diff --git a/.gitattributes b/.gitattributes index e1e127f..dd71303 100644 --- a/.gitattributes +++ b/.gitattributes @@ -23,15 +23,15 @@ doc/doxyfooter -text /missing -text /rules.make -text src/H5Block.c -text +src/H5Block.f90 -text src/H5Block.h -text src/H5BlockErrors.h -text src/H5BlockF.c -text -src/H5BlockF90.inc -text src/H5BlockPrivate.h -text src/H5BlockReadWrite.c -text +src/H5BlockReadWrite.f90 -text src/H5BlockReadWrite.h -text src/H5BlockReadWriteF.c -text -src/H5BlockReadWriteF90.inc -text src/H5BlockTypes.h -text src/H5MultiBlock.c -text src/H5MultiBlock.h -text @@ -41,15 +41,20 @@ src/H5MultiBlockReadWrite.c -text src/H5MultiBlockReadWrite.h -text src/H5MultiBlockTypes.h -text src/H5Part.c -text +src/H5Part.f90 -text src/H5Part.h -text +src/H5PartAttrib.c -text +src/H5PartAttrib.f90 -text +src/H5PartAttrib.h -text +src/H5PartAttribF.c -text src/H5PartErrors.h -text src/H5PartF.c -text -src/H5PartF90.inc -text src/H5PartPrivate.h -text src/H5PartTypes.h -text src/Makefile.am -text src/TestUnderscore.f -text src/TestUnderscoreC.c -text +src/generate-attr.py -text src/generate-h5bl-readwrite.py -text src/generate-h5multi-readwrite.py -text test/Bench.c -text @@ -68,6 +73,13 @@ test/H5test.cc -text test/H5testF.f -text test/H5testFpar.F90 -text test/Makefile.am -text +test/params.h -text +test/test.c -text +test/testframe.c -text +test/testframe.h -text +test/write.c -text +tools/H5BlockBench.c -text +tools/H5PartBench.c -text tools/Makefile.am -text tools/README -text tools/h5pAttrib.cc -text diff --git a/configure.ac b/configure.ac index 252e946..9f935d4 100644 --- a/configure.ac +++ b/configure.ac @@ -79,7 +79,6 @@ SAVE_MPIFC=$MPIFC SAVE_MPILIB=$MPILIB SAVE_MPIINC=$MPIINC SAVE_CFLAGS=$CFLAGS -CFLAGS='' SAVE_FFLAGS=$FFLAGS SAVE_MPIROOT=$MPIROOT SAVE_HDF5ROOT=$HDF5ROOT @@ -392,15 +391,15 @@ if test "X$USE_PARALLEL" = "Xyes"; then fi MTARGET="libpH5Part.a" - TTARGET="H5PartTestP H5PartAndreasTest Bench" - TTARGET="${TTARGET} H5BlockTestAttributes" - TTARGET="${TTARGET} H5BlockParTestScalarField" + TTARGET="test" # parallel + fortran if test "X$USE_FORTRAN" = "Xyes"; then AC_PATH_PROGS([MPIFC], [mpxlf_r mpif90], [], [$PATH]) + FFLAGS="${FFLAGS} -DPARALLEL_IO" + if test -z "${MPIFC}" ; then if test -e "${MPIROOT}/bin/mpif90"; then MPIFC=${MPIROOT}/bin/mpif90 @@ -419,28 +418,29 @@ if test "X$USE_PARALLEL" = "Xyes"; then fi MTARGET="${MTARGET} libpH5PartF.a" - TTARGET="${TTARGET} H5testFpar" - TTARGET="${TTARGET} H5BlockParTestScalarFieldF" + TTARGET="${TTARGET} testf" fi else # --enable-parallel=no AC_MSG_RESULT([no]) MTARGET="libH5Part.a" - TTARGET="H5PartTest H5test" - TTARGET="${TTARGET} H5BlockTestAttributes" + TTARGET="test" if test "X$USE_FORTRAN" = "Xyes"; then MTARGET="${MTARGET} libH5PartF.a" - TTARGET="${TTARGET} H5testF" - TTARGET="${TTARGET} H5BlockTestAttributesF" - fi + TTARGET="${TTARGET} testf" + fi fi -AC_MSG_CHECKING([wheter tools are enabled]) +AC_MSG_CHECKING([whether tools are enabled]) if test "X$USE_TOOLS" = "Xyes"; then AC_MSG_RESULT([yes]) - BUILD_TOOLS="h5pAttrib h5pToGNUplot # homdynToH5p" + BUILD_TOOLS="h5pAttrib h5pToGNUplot homdynToH5p" + # tools + parallel + if test "X$USE_PARALLEL" = "Xyes"; then + BUILD_TOOLS="${BUILD_TOOLS} H5PartBench H5BlockBench" + fi else AC_MSG_RESULT([no]) fi @@ -506,6 +506,8 @@ if test -n "$ZLIBROOT"; then LDFLAGS="$LDFLAGS -L$ZLIBROOT/lib" fi +FCFLAGS=${FFLAGS} + ############################################################################### #################### MISC SETTINGS - path, flags, etc ######################### @@ -570,16 +572,6 @@ if test -n "$SAVE_LDFLAGS"; then LDFLAGS=$SAVE_LDFLAGS fi -if test -n "$MPICXX"; then -TOOLS_CXX=$MPICXX -TOOLS_H5PART_LIB="-lpH5Part" -TOOLS_HDFLIB="-L$HDF5ROOT/lib -lhdf5" -else -TOOLS_CXX=$CXX -TOOLS_H5PART_LIB="-lH5Part" -TOOLS_HDFLIB="-L$HDF5ROOT/lib -lhdf5" -fi - ############################################################################### ############## EXPORTING VARIABLES & CREATING OUTPUT FILES #################### ############################################################################### @@ -607,9 +599,6 @@ AC_SUBST(H5P_LIB_LOC) AC_SUBST(UNDERSCORE_H) AC_SUBST(BUILD_TOOLS) AC_SUBST(LDFLAGS) -AC_SUBST(TOOLS_CXX) -AC_SUBST(TOOLS_H5PART_LIB) -AC_SUBST(TOOLS_HDFLIB) # Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'), # substituting the output variable values. diff --git a/doc/Doxyfile b/doc/Doxyfile index 8f1ad71..c06cfb8 100644 --- a/doc/Doxyfile +++ b/doc/Doxyfile @@ -58,8 +58,8 @@ HIDE_SCOPE_NAMES = NO SHOW_INCLUDE_FILES = NO INLINE_INFO = YES SORT_MEMBER_DOCS = YES -SORT_BRIEF_DOCS = NO -SORT_BY_SCOPE_NAME = NO +SORT_BRIEF_DOCS = YES +SORT_BY_SCOPE_NAME = YES GENERATE_TODOLIST = YES GENERATE_TESTLIST = YES GENERATE_BUGLIST = YES @@ -83,10 +83,15 @@ WARN_LOGFILE = # configuration options related to the input files #--------------------------------------------------------------------------- INPUT += ../src/H5Part.c +INPUT += ../src/H5PartAttrib.c INPUT += ../src/H5Block.c -INPUT += ../src/H5MultiBlock.c INPUT += ../src/H5BlockReadWrite.c +INPUT += ../src/H5MultiBlock.c INPUT += ../src/H5MultiBlockReadWrite.c +INPUT += ../src/H5Part.f90 +INPUT += ../src/H5PartAttrib.f90 +INPUT += ../src/H5Block.f90 +INPUT += ../src/H5BlockReadWrite.f90 FILE_PATTERNS = RECURSIVE = YES EXCLUDE = @@ -200,7 +205,7 @@ SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- -TAGFILES = YES +TAGFILES = GENERATE_TAGFILE = ALLEXTERNALS = NO EXTERNAL_GROUPS = YES @@ -208,12 +213,12 @@ PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- -CLASS_DIAGRAMS = YES -HIDE_UNDOC_RELATIONS = YES -HAVE_DOT = YES -CLASS_GRAPH = YES -COLLABORATION_GRAPH = YES -GROUP_GRAPHS = YES +CLASS_DIAGRAMS = NO +HIDE_UNDOC_RELATIONS = NO +HAVE_DOT = NO +CLASS_GRAPH = NO +COLLABORATION_GRAPH = NO +GROUP_GRAPHS = NO UML_LOOK = NO TEMPLATE_RELATIONS = NO INCLUDE_GRAPH = NO @@ -222,7 +227,7 @@ CALL_GRAPH = NO GRAPHICAL_HIERARCHY = YES DIRECTORY_GRAPH = YES DOT_IMAGE_FORMAT = png -DOT_PATH = /Applications/Graphviz.app/Contents/MacOS +DOT_PATH = DOTFILE_DIRS = MAX_DOT_GRAPH_WIDTH = 1024 MAX_DOT_GRAPH_HEIGHT = 1024 diff --git a/src/H5Block.c b/src/H5Block.c index 6eb9b59..b0bdaae 100644 --- a/src/H5Block.c +++ b/src/H5Block.c @@ -16,11 +16,11 @@ /*! \ingroup h5block_c_api - \defgroup h5block_write File Writing + \defgroup h5block_model Setting up the Data Model */ /*! \ingroup h5block_c_api - \defgroup h5block_read File Reading + \defgroup h5block_data Reading and Writing Datasets */ /*! \ingroup h5block_c_api @@ -81,7 +81,7 @@ */ static h5part_int64_t -_file_is_valid ( +_H5Block_file_is_valid ( const H5PartFile *f /*!< IN: file handle */ ) { @@ -114,7 +114,7 @@ _H5Block_init ( h5part_int64_t herr; struct H5BlockStruct *b; - herr = _file_is_valid ( f ); + herr = _H5Block_file_is_valid ( f ); if ( herr == H5PART_SUCCESS ) return H5PART_SUCCESS; if ( (f == 0) || (f->file == 0) ) return HANDLE_H5PART_BADFD_ERR; @@ -719,7 +719,7 @@ _release_hyperslab ( } /*! - \ingroup h5block_write + \ingroup h5block_model Define the field layout given the dense index space at the actual time step. @@ -770,7 +770,7 @@ H5BlockDefine3DFieldLayout( } /*! - \ingroup h5block_write + \ingroup h5block_model Define the chunk dimensions and enable chunking in the underlying HDF5 dataset. @@ -808,7 +808,7 @@ H5BlockDefine3DChunkDims( } /*! - \ingroup h5block_read + \ingroup h5block_model Lookup the chunk dimensions of the underlying HDF5 dataset. @@ -867,7 +867,7 @@ H5BlockGet3DChunkDims( } /*! - \ingroup h5block_read + \ingroup h5block_model Return partition of processor \c proc as specified with \c H5BlockDefine3dLayout(). @@ -907,7 +907,7 @@ H5Block3dGetPartitionOfProc ( } /*! - \ingroup h5block_read + \ingroup h5block_model Return reduced (ghost-zone free) partition of processor \c proc as specified with \c H5BlockDefine3dLayout(). @@ -948,7 +948,7 @@ H5Block3dGetReducedPartitionOfProc ( /*! - \ingroup h5block_read + \ingroup h5block_model Returns the processor computing the reduced (ghostzone-free) partition given by the coordinates \c i, \c j and \c k. @@ -1461,7 +1461,7 @@ _H5Block_write_data ( /********************** query information about available fields *************/ /*! - \ingroup h5block_read + \ingroup h5block_model Query number of fields in current time step. @@ -1548,7 +1548,7 @@ _get_field_info ( } /*! - \ingroup h5block_read + \ingroup h5block_model Get the name, rank and dimensions of the field specified by the index \c idx. @@ -1589,7 +1589,7 @@ H5BlockGetFieldInfo ( } /*! - \ingroup h5block_read + \ingroup h5block_model Get the rank and dimensions of the field specified by its name. @@ -1715,7 +1715,7 @@ H5BlockWriteFieldAttribString ( */ h5part_int64_t H5BlockGetNumFieldAttribs ( - H5PartFile *f, /*!< IN: file handle */ + H5PartFile *f, /* \defgroup h5block_f90_api H5Block F90 API + +!> \ingroup h5block_f90_api +!! \defgroup h5blockf_model Setting up the Data Model +!< + +!> \ingroup h5block_f90_api +!! \defgroup h5blockf_data Reading and Writing Datasets +!< + +!> \ingroup h5block_f90_api +!! \defgroup h5blockf_attrib Reading and Writing Attributes +!< + + +!!!!!!!! Setting up the Data Model !!!!!!!! + +!> \ingroup h5blockf_model +!! See \ref H5BlockDefine3DFieldLayout +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_define3dlayout ( filehandle, i_start, i_end, j_start, j_end, k_start, k_end ) + INTEGER*8, INTENT(IN) :: filehandle + INTEGER*8, INTENT(IN) :: i_start + INTEGER*8, INTENT(IN) :: i_end + INTEGER*8, INTENT(IN) :: j_start + INTEGER*8, INTENT(IN) :: j_end + INTEGER*8, INTENT(IN) :: k_start + INTEGER*8, INTENT(IN) :: k_end +END FUNCTION + +!> \ingroup h5blockf_model +!! See \ref H5BlockDefine3DChunkDims +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_define3dchunkdims ( filehandle, i, j, k ) + INTEGER*8, INTENT(IN) :: filehandle + INTEGER*8, INTENT(IN) :: i + INTEGER*8, INTENT(IN) :: j + INTEGER*8, INTENT(IN) :: k +END FUNCTION + +!> \ingroup h5blockf_model +!! See \ref H5Block3dGetPartitionOfProc +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_get_partition_of_proc ( filehandle, proc, i_start, i_end, j_start, j_end, k_start, k_end ) + INTEGER*8, INTENT(IN) :: filehandle + INTEGER*8, INTENT(OUT) :: proc + INTEGER*8, INTENT(OUT) :: i_start + INTEGER*8, INTENT(OUT) :: i_end + INTEGER*8, INTENT(OUT) :: j_start + INTEGER*8, INTENT(OUT) :: j_end + INTEGER*8, INTENT(OUT) :: k_start + INTEGER*8, INTENT(OUT) :: k_end + END FUNCTION + +!> \ingroup h5blockf_model +!! See \ref H5Block3dGetReducedPartitionOfProc +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_get_reduced_partition_of_proc ( filehandle, proc, i_start, i_end, j_start, j_end, k_start, k_end ) + INTEGER*8, INTENT(IN) :: filehandle + INTEGER*8, INTENT(OUT) :: proc + INTEGER*8, INTENT(OUT) :: i_start + INTEGER*8, INTENT(OUT) :: i_end + INTEGER*8, INTENT(OUT) :: j_start + INTEGER*8, INTENT(OUT) :: j_end + INTEGER*8, INTENT(OUT) :: k_start + INTEGER*8, INTENT(OUT) :: k_end +END FUNCTION + +!> \ingroup h5blockf_model +!! See \ref H5Block3dGetProcOf +!! \return rank of processor error code +!< +INTEGER*8 FUNCTION h5bl_get_proc_of ( filehandle, i, j, k ) + INTEGER*8, INTENT(IN) :: filehandle + INTEGER*8, INTENT(IN) :: i + INTEGER*8, INTENT(IN) :: j + INTEGER*8, INTENT(IN) :: k +END FUNCTION + +!> \ingroup h5blockf_model +!! See \ref H5BlockGetNumFields +!! \return number of fields or error code +!< +INTEGER*8 FUNCTION h5bl_getnumfields ( filehandle ) + INTEGER*8, INTENT(IN) :: filehandle +END FUNCTION + +!> \ingroup h5blockf_model +!! See \ref H5BlockGetFieldInfo +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_getfieldinfo ( filehandle, idx, field_name, grid_rank, grid_dims, field_dims ) + INTEGER*8, INTENT(IN) :: filehandle + INTEGER*8, INTENT(IN) :: idx + CHARACTER(LEN=*), INTENT(OUT) :: field_name + INTEGER*8, INTENT(OUT) :: grid_rank + INTEGER*8, INTENT(OUT) :: grid_dims(*) + INTEGER*8, INTENT(OUT) :: field_dims +END FUNCTION + +!> \ingroup h5blockf_model +!! See \ref H5BlockHasFieldData +!! \return 0 if false, 1 if true, or error code +!< +INTEGER*8 FUNCTION h5bl_has_fielddata ( filehandle ) + INTEGER*8, INTENT(IN) :: filehandle +END FUNCTION + + +!!!!!!!! Reading and Writing Attributes !!!!!!!! + +!> \ingroup h5blockf_attrib +!! See \ref H5BlockWriteFieldAttribString +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_writefieldattrib_string ( filehandle, field_name, attrib_name, attrib_value ) + INTEGER*8, INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute + CHARACTER(LEN=*), INTENT(IN) :: attrib_value ! The array of data to write into the attribute +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5BlockGetNumFieldAttribs +!! \return number of attributes or error code +!< +INTEGER*8 FUNCTION h5bl_getnfieldattribs ( filehandle, field_name ) + INTEGER*8, INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5BlockGetFieldAttribInfo +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_getfieldattribinfo ( filehandle, field_name, idx, attrib_name, attrib_nelem) + INTEGER*8,INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field + INTEGER*8,INTENT(IN) :: idx ! index of the attribute being queried + CHARACTER(LEN=*), INTENT(OUT):: attrib_name ! The name of the attribute + INTEGER*8,INTENT(OUT):: attrib_nelem ! Number of elements in the attrib array +END FUNCTION + +!> \ingroup h5blockf_attrib +!! Read the attribute \c attrib_name from the field \c field_name at the +!! current timestep, and store the int64 value in \c attrib_value. +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_readfieldattrib_i8 ( filehandle, field_name, attrib_name, attrib_value ) + INTEGER*8,INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read + INTEGER*8,INTENT(OUT):: attrib_value(*)! the attribute data will be read into this array +END FUNCTION + +!> \ingroup h5blockf_attrib +!! Read the attribute \c attrib_name from the field \c field_name at the +!! current timestep, and store the float64 value in \c attrib_value. +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_readfieldattrib_r8 ( filehandle, field_name, attrib_name, attrib_value ) + INTEGER*8,INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read + REAL*8, INTENT(OUT):: attrib_value(*)! the attribute data will be read into this array +END FUNCTION + +!> \ingroup h5blockf_attrib +!! Read the attribute \c attrib_name from the field \c field_name at the +!! current timestep, and store the string value in \c attrib_value. +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_readfieldattrib_string ( filehandle, field_name, attrib_name, attrib_value ) + INTEGER*8, INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read + CHARACTER(LEN=*), INTENT(IN) :: attrib_value ! The array of data to write into the attribute +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5Block3dGetFieldSpacing +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_get_field_spacing ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: name + REAL*8, INTENT(OUT) :: x + REAL*8, INTENT(OUT) :: y + REAL*8, INTENT(OUT) :: z +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5Block3dSetFieldSpacing +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_set_field_spacing ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: name + REAL*8, INTENT(IN) :: x + REAL*8, INTENT(IN) :: y + REAL*8, INTENT(IN) :: z +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5Block3dGetFieldOrigin +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_get_field_origin ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: name + REAL*8, INTENT(OUT) :: x + REAL*8, INTENT(OUT) :: y + REAL*8, INTENT(OUT) :: z +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5Block3dSetFieldOrigin +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_set_field_origin ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle + CHARACTER(LEN=*), INTENT(IN) :: name + REAL*8, INTENT(IN) :: x + REAL*8, INTENT(IN) :: y + REAL*8, INTENT(IN) :: z +END FUNCTION + + diff --git a/src/H5Block.h b/src/H5Block.h index 9394ebf..94ce9a5 100644 --- a/src/H5Block.h +++ b/src/H5Block.h @@ -1,5 +1,5 @@ -#ifndef __H5BLOCK_H -#define __H5BLOCK_H +#ifndef _H5BLOCK_H_ +#define _H5BLOCK_H_ #ifdef __cplusplus extern "C" { diff --git a/src/H5BlockErrors.h b/src/H5BlockErrors.h index 43e39de..660913d 100644 --- a/src/H5BlockErrors.h +++ b/src/H5BlockErrors.h @@ -1,7 +1,7 @@ -#ifndef __H5BLOCKERRORS_H -#define __H5BLOCKERRORS_H +#ifndef _H5BLOCK_ERRORS_H_ +#define _H5BLOCK_ERRORS_H_ -#define _err_handler H5PartGetErrorHandler() +extern h5part_error_handler _err_handler; #define CHECK_LAYOUT( f ) \ if ( ! f->block->have_layout ) \ diff --git a/src/H5BlockF90.inc b/src/H5BlockF90.inc deleted file mode 100644 index cec5ff7..0000000 --- a/src/H5BlockF90.inc +++ /dev/null @@ -1,143 +0,0 @@ - -INCLUDE 'H5BlockReadWriteF90.inc' - -INTERFACE - -INTEGER*8 FUNCTION h5bl_define3dlayout ( filehandle, i_start, i_end, j_start, j_end, k_start, k_end ) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: i_start - INTEGER*8, INTENT(IN) :: i_end - INTEGER*8, INTENT(IN) :: j_start - INTEGER*8, INTENT(IN) :: j_end - INTEGER*8, INTENT(IN) :: k_start - INTEGER*8, INTENT(IN) :: k_end -END FUNCTION - -INTEGER*8 FUNCTION h5bl_define3dchunkdims ( filehandle, i, j, k ) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: i - INTEGER*8, INTENT(IN) :: j - INTEGER*8, INTENT(IN) :: k -END FUNCTION - -INTEGER*8 FUNCTION h5bl_get_partition_of_proc ( filehandle, proc, i_start, i_end, j_start, j_end, k_start, k_end ) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(OUT) :: proc - INTEGER*8, INTENT(OUT) :: i_start - INTEGER*8, INTENT(OUT) :: i_end - INTEGER*8, INTENT(OUT) :: j_start - INTEGER*8, INTENT(OUT) :: j_end - INTEGER*8, INTENT(OUT) :: k_start - INTEGER*8, INTENT(OUT) :: k_end -END FUNCTION - -INTEGER*8 FUNCTION h5bl_get_reduced_partition_of_proc ( filehandle, proc, i_start, i_end, j_start, j_end, k_start, k_end ) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(OUT) :: proc - INTEGER*8, INTENT(OUT) :: i_start - INTEGER*8, INTENT(OUT) :: i_end - INTEGER*8, INTENT(OUT) :: j_start - INTEGER*8, INTENT(OUT) :: j_end - INTEGER*8, INTENT(OUT) :: k_start - INTEGER*8, INTENT(OUT) :: k_end -END FUNCTION - -INTEGER*8 FUNCTION h5bl_get_proc_of ( filehandle, i, j, k ) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: i - INTEGER*8, INTENT(IN) :: j - INTEGER*8, INTENT(IN) :: k -END FUNCTION - -INTEGER*8 FUNCTION h5bl_getnumfields ( filehandle ) - INTEGER*8, INTENT(IN) :: filehandle -END FUNCTION - -INTEGER*8 FUNCTION h5bl_getfieldinfo ( filehandle, idx, field_name, grid_rank, grid_dims, field_dims ) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: idx - CHARACTER(LEN=*), INTENT(OUT) :: field_name - INTEGER*8, INTENT(OUT) :: grid_rank - INTEGER*8, INTENT(OUT) :: grid_dims(*) - INTEGER*8, INTENT(OUT) :: field_dims -END FUNCTION - -INTEGER*8 FUNCTION h5bl_writefieldattrib_string ( filehandle, field_name, attrib_name, attrib_value ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - CHARACTER(LEN=*), INTENT(IN) :: attrib_value ! The array of data to write into the attribute -END FUNCTION - -INTEGER*8 FUNCTION h5bl_getnfieldattribs ( filehandle, field_name ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field -END FUNCTION - -INTEGER*8 FUNCTION h5bl_getfieldattribinfo ( filehandle, field_name, idx, attrib_name, attrib_nelem) - INTEGER*8,INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - INTEGER*8,INTENT(IN) :: idx ! index of the attribute being queried - CHARACTER(LEN=*), INTENT(OUT):: attrib_name ! The name of the attribute - INTEGER*8,INTENT(OUT):: attrib_nelem ! Number of elements in the attrib array -END FUNCTION - -INTEGER*8 FUNCTION h5bl_readfieldattrib_i8 ( filehandle, field_name, attrib_name, attrib_value ) - INTEGER*8,INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read - INTEGER*8,INTENT(OUT):: attrib_value(*)! the attribute data will be read into this array -END FUNCTION - -INTEGER*8 FUNCTION h5bl_readfieldattrib_r8 ( filehandle, field_name, attrib_name, attrib_value ) - INTEGER*8,INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read - REAL*8, INTENT(OUT):: attrib_value(*)! the attribute data will be read into this array -END FUNCTION - -INTEGER*8 FUNCTION h5bl_readfieldattrib_string ( filehandle, field_name, attrib_name, attrib_value ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read - CHARACTER(LEN=*), INTENT(IN) :: attrib_value ! The array of data to write into the attribute -END FUNCTION - -INTEGER*8 FUNCTION h5bl_has_fielddata ( filehandle ) - INTEGER*8, INTENT(IN) :: filehandle -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_get_field_spacing ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*8, INTENT(OUT) :: x - REAL*8, INTENT(OUT) :: y - REAL*8, INTENT(OUT) :: z -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_set_field_spacing ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*8, INTENT(IN) :: x - REAL*8, INTENT(IN) :: y - REAL*8, INTENT(IN) :: z -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_get_field_origin ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*8, INTENT(OUT) :: x - REAL*8, INTENT(OUT) :: y - REAL*8, INTENT(OUT) :: z -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_set_field_origin ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*8, INTENT(IN) :: x - REAL*8, INTENT(IN) :: y - REAL*8, INTENT(IN) :: z -END FUNCTION - -END INTERFACE - diff --git a/src/H5BlockPrivate.h b/src/H5BlockPrivate.h index 167373b..e4d666c 100644 --- a/src/H5BlockPrivate.h +++ b/src/H5BlockPrivate.h @@ -1,5 +1,5 @@ -#ifndef __H5BLOCKPRIVATE_H -#define __H5BLOCKPRIVATE_H +#ifndef _H5BLOCK_PRIVATE_H_ +#define _H5BLOCK_PRIVATE_H_ #define H5BLOCK_GROUPNAME_BLOCK "Block" diff --git a/src/H5BlockReadWrite.c b/src/H5BlockReadWrite.c index 69b9887..5118a4a 100644 --- a/src/H5BlockReadWrite.c +++ b/src/H5BlockReadWrite.c @@ -13,7 +13,7 @@ #include "H5BlockErrors.h" /*! - \ingroup h5block_write + \ingroup h5block_data Write a 3-dimensional field \c name from the buffer starting at \c data to the current time-step using the defined field layout. Values are @@ -49,7 +49,7 @@ H5Block3dWriteScalarFieldFloat64 ( } /*! - \ingroup h5block_read + \ingroup h5block_data Read a 3-dimensional field \c name into the buffer starting at \c data from the current time-step using the defined field layout. Values are @@ -84,7 +84,7 @@ H5Block3dReadScalarFieldFloat64 ( } /*! - \ingroup h5block_write + \ingroup h5block_data */ /*! Write a 3-dimensional field \c name with 3-dimensional vectors as values @@ -128,7 +128,7 @@ H5Block3dWrite3dVectorFieldFloat64 ( } /*! - \ingroup h5block_read + \ingroup h5block_data */ /*! Read a 3-dimensional field \c name with 3-dimensional vectors as values @@ -171,7 +171,7 @@ H5Block3dRead3dVectorFieldFloat64 ( } /*! - \ingroup h5block_write + \ingroup h5block_data Write a 3-dimensional field \c name from the buffer starting at \c data to the current time-step using the defined field layout. Values are @@ -207,7 +207,7 @@ H5Block3dWriteScalarFieldFloat32 ( } /*! - \ingroup h5block_read + \ingroup h5block_data Read a 3-dimensional field \c name into the buffer starting at \c data from the current time-step using the defined field layout. Values are @@ -242,7 +242,7 @@ H5Block3dReadScalarFieldFloat32 ( } /*! - \ingroup h5block_write + \ingroup h5block_data */ /*! Write a 3-dimensional field \c name with 3-dimensional vectors as values @@ -286,7 +286,7 @@ H5Block3dWrite3dVectorFieldFloat32 ( } /*! - \ingroup h5block_read + \ingroup h5block_data */ /*! Read a 3-dimensional field \c name with 3-dimensional vectors as values @@ -329,7 +329,7 @@ H5Block3dRead3dVectorFieldFloat32 ( } /*! - \ingroup h5block_write + \ingroup h5block_data Write a 3-dimensional field \c name from the buffer starting at \c data to the current time-step using the defined field layout. Values are @@ -365,7 +365,7 @@ H5Block3dWriteScalarFieldInt64 ( } /*! - \ingroup h5block_read + \ingroup h5block_data Read a 3-dimensional field \c name into the buffer starting at \c data from the current time-step using the defined field layout. Values are @@ -400,7 +400,7 @@ H5Block3dReadScalarFieldInt64 ( } /*! - \ingroup h5block_write + \ingroup h5block_data */ /*! Write a 3-dimensional field \c name with 3-dimensional vectors as values @@ -444,7 +444,7 @@ H5Block3dWrite3dVectorFieldInt64 ( } /*! - \ingroup h5block_read + \ingroup h5block_data */ /*! Read a 3-dimensional field \c name with 3-dimensional vectors as values @@ -487,7 +487,7 @@ H5Block3dRead3dVectorFieldInt64 ( } /*! - \ingroup h5block_write + \ingroup h5block_data Write a 3-dimensional field \c name from the buffer starting at \c data to the current time-step using the defined field layout. Values are @@ -523,7 +523,7 @@ H5Block3dWriteScalarFieldInt32 ( } /*! - \ingroup h5block_read + \ingroup h5block_data Read a 3-dimensional field \c name into the buffer starting at \c data from the current time-step using the defined field layout. Values are @@ -558,7 +558,7 @@ H5Block3dReadScalarFieldInt32 ( } /*! - \ingroup h5block_write + \ingroup h5block_data */ /*! Write a 3-dimensional field \c name with 3-dimensional vectors as values @@ -602,7 +602,7 @@ H5Block3dWrite3dVectorFieldInt32 ( } /*! - \ingroup h5block_read + \ingroup h5block_data */ /*! Read a 3-dimensional field \c name with 3-dimensional vectors as values diff --git a/src/H5BlockReadWrite.f90 b/src/H5BlockReadWrite.f90 new file mode 100644 index 0000000..f3be29b --- /dev/null +++ b/src/H5BlockReadWrite.f90 @@ -0,0 +1,224 @@ + +!> \ingroup h5blockf_data +!! See \ref H5Block3dWriteScalarFieldFloat64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_r8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*8, INTENT(IN) :: data(*) !< the array of data +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dReadScalarFieldFloat64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_r8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*8, INTENT(OUT) :: data(*) !< buffer to read the data into +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dWrite3dVectorFieldFloat64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_r8 ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*8, INTENT(IN) :: x(*) !< the array of x data to write + REAL*8, INTENT(IN) :: y(*) !< the array of y data to write + REAL*8, INTENT(IN) :: z(*) !< the array of z data to write +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dRead3dVectorFieldFloat64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_r8 ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*8, INTENT(OUT) :: x(*) !< buffer to read the x data into + REAL*8, INTENT(OUT) :: y(*) !< buffer to read the y data into + REAL*8, INTENT(OUT) :: z(*) !< buffer to read the z data into +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dWriteScalarFieldFloat32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_r4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*4, INTENT(IN) :: data(*) !< the array of data +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dReadScalarFieldFloat32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_r4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*4, INTENT(OUT) :: data(*) !< buffer to read the data into +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dWrite3dVectorFieldFloat32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_r4 ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*4, INTENT(IN) :: x(*) !< the array of x data to write + REAL*4, INTENT(IN) :: y(*) !< the array of y data to write + REAL*4, INTENT(IN) :: z(*) !< the array of z data to write +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dRead3dVectorFieldFloat32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_r4 ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*4, INTENT(OUT) :: x(*) !< buffer to read the x data into + REAL*4, INTENT(OUT) :: y(*) !< buffer to read the y data into + REAL*4, INTENT(OUT) :: z(*) !< buffer to read the z data into +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dWriteScalarFieldInt64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_i8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*8, INTENT(IN) :: data(*) !< the array of data +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dReadScalarFieldInt64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_i8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*8, INTENT(OUT) :: data(*) !< buffer to read the data into +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dWrite3dVectorFieldInt64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_i8 ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*8, INTENT(IN) :: x(*) !< the array of x data to write + INTEGER*8, INTENT(IN) :: y(*) !< the array of y data to write + INTEGER*8, INTENT(IN) :: z(*) !< the array of z data to write +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dRead3dVectorFieldInt64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_i8 ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*8, INTENT(OUT) :: x(*) !< buffer to read the x data into + INTEGER*8, INTENT(OUT) :: y(*) !< buffer to read the y data into + INTEGER*8, INTENT(OUT) :: z(*) !< buffer to read the z data into +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dWriteScalarFieldInt32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_i4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*4, INTENT(IN) :: data(*) !< the array of data +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dReadScalarFieldInt32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_i4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*4, INTENT(OUT) :: data(*) !< buffer to read the data into +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dWrite3dVectorFieldInt32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_i4 ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*4, INTENT(IN) :: x(*) !< the array of x data to write + INTEGER*4, INTENT(IN) :: y(*) !< the array of y data to write + INTEGER*4, INTENT(IN) :: z(*) !< the array of z data to write +END FUNCTION + +!> \ingroup h5blockf_data +!! See \ref H5Block3dRead3dVectorFieldInt32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_i4 ( filehandle, name, x, y, z ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*4, INTENT(OUT) :: x(*) !< buffer to read the x data into + INTEGER*4, INTENT(OUT) :: y(*) !< buffer to read the y data into + INTEGER*4, INTENT(OUT) :: z(*) !< buffer to read the z data into +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5BlockWriteFieldAttribFloat64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_writefieldattrib_r8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: field_name !< the name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute + REAL*8, INTENT(IN) :: attrib_value(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: attrib_nelem !< the number of elements in the array +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5BlockWriteFieldAttribFloat32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_writefieldattrib_r4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: field_name !< the name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute + REAL*4, INTENT(IN) :: attrib_value(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: attrib_nelem !< the number of elements in the array +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5BlockWriteFieldAttribInt64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_writefieldattrib_i8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: field_name !< the name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute + INTEGER*8, INTENT(IN) :: attrib_value(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: attrib_nelem !< the number of elements in the array +END FUNCTION + +!> \ingroup h5blockf_attrib +!! See \ref H5BlockWriteFieldAttribInt32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5bl_writefieldattrib_i4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: field_name !< the name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute + INTEGER*4, INTENT(IN) :: attrib_value(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: attrib_nelem !< the number of elements in the array +END FUNCTION diff --git a/src/H5BlockReadWrite.h b/src/H5BlockReadWrite.h index 8f9d9d8..9025ff4 100644 --- a/src/H5BlockReadWrite.h +++ b/src/H5BlockReadWrite.h @@ -1,6 +1,6 @@ -#ifndef __H5BLOCKREADWRITE_H -#define __H5BLOCKREADWRITE_H +#ifndef _H5BLOCK_READWRITE_H_ +#define _H5BLOCK_READWRITE_H_ #ifdef __cplusplus extern "C" { diff --git a/src/H5BlockReadWriteF90.inc b/src/H5BlockReadWriteF90.inc deleted file mode 100644 index 457dd17..0000000 --- a/src/H5BlockReadWriteF90.inc +++ /dev/null @@ -1,148 +0,0 @@ - -INTERFACE - -INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_r8 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*8, INTENT(IN) :: data(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_r8 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*8, INTENT(OUT) :: data(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_r8 ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*8, INTENT(IN) :: x(*) - REAL*8, INTENT(IN) :: y(*) - REAL*8, INTENT(IN) :: z(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_r8 ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*8, INTENT(OUT) :: x(*) - REAL*8, INTENT(OUT) :: y(*) - REAL*8, INTENT(OUT) :: z(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_r4 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*4, INTENT(IN) :: data(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_r4 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*4, INTENT(OUT) :: data(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_r4 ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*4, INTENT(IN) :: x(*) - REAL*4, INTENT(IN) :: y(*) - REAL*4, INTENT(IN) :: z(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_r4 ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - REAL*4, INTENT(OUT) :: x(*) - REAL*4, INTENT(OUT) :: y(*) - REAL*4, INTENT(OUT) :: z(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_i8 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - INTEGER*8, INTENT(IN) :: data(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_i8 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - INTEGER*8, INTENT(OUT) :: data(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_i8 ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - INTEGER*8, INTENT(IN) :: x(*) - INTEGER*8, INTENT(IN) :: y(*) - INTEGER*8, INTENT(IN) :: z(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_i8 ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - INTEGER*8, INTENT(OUT) :: x(*) - INTEGER*8, INTENT(OUT) :: y(*) - INTEGER*8, INTENT(OUT) :: z(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_i4 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - INTEGER*4, INTENT(IN) :: data(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_i4 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - INTEGER*4, INTENT(OUT) :: data(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_i4 ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - INTEGER*4, INTENT(IN) :: x(*) - INTEGER*4, INTENT(IN) :: y(*) - INTEGER*4, INTENT(IN) :: z(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_i4 ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - INTEGER*4, INTENT(OUT) :: x(*) - INTEGER*4, INTENT(OUT) :: y(*) - INTEGER*4, INTENT(OUT) :: z(*) -END FUNCTION - -INTEGER*8 FUNCTION h5bl_writefieldattrib_r8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - REAL*8, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array -END FUNCTION - -INTEGER*8 FUNCTION h5bl_writefieldattrib_r4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - REAL*4, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array -END FUNCTION - -INTEGER*8 FUNCTION h5bl_writefieldattrib_i8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - INTEGER*8, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array -END FUNCTION - -INTEGER*8 FUNCTION h5bl_writefieldattrib_i4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - INTEGER*4, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array -END FUNCTION - -END INTERFACE diff --git a/src/H5BlockTypes.h b/src/H5BlockTypes.h index 40b4a70..60b2f11 100644 --- a/src/H5BlockTypes.h +++ b/src/H5BlockTypes.h @@ -1,5 +1,5 @@ -#ifndef __H5BLOCKTYPES_H -#define __H5BLOCKTYPES_H +#ifndef _H5BLOCK_TYPES_H +#define _H5BLOCK_TYPES_H struct H5BlockPartition { h5part_int64_t i_start; diff --git a/src/H5MultiBlock.c b/src/H5MultiBlock.c index ae666e2..938fe13 100644 --- a/src/H5MultiBlock.c +++ b/src/H5MultiBlock.c @@ -28,12 +28,14 @@ /*! \ingroup h5multiblock_c_api - \defgroup h5multiblock_write File Writing + \defgroup h5multiblock_model Setting up the Data Model */ + /*! \ingroup h5multiblock_c_api - \defgroup h5multiblock_read File Reading + \defgroup h5multiblock_data Reading and Writing Datasets */ + /*! \ingroup h5multiblock_c_api \defgroup h5multiblock_attrib Reading and Writing Attributes @@ -89,7 +91,7 @@ \return H5PART_SUCCESS or error code */ static h5part_int64_t -_file_is_valid ( +_H5MultiBlock_file_is_valid ( const H5PartFile *f /*!< IN: file handle */ ) { @@ -1055,7 +1057,7 @@ _H5MultiBlock_write_data ( *******************************************************************************/ /*! - \ingroup h5multiblock_write + \ingroup h5multiblock_model Define the radius for halo exchanges between the blocks. Blocks on the edges of the field will be padded with zero values out to the radius. @@ -1083,7 +1085,7 @@ H5MultiBlock3dDefineRadius ( } /*! - \ingroup h5multiblock_write + \ingroup h5multiblock_model Define the radii for halo exchanges between the blocks. Blocks on the edges of the field will be padded with zero values out to the radius. @@ -1115,7 +1117,7 @@ H5MultiBlock3dDefineRadii ( } /*! - \ingroup h5multiblock_write + \ingroup h5multiblock_model Define the field and block dimensions for writing. @@ -1151,7 +1153,7 @@ H5MultiBlock3dDefineDims ( } /*! - \ingroup h5multiblock_read + \ingroup h5multiblock_model Returns the field dimensions of the last field that was read. @@ -1180,7 +1182,7 @@ H5MultiBlock3dGetFieldDims( } /*! - \ingroup h5multiblock_read + \ingroup h5multiblock_model Returns the block dimensions of the last field that was read. @@ -1210,7 +1212,7 @@ H5MultiBlock3dGetBlockDims( } /*! - \ingroup h5multiblock_read + \ingroup h5multiblock_model Return the offsets for the block belonging to processor \c proc. @@ -1240,7 +1242,7 @@ H5MultiBlock3dGetOffsetsOfProc ( } /*! - \ingroup h5multiblock_c_api + \ingroup h5multiblock_model Finds a 3D block decomposition for an arbitrary number of processors \c nprocs. @@ -1266,7 +1268,7 @@ H5MultiBlock3dCalculateDecomp ( } /*! - \ingroup h5multiblock_read + \ingroup h5multiblock_data Frees a \c block that was allocated during a read. @@ -1283,7 +1285,7 @@ H5MultiBlockFree ( } /*! - \ingroup h5multiblock_c_api + \ingroup h5multiblock_model Shifts the assignment of procs to blocks within the field. diff --git a/src/H5MultiBlock.h b/src/H5MultiBlock.h index 127cc4a..978230a 100644 --- a/src/H5MultiBlock.h +++ b/src/H5MultiBlock.h @@ -1,5 +1,5 @@ -#ifndef __H5MULTIBLOCK_H -#define __H5MULTIBLOCK_H +#ifndef _H5MULTIBLOCK_H_ +#define _H5MULTIBLOCK_H_ #ifdef __cplusplus extern "C" { diff --git a/src/H5MultiBlockErrors.h b/src/H5MultiBlockErrors.h index bf8a491..36b7288 100644 --- a/src/H5MultiBlockErrors.h +++ b/src/H5MultiBlockErrors.h @@ -1,7 +1,7 @@ -#ifndef __H5MULTIBLOCKERRORS_H -#define __H5MULTIBLOCKERRORS_H +#ifndef _H5MULTIBLOCK_ERRORS_H_ +#define _H5MULTIBLOCK_ERRORS_H_ -#define _err_handler H5PartGetErrorHandler() +extern h5part_error_handler _err_handler; #define CHECK_DECOMP( f ) \ if ( ! f->multiblock->have_decomp ) \ diff --git a/src/H5MultiBlockPrivate.h b/src/H5MultiBlockPrivate.h index 340a95c..bbcfbea 100644 --- a/src/H5MultiBlockPrivate.h +++ b/src/H5MultiBlockPrivate.h @@ -1,5 +1,5 @@ -#ifndef __H5MULTIBLOCKPRIVATE_H -#define __H5MULTIBLOCKPRIVATE_H +#ifndef _H5MULTIBLOCK_PRIVATE_H_ +#define _H5MULTIBLOCK_PRIVATE_H_ #define MULTIBLOCK_INIT( f ) { \ h5part_int64_t herr = _H5MultiBlock_init ( f ); \ diff --git a/src/H5MultiBlockReadWrite.h b/src/H5MultiBlockReadWrite.h index 6da6ce6..eed85ee 100644 --- a/src/H5MultiBlockReadWrite.h +++ b/src/H5MultiBlockReadWrite.h @@ -1,6 +1,6 @@ -#ifndef __H5MULTIBLOCKREADWRITE_H -#define __H5MULTIBLOCKREADWRITE_H +#ifndef _H5MULTIBLOCK_READWRITE_H_ +#define _H5MULTIBLOCK_READWRITE_H_ #ifdef __cplusplus extern "C" { diff --git a/src/H5MultiBlockTypes.h b/src/H5MultiBlockTypes.h index 37305f5..d5cb158 100644 --- a/src/H5MultiBlockTypes.h +++ b/src/H5MultiBlockTypes.h @@ -1,5 +1,5 @@ -#ifndef __H5MULTIBLOCKTYPES_H -#define __H5MULTIBLOCKTYPES_H +#ifndef _H5MULTIBLOCK_TYPES_H_ +#define _H5MULTIBLOCK_TYPES_H_ struct H5MultiBlockStruct { h5part_int64_t halo_radii[3]; diff --git a/src/H5Part.c b/src/H5Part.c index 661d852..f7586c1 100644 --- a/src/H5Part.c +++ b/src/H5Part.c @@ -19,6 +19,7 @@ Developed by:
  • Wes Bethel (NERSC/LBNL)
  • John Shalf (NERSC/LBNL)
  • Cristina Siegerist (NERSC/LBNL)
    • +
  • Mark Howison (NERSC/LBNL)
    • @@ -39,8 +40,6 @@ Papers: For further information contact: h5part -Last modified on April 19, 2007. - */ @@ -50,15 +49,15 @@ Last modified on April 19, 2007. */ /*! \ingroup h5part_c_api - \defgroup h5part_openclose File Opening and Closing + \defgroup h5part_open File Opening and Closing */ /*! \ingroup h5part_c_api - \defgroup h5part_write File Writing + \defgroup h5part_model Setting up the Data Model */ /*! \ingroup h5part_c_api - \defgroup h5part_read File Reading + \defgroup h5part_data Readind and Writing Datasets */ /*! \ingroup h5part_c_api @@ -90,16 +89,17 @@ Last modified on April 19, 2007. #define close _close #endif /* WIN32 */ -#include "H5PartTypes.h" #include "H5Part.h" #include "H5PartPrivate.h" #include "H5PartErrors.h" +/********* Global Variable Declarations *************/ +h5part_error_handler _err_handler = H5PartReportErrorHandler; + /********* Private Variable Declarations *************/ -static unsigned _debug = 0; +static unsigned _debug = H5PART_VERB_ERROR; static h5part_int64_t _h5part_errno = H5PART_SUCCESS; -static h5part_error_handler _err_handler = H5PartReportErrorHandler; static char *__funcname; /********** Declaration of private functions ******/ @@ -110,8 +110,8 @@ _init( ); static h5part_int64_t -_file_is_valid ( - const H5PartFile *f +_reset_view ( + H5PartFile *f ); /* @@ -149,13 +149,9 @@ _H5Part_open_file ( memset (f, 0, sizeof (H5PartFile)); f->flags = flags; - f->throttle = 0; - f->groupname_step = strdup ( H5PART_GROUPNAME_STEP ); - if( f->groupname_step == NULL ) { - HANDLE_H5PART_NOMEM_ERR; - goto error_cleanup; - } + /* set default step name */ + strncpy ( f->groupname_step, H5PART_GROUPNAME_STEP, H5PART_STEPNAME_LEN ); f->stepno_width = 0; f->xfer_prop = f->create_prop = H5P_DEFAULT; @@ -224,19 +220,30 @@ _H5Part_open_file ( } } - if (flags & H5PART_FS_LUSTRE) { + if ( flags & H5PART_FS_LUSTRE ) + { /* extend the btree size so that metadata pieces are - * close to the 1MB stripe width */ + * close to the alignment value */ + unsigned int btree_ik = (align - 256) / 96; + unsigned int btree_bytes = 64 + 96*btree_ik; + if ( btree_bytes > align ) { + HANDLE_H5PART_INVALID_ERR( + "btree_ik", btree_ik ); + goto error_cleanup; + } + if (f->myproc == 0) { _H5Part_print_info ( - "Setting HDF5 btree parameter to %d", - H5PART_BTREE_IK ); + "Setting HDF5 btree parameter to %u", + btree_ik ); _H5Part_print_info ( - "Extending HDF5 btree size to %d bytes at rank 3", - 24+16*H5PART_BTREE_IK+40*(2*H5PART_BTREE_IK + 1) ); + "Extending HDF5 btree size to %u bytes at rank 3", + btree_bytes ); } + f->create_prop = H5Pcreate(H5P_FILE_CREATE); H5Pset_istore_k (f->create_prop, H5PART_BTREE_IK); + #ifndef H5_USE_16_API /* defer metadata cache flushing until file close */ H5AC_cache_config_t cache_config; @@ -249,14 +256,14 @@ _H5Part_open_file ( cache_config.flash_incr_mode = H5C_flash_incr__off; cache_config.decr_mode = H5C_decr__off; H5Pset_mdc_config (f->access_prop, &cache_config); -#else +#else // H5_USE_16_API _H5Part_print_info ( "Unable to defer metadata write: need HDF5 1.8"); -#endif +#endif // H5_USE_16_API } f->comm = comm; -#endif +#endif // PARALLEL_IO } else { f->comm = 0; f->nprocs = 1; @@ -326,13 +333,14 @@ _H5Part_open_file ( HANDLE_H5F_OPEN_ERR ( filename, flags ); goto error_cleanup; } - f->mode = flags; + f->nparticles = 0; f->timegroup = -1; - f->shape = 0; + f->shape = H5S_ALL; f->diskshape = H5S_ALL; f->memshape = H5S_ALL; f->viewstart = -1; f->viewend = -1; + f->throttle = 0; _H5Part_print_debug ( "Proc[%d]: Opened file \"%s\" val=%lld", @@ -344,9 +352,6 @@ _H5Part_open_file ( error_cleanup: if (f != NULL ) { - if (f->groupname_step) { - free (f->groupname_step); - } if (f->pnparticles != NULL) { free (f->pnparticles); } @@ -357,7 +362,7 @@ _H5Part_open_file ( #ifdef PARALLEL_IO /*! - \ingroup h5part_openclose + \ingroup h5part_open Opens file with specified filename. @@ -392,7 +397,7 @@ H5PartOpenFileParallel ( } /*! - \ingroup h5part_openclose + \ingroup h5part_open Opens file with specified filename, and also specifices an alignment value used for HDF5 tuning parameters. @@ -416,7 +421,7 @@ H5PartOpenFileParallelAlign ( #endif /*! - \ingroup h5part_openclose + \ingroup h5part_open Opens file with specified filename. @@ -452,7 +457,7 @@ H5PartOpenFile ( } /*! - \ingroup h5part_openclose + \ingroup h5part_open Opens file with specified filename, and also specifices an alignment value used for HDF5 tuning parameters. @@ -479,8 +484,8 @@ H5PartOpenFileAlign ( \return \c H5PART_SUCCESS or error code */ -static h5part_int64_t -_file_is_valid ( +h5part_int64_t +_H5Part_file_is_valid ( const H5PartFile *f /*!< filehandle to check validity of */ ) { @@ -493,7 +498,7 @@ _file_is_valid ( } /*! - \ingroup h5part_openclose + \ingroup h5part_open Closes an open file. @@ -524,7 +529,7 @@ H5PartCloseFile ( } #endif - if( f->shape > 0 ) { + if( f->shape != H5S_ALL ) { r = H5Sclose( f->shape ); if ( r < 0 ) HANDLE_H5S_CLOSE_ERR; f->shape = 0; @@ -539,6 +544,11 @@ H5PartCloseFile ( if ( r < 0 ) HANDLE_H5S_CLOSE_ERR; f->diskshape = 0; } + if( f->memshape != H5S_ALL ) { + r = H5Sclose( f->memshape ); + if ( r < 0 ) HANDLE_H5S_CLOSE_ERR; + f->memshape = 0; + } if( f->xfer_prop != H5P_DEFAULT ) { r = H5Pclose( f->xfer_prop ); if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->xfer_prop" ); @@ -559,9 +569,6 @@ H5PartCloseFile ( if ( r < 0 ) HANDLE_H5F_CLOSE_ERR; f->file = 0; } - if (f->groupname_step) { - free (f->groupname_step); - } if( f->pnparticles ) { free( f->pnparticles ); } @@ -570,60 +577,99 @@ H5PartCloseFile ( return _h5part_errno; } +h5part_int64_t +H5PartFileIsValid ( + H5PartFile *f + ) { + return _H5Part_file_is_valid(f); +} + /*============== File Writing Functions ==================== */ +h5part_int64_t +_H5Part_get_step_name( + H5PartFile *f, + const h5part_int64_t step, + char *name + ) { + + /* Work around sprintf bug on older systems */ + if (f->stepno_width == 0 && step == 0) { + sprintf ( + name, + "%s#%0*lld", + f->groupname_step, 1, (long long) step ); + } + else { + sprintf ( + name, + "%s#%0*lld", + f->groupname_step, f->stepno_width, (long long) step ); + } + + return H5PART_SUCCESS; +} + h5part_int64_t H5PartDefineStepName ( H5PartFile *f, const char *name, const h5part_int64_t width ) { - f->groupname_step = strdup ( name ); - if( f->groupname_step == NULL ) { - return HANDLE_H5PART_NOMEM_ERR; + + CHECK_FILEHANDLE ( f ); + + h5part_int64_t len = H5PART_STEPNAME_LEN - width - 2; + if ( strlen(name) > len ) { + _H5Part_print_warn ( + "Step name has been truncated to fit within %d chars.", + H5PART_STEPNAME_LEN ); } + + strncpy ( f->groupname_step, name, len ); f->stepno_width = (int)width; + + _H5Part_print_debug ( "Step name defined as '%s'", f->groupname_step ); return H5PART_SUCCESS; } -/*! - \ingroup h5part_write - - Set number of particles for current time-step. - - This function's sole purpose is to prevent - needless creation of new HDF5 DataSpace handles if the number of - particles is invariant throughout the simulation. That's its only reason - for existence. After you call this subroutine, all subsequent - operations will assume this number of particles will be written. - - - \return \c H5PART_SUCCESS or error code - */ -h5part_int64_t -H5PartSetNumParticles ( - H5PartFile *f, /*!< [in] Handle to open file */ - h5part_int64_t nparticles /*!< [in] Number of particles */ +static h5part_int64_t +_set_num_particles ( + H5PartFile *f, /*!< [in] Handle to open file */ + const h5part_int64_t nparticles, /*!< [in] Number of particles */ + const h5part_int64_t _stride ) { - SET_FNAME ( "H5PartSetNumParticles" ); - int r; -#ifdef PARALLEL_IO -#ifdef HDF5V160 - hssize_t start[1]; -#else - hsize_t start[1]; -#endif + int ret; + h5part_int64_t herr; - hsize_t stride[1]; - hsize_t count[1]; - hsize_t total; + hsize_t count; +#ifdef HDF5V160 + hssize_t start; +#else + hsize_t start; +#endif + hsize_t stride; hsize_t dmax = H5S_UNLIMITED; + +#ifdef PARALLEL_IO + hsize_t total; register int i; #endif - CHECK_FILEHANDLE( f ); + if ( nparticles <= 0 ) + return HANDLE_H5PART_INVALID_ERR ( "nparticles", nparticles ); + + /* prevent invalid stride value */ + if (_stride < 1) + { + _H5Part_print_warn ( + "Stride < 1 was specified: changing to 1." ); + stride = 1; + } else { + stride = (hsize_t) _stride; + } #ifndef PARALLEL_IO /* @@ -632,28 +678,46 @@ H5PartSetNumParticles ( for parallel IO, this is going to cause problems because we don't know if things have changed globally */ - if ( f->nparticles == nparticles ) { + if ( f->nparticles == nparticles && stride == 1 ) { + _H5Part_print_debug ( + "Serial mode: skipping unnecessary view creation" ); return H5PART_SUCCESS; } #endif - if ( f->diskshape != H5S_ALL ) { - r = H5Sclose( f->diskshape ); - if ( r < 0 ) return HANDLE_H5S_CLOSE_ERR; - f->diskshape = H5S_ALL; + + herr = _reset_view ( f ); + if ( herr < 0 ) return herr; + + f->nparticles = (hsize_t) nparticles; + + /* declare local memory datasize with striding */ + count = f->nparticles * stride; + f->memshape = H5Screate_simple ( 1, &count, &dmax ); + if ( f->memshape < 0 ) + return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles ); + + /* we need a hyperslab selection if there is striding + * (otherwise, the default H5S_ALL selection is ok) + */ + if ( stride > 1 ) + { + start = 0; + count = f->nparticles; + herr = H5Sselect_hyperslab ( + f->memshape, + H5S_SELECT_SET, + &start, + &stride, + &count, NULL ); + if ( herr < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR; } - if(f->memshape != H5S_ALL) { - r = H5Sclose( f->memshape ); - if ( r < 0 ) return HANDLE_H5S_CLOSE_ERR; - f->memshape = H5S_ALL; - } - if( f->shape ) { - r = H5Sclose(f->shape); - if ( r < 0 ) return HANDLE_H5S_CLOSE_ERR; - } - f->nparticles =(hsize_t) nparticles; + #ifndef PARALLEL_IO - f->shape = H5Screate_simple (1, &(f->nparticles), NULL); - if ( f->shape < 0 ) HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles ); + count = f->nparticles; + f->shape = H5Screate_simple ( 1, &count, NULL ); + if ( f->shape < 0 ) HANDLE_H5S_CREATE_SIMPLE_ERR ( count ); + f->viewstart = 0; + f->viewend = nparticles - 1; // view range is *inclusive* #else /* PARALLEL_IO */ /* The Gameplan here is to declare the overall size of the on-disk @@ -670,27 +734,26 @@ H5PartSetNumParticles ( acquire the number of particles to be written from each MPI process */ - r = MPI_Allgather ( + ret = MPI_Allgather ( &nparticles, 1, MPI_LONG_LONG, f->pnparticles, 1, MPI_LONG_LONG, - f->comm); - if ( r != MPI_SUCCESS) { - return HANDLE_MPI_ALLGATHER_ERR; - } + f->comm ); + if ( ret != MPI_SUCCESS) return HANDLE_MPI_ALLGATHER_ERR; + if ( f->myproc == 0 ) { _H5Part_print_debug ( "Particle offsets:" ); - for(i=0;inprocs;i++) + for ( i=0; inprocs; i++ ) _H5Part_print_debug ( "\t[%d] np=%lld", i, (long long) f->pnparticles[i] ); } - /* should I create a selection here? */ /* compute start offsets */ - stride[0] = 1; - start[0] = 0; + start = 0; for (i=0; imyproc; i++) { - start[0] += f->pnparticles[i]; + start += f->pnparticles[i]; } + f->viewstart = start; + f->viewend = start + f->nparticles - 1; // view range is *inclusive* /* compute total nparticles */ total = 0; @@ -698,38 +761,125 @@ H5PartSetNumParticles ( total += f->pnparticles[i]; } - /* declare overall datasize */ - f->shape = H5Screate_simple (1, &total, &total); - if (f->shape < 0) return HANDLE_H5S_CREATE_SIMPLE_ERR ( total ); + if ( stride > 1 ) count = stride * total; + else count = total; + /* declare overall datasize */ + f->shape = H5Screate_simple (1, &count, NULL); + if ( f->shape < 0 ) return HANDLE_H5S_CREATE_SIMPLE_ERR ( count ); /* declare overall data size but then will select a subset */ - f->diskshape = H5Screate_simple (1, &total, &total); - if (f->diskshape < 0) return HANDLE_H5S_CREATE_SIMPLE_ERR ( total ); + f->diskshape = H5Screate_simple (1, &count, NULL); + if ( f->diskshape < 0 ) return HANDLE_H5S_CREATE_SIMPLE_ERR ( count ); - /* declare local memory datasize */ - f->memshape = H5Screate_simple (1, &(f->nparticles), &dmax); - if (f->memshape < 0) - return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles ); - - count[0] = nparticles; - r = H5Sselect_hyperslab ( + count = nparticles; + stride = 1; + herr = H5Sselect_hyperslab ( f->diskshape, H5S_SELECT_SET, - start, - stride, - count, NULL ); - if ( r < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR; + &start, + &stride, + &count, NULL ); + if ( herr < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR; if ( f->timegroup < 0 ) { - r = _H5Part_set_step ( f, 0 ); - if ( r < 0 ) return r; - + herr = _H5Part_set_step ( f, 0 ); + if ( herr < 0 ) return herr; } #endif return H5PART_SUCCESS; } +/*! + \ingroup h5part_model + + Set the number of particles for the current time-step. + After you call this subroutine, all subsequent + operations will assume this number of particles will be written. + + For the parallel library, the \a nparticles value is the number of + particles that the \e individual task will write. You can use + a different value on different tasks. + This function uses an \c MPI_Allgather + call to aggregate each tasks number of particles and determine + the appropiate offsets. Because of the use of this MPI collective, + it is advisable to call this function as + few times as possible when running at large concurrency. + + This function assumes that your particles' data fields are in stored in + contiguous 1D arrays. + For instance, the fields $x$ and $y$ for your particles are stored + in separate arrays \c x[] and \c y[]. + + If instead you store your particles as tuples, so that the values + are arranged $x_1,y_1,x_2,y_2$... than you need to setup striding + (in this case with value 2) using \ref H5PartSetNumParticlesStrided. + + \return \c H5PART_SUCCESS or error code + */ +h5part_int64_t +H5PartSetNumParticles ( + H5PartFile *f, /*!< [in] Handle to open file */ + const h5part_int64_t nparticles /*!< [in] Number of particles */ + ) { + + SET_FNAME ( "H5PartSetNumParticles" ); + CHECK_FILEHANDLE( f ); + + h5part_int64_t herr; + h5part_int64_t stride = 1; + + herr = _set_num_particles ( f, nparticles, stride ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + +/*! + \ingroup h5part_model + + Set the number of particles for the current time-step. + After you call this subroutine, all subsequent + operations will assume this number of particles will be written. + + For the parallel library, the \a nparticles value is the number of + particles that the \e individual task will write. You can use + a different value on different tasks. + This function uses an \c MPI_Allgather + call to aggregate each tasks number of particles and determine + the appropiate offsets. Because of the use of this MPI collective, + it is advisable to call this function as + few times as possible when running at large concurrency. + + This function assumes that your particles' data fields are + stored tuples. For instance, the fields $x$ and $y$ of your + particles are arranged $x_1,y_1,x_2,y_2$... in a single data + array. In this example, the stride value would be 2. + + If you instead have a separate array for each fields, + such as \c x[] and \c y[], + use \ref H5PartSetNumParticles. + + \return \c H5PART_SUCCESS or error code + */ +h5part_int64_t +H5PartSetNumParticlesStrided ( + H5PartFile *f, /*!< [in] Handle to open file */ + const h5part_int64_t nparticles, /*!< [in] Number of particles */ + const h5part_int64_t stride /*!< [in] Stride (e.g. number of fields in the particle array) */ + ) { + + SET_FNAME ( "H5PartSetNumParticlesStrided" ); + CHECK_FILEHANDLE( f ); + + h5part_int64_t herr; + + herr = _set_num_particles ( f, nparticles, stride ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + static h5part_int64_t _write_data ( H5PartFile *f, /*!< IN: Handle to open file */ @@ -744,6 +894,13 @@ _write_data ( "timestep %lld", name, (long long)f->timestep ); + if ( f->shape == H5S_ALL ) { + _H5Part_print_warn ( + "The view is unset or invalid: please " + "set the view or specify a number of particles." ); + return HANDLE_H5PART_BAD_VIEW_ERR ( f->viewstart, f->viewend ); + } + #ifndef H5_USE_16_API htri_t exists = H5Lexists ( f->timegroup, name, H5P_DEFAULT ); if ( exists > 0 ) return HANDLE_H5D_EXISTS_ERR ( name, f->timestep ); @@ -767,9 +924,9 @@ _write_data ( if ( dataset_id < 0 ) return HANDLE_H5D_CREATE_ERR ( name, f->timestep ); -#if PARALLEL_IO - herr = _H5Part_start_throttle( f ); - if (herr < 0) return herr; +#ifdef PARALLEL_IO + herr = _H5Part_start_throttle ( f ); + if ( herr < 0 ) return herr; #endif herr = H5Dwrite ( @@ -780,9 +937,9 @@ _write_data ( f->xfer_prop, array ); -#if PARALLEL_IO - herr = _H5Part_end_throttle( f ); - if (herr < 0) return herr; +#ifdef PARALLEL_IO + herr = _H5Part_end_throttle ( f ); + if ( herr < 0 ) return herr; #endif if ( herr < 0 ) return HANDLE_H5D_WRITE_ERR ( name, f->timestep ); @@ -796,7 +953,7 @@ _write_data ( } /*! - \ingroup h5part_write + \ingroup h5part_data Write array of 64 bit floating point data to file. @@ -842,7 +999,7 @@ H5PartWriteDataFloat64 ( } /*! - \ingroup h5part_write + \ingroup h5part_data Write array of 32 bit floating point data to file. @@ -888,7 +1045,7 @@ H5PartWriteDataFloat32 ( } /*! - \ingroup h5part_write + \ingroup h5part_data Write array of 64 bit integer data to file. @@ -935,7 +1092,7 @@ H5PartWriteDataInt64 ( } /*! - \ingroup h5part_write + \ingroup h5part_data Write array of 32 bit integer data to file. @@ -1009,34 +1166,34 @@ h5part_int64_t _H5Part_normalize_h5_type ( hid_t type ) { + H5T_class_t tclass = H5Tget_class ( type ); int size = H5Tget_size ( type ); - switch ( tclass ){ + switch ( tclass ) { case H5T_INTEGER: - if ( size==8 ) { - return H5PART_INT64; - } - else if ( size==1 ) { - return H5PART_CHAR; - } - break; + if ( size==8 ) { + return H5PART_INT64; + } + else if ( size==1 ) { + return H5PART_CHAR; + } + break; case H5T_FLOAT: - if ( size==8 ) { - return H5PART_FLOAT64; - } - else if ( size==4 ) { - return H5PART_FLOAT32; - } - break; + if ( size==8 ) { + return H5PART_FLOAT64; + } + else if ( size==4 ) { + return H5PART_FLOAT32; + } + break; case H5T_STRING: - return H5PART_STRING; + return H5PART_STRING; default: - ; /* NOP */ + ;/* NOP */ } - _H5Part_print_warn ( "Unknown type %d", (int)type ); - return -1; + return HANDLE_H5PART_TYPE_ERR; } h5part_int64_t @@ -1051,8 +1208,6 @@ _H5Part_read_attrib ( hid_t attrib_id; hid_t space_id; hid_t type_id; - hid_t mytype; - hsize_t nelem; #ifndef H5_USE_16_API if (! H5Aexists ( id, attrib_name )) { @@ -1070,9 +1225,6 @@ _H5Part_read_attrib ( space_id = H5Aget_space ( attrib_id ); if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR; - nelem = H5Sget_simple_extent_npoints ( space_id ); - if ( nelem < 0 ) return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR; - herr = H5Aread ( attrib_id, type_id, attrib_value ); if ( herr < 0 ) return HANDLE_H5A_READ_ERR; @@ -1085,43 +1237,6 @@ _H5Part_read_attrib ( herr = H5Aclose ( attrib_id ); if ( herr < 0 ) return HANDLE_H5A_CLOSE_ERR; - -/* if ( attrib_id <= 0 ) return HANDLE_H5A_OPEN_NAME_ERR( attrib_name ); */ - -/* mytype = H5Aget_type ( attrib_id ); */ -/* if ( mytype < 0 ) return HANDLE_H5A_GET_TYPE_ERR; */ - -/* space_id = H5Aget_space ( attrib_id ); */ -/* if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR; */ - -/* nelem = H5Sget_simple_extent_npoints ( space_id ); */ -/* if ( nelem < 0 ) return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR; */ - -/* type_id = _H5Part_normalize_h5_type ( mytype ); */ - -/* herr = H5Aread (attrib_id, type_id, attrib_value ); */ -/* if ( herr < 0 ) return HANDLE_H5A_READ_ERR; */ - -/* /\* _H5Part_close_h5_type( type_id ); *\/ */ - -/* if( type_id != H5T_NATIVE_CHAR && */ -/* type_id != H5T_NATIVE_INT64 && */ -/* type_id != H5T_NATIVE_FLOAT && */ -/* type_id != H5T_NATIVE_DOUBLE ) */ -/* { */ -/* herr = H5Tclose ( type_id ); */ -/* if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR; */ -/* } */ - -/* herr = H5Sclose ( space_id ); */ -/* if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; */ - -/* herr = H5Tclose ( mytype ); */ -/* if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR; */ - -/* herr = H5Aclose ( attrib_id ); */ -/* if ( herr < 0 ) return HANDLE_H5A_CLOSE_ERR; */ - return H5PART_SUCCESS; } @@ -1134,34 +1249,36 @@ _H5Part_write_attrib ( const hsize_t attrib_nelem ) { - herr_t herr; - h5part_int64_t h5err; + h5part_int64_t herr; hid_t space_id; hid_t attrib_id; hid_t type = attrib_type; - if (attrib_type == H5T_STRING) { - h5err = _H5Part_make_string_type(&type, attrib_nelem); - if ( h5err < 0 ) return h5err; + if ( attrib_type == H5PART_STRING ) + { + herr = _H5Part_make_string_type ( &type, attrib_nelem ); + if ( herr < 0 ) return herr; + space_id = H5Screate (H5S_SCALAR); if ( space_id < 0 ) return HANDLE_H5S_CREATE_SCALAR_ERR; } else { - space_id = H5Screate_simple (1, &attrib_nelem, NULL); + space_id = H5Screate_simple ( 1, &attrib_nelem, NULL ); if ( space_id < 0 ) return HANDLE_H5S_CREATE_SIMPLE_ERR ( attrib_nelem ); } - attrib_id = H5Acreate( id, - attrib_name, - type, - space_id, - H5P_DEFAULT + attrib_id = H5Acreate( + id, + attrib_name, + type, + space_id, + H5P_DEFAULT #ifndef H5_USE_16_API - , H5P_DEFAULT + , H5P_DEFAULT #endif - ); + ); if ( attrib_id < 0 ) return HANDLE_H5A_CREATE_ERR ( attrib_name ); @@ -1174,7 +1291,7 @@ _H5Part_write_attrib ( herr = H5Sclose ( space_id ); if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; - if (attrib_type == H5T_STRING) { + if ( attrib_type == H5PART_STRING ) { herr = H5Tclose ( type ); if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR; } @@ -1182,6 +1299,59 @@ _H5Part_write_attrib ( return H5PART_SUCCESS; } +h5part_int64_t +_H5Part_write_file_attrib ( + H5PartFile *f, + const char *name, + const hid_t type, + const void *value, + const hsize_t nelem + ) { + + hid_t group_id = H5Gopen ( f->file, "/" +#ifndef H5_USE_16_API + , H5P_DEFAULT +#endif + ); + + if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR( "/" ); + + h5part_int64_t herr = _H5Part_write_attrib ( + group_id, + name, + type, + value, + nelem ); + if ( herr < 0 ) return herr; + + herr = H5Gclose ( group_id ); + if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR; + + return H5PART_SUCCESS; +} + +h5part_int64_t +_H5Part_write_step_attrib ( + H5PartFile *f, + const char *name, + const hid_t type, + const void *value, + const hsize_t nelem + ) { + + CHECK_TIMEGROUP( f ); + + h5part_int64_t herr = _H5Part_write_attrib ( + f->timegroup, + name, + type, + value, + nelem ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + h5part_int64_t _H5Part_get_attrib_info ( hid_t id, @@ -1223,6 +1393,7 @@ _H5Part_get_attrib_info ( if ( mytype < 0 ) return HANDLE_H5A_GET_TYPE_ERR; *attrib_type = _H5Part_normalize_h5_type ( mytype ); + if ( *attrib_type < 0 ) return *attrib_type; herr = H5Tclose ( mytype ); if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR; @@ -1232,28 +1403,25 @@ _H5Part_get_attrib_info ( return H5PART_SUCCESS; } +/*! + }@ +*/ /********************** attribute API ****************************************/ /*! \ingroup h5part_attrib - Writes a string attribute bound to a file. - - This function creates a new attribute \c name with the string \c value as - content. The attribute is bound to the file associated with the file handle - \c f. - - If the attribute already exists an error will be returned. There - is currently no way to change the content of an existing attribute. + Writes an attribute \c name with the string \c value to + the file root ("/"). \return \c H5PART_SUCCESS or error code */ h5part_int64_t H5PartWriteFileAttribString ( H5PartFile *f, /*!< [in] Handle to open file */ - const char *attrib_name,/*!< [in] Name of attribute to create */ - const char *attrib_value/*!< [in] Value of attribute */ + const char *name, /*!< [in] Name of attribute to create */ + const char *value /*!< [in] Value of attribute */ ) { SET_FNAME ( "H5PartWriteFileAttribString" ); @@ -1261,39 +1429,25 @@ H5PartWriteFileAttribString ( CHECK_FILEHANDLE ( f ); CHECK_WRITABLE_MODE( f ); - hid_t group_id = H5Gopen ( f->file, "/" -#ifndef H5_USE_16_API - , H5P_DEFAULT -#endif - ); - - if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR( "/" ); - - h5part_int64_t herr = _H5Part_write_attrib ( - group_id, - attrib_name, - H5T_STRING, - attrib_value, - strlen ( attrib_value ) + 1 ); + h5part_int64_t herr = _H5Part_write_file_attrib ( + f, + name, + H5PART_STRING, + value, + strlen ( value ) + 1 ); if ( herr < 0 ) return herr; - herr = H5Gclose ( group_id ); - if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR; - return H5PART_SUCCESS; } /*! \ingroup h5part_attrib - Writes a string attribute bound to the current time-step. - - If the attribute already exists an error will be returned. There - is currently no way to change the content of an existing attribute. + Writes an attribute \c name with the string \c value to + the current timestep. \return \c H5PART_SUCCESS or error code */ - h5part_int64_t H5PartWriteStepAttribString ( H5PartFile *f, /*!< [in] Handle to open file */ @@ -1305,12 +1459,11 @@ H5PartWriteStepAttribString ( CHECK_FILEHANDLE ( f ); CHECK_WRITABLE_MODE( f ); - CHECK_TIMEGROUP( f ); - h5part_int64_t herr = _H5Part_write_attrib ( - f->timegroup, + h5part_int64_t herr = _H5Part_write_step_attrib ( + f, name, - H5T_STRING, + H5PART_STRING, value, strlen ( value ) + 1 ); if ( herr < 0 ) return herr; @@ -1321,115 +1474,43 @@ H5PartWriteStepAttribString ( /*! \ingroup h5part_attrib - Writes an int32 attribute bound to the current time-step. + Writes an attribute \c name with values in the array \c data + of \c nelem elements to + the current timestep. - If the attribute already exists an error will be returned. There - is currently no way to change the content of an existing attribute. + The type of \c data must ve specified using one of the folowing + macros: + + - \c H5PART_FLOAT64 (for \c h5part_float64_t) + - \c H5PART_FLOAT32 (for \c h5part_float32_t) + - \c H5PART_INT64 (for \c h5part_int64_t) + - \c H5PART_INT32 (for \c h5part_int32_t) + - \c H5PART_CHAR (for \c char) + - \c H5PART_STRING (for \c char*) \return \c H5PART_SUCCESS or error code */ - -h5part_int64_t -H5PartWriteStepAttribInt32 ( - H5PartFile *f, /*!< [in] Handle to open file */ - const char *name, /*!< [in] Name of attribute to create */ - const h5part_int32_t value /*!< [in] Value of attribute */ - ) { - - SET_FNAME ( "H5PartWriteStepAttribInt32" ); - - CHECK_FILEHANDLE ( f ); - CHECK_WRITABLE_MODE( f ); - CHECK_TIMEGROUP( f ); - - h5part_int64_t herr = _H5Part_write_attrib ( - f->timegroup, - name, - H5T_NATIVE_INT32, - &value, - 1 ); - if ( herr < 0 ) return herr; - - return H5PART_SUCCESS; -} - -/*! - \ingroup h5part_attrib - - Writes a float32 attribute bound to the current time-step. - - If the attribute already exists an error will be returned. There - is currently no way to change the content of an existing attribute. - - \return \c H5PART_SUCCESS or error code -*/ - -h5part_int64_t -H5PartWriteStepAttribFloat32 ( - H5PartFile *f, /*!< [in] Handle to open file */ - const char *name, /*!< [in] Name of attribute to create */ - const h5part_float32_t value /*!< [in] Value of attribute */ - ) { - - SET_FNAME ( "H5PartWriteStepAttribFloat32" ); - - CHECK_FILEHANDLE ( f ); - CHECK_WRITABLE_MODE( f ); - CHECK_TIMEGROUP( f ); - - h5part_int64_t herr = _H5Part_write_attrib ( - f->timegroup, - name, - H5T_NATIVE_FLOAT, - &value, - 1 ); - if ( herr < 0 ) return herr; - - return H5PART_SUCCESS; -} - -/*! - \ingroup h5part_attrib - - Writes a attribute bound to the current time-step. - - This function creates a new attribute \c name with the string \c value as - content. The attribute is bound to the current time step in the file given - by the file handle \c f. - - The value of the attribute is given the parameter \c type, which must be one - of \c H5T_NATIVE_DOUBLE, \c H5T_NATIVE_INT64 of \c H5T_NATIVE_CHAR, the array - \c value and the number of elements \c nelem in the array. - - If the attribute already exists an error will be returned. There - is currently no way to change the content of an existing attribute. - - \return \c H5PART_SUCCESS or error code -*/ - h5part_int64_t H5PartWriteStepAttrib ( H5PartFile *f, /*!< [in] Handle to open file */ - const char *attrib_name, /*!< [in] Name of attribute */ - const h5part_int64_t attrib_type,/*!< [in] Type of value. */ - const void *attrib_value, /*!< [in] Value of attribute */ - const h5part_int64_t attrib_nelem/*!< [in] Number of elements */ + const char *name, /*!< [in] Name of attribute */ + const h5part_int64_t type, /*!< [in] Type of values */ + const void *data, /*!< [in] Array of attribute values */ + const h5part_int64_t nelem /*!< [in] Number of array elements */ ){ SET_FNAME ( "H5PartWriteStepAttrib" ); - h5part_int64_t herr; - CHECK_FILEHANDLE ( f ); CHECK_WRITABLE_MODE( f ); CHECK_TIMEGROUP( f ); - herr = _H5Part_write_attrib ( - f->timegroup, - attrib_name, - (const hid_t)attrib_type, - attrib_value, - attrib_nelem ); + h5part_int64_t herr = _H5Part_write_step_attrib ( + f, + name, + (const hid_t)type, + data, + nelem ); if ( herr < 0 ) return herr; return H5PART_SUCCESS; @@ -1438,58 +1519,44 @@ H5PartWriteStepAttrib ( /*! \ingroup h5part_attrib - Writes a attribute bound to a file. + Writes an attribute \c name with values in the array \c data + of \c nelem elements to + the file root ("/"). - This function creates a new attribute \c name with the string \c value as - content. The attribute is bound to the file file given by the file handle - \c f. + The type of \c data must ve specified using one of the folowing + macros: - The value of the attribute is given the parameter \c type, which must be one - of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64 of H5T_NATIVE_CHAR, the array \c value - and the number of elements \c nelem in the array. - - If the attribute already exists an error will be returned. There - is currently no way to change the content of an existing attribute. + - \c H5PART_FLOAT64 (for \c h5part_float64_t) + - \c H5PART_FLOAT32 (for \c h5part_float32_t) + - \c H5PART_INT64 (for \c h5part_int64_t) + - \c H5PART_INT32 (for \c h5part_int32_t) + - \c H5PART_CHAR (for \c char) + - \c H5PART_STRING (for \c char*) \return \c H5PART_SUCCESS or error code */ - h5part_int64_t H5PartWriteFileAttrib ( H5PartFile *f, /*!< [in] Handle to open file */ - const char *attrib_name, /*!< [in] Name of attribute */ - const h5part_int64_t attrib_type,/*!< [in] Type of value. */ - const void *attrib_value, /*!< [in] Value of attribute */ - const h5part_int64_t attrib_nelem/*!< [in] Number of elements */ + const char *name, /*!< [in] Name of attribute */ + const h5part_int64_t type, /*!< [in] Type of values */ + const void *data, /*!< [in] Array of attribute values */ + const h5part_int64_t nelem /*!< [in] Number of array elements */ ) { SET_FNAME ( "H5PartWriteFileAttrib" ); - h5part_int64_t herr; - hid_t group_id; - CHECK_FILEHANDLE ( f ); CHECK_WRITABLE_MODE ( f ); - group_id = H5Gopen(f->file,"/" -#ifndef H5_USE_16_API - , H5P_DEFAULT -#endif - ); - - if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR( "/" ); - - herr = _H5Part_write_attrib ( - group_id, - attrib_name, - (const hid_t)attrib_type, - attrib_value, - attrib_nelem ); + h5part_int64_t herr = _H5Part_write_file_attrib ( + f, + name, + (const hid_t)type, + data, + nelem ); if ( herr < 0 ) return herr; - herr = H5Gclose ( group_id ); - if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR; - return H5PART_SUCCESS; } @@ -1506,10 +1573,10 @@ H5PartGetNumStepAttribs ( ) { SET_FNAME ( "H5PartGetNumStepAttribs" ); - h5part_int64_t nattribs; - CHECK_FILEHANDLE ( f ); + h5part_int64_t nattribs; + nattribs = H5Aget_num_attrs(f->timegroup); if ( nattribs < 0 ) HANDLE_H5A_GET_NUM_ATTRS_ERR; @@ -1664,13 +1731,11 @@ H5PartReadStepAttrib ( ) { SET_FNAME ( "H5PartReadStepAttrib" ); + CHECK_FILEHANDLE( f ); h5part_int64_t herr; - CHECK_FILEHANDLE( f ); - - herr = _H5Part_read_attrib ( f->timegroup, - attrib_name, attrib_value ); + herr = _H5Part_read_attrib ( f->timegroup, attrib_name, attrib_value ); if ( herr < 0 ) return herr; return H5PART_SUCCESS; @@ -1733,23 +1798,10 @@ _H5Part_set_step ( const h5part_int64_t step /*!< [in] Time-step to set. */ ) { - char name[128]; + char stepname[H5PART_STEPNAME_LEN]; + _H5Part_get_step_name(f, step, stepname); - /* Work around sprintf bug on older systems */ - if (f->stepno_width == 0 && step == 0) { - sprintf ( - name, - "%s#%0*lld", - f->groupname_step, 1, (long long) step ); - } - else { - sprintf ( - name, - "%s#%0*lld", - f->groupname_step, f->stepno_width, (long long) step ); - } - - if ( (!(f->mode & H5PART_READ)) && _H5Part_have_group ( f->file, name ) ) { + if ( (!(f->flags & H5PART_READ)) && _H5Part_have_group ( f->file, stepname ) ) { return HANDLE_H5PART_STEP_EXISTS_ERR ( step ); } @@ -1760,20 +1812,20 @@ _H5Part_set_step ( f->timegroup = -1; f->timestep = step; - if( f->mode & H5PART_READ ) { + if ( f->flags & H5PART_READ ) { _H5Part_print_debug ( "Proc[%d]: Set step to #%lld for file %lld", f->myproc, (long long)step, (long long)(size_t) f ); - f->timegroup = H5Gopen ( f->file, name + f->timegroup = H5Gopen ( f->file, stepname #ifndef H5_USE_16_API , H5P_DEFAULT #endif ); if ( f->timegroup < 0 ) - return HANDLE_H5G_OPEN_ERR( name ); + return HANDLE_H5G_OPEN_ERR( stepname ); } else { _H5Part_print_debug ( @@ -1783,7 +1835,7 @@ _H5Part_set_step ( (long long)(size_t) f ); f->timegroup = H5Gcreate( f->file, - name, + stepname, 0 #ifndef H5_USE_16_API , H5P_DEFAULT, H5P_DEFAULT @@ -1791,14 +1843,14 @@ _H5Part_set_step ( ); if ( f->timegroup < 0 ) - return HANDLE_H5G_CREATE_ERR ( name ); + return HANDLE_H5G_CREATE_ERR ( stepname ); } return H5PART_SUCCESS; } /*! - \ingroup h5part_read + \ingroup h5part_model Set the current time-step. @@ -1856,11 +1908,12 @@ _H5Part_have_group ( #ifndef H5_USE_16_API herr_t _H5Part_iteration_operator2 ( - hid_t group_id, /*!< [in] parent object id */ - const char *member_name, /*!< [in] child object name */ - const H5L_info_t *linfo, /*!< link info */ - void *operator_data ) /*!< [in,out] data passed to the iterator */ -{ + hid_t group_id, /*!< [in] parent object id */ + const char *member_name, /*!< [in] child object name */ + const H5L_info_t *linfo, /*!< link info */ + void *operator_data /*!< [in,out] data passed to the iterator */ + ) { + struct _iter_op_data *data = (struct _iter_op_data*)operator_data; herr_t herr = 0; @@ -1891,6 +1944,7 @@ _H5Part_iteration_operator2 ( case H5L_TYPE_EXTERNAL: { char *targbuf = (char*) malloc( linfo->u.val_size ); + if ( targbuf == NULL ) return (herr_t)HANDLE_H5PART_NOMEM_ERR; if(H5Lget_val(group_id, member_name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { @@ -1966,52 +2020,53 @@ _H5Part_iteration_operator ( hid_t group_id, /*!< [in] parent object id */ const char *member_name,/*!< [in] child object name */ void *operator_data /*!< [in,out] data passed to the iterator */ - ) -{ - struct _iter_op_data *data = (struct _iter_op_data*)operator_data; - herr_t herr; + ) { + + struct _iter_op_data *data = (struct _iter_op_data*)operator_data; + herr_t herr; /* printf( "%d GROUP ITERATOR %s %d\n", __LINE__, member_name, data->type ); */ - if ( data->type != H5G_UNKNOWN ) { - + if ( data->type != H5G_UNKNOWN ) + { #ifndef H5_USE_16_API - H5O_info_t objinfo; + H5O_info_t objinfo; - hid_t obj_id = H5Oopen(group_id, member_name, H5P_DEFAULT); - if ( obj_id < 0 ) - return (herr_t)HANDLE_H5G_OPEN_ERR ( member_name ); + hid_t obj_id = H5Oopen(group_id, member_name, H5P_DEFAULT); + if ( obj_id < 0 ) + return (herr_t)HANDLE_H5G_OPEN_ERR ( member_name ); - herr = H5Oget_info ( obj_id, &objinfo ); - if ( herr < 0 ) - return (herr_t)HANDLE_H5G_GET_OBJINFO_ERR ( member_name ); + herr = H5Oget_info ( obj_id, &objinfo ); + if ( herr < 0 ) + return (herr_t)HANDLE_H5G_GET_OBJINFO_ERR ( member_name ); - H5Oclose( obj_id ); + H5Oclose( obj_id ); #else - H5G_stat_t objinfo; - herr = H5Gget_objinfo( group_id, member_name, 1, &objinfo ); - if ( herr < 0 ) return (herr_t)HANDLE_H5G_GET_OBJINFO_ERR ( member_name ); + H5G_stat_t objinfo; + herr = H5Gget_objinfo( group_id, member_name, 1, &objinfo ); + if ( herr < 0 ) + return (herr_t)HANDLE_H5G_GET_OBJINFO_ERR ( member_name ); #endif + if ( objinfo.type != data->type ) + return 0; /* don't count, continue iteration */ + } - if ( objinfo.type != data->type ) - { - return 0;/* don't count, continue iteration */ - } - } - - if ( data->name && (data->stop_idx == data->count) ) { - memset ( data->name, 0, data->len ); - strncpy ( data->name, member_name, data->len-1 ); + if ( data->name && (data->stop_idx == data->count) ) + { + memset ( data->name, 0, data->len ); + strncpy ( data->name, member_name, data->len-1 ); - return 1; /* stop iteration */ - } - /* count only if pattern is NULL or member name matches */ - if ( !data->pattern || - (strncmp (member_name, data->pattern, strlen(data->pattern)) == 0) - ) { - data->count++; - } - return 0; /* continue iteration */ + return 1; /* stop iteration */ + } + + /* count only if pattern is NULL or member name matches */ + if ( !data->pattern || + (strncmp (member_name, data->pattern, strlen(data->pattern)) == 0) + ) { + data->count++; + } + + return 0; /* continue iteration */ } /*! @@ -2054,9 +2109,6 @@ _H5Part_get_num_objects_matching_pattern ( data.type = type; data.pattern = pattern; -/* herr = H5Giterate ( group_id, group_name, &idx, */ -/* _H5Part_iteration_operator, &data ); */ - #ifndef H5_USE_16_API hid_t child_id = H5Gopen( group_id, group_name, H5P_DEFAULT ); if ( child_id < 0 ) return child_id; @@ -2079,7 +2131,8 @@ _H5Part_get_num_objects_matching_pattern ( /*! \ingroup h5part_kernel - Iterator for \c H5Giterate(). + \return 1 on success + 0 for no entry */ h5part_int64_t _H5Part_get_object_name ( @@ -2101,40 +2154,35 @@ _H5Part_get_object_name ( data.name = obj_name; data.len = (size_t)len_obj_name; -/* herr = H5Giterate ( group_id, group_name, &iterator_idx, */ -/* _H5Part_iteration_operator, &data ); */ - #ifndef H5_USE_16_API - hid_t child_id = H5Gopen( group_id, group_name, H5P_DEFAULT ); + hid_t child_id = H5Gopen ( group_id, group_name, H5P_DEFAULT ); if ( child_id < 0 ) return child_id; - herr = H5Literate( child_id, H5_INDEX_NAME, H5_ITER_INC, 0, + herr = H5Literate ( child_id, H5_INDEX_NAME, H5_ITER_INC, 0, _H5Part_iteration_operator2, &data ); #else herr = H5Giterate ( group_id, group_name, &iterator_idx, _H5Part_iteration_operator, &data ); #endif - - if ( herr < 0 ) return (h5part_int64_t)herr; - - if ( herr == 0 ) HANDLE_H5PART_NOENTRY_ERR( group_name, - type, idx ); + if ( herr < 0 ) { + return HANDLE_H5L_ITERATE_ERR; + } + else if ( herr == 0 ) return 0; #ifndef H5_USE_16_API - H5Gclose( child_id ); + herr = H5Gclose ( child_id ); + if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR; #endif - return H5PART_SUCCESS; + return 1; } /*! - \ingroup h5part_read + \ingroup h5part_model - Query whether a particular step already exists in the file - \c f. + Query whether a particular \a step already exists in + the file \a f. - It works for both reading and writing of files - - \return true or false + \return 0 or 1 */ h5part_int64_t H5PartHasStep ( @@ -2146,20 +2194,15 @@ H5PartHasStep ( CHECK_FILEHANDLE( f ); - char name[128]; - /* Work around sprintf bug on older systems */ - if (f->stepno_width == 0 && step == 0) { - sprintf ( name, "%s#%0*lld", f->groupname_step, 1, (long long) step ); - } - else { - sprintf ( name, "%s#%0*lld", f->groupname_step, f->stepno_width, (long long) step ); - } - return _H5Part_have_group ( f->file, name ); + char stepname[H5PART_STEPNAME_LEN]; + _H5Part_get_step_name(f, step, stepname); + + return _H5Part_have_group ( f->file, stepname ); } /*! - \ingroup h5part_read + \ingroup h5part_model Get the number of time-steps that are currently stored in the file \c f. @@ -2186,7 +2229,7 @@ H5PartGetNumSteps ( } /*! - \ingroup h5part_read + \ingroup h5part_model Get the number of datasets that are stored at the current time-step. @@ -2200,29 +2243,16 @@ H5PartGetNumDatasets ( SET_FNAME ( "H5PartGetNumDatasets" ); - char stepname[128]; - CHECK_FILEHANDLE( f ); - - /* Work around sprintf bug on older systems */ - if (f->stepno_width == 0 && f->timestep == 0) { - sprintf ( - stepname, - "%s#%0*lld", - f->groupname_step, 1, (long long) f->timestep ); - } - else { - sprintf ( - stepname, - "%s#%0*lld", - f->groupname_step, f->stepno_width, (long long) f->timestep ); - } + + char stepname[H5PART_STEPNAME_LEN]; + _H5Part_get_step_name(f, f->timestep, stepname); return _H5Part_get_num_objects ( f->file, stepname, H5G_DATASET ); } /*! - \ingroup h5part_read + \ingroup h5part_model This reads the name of a dataset specified by it's index in the current time-step. @@ -2241,41 +2271,40 @@ H5PartGetDatasetName ( SET_FNAME ( "H5PartGetDatasetName" ); - char stepname[128]; - CHECK_FILEHANDLE ( f ); CHECK_TIMEGROUP ( f ); - /* Work around sprintf bug on older systems */ - if (f->stepno_width == 0 && f->timestep == 0) { - sprintf ( - stepname, - "%s#%0*lld", - f->groupname_step, 1, (long long) f->timestep ); - } - else { - sprintf ( - stepname, - "%s#%0*lld", - f->groupname_step, f->stepno_width, (long long) f->timestep ); - } + char stepname[H5PART_STEPNAME_LEN]; + _H5Part_get_step_name(f, f->timestep, stepname); - return _H5Part_get_object_name ( + h5part_int64_t herr = _H5Part_get_object_name ( f->file, stepname, H5G_DATASET, idx, name, len_of_name ); + if ( herr == 0 ) HANDLE_H5PART_NOENTRY_ERR( + stepname, H5G_DATASET, idx ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; } /*! - \ingroup h5part_read + \ingroup h5part_model - Gets the name, type and number of elements of a dataset specified by it's - index in the current time-step. + Gets the name, type and number of elements of a dataset based on its + index in the current timestep. - Type is one of \c H5T_NATIVE_DOUBLE or \c H5T_NATIVE_INT64. + Type is one of the following macros: + + - \c H5PART_FLOAT64 (for \c h5part_float64_t) + - \c H5PART_FLOAT32 (for \c h5part_float32_t) + - \c H5PART_INT64 (for \c h5part_int64_t) + - \c H5PART_INT32 (for \c h5part_int32_t) + - \c H5PART_CHAR (for \c char) + - \c H5PART_STRING (for \c char*) \return \c H5PART_SUCCESS */ @@ -2293,127 +2322,69 @@ H5PartGetDatasetInfo ( SET_FNAME ( "H5PartGetDatasetInfo" ); h5part_int64_t herr; - hid_t dataset_id; - hid_t mytype; - char step_name[128]; + hid_t dataset; + hid_t space; + hid_t h5type; CHECK_FILEHANDLE ( f ); CHECK_TIMEGROUP ( f ); - /* Work around sprintf bug on older systems */ - if (f->stepno_width == 0 && f->timestep == 0) { - sprintf ( - step_name, - "%s#%0*lld", - f->groupname_step, 1, (long long) f->timestep ); - } - else { - sprintf ( - step_name, - "%s#%0*lld", - f->groupname_step, f->stepno_width, (long long) f->timestep ); - } + char stepname[H5PART_STEPNAME_LEN]; + _H5Part_get_step_name(f, f->timestep, stepname); herr = _H5Part_get_object_name ( f->file, - step_name, + stepname, H5G_DATASET, idx, dataset_name, len_dataset_name ); - if ( herr < 0 ) return herr; + if ( herr == 0 ) { + return HANDLE_H5PART_NOENTRY_ERR( stepname, H5G_DATASET, idx ); + } + else if ( herr < 0 ) return herr; - *nelem = _H5Part_get_num_particles ( f ); - if ( *nelem < 0 ) return *nelem; - - dataset_id = H5Dopen( f->timegroup, dataset_name + dataset = H5Dopen( f->timegroup, dataset_name #ifndef H5_USE_16_API - , H5P_DEFAULT + , H5P_DEFAULT #endif - ); + ); + if ( dataset < 0 ) HANDLE_H5D_OPEN_ERR ( dataset_name ); - if ( dataset_id < 0 ) HANDLE_H5D_OPEN_ERR ( dataset_name ); + h5type = H5Dget_type ( dataset ); + if ( h5type < 0 ) HANDLE_H5D_GET_TYPE_ERR; - mytype = H5Dget_type ( dataset_id ); - if ( mytype < 0 ) HANDLE_H5D_GET_TYPE_ERR; + if ( type ) *type = _H5Part_normalize_h5_type ( h5type ); + if ( *type < 0 ) return *type; - if ( type ) *type = _H5Part_normalize_h5_type ( mytype ); + if ( nelem ) + { + space = H5Dget_space ( dataset ); + if ( space < 0 ) return HANDLE_H5D_GET_SPACE_ERR; - herr = H5Tclose(mytype); + *nelem = H5Sget_simple_extent_npoints ( space ); + if ( *nelem < 0 ) + return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR; + + herr = H5Sclose ( space ); + if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; + } + + herr = H5Tclose ( h5type ); if ( herr < 0 ) HANDLE_H5T_CLOSE_ERR; - herr = H5Dclose(dataset_id); + herr = H5Dclose ( dataset ); if ( herr < 0 ) HANDLE_H5D_CLOSE_ERR; return H5PART_SUCCESS; } -static hid_t -_get_diskshape_for_reading ( - H5PartFile *f, - hid_t dataset +static h5part_int64_t +_H5Part_has_view ( + H5PartFile *f ) { - herr_t r; - - hid_t space = H5Dget_space(dataset); - if ( space < 0 ) return (hid_t)HANDLE_H5D_GET_SPACE_ERR; - - if ( H5PartHasView(f) ){ - hsize_t stride; - hsize_t count; -#ifdef HDF5V160 - hssize_t start; -#else - hsize_t start; -#endif - _H5Part_print_debug ( "Selection is available" ); - - /* so, is this selection inclusive or exclusive? */ - start = f->viewstart; - count = f->viewend - f->viewstart; /* to be inclusive */ - stride=1; - - /* now we select a subset */ - if ( f->diskshape > 0 ) { - r = H5Sselect_hyperslab ( - f->diskshape, H5S_SELECT_SET, - &start, &stride, &count, NULL); - if ( r < 0 ) return (hid_t)HANDLE_H5S_SELECT_HYPERSLAB_ERR; - } - /* now we select a subset */ - r = H5Sselect_hyperslab ( - space,H5S_SELECT_SET, - &start, &stride, &count, NULL ); - if ( r < 0 ) return (hid_t)HANDLE_H5S_SELECT_HYPERSLAB_ERR; - - _H5Part_print_debug ( - "Selection: range=%d:%d, npoints=%d s=%d", - (int)f->viewstart,(int)f->viewend, - (int)H5Sget_simple_extent_npoints(space), - (int)H5Sget_select_npoints(space) ); - } else { - _H5Part_print_debug ( "Selection" ); - } - return space; -} - -static hid_t -_get_memshape_for_reading ( - H5PartFile *f, - hid_t dataset - ) { - - if(H5PartHasView(f)) { - hsize_t dmax=H5S_UNLIMITED; - hsize_t len = f->viewend - f->viewstart; - hid_t r = H5Screate_simple(1,&len,&dmax); - if ( r < 0 ) return (hid_t)HANDLE_H5S_CREATE_SIMPLE_ERR ( len ); - return r; - } - else { - return H5S_ALL; - } + return ( f->viewstart >= 0 ) && ( f->viewend >= 0 ); } h5part_int64_t @@ -2425,30 +2396,24 @@ _H5Part_get_num_particles ( hid_t space_id; hid_t dataset_id; char dataset_name[128]; - char step_name[128]; hsize_t nparticles; - /* Get first dataset in current time-step */ - if (f->stepno_width == 0 && f->timestep == 0) { - sprintf ( - step_name, - "%s#%0*lld", - f->groupname_step, 1, (long long) f->timestep ); - } - else { - sprintf ( - step_name, - "%s#%0*lld", - f->groupname_step, f->stepno_width, (long long) f->timestep ); - } + char stepname[H5PART_STEPNAME_LEN]; + _H5Part_get_step_name(f, f->timestep, stepname); herr = _H5Part_get_object_name ( f->file, - step_name, + stepname, H5G_DATASET, 0, dataset_name, sizeof (dataset_name) ); if ( herr < 0 ) return herr; + else if ( herr == 0 ) { + _H5Part_print_warn ( + "There are no datasets in timestep %s: " + "reporting 0 particles.", stepname ); + return 0; + } dataset_id = H5Dopen ( f->timegroup, dataset_name #ifndef H5_USE_16_API @@ -2459,22 +2424,31 @@ _H5Part_get_num_particles ( if ( dataset_id < 0 ) return HANDLE_H5D_OPEN_ERR ( dataset_name ); - space_id = _get_diskshape_for_reading ( f, dataset_id ); - if ( space_id < 0 ) return (h5part_int64_t)space_id; - - if ( H5PartHasView ( f ) ) { - nparticles = H5Sget_select_npoints ( space_id ); + /* if a view exists, use its size as the number of particles */ + if ( _H5Part_has_view ( f ) ) { + nparticles = H5Sget_select_npoints ( f->diskshape ); if ( nparticles < 0 ) return HANDLE_H5S_GET_SELECT_NPOINTS_ERR; + if ( nparticles != f->viewend - f->viewstart + 1 ) + _H5Part_print_warn ( + "Number of particles (%lld) does not agree " + "with view range.", nparticles ); + return HANDLE_H5PART_BAD_VIEW_ERR ( + f->viewstart, f->viewend); } + /* otherwise, report all particles on disk in the first dataset + * for this timestep */ else { + space_id = H5Dget_space ( dataset_id ); + if ( space_id < 0 ) return HANDLE_H5D_GET_SPACE_ERR; + nparticles = H5Sget_simple_extent_npoints ( space_id ); if ( nparticles < 0 ) return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR; - } - if ( space_id != H5S_ALL ) { + herr = H5Sclose ( space_id ); if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; } + herr = H5Dclose ( dataset_id ); if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR; @@ -2482,11 +2456,18 @@ _H5Part_get_num_particles ( } /*! - \ingroup h5part_read + \ingroup h5part_model - This gets the number of particles stored in the current timestep. - It will arbitrarily select a time-step if you haven't already set - the timestep with \c H5PartSetStep(). + This function returns the number of particles in the first dataset of + the current timestep (or in the first timestep if none has been set). + + If you have neither set the number of particles (read or write) + nor set a view (read-only), then this returns the total number of + elements on disk of the first dataset if is exists. Otherwise, + it returns 0. + + If you have set a view, this return the number of particles + in the view. \return number of particles in current timestep or an error code. @@ -2511,33 +2492,36 @@ H5PartGetNumParticles ( static h5part_int64_t _reset_view ( H5PartFile *f /*!< [in] Handle to open file */ - ) { + ) { herr_t herr = 0; f->viewstart = -1; f->viewend = -1; - if ( f->shape != 0 ){ - herr = H5Sclose(f->shape); + + if ( f->shape != H5S_ALL ) { + herr = H5Sclose ( f->shape ); if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; - f->shape=0; + f->shape = H5S_ALL; } - if(f->diskshape!=0 && f->diskshape!=H5S_ALL){ - herr = H5Sclose(f->diskshape); + + if ( f->diskshape != H5S_ALL ) { + herr = H5Sclose ( f->diskshape ); if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; - f->diskshape=H5S_ALL; + f->diskshape = H5S_ALL; } - f->diskshape = H5S_ALL; - if(f->memshape!=0 && f->memshape!=H5S_ALL){ + + if ( f->memshape != H5S_ALL ){ herr = H5Sclose ( f->memshape ); if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; - f->memshape=H5S_ALL; + f->memshape = H5S_ALL; } + return H5PART_SUCCESS; } /*! - \ingroup h5part_read + \ingroup h5part_model */ h5part_int64_t H5PartResetView ( @@ -2552,7 +2536,7 @@ H5PartResetView ( } /*! - \ingroup h5part_read + \ingroup h5part_model */ h5part_int64_t H5PartHasView ( @@ -2560,10 +2544,10 @@ H5PartHasView ( ) { SET_FNAME ( "H5PartHasView" ); - CHECK_FILEHANDLE( f ); + CHECK_FILEHANDLE ( f ); CHECK_READONLY_MODE ( f ); - return ( f->viewstart >= 0 ) && ( f->viewend >= 0 ); + return _H5Part_has_view ( f ); } static h5part_int64_t @@ -2572,9 +2556,11 @@ _set_view ( h5part_int64_t start, /*!< [in] Start particle */ h5part_int64_t end /*!< [in] End particle */ ) { + h5part_int64_t herr = 0; hsize_t total; hsize_t stride = 1; + hsize_t hstart; hsize_t dmax = H5S_UNLIMITED; _H5Part_print_debug ( @@ -2596,11 +2582,13 @@ _set_view ( total = (hsize_t) _H5Part_get_num_particles ( f ); if ( total < 0 ) return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total ); - if ( start == -1 ) start = 0; - if ( end == -1 ) end = total; - _H5Part_print_debug ( "Total nparticles=%lld", (long long)total ); + if ( total == 0 ) return H5PART_SUCCESS; + + if ( start == -1 ) start = 0; + if ( end == -1 ) end = total - 1; // range is *inclusive* + /* so, is this selection inclusive or exclusive? it appears to be inclusive for both ends of the range. */ @@ -2617,38 +2605,115 @@ _set_view ( f->nparticles = end - start + 1; /* declare overall datasize */ - f->shape = H5Screate_simple ( 1, &total, &total ); + f->shape = H5Screate_simple ( 1, &total, NULL ); if ( f->shape < 0 ) return HANDLE_H5S_CREATE_SIMPLE_ERR ( total ); - /* declare overall data size but then will select a subset */ - f->diskshape = H5Screate_simple ( 1, &total, &total ); + /* declare overall data size but then select a subset */ + f->diskshape = H5Screate_simple ( 1, &total, NULL ); if ( f->diskshape < 0 ) return HANDLE_H5S_CREATE_SIMPLE_ERR ( total ); - /* declare local memory datasize */ - f->memshape = H5Screate_simple(1,&(f->nparticles),&dmax); - if ( f->memshape < 0 ) - return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles ); - + total = (hsize_t)f->nparticles; + hstart = (size_t)start; herr = H5Sselect_hyperslab ( f->diskshape, H5S_SELECT_SET, - (hsize_t*)&start, + &hstart, &stride, &total, NULL ); if ( herr < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR; + /* declare local memory datasize */ + f->memshape = H5Screate_simple ( 1, &total, &dmax ); + if ( f->memshape < 0 ) + return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles ); + + return H5PART_SUCCESS; +} + +static h5part_int64_t +_set_view_indices ( + H5PartFile *f, /*!< [in] Handle to open file */ + const hsize_t *indices, /*!< [in] List of indices */ + h5part_int64_t nelems /*!< [in] Size of list */ + ) { + + h5part_int64_t herr = 0; + hsize_t total; + hsize_t dmax = H5S_UNLIMITED; + + herr = _reset_view ( f ); + if ( herr < 0 ) return herr; + + if ( indices == NULL ) { + _H5Part_print_warn ( + "View indices array is null: reseting view." ); + return H5PART_SUCCESS; + } + + /* + View has been reset so H5PartGetNumParticles will tell + us the total number of particles. + + For now, we interpret start=-1 to mean 0 and + end==-1 to mean end of file + */ + total = (hsize_t) _H5Part_get_num_particles ( f ); + if ( total < 0 ) return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total ); + + _H5Part_print_debug ( "Total nparticles=%lld", (long long)total ); + + if ( total == 0 ) return H5PART_SUCCESS; + + /* check length of list */ + if ( nelems < 0 ) { + _H5Part_print_warn ( + "Array of view indices has length < 0: " + "resetting view."); + f->nparticles = 0; + } else { + f->nparticles = (hsize_t) nelems; + } + + /* declare overall datasize */ + f->shape = H5Screate_simple ( 1, &total, NULL ); + if ( f->shape < 0 ) + return HANDLE_H5S_CREATE_SIMPLE_ERR ( total ); + + /* declare overall data size but then will select a subset */ + f->diskshape = H5Screate_simple ( 1, &total, NULL ); + if ( f->diskshape < 0 ) + return HANDLE_H5S_CREATE_SIMPLE_ERR ( total ); + + /* declare local memory datasize */ + total = (size_t)f->nparticles; + f->memshape = H5Screate_simple (1, &total, &dmax ); + if ( f->memshape < 0 ) + return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles ); + + if ( nelems > 0 ) { + herr = H5Sselect_elements ( + f->diskshape, + H5S_SELECT_SET, + nelems, + indices ); + } else { + herr = H5Sselect_none ( f->diskshape ); + } + if ( herr < 0 ) return HANDLE_H5S_SELECT_ELEMENTS_ERR; + return H5PART_SUCCESS; } /*! - \ingroup h5part_read + \ingroup h5part_model For parallel I/O or for subsetting operations on the datafile, the \c H5PartSetView() function allows you to define a subset of the total - particle dataset to read. The concept of "view" works for both serial + particle dataset to operate on. + The concept of "view" works for both serial and for parallel I/O. The "view" will remain in effect until a new view is set, or the number of particles in a dataset changes, or the view is "unset" by calling \c H5PartSetView(file,-1,-1); @@ -2658,7 +2723,8 @@ _set_view ( reads). However, after you set a view, it will return the number of particles contained in the view. - The range is inclusive (the start and the end index). + The range is \e inclusive: the end value is the last index of the + data. \return \c H5PART_SUCCESS or error code */ @@ -2672,7 +2738,6 @@ H5PartSetView ( SET_FNAME ( "H5PartSetView" ); CHECK_FILEHANDLE( f ); - CHECK_READONLY_MODE ( f ); if ( f->timegroup < 0 ) { h5part_int64_t herr = _H5Part_set_step ( f, 0 ); @@ -2683,14 +2748,51 @@ H5PartSetView ( } /*! - \ingroup h5part_read + \ingroup h5part_model + + For parallel I/O or for subsetting operations on the datafile, + this function allows you to define a subset of the total + dataset to operate on by specifying a list of indices. + The concept of "view" works for both serial + and for parallel I/O. The "view" will remain in effect until a new view + is set, or the number of particles in a dataset changes, or the view is + "unset" by calling \c H5PartSetViewIndices(NULL,0); + + Before you set a view, the \c H5PartGetNumParticles() will return the + total number of particles in the current time-step (even for the parallel + reads). However, after you set a view, it will return the number of + particles contained in the view. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartSetViewIndices ( + H5PartFile *f, /*!< [in] Handle to open file */ + const hsize_t *indices, /*!< [in] List of indices */ + h5part_int64_t nelems /*!< [in] Size of list */ + ) { + + SET_FNAME ( "H5PartSetViewIndices" ); + + CHECK_FILEHANDLE( f ); + + if ( f->timegroup < 0 ) { + h5part_int64_t herr = _H5Part_set_step ( f, 0 ); + if ( herr < 0 ) return herr; + } + + return _set_view_indices ( f, indices, nelems ); +} + +/*! + \ingroup h5part_model Allows you to query the current view. Start and End will be \c -1 if there is no current view established. Use \c H5PartHasView() to see if the view is smaller than the total dataset. - \return the number of elements in the view + \return the number of elements in the view */ h5part_int64_t H5PartGetView ( @@ -2724,13 +2826,13 @@ H5PartGetView ( } if ( start ) *start = viewstart; - if ( end ) *end = viewend; + if ( end ) *end = viewend; - return viewend - viewstart; + return viewend - viewstart + 1; // view range is *inclusive* } /*! - \ingroup h5part_read + \ingroup h5part_model If it is too tedious to manually set the start and end coordinates for a view, the \c H5SetCanonicalView() will automatically select an @@ -2756,7 +2858,6 @@ H5PartSetCanonicalView ( h5part_int64_t herr; CHECK_FILEHANDLE( f ); - CHECK_READONLY_MODE ( f ) herr = _reset_view ( f ); if ( herr < 0 ) return HANDLE_H5PART_SET_VIEW_ERR( herr, -1, -1 ); @@ -2764,17 +2865,22 @@ H5PartSetCanonicalView ( #ifdef PARALLEL_IO h5part_int64_t start = 0; h5part_int64_t end = 0; - h5part_int64_t n = 0; + h5part_int64_t total = 0; + h5part_int64_t pertask = 0; int i = 0; if ( f->timegroup < 0 ) { herr = _H5Part_set_step ( f, 0 ); if ( herr < 0 ) return herr; } - n = _H5Part_get_num_particles ( f ); - if ( n < 0 ) return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( n ); - /* - now lets query the attributes for this group to see if there + + /* returns all particles (aggregated across all tasks) */ + total = _H5Part_get_num_particles ( f ); + if ( total < 0 ) + return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total ); + +#if 0 + /* now lets query the attributes for this group to see if there is a 'pnparticles' group that contains the offsets for the processors. */ @@ -2790,6 +2896,12 @@ H5PartSetCanonicalView ( f->pnparticles[i] = n; } } +#endif + + total /= f->nprocs; + for ( i=0; inprocs; i++ ) { + f->pnparticles[i] = total; + } for ( i = 0; i < f->myproc; i++ ){ start += f->pnparticles[i]; @@ -2811,7 +2923,8 @@ _read_data ( const hid_t type ) { - herr_t herr; + h5part_int64_t herr; + hsize_t ndisk, nread, nmem; hid_t dataset_id; hid_t space_id; hid_t memspace_id; @@ -2820,6 +2933,7 @@ _read_data ( h5part_int64_t h5err = _H5Part_set_step ( f, f->timestep ); if ( h5err < 0 ) return h5err; } + dataset_id = H5Dopen ( f->timegroup, name #ifndef H5_USE_16_API , H5P_DEFAULT @@ -2828,15 +2942,69 @@ _read_data ( if ( dataset_id < 0 ) return HANDLE_H5D_OPEN_ERR ( name ); - space_id = _get_diskshape_for_reading ( f, dataset_id ); - if ( space_id < 0 ) return (h5part_int64_t)space_id; + /* default spaces, if not using a view selection */ + memspace_id = H5S_ALL; + space_id = H5Dget_space ( dataset_id ); + if ( space_id < 0 ) return HANDLE_H5D_GET_SPACE_ERR; - memspace_id = _get_memshape_for_reading ( f, dataset_id ); - if ( memspace_id < 0 ) return (h5part_int64_t)memspace_id; + /* get the number of elements on disk for the datset */ + ndisk = H5Sget_simple_extent_npoints ( space_id ); + if ( ndisk < 0 ) return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR; -#if PARALLEL_IO - herr = _H5Part_start_throttle( f ); - if (herr < 0) return herr; + if ( f->diskshape != H5S_ALL ) + { + nread = H5Sget_select_npoints ( f->diskshape ); + if ( nread < 0 ) return HANDLE_H5S_GET_SELECT_NPOINTS_ERR; + + /* make sure the disk space selected by the view doesn't + * exceed the size of the dataset */ + if ( nread <= ndisk ) { + /* we no longer need the dataset space... */ + herr = H5Sclose ( space_id ); + if ( herr < 0 ) HANDLE_H5S_CLOSE_ERR; + /* ...because it's safe to use the view selection */ + space_id = f->diskshape; + } else { + /* the view selection is too big? + * fall back to using the dataset space */ + _H5Part_print_warn ( + "Ignoring view: dataset[%s] has fewer " + "elements on disk (%lld) than are selected " + "(%lld).", + name, (long long)ndisk, (long long)nread ); + nread = ndisk; + } + } + else { + /* since the view selection is H5S_ALL, we will + * read all available elements in the dataset space */ + nread = ndisk; + } + + if ( f->memshape != H5S_ALL ) + { + nmem = H5Sget_select_npoints ( f->memshape ); + if ( nmem < 0 ) return HANDLE_H5S_GET_SELECT_NPOINTS_ERR; + + /* make sure the memory space selected by the view has + * enough capacity for the read */ + if ( nmem >= nread ) { + memspace_id = f->memshape; + } else { + /* the view selection is too small? + * fall back to using H5S_ALL */ + _H5Part_print_warn ( + "Ignoring view: dataset[%s] has more " + "elements selected (%lld) than are available " + "in memory (%lld).", + name, (long long)nread, (long long)nmem ); + memspace_id == H5S_ALL; + } + } + +#ifdef PARALLEL_IO + herr = _H5Part_start_throttle ( f ); + if ( herr < 0 ) return herr; #endif herr = H5Dread ( @@ -2848,23 +3016,18 @@ _read_data ( (get hyperslab if needed) */ f->xfer_prop, /* ignore... its for parallel reads */ array ); - -#if PARALLEL_IO - herr = _H5Part_end_throttle( f ); - if (herr < 0) return herr; -#endif - if ( herr < 0 ) return HANDLE_H5D_READ_ERR ( name, f->timestep ); - if ( space_id != H5S_ALL ) { - herr = H5Sclose (space_id ); +#ifdef PARALLEL_IO + herr = _H5Part_end_throttle ( f ); + if ( herr < 0 ) return herr; +#endif + + if ( space_id != f->diskshape ) { + herr = H5Sclose ( space_id ); if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; } - if ( memspace_id != H5S_ALL ) - herr = H5Sclose ( memspace_id ); - if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR; - herr = H5Dclose ( dataset_id ); if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR; @@ -2872,7 +3035,7 @@ _read_data ( } /*! - \ingroup h5part_read + \ingroup h5part_data Read array of 64 bit floating point data from file. @@ -2903,7 +3066,7 @@ H5PartReadDataFloat64 ( } /*! - \ingroup h5part_read + \ingroup h5part_data Read array of 32 bit floating point data from file. @@ -2934,7 +3097,7 @@ H5PartReadDataFloat32 ( } /*! - \ingroup h5part_read + \ingroup h5part_data Read array of 64 bit integer data from file. @@ -2965,7 +3128,7 @@ H5PartReadDataInt64 ( } /*! - \ingroup h5part_read + \ingroup h5part_data Read array of 32 bit integer data from file. @@ -2996,16 +3159,12 @@ H5PartReadDataInt32 ( } /*! - \ingroup h5part_read + \ingroup h5part_data - This is the mongo read function that pulls in all of the data for a - given timestep in one shot. It also takes the timestep as an argument - and will call \c H5PartSetStep() internally so that you don't have to - make that call separately. - - \note - See also \c H5PartReadDataInt64() and \c H5PartReadDataFloat64() if you want - to just read in one of the many datasets. + This is an aggregate read function that pulls in all of the data for a + typical particle timestep in one shot. + It also takes the timestep as an argument + and will call \ref H5PartSetStep internally. \return \c H5PART_SUCCESS or error code */ @@ -3067,10 +3226,12 @@ H5PartReadParticleStep ( parallel file system. Throttling only works with the H5PART_VFD_MPIPOSIX or - H5PART_VFD_MPIIO_IND drivers. + H5PART_VFD_MPIIO_IND drivers and is only available in + the parallel library. \return \c H5PART_SUCCESS */ +#ifdef PARALLEL_IO h5part_int64_t H5PartSetThrottle ( H5PartFile *f, @@ -3080,16 +3241,19 @@ H5PartSetThrottle ( SET_FNAME( "H5PartSetThrottle" ); CHECK_FILEHANDLE ( f ); - if (f->flags & H5PART_VFD_MPIIO_IND || f->flags & H5PART_VFD_MPIPOSIX) { + if ( f->flags & H5PART_VFD_MPIIO_IND || f->flags & H5PART_VFD_MPIPOSIX ) { f->throttle = factor; + _H5Part_print_info ( + "Throttling set with factor '%d'", f->throttle ); } else { - _H5Part_print_warn ("Throttling is not permitted in MPI-IO collective mode."); + _H5Part_print_warn ( + "Throttling is only permitted with the MPI-POSIX " + "or MPI-IO Independent VFD." ); } return H5PART_SUCCESS; } -#if PARALLEL_IO h5part_int64_t _H5Part_start_throttle ( H5PartFile *f @@ -3147,10 +3311,10 @@ _H5Part_end_throttle ( } return H5PART_SUCCESS; } -#endif +#endif // PARALLEL_IO /*! - \ingroup h5part_errhandle + \ingroup h5part_open Set verbosity level to \c level. @@ -3256,7 +3420,7 @@ H5PartAbortErrorHandler ( vfprintf ( stderr, fmt, ap ); fprintf ( stderr, "\n" ); } - exit (-(int)_h5part_errno); + exit ( (int)_h5part_errno ); } /*! diff --git a/src/H5Part.f90 b/src/H5Part.f90 new file mode 100644 index 0000000..e44b82d --- /dev/null +++ b/src/H5Part.f90 @@ -0,0 +1,439 @@ +! Declaration of subroutines for Fortran Bindings + +!> \defgroup h5part_f90_api H5Part F90 API + +!> \ingroup h5part_f90_api +!! \defgroup h5partf_open File Opening and Closing +!< + +!> \ingroup h5part_f90_api +!! \defgroup h5partf_model Setting up the Data Model +!< + +!> \ingroup h5part_f90_api +!! \defgroup h5partf_data Reading and Writing Datasets +!< + +!> \ingroup h5part_f90_api +!! \defgroup h5partf_attrib Reading and Writing Attributes +!< + + +!!!!!!!! File Opening and Closing !!!!!!!! + +!> \ingroup h5partf_open +!! Opens a file for reading. See \ref H5PartOpenFile +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_openr ( filename ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for reading +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a file for writing in truncate mode. See \ref H5PartOpenFile +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_openw ( filename ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for writing +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a file for writing in append mode. See \ref H5PartOpenFile +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_opena ( filename ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for appending +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a parallel file for reading. +!! See \ref H5PartOpenFileParallel +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_openr_par ( filename, mpi_communicator ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for reading + INTEGER, INTENT(IN) :: mpi_communicator !< the MPI communicator used by the program +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a parallel file for writing in truncate mode. +!! See \ref H5PartOpenFileParallel +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_openw_par ( filename, mpi_communicator ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for writing + INTEGER, INTENT(IN) :: mpi_communicator !< the MPI_Communicator used by the program +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a parallel file for writing in append mode. +!! See \ref H5PartOpenFileParallel +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_opena_par ( filename, mpi_communicator ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for appending + INTEGER, INTENT(IN) :: mpi_communicator !< the MPI_Communicator used by the program +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a file for reading and specifies an HDF5 alignment. +!! See \ref H5PartOpenFileAlign +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_openr_align ( filename, align ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for reading + INTEGER*8, INTENT(IN) :: align !< alignment value in bytes +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a file for writing in truncate mode and specifies an HDF5 alignment. +!! See \ref H5PartOpenFileAlign +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_openw_align ( filename, align ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for writing + INTEGER*8, INTENT(IN) :: align !< alignment value in bytes +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a file for writing in append mode and specifies an HDF5 alignment. +!! See \ref H5PartOpenFileAlign +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_opena_align ( filename, align ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for appending + INTEGER*8, INTENT(IN) :: align !< alignment value in bytes +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a parallel file for reading and specifies an HDF5 alignment. +!! See \ref H5PartOpenFileParallelAlign +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_openr_par_align ( filename, mpi_communicator, align ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for reading + INTEGER, INTENT(IN) :: mpi_communicator !< the MPI_Communicator used by the program + INTEGER*8, INTENT(IN) :: align !< alignment value in bytes +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a parallel file for writing in truncate mode and specifies +!! an HDF5 alignment. +!! See \ref H5PartOpenFileParallelAlign +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_openw_par_align ( filename, mpi_communicator, align, flags ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for writing + INTEGER, INTENT(IN) :: mpi_communicator !< the MPI_Communicator used by the program + INTEGER*8, INTENT(IN) :: align !< alignment value in bytes + CHARACTER(LEN=*), INTENT(IN) :: flags !< additional flags +END FUNCTION + +!> \ingroup h5partf_open +!! Opens a parallel file for writing in append mode and specifies +!! an HDF5 alignment. +!! See \ref H5PartOpenFileParallelAlign +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_opena_par_align ( filename, mpi_communicator, align, flags ) + CHARACTER(LEN=*), INTENT(IN) :: filename !< the filename to open for appending + INTEGER, INTENT(IN) :: mpi_communicator !< the MPI_Communicator used by the program + INTEGER*8, INTENT(IN) :: align !< alignment value in bytes + CHARACTER(LEN=*), INTENT(IN) :: flags !< additional flags +END FUNCTION + +!> \ingroup h5partf_open +!! Closes a file. See \ref H5PartCloseFile +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_close ( filehandle ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open +END FUNCTION + +!> \ingroup h5partf_open +!! See \ref H5PartSetVerbosityLevel +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_set_verbosity_level ( level ) + INTEGER*8, INTENT(IN) :: level !< the level from 0 (no output) to 5 (most detailed) +END FUNCTION + + +!!!!!!!! Setting up the Data Model !!!!!!!! + +!> \ingroup h5partf_model +!! See \ref H5PartSetNumParticles +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_setnpoints ( filehandle, npoints ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(IN) :: npoints !< the number of particles on *this* processor +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartSetNumParticlesStrided +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_setnpoints_strided ( filehandle, npoints, stride ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(IN) :: npoints !< the number of particles on *this* processor + INTEGER*8, INTENT(IN) :: stride !< the stride value (e.g. the number of fields in the particle data array) +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartSetStep +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_setstep (filehandle,step) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(IN) :: step !< a timestep value >= 1 +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartGetNumSteps +!! \return the number of steps or error code +!< +INTEGER*8 FUNCTION h5pt_getnsteps (filehandle) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartGetNumDatasets +!! \return the number of datasets or error code +!< +INTEGER*8 FUNCTION h5pt_getndatasets (filehandle) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartGetNumParticles +!! \return the number of particles or error code +!< +INTEGER*8 FUNCTION h5pt_getnpoints (filehandle) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartGetDatasetName +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_getdatasetname (filehandle,index,name) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(IN) :: index !< index of dataset to query (starting from 0) + CHARACTER(LEN=*), INTENT(OUT) :: name !< buffer to read the dataset name into +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartSetView +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_setview (filehandle,start,end) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(IN) :: start !< offset of the first particle in the view + INTEGER*8, INTENT(IN) :: end !< offset of the last particle in the view (inclusive) +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartSetViewIndices +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_setview_indices (filehandle,indices,nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(IN) :: indices(*) !< list of indicies to select in this view + INTEGER*8, INTENT(IN) :: nelem !< number of particles in the list +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartResetView +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_resetview (filehandle) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartResetView +!! \return 1 if true, 0 if false, or error code +!< +INTEGER*8 FUNCTION h5pt_hasview (filehandle) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open +END FUNCTION + +!> \ingroup h5partf_model +!! See \ref H5PartGetView +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_getview (filehandle,start,end) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(OUT) :: start !< buffer to store the offset of the first particle in the view + INTEGER*8, INTENT(OUT) :: end !< buffer to store the offset of the last particle in the view (inclusive) +END FUNCTION + + +!!!!!!!! Reading and Writing Datasets !!!!!!!! + +!> \ingroup h5partf_data +!! See \ref H5PartWriteDataFloat64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_writedata_r8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*8, INTENT(IN) :: data(*) !< the array of float64 data to write +END FUNCTION + +!> \ingroup h5partf_data +!! See \ref H5PartWriteDataFloat32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_writedata_r4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL, INTENT(IN) :: data(*) !< the array of float32 data to write +END FUNCTION + +!> \ingroup h5partf_data +!! See \ref H5PartWriteDataInt64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_writedata_i8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*8, INTENT(IN) :: data(*) !< the array of int64 data to write +END FUNCTION + +!> \ingroup h5partf_data +!! See \ref H5PartWriteDataInt32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_writedata_i4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER, INTENT(IN) :: data(*) !< the array of int32 data to write +END FUNCTION + + +!> \ingroup h5partf_data +!! See \ref H5PartReadDataFloat64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_readdata_r8 (filehandle,name,data) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL*8, INTENT(OUT) :: data(*) !< array to read float64 data into +END FUNCTION + +!> \ingroup h5partf_data +!! See \ref H5PartReadDataFloat32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_readdata_r4 (filehandle,name,data) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + REAL, INTENT(OUT) :: data(*) !< array to read float32 data into +END FUNCTION + +!> \ingroup h5partf_data +!! See \ref H5PartReadDataInt64 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_readdata_i8 (filehandle,name,data) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER*8, INTENT(OUT) :: data(*) !< array to read int64 data into +END FUNCTION + +!> \ingroup h5partf_data +!! See \ref H5PartReadDataInt32 +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_readdata_i4 (filehandle,name,data) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + INTEGER, INTENT(OUT) :: data(*) !< array to read int32 data into +END FUNCTION + + +!!!!!!!! Reading and Writing Attributes !!!!!!!! + +!> \ingroup h5partf_attrib +!! See \ref H5PartWriteFileAttribString +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_writefileattrib_string (filehandle,attrib_name,attrib_value) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + CHARACTER(LEN=*), INTENT(IN) :: value !< the string value to store +END FUNCTION + +!> \ingroup h5partf_attrib +!! See \ref H5PartWriteStepAttribString +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_writestepattrib_string (filehandle,attrib_name,attrib_value) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + CHARACTER(LEN=*), INTENT(IN) :: value !< the string value to store +END FUNCTION + +!> \ingroup h5partf_attrib +!! Reads the attribute \c name in the file root ("/") +!! into the string buffer \c value. +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_readfileattrib_string (filehandle,attrib_name,attrib_value) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + CHARACTER(LEN=*), INTENT(OUT) :: value !< buffer to read the string value into +END FUNCTION + +!> \ingroup h5partf_attrib +!! Reads the attribute \c name in the current step +!! into the string buffer \c value. +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_readstepattrib_string (filehandle,attrib_name,attrib_value) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + CHARACTER(LEN=*), INTENT(OUT) :: value !< buffer to read the string value into +END FUNCTION + +!> \ingroup h5partf_attrib +!! See \ref H5PartGetNumStepAttribs +!! \return number of attributes or error code +!< +INTEGER*8 FUNCTION h5pt_getnstepattribs (filehandle) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open +END FUNCTION + +!> \ingroup h5partf_attrib +!! See \ref H5PartGetNumFileAttribs +!! \return number of attributes or error code +!< +INTEGER*8 FUNCTION h5pt_getnfileattribs (filehandle) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open +END FUNCTION + +!> \ingroup h5partf_attrib +!! See \ref H5PartGetStepAttribInfo +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_getstepattribinfo (filehandle,idx,attrib_name,attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(IN) :: index !< index of the attribute to query (starting from 0) + CHARACTER(LEN=*), INTENT(OUT) :: name !< buffer to read the attribute name into + INTEGER*8, INTENT(OUT) :: nelem !< number of elements in the attribute's array +END FUNCTION + +!> \ingroup h5partf_attrib +!! See \ref H5PartGetFileAttribInfo +!! \return 0 on success or error code +!< +INTEGER*8 FUNCTION h5pt_getfileattribinfo (filehandle,idx,attrib_name,attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open + INTEGER*8, INTENT(IN) :: index !< index of the attribute to query (starting from 0) + CHARACTER(LEN=*), INTENT(OUT) :: name !< buffer to read the attribute name into + INTEGER*8, INTENT(OUT) :: nelem !< number of elements in the attribute's array +END FUNCTION + + diff --git a/src/H5Part.h b/src/H5Part.h index 735bde7..f39b9d7 100644 --- a/src/H5Part.h +++ b/src/H5Part.h @@ -10,12 +10,17 @@ extern "C" { #endif #include "H5PartTypes.h" - +#include "H5PartAttrib.h" #include "H5Block.h" #ifdef PARALLEL_IO #include "H5MultiBlock.h" #endif +#define H5PART_VER_STRING "1.5.0" +#define H5PART_VER_MAJOR 1 +#define H5PART_VER_MINOR 5 +#define H5PART_VER_RELEASE 0 + /* error values */ #define H5PART_SUCCESS 0 #define H5PART_ERR_NOMEM -12 @@ -24,6 +29,8 @@ extern "C" { #define H5PART_ERR_INIT -200 #define H5PART_ERR_NOENTRY -201 +#define H5PART_ERR_NOTYPE -210 +#define H5PART_ERR_BAD_VIEW -220 #define H5PART_ERR_MPI -300 #define H5PART_ERR_HDF5 -400 @@ -50,7 +57,7 @@ extern "C" { #define H5PART_FLOAT64 ((h5part_int64_t)H5T_NATIVE_DOUBLE) #define H5PART_FLOAT32 ((h5part_int64_t)H5T_NATIVE_FLOAT) #define H5PART_CHAR ((h5part_int64_t)H5T_NATIVE_CHAR) -#define H5PART_STRING ((h5part_int64_t)H5T_STRING) +#define H5PART_STRING ((h5part_int64_t)H5T_C_S1) /*========== File Opening/Closing ===============*/ H5PartFile* @@ -107,6 +114,13 @@ H5PartSetNumParticles ( const h5part_int64_t nparticles ); +h5part_int64_t +H5PartSetNumParticlesStrided ( + H5PartFile *f, /*!< [in] Handle to open file */ + const h5part_int64_t nparticles, /*!< [in] Number of particles */ + const h5part_int64_t stride /*!< [in] Stride (e.g. number of fields in the particle array) */ + ); + h5part_int64_t H5PartWriteDataFloat64 ( H5PartFile *f, @@ -188,6 +202,12 @@ H5PartSetView ( const h5part_int64_t end ); +h5part_int64_t +H5PartSetViewIndices ( + H5PartFile *f, /*!< [in] Handle to open file */ + const hsize_t *indices, /*!< [in] List of indices */ + h5part_int64_t nelems /*!< [in] Size of list */ + ); h5part_int64_t H5PartGetView ( @@ -292,20 +312,6 @@ H5PartWriteStepAttribString ( const char *value ); -h5part_int64_t -H5PartWriteStepAttribInt32 ( - H5PartFile *f, - const char *name, - const h5part_int32_t value - ); - -h5part_int64_t -H5PartWriteStepAttribFloat32 ( - H5PartFile *f, - const char *name, - const h5part_float32_t value - ); - h5part_int64_t H5PartGetNumStepAttribs ( /* for current filestep */ H5PartFile *f diff --git a/src/H5PartAttrib.c b/src/H5PartAttrib.c new file mode 100644 index 0000000..57735a7 --- /dev/null +++ b/src/H5PartAttrib.c @@ -0,0 +1,265 @@ + +#include +#include + +#include +#include "H5Part.h" +#include "H5PartErrors.h" +#include "H5PartPrivate.h" + + +/*! + \ingroup h5part_attrib + + Writes a \c value of type floating points (64-bit) + to the root ("/") of the file + as attribute \c name. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWriteFileAttribFloat64 ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_float64_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWriteFileAttribFloat64" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_file_attrib ( + f, + name, + H5T_NATIVE_DOUBLE, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + +/*! + \ingroup h5part_attrib + + Writes a \c value of type floating points (32-bit) + to the root ("/") of the file + as attribute \c name. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWriteFileAttribFloat32 ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_float32_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWriteFileAttribFloat32" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_file_attrib ( + f, + name, + H5T_NATIVE_FLOAT, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + +/*! + \ingroup h5part_attrib + + Writes a \c value of type integers (64-bit) + to the root ("/") of the file + as attribute \c name. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWriteFileAttribInt64 ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_int64_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWriteFileAttribInt64" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_file_attrib ( + f, + name, + H5T_NATIVE_INT64, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + +/*! + \ingroup h5part_attrib + + Writes a \c value of type integers (32-bit) + to the root ("/") of the file + as attribute \c name. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWriteFileAttribInt32 ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_int32_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWriteFileAttribInt32" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_file_attrib ( + f, + name, + H5T_NATIVE_INT32, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + +/*! + \ingroup h5part_attrib + + Writes a \c value of type floating points (64-bit) + to the root ("/") of the file + as attribute \c name. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWriteStepAttribFloat64 ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_float64_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWriteStepAttribFloat64" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_step_attrib ( + f, + name, + H5T_NATIVE_DOUBLE, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + +/*! + \ingroup h5part_attrib + + Writes a \c value of type floating points (32-bit) + to the root ("/") of the file + as attribute \c name. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWriteStepAttribFloat32 ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_float32_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWriteStepAttribFloat32" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_step_attrib ( + f, + name, + H5T_NATIVE_FLOAT, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + +/*! + \ingroup h5part_attrib + + Writes a \c value of type integers (64-bit) + to the root ("/") of the file + as attribute \c name. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWriteStepAttribInt64 ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_int64_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWriteStepAttribInt64" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_step_attrib ( + f, + name, + H5T_NATIVE_INT64, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} + +/*! + \ingroup h5part_attrib + + Writes a \c value of type integers (32-bit) + to the root ("/") of the file + as attribute \c name. + + \return \c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWriteStepAttribInt32 ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_int32_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWriteStepAttribInt32" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_step_attrib ( + f, + name, + H5T_NATIVE_INT32, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} diff --git a/src/H5PartAttrib.f90 b/src/H5PartAttrib.f90 new file mode 100644 index 0000000..23fb8b6 --- /dev/null +++ b/src/H5PartAttrib.f90 @@ -0,0 +1,168 @@ + +!< \ingroup h5partf_attrib +!! See \ref H5PartWritefileAttribFloat64 +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_writefileattrib_r8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + REAL*8, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION + +!< \ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_readfileattrib_r8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + REAL*8, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION + +!< \ingroup h5partf_attrib +!! See \ref H5PartWritefileAttribFloat32 +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_writefileattrib_r4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + REAL*4, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION + +!< \ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_readfileattrib_r4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + REAL*4, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION + +!< \ingroup h5partf_attrib +!! See \ref H5PartWritefileAttribInt64 +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_writefileattrib_i8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + INTEGER*8, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION + +!< \ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_readfileattrib_i8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + INTEGER*8, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION + +!< \ingroup h5partf_attrib +!! See \ref H5PartWritefileAttribInt32 +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_writefileattrib_i4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + INTEGER*4, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION + +!< \ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_readfileattrib_i4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + INTEGER*4, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION + +!< \ingroup h5partf_attrib +!! See \ref H5PartWritestepAttribFloat64 +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_writestepattrib_r8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + REAL*8, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION + +!< \ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_readstepattrib_r8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + REAL*8, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION + +!< \ingroup h5partf_attrib +!! See \ref H5PartWritestepAttribFloat32 +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_writestepattrib_r4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + REAL*4, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION + +!< \ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_readstepattrib_r4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + REAL*4, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION + +!< \ingroup h5partf_attrib +!! See \ref H5PartWritestepAttribInt64 +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_writestepattrib_i8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + INTEGER*8, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION + +!< \ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_readstepattrib_i8 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + INTEGER*8, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION + +!< \ingroup h5partf_attrib +!! See \ref H5PartWritestepAttribInt32 +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_writestepattrib_i4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + INTEGER*4, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION + +!< \ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_readstepattrib_i4 ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + INTEGER*4, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION diff --git a/src/H5PartAttrib.h b/src/H5PartAttrib.h new file mode 100644 index 0000000..a625d1d --- /dev/null +++ b/src/H5PartAttrib.h @@ -0,0 +1,71 @@ + +#ifndef _H5PART_ATTRIB_H_ +#define _H5PART_ATTRIB_H_ + +#ifdef __cplusplus +extern "C" { +#endif + + +h5part_int64_t +H5PartWriteFileAttribFloat64 ( + H5PartFile *f, + const char *name, + const h5part_float64_t data + ); + +h5part_int64_t +H5PartWriteFileAttribFloat32 ( + H5PartFile *f, + const char *name, + const h5part_float32_t data + ); + +h5part_int64_t +H5PartWriteFileAttribInt64 ( + H5PartFile *f, + const char *name, + const h5part_int64_t data + ); + +h5part_int64_t +H5PartWriteFileAttribInt32 ( + H5PartFile *f, + const char *name, + const h5part_int32_t data + ); + +h5part_int64_t +H5PartWriteStepAttribFloat64 ( + H5PartFile *f, + const char *name, + const h5part_float64_t data + ); + +h5part_int64_t +H5PartWriteStepAttribFloat32 ( + H5PartFile *f, + const char *name, + const h5part_float32_t data + ); + +h5part_int64_t +H5PartWriteStepAttribInt64 ( + H5PartFile *f, + const char *name, + const h5part_int64_t data + ); + +h5part_int64_t +H5PartWriteStepAttribInt32 ( + H5PartFile *f, + const char *name, + const h5part_int32_t data + ); + + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/src/H5PartAttribF.c b/src/H5PartAttribF.c new file mode 100644 index 0000000..64c3e07 --- /dev/null +++ b/src/H5PartAttribF.c @@ -0,0 +1,421 @@ + +#include "H5Part.h" +#include "H5PartPrivate.h" +#include "Underscore.h" + +#if defined(F77_SINGLE_UNDERSCORE) +#define F77NAME(a,b) a +#elif defined(F77_CRAY_UNDERSCORE) +#define F77NAME(a,b) b +#elif defined(F77_NO_UNDERSCORE) +#else +#error Error, no way to determine how to construct fortran bindings +#endif + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writefileattrib_r8 F77NAME ( \ + h5pt_writefileattrib_r8_, \ + H5PT_WRITEFILEATTRIB_R8 ) +#endif + +h5part_int64_t +h5pt_writefileattrib_r8 ( + h5part_int64_t *f, + const char *name, + const h5part_float64_t *data, + const h5part_float64_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWriteFileAttrib ( + filehandle, name2, H5PART_FLOAT64, data, *nelem); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writefileattrib_r8 F77NAME ( \ + h5pt_writefileattrib_r8_, \ + H5PT_WRITEFILEATTRIB_R8 ) +#endif + +h5part_int64_t +h5pt_readfileattrib_r8 ( + h5part_int64_t *f, + const char *name, + const h5part_float64_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartReadFileAttrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writefileattrib_r4 F77NAME ( \ + h5pt_writefileattrib_r4_, \ + H5PT_WRITEFILEATTRIB_R4 ) +#endif + +h5part_int64_t +h5pt_writefileattrib_r4 ( + h5part_int64_t *f, + const char *name, + const h5part_float32_t *data, + const h5part_float32_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWriteFileAttrib ( + filehandle, name2, H5PART_FLOAT32, data, *nelem); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writefileattrib_r4 F77NAME ( \ + h5pt_writefileattrib_r4_, \ + H5PT_WRITEFILEATTRIB_R4 ) +#endif + +h5part_int64_t +h5pt_readfileattrib_r4 ( + h5part_int64_t *f, + const char *name, + const h5part_float32_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartReadFileAttrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writefileattrib_i8 F77NAME ( \ + h5pt_writefileattrib_i8_, \ + H5PT_WRITEFILEATTRIB_I8 ) +#endif + +h5part_int64_t +h5pt_writefileattrib_i8 ( + h5part_int64_t *f, + const char *name, + const h5part_int64_t *data, + const h5part_int64_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWriteFileAttrib ( + filehandle, name2, H5PART_INT64, data, *nelem); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writefileattrib_i8 F77NAME ( \ + h5pt_writefileattrib_i8_, \ + H5PT_WRITEFILEATTRIB_I8 ) +#endif + +h5part_int64_t +h5pt_readfileattrib_i8 ( + h5part_int64_t *f, + const char *name, + const h5part_int64_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartReadFileAttrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writefileattrib_i4 F77NAME ( \ + h5pt_writefileattrib_i4_, \ + H5PT_WRITEFILEATTRIB_I4 ) +#endif + +h5part_int64_t +h5pt_writefileattrib_i4 ( + h5part_int64_t *f, + const char *name, + const h5part_int32_t *data, + const h5part_int32_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWriteFileAttrib ( + filehandle, name2, H5PART_INT32, data, *nelem); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writefileattrib_i4 F77NAME ( \ + h5pt_writefileattrib_i4_, \ + H5PT_WRITEFILEATTRIB_I4 ) +#endif + +h5part_int64_t +h5pt_readfileattrib_i4 ( + h5part_int64_t *f, + const char *name, + const h5part_int32_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartReadFileAttrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writestepattrib_r8 F77NAME ( \ + h5pt_writestepattrib_r8_, \ + H5PT_WRITESTEPATTRIB_R8 ) +#endif + +h5part_int64_t +h5pt_writestepattrib_r8 ( + h5part_int64_t *f, + const char *name, + const h5part_float64_t *data, + const h5part_float64_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWriteStepAttrib ( + filehandle, name2, H5PART_FLOAT64, data, *nelem); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writestepattrib_r8 F77NAME ( \ + h5pt_writestepattrib_r8_, \ + H5PT_WRITESTEPATTRIB_R8 ) +#endif + +h5part_int64_t +h5pt_readstepattrib_r8 ( + h5part_int64_t *f, + const char *name, + const h5part_float64_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartReadStepAttrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writestepattrib_r4 F77NAME ( \ + h5pt_writestepattrib_r4_, \ + H5PT_WRITESTEPATTRIB_R4 ) +#endif + +h5part_int64_t +h5pt_writestepattrib_r4 ( + h5part_int64_t *f, + const char *name, + const h5part_float32_t *data, + const h5part_float32_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWriteStepAttrib ( + filehandle, name2, H5PART_FLOAT32, data, *nelem); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writestepattrib_r4 F77NAME ( \ + h5pt_writestepattrib_r4_, \ + H5PT_WRITESTEPATTRIB_R4 ) +#endif + +h5part_int64_t +h5pt_readstepattrib_r4 ( + h5part_int64_t *f, + const char *name, + const h5part_float32_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartReadStepAttrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writestepattrib_i8 F77NAME ( \ + h5pt_writestepattrib_i8_, \ + H5PT_WRITESTEPATTRIB_I8 ) +#endif + +h5part_int64_t +h5pt_writestepattrib_i8 ( + h5part_int64_t *f, + const char *name, + const h5part_int64_t *data, + const h5part_int64_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWriteStepAttrib ( + filehandle, name2, H5PART_INT64, data, *nelem); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writestepattrib_i8 F77NAME ( \ + h5pt_writestepattrib_i8_, \ + H5PT_WRITESTEPATTRIB_I8 ) +#endif + +h5part_int64_t +h5pt_readstepattrib_i8 ( + h5part_int64_t *f, + const char *name, + const h5part_int64_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartReadStepAttrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writestepattrib_i4 F77NAME ( \ + h5pt_writestepattrib_i4_, \ + H5PT_WRITESTEPATTRIB_I4 ) +#endif + +h5part_int64_t +h5pt_writestepattrib_i4 ( + h5part_int64_t *f, + const char *name, + const h5part_int32_t *data, + const h5part_int32_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWriteStepAttrib ( + filehandle, name2, H5PART_INT32, data, *nelem); + + free ( name2 ); + return herr; +} + +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_writestepattrib_i4 F77NAME ( \ + h5pt_writestepattrib_i4_, \ + H5PT_WRITESTEPATTRIB_I4 ) +#endif + +h5part_int64_t +h5pt_readstepattrib_i4 ( + h5part_int64_t *f, + const char *name, + const h5part_int32_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartReadStepAttrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} diff --git a/src/H5PartErrors.h b/src/H5PartErrors.h index aa62179..5c1d2f9 100644 --- a/src/H5PartErrors.h +++ b/src/H5PartErrors.h @@ -1,22 +1,23 @@ -#ifndef __H5PARTERRORS_H -#define __H5PARTERRORS_H +#ifndef __H5PART_ERRORS_H +#define __H5PART_ERRORS_H +extern h5part_error_handler _err_handler; /***************** Error Handling ***************/ #define CHECK_FILEHANDLE( f ) \ - if ( _file_is_valid ( f ) != H5PART_SUCCESS ) \ + if ( _H5Part_file_is_valid ( f ) != H5PART_SUCCESS ) \ return HANDLE_H5PART_BADFD_ERR; #define CHECK_WRITABLE_MODE( f ) \ - if ( f->mode==H5PART_READ ) \ + if ( f->flags & H5PART_READ ) \ return (*_err_handler) ( \ _H5Part_get_funcname(), \ H5PART_ERR_INVAL, \ - "Attempting to write to read-only file" ); + "Attempting to write to read-only file." ); #define CHECK_READONLY_MODE( f ) \ - if ( ! f->mode==H5PART_READ ) \ + if ( ! (f->flags & H5PART_READ) ) \ return (*_err_handler) ( \ _H5Part_get_funcname(), \ H5PART_ERR_INVAL, \ @@ -43,6 +44,13 @@ H5PART_ERR_INIT, \ "Cannot initialize H5Part." ); +#define HANDLE_H5PART_INVALID_ERR( name, value ) \ + (*_err_handler) ( \ + _H5Part_get_funcname(), \ + H5PART_ERR_INVAL, \ + "Invalid value '%lld' for '%s'.", \ + (long long)value, name); + #define HANDLE_H5PART_NOMEM_ERR \ (*_err_handler) ( \ _H5Part_get_funcname(), \ @@ -75,6 +83,13 @@ "Cannot set view to (%lld, %lld).", \ (long long)start, (long long)end ); +#define HANDLE_H5PART_BAD_VIEW_ERR( start, end ) \ + (*_err_handler) ( \ + _H5Part_get_funcname(), \ + H5PART_ERR_BAD_VIEW, \ + "Problem with existing view (%lld, %lld).", \ + (long long)start, (long long)end ); + #define HANDLE_H5PART_GET_NUM_PARTICLES_ERR( rc ) \ (*_err_handler) ( \ _H5Part_get_funcname(), \ @@ -88,6 +103,12 @@ "No entry with index %lld and type %d in group %s!", \ (long long)idx, type, group_name ); +#define HANDLE_H5PART_TYPE_ERR \ + (*_err_handler) ( \ + _H5Part_get_funcname(), \ + H5PART_ERR_NOTYPE, \ + "Encountered unkown data type!"); + /**************** HDF5 *********************/ /* H5A: Attribute */ #define HANDLE_H5A_CLOSE_ERR \ @@ -318,7 +339,7 @@ (*_err_handler) ( \ _H5Part_get_funcname(), \ H5PART_ERR_HDF5, \ - "Cannot determine the number of elements in dataspace selection." ); + "Cannot determine number of elements in dataspace selection." ); #define HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR \ (*_err_handler) ( \ @@ -330,7 +351,13 @@ (*_err_handler) ( \ _H5Part_get_funcname(), \ H5PART_ERR_HDF5, \ - "Cannot set select hyperslap region or add the specified region" ); + "Cannot select hyperslap region of dataspace." ); + +#define HANDLE_H5S_SELECT_ELEMENTS_ERR \ + (*_err_handler) ( \ + _H5Part_get_funcname(), \ + H5PART_ERR_HDF5, \ + "Cannot select elements in dataspace." ); /* H5T: type */ #define HANDLE_H5T_STRING_ERR \ @@ -345,6 +372,12 @@ H5PART_ERR_HDF5, \ "Cannot release datatype." ); +/* H5L */ +#define HANDLE_H5L_ITERATE_ERR \ + (*_err_handler) ( \ + _H5Part_get_funcname(), \ + H5PART_ERR_HDF5, \ + "Cannot iterate through group." ); /* MPI */ #define HANDLE_MPI_ALLGATHER_ERR \ diff --git a/src/H5PartF.c b/src/H5PartF.c index 6f13a4d..9b85b9f 100755 --- a/src/H5PartF.c +++ b/src/H5PartF.c @@ -60,6 +60,9 @@ #define h5pt_setnpoints F77NAME ( \ h5pt_setnpoints_, \ H5PT_SETNPOINTS ) +#define h5pt_setnpoints_strided F77NAME ( \ + h5pt_setnpoints_strided_, \ + H5PT_SETNPOINTS_STRIDED ) #define h5pt_setstep F77NAME ( \ h5pt_setstep_, \ H5PT_SETSTEP ) @@ -89,14 +92,14 @@ #define h5pt_getdatasetname F77NAME ( \ h5pt_getdatasetname_, \ H5PT_GETDATASETNAME ) -#define h5pt_getnumpoints F77NAME ( \ - h5pt_getnumpoints_, \ - H5PT_GETNUMPOINTS ) /* Views and parallelism */ #define h5pt_setview F77NAME ( \ h5pt_setview_, \ H5PT_SETVIEW ) +#define h5pt_setview_indices F77NAME ( \ + h5pt_setview_indices_, \ + H5PT_SETVIEW_INDICES ) #define h5pt_resetview F77NAME ( \ h5pt_resetview_, \ H5PT_RESETVIEW ) @@ -122,21 +125,9 @@ H5PT_READDATA_I4 ) /* Writing attributes */ -#define h5pt_writefileattrib_r8 F77NAME ( \ - h5pt_writefileattrib_r8_, \ - H5PT_WRITEFILEATTRIB_R8 ) -#define h5pt_writefileattrib_i8 F77NAME ( \ - h5pt_writefileattrib_i8_, \ - H5PT_WRITEFILEATTRIB_I8 ) #define h5pt_writefileattrib_string F77NAME ( \ h5pt_writefileattrib_string_, \ H5PT_writefileattrib_string ) -#define h5pt_writestepattrib_r8 F77NAME ( \ - h5pt_writestepattrib_r8_, \ - H5PT_WRITESTEPATTRIB_R8 ) -#define h5pt_writestepattrib_i8 F77NAME ( \ - h5pt_writestepattrib_i8_, \ - H5PT_WRITESTEPATTRIB_I8 ) #define h5pt_writestepattrib_string F77NAME ( \ h5pt_writestepattrib_string_, \ H5PT_WRITESTEPATTRIB_STRING ) @@ -154,27 +145,9 @@ #define h5pt_getfileattribinfo F77NAME ( \ h5pt_getfileattribinfo_, \ H5PT_GETFILEATTRIBINFO ) -#define h5pt_readstepattrib F77NAME ( \ - h5pt_readstepattrib_, \ - H5PT_READSTEPATTRIB ) -#define h5pt_readstepattrib_r8 F77NAME ( \ - h5pt_readstepattrib_r8_, \ - H5PT_READSTEPATTRIB_R8 ) -#define h5pt_readstepattrib_i8 F77NAME ( \ - h5pt_readstepattrib_i8_, \ - H5PT_READSTEPATTRIB_I8 ) #define h5pt_readstepattrib_string F77NAME ( \ h5pt_readstepattrib_string_, \ H5PT_READSTEPATTRIB_STRING ) -#define h5pt_readfileattrib F77NAME ( \ - h5pt_readfileattrib_, \ - H5PT_READFILEATTRIB ) -#define h5pt_readfileattrib_r8 F77NAME ( \ - h5pt_readfileattrib_r8_, \ - H5PT_READFILEATTRIB_R8 ) -#define h5pt_readfileattrib_i8 F77NAME ( \ - h5pt_readfileattrib_i8_, \ - H5PT_READFILEATTRIB_I8 ) #define h5pt_readfileattrib_string F77NAME ( \ h5pt_readfileattrib_string_, \ H5PT_READFILEATTRIB_STRING ) @@ -480,6 +453,18 @@ h5pt_setnpoints ( return H5PartSetNumParticles ( filehandle, *np ); } +h5part_int64_t +h5pt_setnpoints_strided ( + const h5part_int64_t *f, + h5part_int64_t *np, + h5part_int64_t *stride + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + return H5PartSetNumParticlesStrided ( filehandle, *np, *stride ); +} + h5part_int64_t h5pt_setstep ( const h5part_int64_t *f, @@ -615,16 +600,6 @@ h5pt_getdatasetname ( return herr; } -h5part_int64_t -h5pt_getnumpoints ( - const h5part_int64_t *f - ) { - - H5PartFile *filehandle = (H5PartFile*)(size_t)*f; - - return H5PartGetNumParticles( filehandle ); -} - /*=============Setting and getting views================*/ h5part_int64_t @@ -639,6 +614,18 @@ h5pt_setview ( return H5PartSetView ( filehandle, *start, *end ); } +h5part_int64_t +h5pt_setview_indices ( + const h5part_int64_t *f, + const h5part_int64_t *indices, + const h5part_int64_t *nelem + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + return H5PartSetViewIndices ( filehandle, indices, *nelem ); +} + h5part_int64_t h5pt_resetview ( const h5part_int64_t *f @@ -749,49 +736,6 @@ h5pt_readdata_i4 ( /*=================== Attributes ================*/ -/* Writeing attributes */ -h5part_int64_t -h5pt_writefileattrib_r8 ( - const h5part_int64_t *f, - const char *attrib_name, - const h5part_float64_t *attrib_value, - const h5part_int64_t *attrib_nelem, - const int l_attrib_name - ) { - - H5PartFile *filehandle = (H5PartFile*)(size_t)*f; - - char *attrib_name2 = _H5Part_strdupfor2c (attrib_name,l_attrib_name); - - h5part_int64_t herr = H5PartWriteFileAttrib ( - filehandle, - attrib_name2, H5T_NATIVE_DOUBLE, attrib_value, *attrib_nelem ); - - free ( attrib_name2 ); - return herr; -} - -h5part_int64_t -h5pt_writefileattrib_i8 ( - const h5part_int64_t *f, - const char *attrib_name, - const h5part_int64_t *attrib_value, - const h5part_int64_t *attrib_nelem, - const int l_attrib_name - ) { - - H5PartFile *filehandle = (H5PartFile*)(size_t)*f; - - char *attrib_name2 = _H5Part_strdupfor2c (attrib_name,l_attrib_name); - - h5part_int64_t herr = H5PartWriteFileAttrib ( - filehandle, - attrib_name2, H5T_NATIVE_INT64, attrib_value, *attrib_nelem ); - - free ( attrib_name2 ); - return herr; -} - h5part_int64_t h5pt_writefileattrib_string ( const h5part_int64_t *f, @@ -814,48 +758,6 @@ h5pt_writefileattrib_string ( return herr; } -h5part_int64_t -h5pt_writestepattrib_r8 ( - const h5part_int64_t *f, - const char *attrib_name, - const h5part_float64_t *attrib_value, - const h5part_int64_t *attrib_nelem, - const int l_attrib_name - ) { - - H5PartFile *filehandle = (H5PartFile*)(size_t)*f; - - char *attrib_name2 = _H5Part_strdupfor2c ( attrib_name, l_attrib_name ); - - h5part_int64_t herr = H5PartWriteStepAttrib ( - filehandle, - attrib_name2, H5T_NATIVE_DOUBLE, attrib_value, *attrib_nelem ); - - free ( attrib_name2 ); - return herr; -} - -h5part_int64_t -h5pt_writestepattrib_i8 ( - const h5part_int64_t *f, - const char *attrib_name, - const h5part_int64_t *attrib_value, - const h5part_int64_t *attrib_nelem, - const int l_attrib_name - ) { - - H5PartFile *filehandle = (H5PartFile*)(size_t)*f; - - char *attrib_name2 = _H5Part_strdupfor2c ( attrib_name, l_attrib_name ); - - h5part_int64_t herr = H5PartWriteStepAttrib ( - filehandle, - attrib_name2, H5T_NATIVE_INT64, attrib_value, *attrib_nelem ); - - free ( attrib_name2 ); - return herr; -} - h5part_int64_t h5pt_writestepattrib_string ( const h5part_int64_t *f, @@ -937,49 +839,6 @@ h5pt_getfileattribinfo ( return herr; } -h5part_int64_t -h5pt_readstepattrib ( - const h5part_int64_t *f, - const char *attrib_name, - void *attrib_value, - const int l_attrib_name - ) { - - H5PartFile *filehandle = (H5PartFile*)(size_t)*f; - - char * attrib_name2 = _H5Part_strdupfor2c (attrib_name,l_attrib_name); - - h5part_int64_t herr = H5PartReadStepAttrib ( - filehandle, attrib_name2, attrib_value ); - - free ( attrib_name2 ); - return herr; -} - -h5part_int64_t -h5pt_readstepattrib_r8 ( - const h5part_int64_t *f, - const char *attrib_name, - h5part_float64_t *attrib_value, - const int l_attrib_name - ) { - - return h5pt_readstepattrib ( - f, attrib_name, attrib_value, l_attrib_name ); -} - -h5part_int64_t -h5pt_readstepattrib_i8 ( - const h5part_int64_t *f, - const char *attrib_name, - h5part_int64_t *attrib_value, - const int l_attrib_name - ) { - - return h5pt_readstepattrib ( - f, attrib_name, attrib_value, l_attrib_name ); -} - h5part_int64_t h5pt_readstepattrib_string ( const h5part_int64_t *f, @@ -988,56 +847,20 @@ h5pt_readstepattrib_string ( const int l_attrib_name, const int l_attrib_value ) { - - h5part_int64_t herr = h5pt_readstepattrib ( - f, attrib_name, attrib_value, l_attrib_name ); - _H5Part_strc2for ( attrib_value, l_attrib_value ); - return herr; -} - - -h5part_int64_t -h5pt_readfileattrib ( - const h5part_int64_t *f, - const char *attrib_name, - void *attrib_value, - const int l_attrib_name - ) { - H5PartFile *filehandle = (H5PartFile*)(size_t)*f; char * attrib_name2 = _H5Part_strdupfor2c (attrib_name,l_attrib_name); - h5part_int64_t herr = H5PartReadFileAttrib ( + h5part_int64_t herr = H5PartReadStepAttrib ( filehandle, attrib_name2, attrib_value ); + _H5Part_strc2for ( attrib_value, l_attrib_value ); + free ( attrib_name2 ); return herr; } -h5part_int64_t -h5pt_readfileattrib_r8 ( - const h5part_int64_t *f, - const char *attrib_name, - h5part_float64_t *attrib_value, - const int l_attrib_name - ) { - return h5pt_readfileattrib ( - f, attrib_name, attrib_value, l_attrib_name ); -} - -h5part_int64_t -h5pt_readfileattrib_i8 ( - const h5part_int64_t *f, - const char *attrib_name, - h5part_int64_t *attrib_value, - const int l_attrib_name - ) { - return h5pt_readfileattrib ( - f, attrib_name, attrib_value, l_attrib_name ); -} - h5part_int64_t h5pt_readfileattrib_string ( const h5part_int64_t *f, @@ -1046,11 +869,17 @@ h5pt_readfileattrib_string ( const int l_attrib_name, const int l_attrib_value ) { - - h5part_int64_t herr = h5pt_readfileattrib ( - f, attrib_name, attrib_value, l_attrib_name ); + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char * attrib_name2 = _H5Part_strdupfor2c (attrib_name,l_attrib_name); + + h5part_int64_t herr = H5PartReadFileAttrib ( + filehandle, attrib_name2, attrib_value ); _H5Part_strc2for ( attrib_value, l_attrib_value ); + + free ( attrib_name2 ); return herr; } diff --git a/src/H5PartF90.inc b/src/H5PartF90.inc deleted file mode 100644 index 3ac5c68..0000000 --- a/src/H5PartF90.inc +++ /dev/null @@ -1,291 +0,0 @@ -! Declaration of subroutines for Fortran Bindings -! open/close interface - -INTERFACE - INTEGER*8 FUNCTION h5pt_openr ( filename ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for reading - END FUNCTION - - INTEGER*8 FUNCTION h5pt_openw ( filename ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for writing - END FUNCTION - - INTEGER*8 FUNCTION h5pt_opena ( filename ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for appending - END FUNCTION - - INTEGER*8 FUNCTION h5pt_openr_par ( filename, mpi_communicator ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for reading - INTEGER, INTENT(IN) :: mpi_communicator ! the MPI_Communicator used by the program - END FUNCTION - - INTEGER*8 FUNCTION h5pt_openw_par ( filename, mpi_communicator ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for writing - INTEGER, INTENT(IN) :: mpi_communicator ! the MPI_Communicator used by the program - END FUNCTION - - INTEGER*8 FUNCTION h5pt_opena_par ( filename, mpi_communicator ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for appending - INTEGER, INTENT(IN) :: mpi_communicator ! the MPI_Communicator used by the program - END FUNCTION - - - INTEGER*8 FUNCTION h5pt_openr_align ( filename, align ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for reading - INTEGER*8, INTENT(IN) :: align ! alignment value in bytes - END FUNCTION - - INTEGER*8 FUNCTION h5pt_openw_align ( filename, align ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for writing - INTEGER*8, INTENT(IN) :: align ! alignment value in bytes - END FUNCTION - - INTEGER*8 FUNCTION h5pt_opena_align ( filename, align ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for appending - INTEGER*8, INTENT(IN) :: align ! alignment value in bytes - END FUNCTION - - INTEGER*8 FUNCTION h5pt_openr_par_align ( filename, mpi_communicator, align ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for reading - INTEGER, INTENT(IN) :: mpi_communicator ! the MPI_Communicator used by the program - INTEGER*8, INTENT(IN) :: align ! alignment value in bytes - END FUNCTION - - INTEGER*8 FUNCTION h5pt_openw_par_align ( filename, mpi_communicator, align, flags ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for writing - INTEGER, INTENT(IN) :: mpi_communicator ! the MPI_Communicator used by the program - INTEGER*8, INTENT(IN) :: align ! alignment value in bytes - CHARACTER(LEN=*), INTENT(IN) :: flags ! additional flags - END FUNCTION - - INTEGER*8 FUNCTION h5pt_opena_par_align ( filename, mpi_communicator, align, flags ) - CHARACTER(LEN=*), INTENT(IN) :: filename ! the filename to open for appending - INTEGER, INTENT(IN) :: mpi_communicator ! the MPI_Communicator used by the program - INTEGER*8, INTENT(IN) :: align ! alignment value in bytes - CHARACTER(LEN=*), INTENT(IN) :: flags ! additional flags - END FUNCTION - - - INTEGER*8 FUNCTION h5pt_close ( filehandle ) - INTEGER*8, INTENT(IN) :: filehandle ! close this open filehandle - END FUNCTION - -!==============Writing and Setting Dataset info======== - - INTEGER*8 FUNCTION h5pt_setnpoints ( filehandle, npoints ) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: npoints ! The number of particles on *this* processor - END FUNCTION - - INTEGER*8 FUNCTION h5pt_setstep (filehandle,step) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: step ! Set the current timestep in the file to this - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writedata_r8 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name ! The name of the data we are writing - REAL*8, INTENT(IN) :: data(*) ! The dataarray to write. The number of - ! elements is presumably set earlier with - ! h5pt_setnpoints(f,npoints) - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writedata_r4 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name ! The name of the data we are writing - REAL, INTENT(IN) :: data(*) ! The dataarray to write. The number of - ! elements is presumably set earlier with - ! h5pt_setnpoints(f,npoints) - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writedata_i8 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name ! The name of the data we are writing - INTEGER*8, INTENT(IN) :: data(*) - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writedata_i4 ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name ! The name of the data we are writing - INTEGER, INTENT(IN) :: data(*) - END FUNCTION - -!==============Reading Data Characteristics============ - - INTEGER*8 FUNCTION h5pt_getnsteps (filehandle) - INTEGER*8, INTENT(IN) :: filehandle - END FUNCTION - - INTEGER*8 FUNCTION h5pt_getndatasets (filehandle) - INTEGER*8, INTENT(IN) :: filehandle - END FUNCTION - -! returns total number of points in this timestep -! If a "view" has been set using h5pt_setview() -! then it returns the number of points that are -! in the current view. - INTEGER*8 FUNCTION h5pt_getnpoints (filehandle) - INTEGER*8, INTENT(IN) :: filehandle - END FUNCTION - - INTEGER*8 FUNCTION h5pt_getdatasetname (filehandle,index,name) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: index ! Index for a given dataset name - CHARACTER(LEN=*), INTENT(OUT) :: name ! returns the name of the dataset at that index - END FUNCTION - -!=============Setting and getting views================ - INTEGER*8 FUNCTION h5pt_setview (filehandle,start,end) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: start ! offset of the first particle in the view - INTEGER*8, INTENT(IN) :: end ! offset of the first particle after the end of the view - END FUNCTION - - INTEGER*8 FUNCTION h5pt_resetview (filehandle) - INTEGER*8, INTENT(IN) :: filehandle ! reset the view on this filehandle to default - END FUNCTION - - INTEGER*8 FUNCTION h5pt_hasview (filehandle) - INTEGER*8, INTENT(IN) :: filehandle - END FUNCTION - - INTEGER*8 FUNCTION h5pt_getview (filehandle,start,end) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(OUT) :: start ! offset of first particle in the view - INTEGER*8, INTENT(OUT) :: end ! offset of first particle beyond the current view - END FUNCTION - -!==============Reading Data========================= - - INTEGER*8 FUNCTION h5pt_readdata_r8 (filehandle,name,data) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name ! The name of the data we are writing - REAL*8, INTENT(OUT) :: data(*) ! The dataarray to read. Number of points - ! read is either the number within the view set - ! by h5pt_setview() or the default (the total - ! number of particles in the file. - END FUNCTION - - INTEGER*8 FUNCTION h5pt_readdata_r4 (filehandle,name,data) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name ! The name of the data we are writing - REAL, INTENT(OUT) :: data(*) ! The dataarray to read. Number of points - ! read is either the number within the view set - ! by h5pt_setview() or the default (the total - ! number of particles in the file. - END FUNCTION - - INTEGER*8 FUNCTION h5pt_readdata_i8 (filehandle,name,data) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name ! The name of the data we are writing - INTEGER*8, INTENT(OUT) :: data(*) ! The dataarray to read. Number of points - ! read is either the number within the view set - ! by h5pt_setview() or the default (the total - ! number of particles in the file. - END FUNCTION - - INTEGER*8 FUNCTION h5pt_readdata_i4 (filehandle,name,data) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name ! The name of the data we are writing - INTEGER, INTENT(OUT) :: data(*) ! The dataarray to read. Number of points - ! read is either the number within the view set - ! by h5pt_setview() or the default (the total - ! number of particles in the file. - END FUNCTION - - -!=================== Attributes ================ - - INTEGER*8 FUNCTION h5pt_writefileattrib_r8 (filehandle,attrib_name,attrib_value,attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - REAL*8, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writefileattrib_i8 (filehandle,attrib_name,attrib_value,attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - INTEGER*8, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writefileattrib_string (filehandle,attrib_name,attrib_value) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - CHARACTER(LEN=*), INTENT(IN) :: attrib_value ! The array of data to write into the attribute - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writestepattrib_r8 (filehandle,attrib_name,attrib_value,attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - REAL*8, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writestepattrib_i8 (filehandle,attrib_name,attrib_value,attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - INTEGER*8, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_writestepattrib_string (filehandle,attrib_name,attrib_value) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - CHARACTER(LEN=*), INTENT(IN) :: attrib_value ! The array of data to write into the attribute - END FUNCTION - - - INTEGER*8 FUNCTION h5pt_getnstepattribs (filehandle) - INTEGER*8, INTENT(IN) :: filehandle - END FUNCTION - - INTEGER*8 FUNCTION h5pt_getnfileattribs (filehandle) - INTEGER*8, INTENT(IN) :: filehandle - END FUNCTION - - INTEGER*8 FUNCTION h5pt_getstepattribinfo (filehandle,idx,attrib_name,attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: idx ! index of the attribute being queried - CHARACTER(LEN=*), INTENT(OUT) :: attrib_name ! The name of the attribute - INTEGER*8, INTENT(OUT) :: attrib_nelem ! Number of elements in the attrib array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_getfileattribinfo (filehandle,idx,attrib_name,attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - INTEGER*8, INTENT(IN) :: idx ! index of the attribute being queried - CHARACTER(LEN=*), INTENT(OUT) :: attrib_name ! The name of the attribute - INTEGER*8, INTENT(OUT) :: attrib_nelem ! Number of elements in the attrib array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_readstepattrib_i8 ( filehandle, attrib_name, attrib_value ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read - INTEGER*8, INTENT(OUT) :: attrib_value(*) ! the attribute data will be read into this array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_readstepattrib_r8 ( filehandle, attrib_name, attrib_value ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read - REAL*8, INTENT(OUT) :: attrib_value(*) ! the attribute data will be read into this array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_readfileattrib_i8 (filehandle, attrib_name, attrib_value ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read - INTEGER*8, INTENT(OUT) :: attrib_value(*) ! the attribute data will be read into this array - END FUNCTION - - INTEGER*8 FUNCTION h5pt_readfileattrib_r8 (filehandle, attrib_name, attrib_value ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! name of the attribute to read - REAL*8, INTENT(OUT) :: attrib_value(*) ! the attribute data will be read into this array - END FUNCTION - - - INTEGER*8 FUNCTION h5pt_set_verbosity_level ( level ) - INTEGER*8, INTENT(IN) :: level - END FUNCTION - -END INTERFACE diff --git a/src/H5PartPrivate.h b/src/H5PartPrivate.h index 15bdf1d..1328154 100644 --- a/src/H5PartPrivate.h +++ b/src/H5PartPrivate.h @@ -1,5 +1,5 @@ -#ifndef __H5PARTPRIVATE_H -#define __H5PARTPRIVATE_H +#ifndef __H5PART_PRIVATE_H +#define __H5PART_PRIVATE_H #if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 6 #define H5_USE_16_API @@ -9,6 +9,11 @@ #define H5PART_BTREE_IK 10000 +h5part_int64_t +_H5Part_file_is_valid ( + const H5PartFile *f + ); + /*! The functions declared here are not part of the API, but may be used in extensions like H5Block. We name these functions "private". @@ -33,6 +38,13 @@ _H5Part_set_step ( const h5part_int64_t step ); +h5part_int64_t +_H5Part_get_step_name( + H5PartFile *f, + const h5part_int64_t step, + char *name + ); + h5part_int64_t _H5Part_get_num_particles ( H5PartFile *f @@ -150,6 +162,11 @@ _H5Part_end_throttle ( H5PartFile *f ); +h5part_error_handler +_H5Part_get_err_handle ( + void + ); + void _H5Part_vprint_error ( const char *fmt, diff --git a/src/H5PartTypes.h b/src/H5PartTypes.h index 6606f7a..60e8288 100644 --- a/src/H5PartTypes.h +++ b/src/H5PartTypes.h @@ -2,8 +2,8 @@ System dependend definitions */ -#ifndef _H5PARTTYPES_H_ -#define _H5PARTTYPES_H_ +#ifndef _H5PART_TYPES_H_ +#define _H5PART_TYPES_H_ #ifdef WIN32 typedef __int64 int64_t; @@ -23,6 +23,8 @@ __attribute__ ((format (printf, 3, 4))) typedef unsigned long MPI_Comm; #endif +#define H5PART_STEPNAME_LEN 64 + struct H5BlockFile; /** @@ -35,22 +37,26 @@ struct H5BlockFile; */ struct H5PartFile { hid_t file; - char *groupname_step; + char groupname_step[H5PART_STEPNAME_LEN]; int stepno_width; int empty; + char flags; + h5part_int64_t timestep; hsize_t nparticles; - + hid_t timegroup; hid_t shape; - unsigned mode; hid_t xfer_prop; hid_t create_prop; hid_t access_prop; + + /* the dataspace on disk for the current view */ hid_t diskshape; - hid_t memshape; /* for parallel I/O (this is on-disk) H5S_ALL - if serial I/O */ + /* the dataspace in memory for the current view */ + hid_t memshape; + h5part_int64_t viewstart; /* -1 if no view is available: A "view" looks */ h5part_int64_t viewend; /* at a subset of the data. */ @@ -75,11 +81,10 @@ struct H5PartFile { int myproc; /** - MPI comnunicator + MPI communicator */ MPI_Comm comm; - char flags; int throttle; struct H5BlockStruct *block; diff --git a/src/Makefile.am b/src/Makefile.am index eeba89e..213f5c7 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -1,37 +1,22 @@ # src level Makefile.am -# PATH SETTING (IMPORTED FROM CONFIGURE) -HDF5ROOT = @HDF5ROOT@ +OBJEXT=o -# COMPILERS -CC = @CC@ - -#INCLUDES -HDFINC = -I$(HDF5ROOT)/include -MPIINC = @MPIINC@ - -INC = $(HDFINC) ${MPIINC} - -# H5Part header file location -H5PINC = -I@prefix@/include - -# COMPILER FLAGS -CFLAGS = @CFLAGS@ ${INC} - -# H5Part compiled library location -H5PLIB = -L@prefix@/lib - -# HDF5 LIBRARY -HDFLIB = -L$(HDF5ROOT)/lib -lhdf5 -lz $(SZLIB) @LDFLAGS@ - -# SZ LIBRARY -SZLIB = @SZLIB@ +INCLUDES = -I@HDF5ROOT@/include @MPIINC@ # Extra files that I wish to include in the dist tar ball. -EXTRA_DIST = TestUnderscoreC.c TestUnderscore.f $(EXTRA_HEADERS) +EXTRA_DIST = TestUnderscoreC.c \ + TestUnderscore.f \ + generate-attr.py \ + generate-h5bl-readwrite.py \ + generate-h5multi-readwrite.py \ + H5Part.f90 \ + H5PartAttrib.f90 \ + H5Block.f90 \ + H5BlockReadWrite.f90 # Files that I don't want to include in the dist tar ball -nodist_include_HEADERS = @UNDERSCORE_H@ +nodist_include_HEADERS = H5PartF.h @UNDERSCORE_H@ # What to build... Will be determined by configure script. lib_LIBRARIES = @MTARGET@ @@ -40,64 +25,51 @@ lib_LIBRARIES = @MTARGET@ EXTRA_LIBRARIES = libH5Part.a libH5PartF.a # Header files that I wish to install in $(prefix)/include -include_HEADERS = H5Part.h H5PartTypes.h H5PartErrors.h \ - H5Block.h H5BlockReadWrite.h H5BlockTypes.h H5BlockErrors.h \ - H5MultiBlock.h H5MultiBlockReadWrite.h H5MultiBlockTypes.h H5MultiBlockErrors.h \ - H5Part.inc H5PartF90.inc \ - H5BlockF90.inc H5BlockReadWriteF90.inc \ - @UNDERSCORE_H@ +include_HEADERS = H5Part.h \ + H5PartTypes.h \ + H5PartErrors.h \ + H5PartAttrib.h \ + H5Block.h \ + H5BlockTypes.h \ + H5BlockErrors.h \ + H5BlockReadWrite.h \ + H5MultiBlock.h \ + H5MultiBlockTypes.h \ + H5MultiBlockErrors.h \ + H5MultiBlockReadWrite.h \ + H5PartF.h \ + @UNDERSCORE_H@ # Listing of all possible headers that I may include -EXTRA_HEADERS = H5PartPrivate.h H5BlockPrivate.h H5MultiBlockPrivate.h +EXTRA_HEADERS = H5PartPrivate.h \ + H5BlockPrivate.h \ + H5MultiBlockPrivate.h \ + H5PartAttrib.h # Listing of sources -libH5Part_a_SOURCES = H5Part.c H5Block.c H5BlockReadWrite.c H5MultiBlock.c H5MultiBlockReadWrite.c -libH5PartF_a_SOURCES = H5PartF.c H5BlockF.c H5BlockReadWriteF.c +libH5Part_a_SOURCES = H5Part.c \ + H5PartAttrib.c \ + H5Block.c \ + H5BlockReadWrite.c \ + H5MultiBlock.c \ + H5MultiBlockReadWrite.c +libH5PartF_a_SOURCES = H5PartF.c \ + H5PartAttribF.c \ + H5BlockF.c \ + H5BlockReadWriteF.c -H5Part.inc: H5PartF90.inc - grep "INTEGER.* FUNCTION" $< | while read type func name rest; do echo " $$type $$name"; done > $@ +H5PartF.h: H5Part.f90 H5PartAttrib.f90 H5Block.f90 H5BlockReadWrite.f90 + awk '/INTEGER\*8 FUNCTION/{print "\t" $$1 " " $$3}' $^ >$@ -# Specific building instruction (What compilers to use...) -# ------------ Serial Lib build commands ------------ -libH5Part.a: H5Part.o H5Block.o H5BlockReadWrite.o H5MultiBlock.o H5MultiBlockReadWrite.o - ${AR} rucs $@ $^ - -libH5PartF.a: H5Part.o H5PartF.o H5Block.o H5BlockF.o H5BlockReadWrite.o H5BlockReadWriteF.o - ${AR} rucs $@ $^ - -%.o : %.c - $(CC) $(CFLAGS) $(INC) -c $< - -H5Part.o: H5Part.c H5Part.h H5PartPrivate.h H5PartTypes.h -H5PartF.o: H5PartF.c Underscore.h H5Part.h -H5Block.o: H5Block.c H5Part.h H5PartPrivate.h H5PartTypes.h H5Block.h H5BlockTypes.h -H5BlockF.o: H5BlockF.c Underscore.h H5Block.h -H5BlockReadWrite.o: H5BlockReadWrite.c H5Part.h H5PartPrivate.h H5PartTypes.h H5Block.h H5BlockPrivate.h H5BlockReadWrite.h H5BlockTypes.h -H5BlockReadWriteF.o: H5BlockF.c Underscore.h H5Block.h H5BlockReadWrite.h -H5MultiBlock.o: H5MultiBlock.c -H5MultiBlockF.o: H5MultiBlockF.c -H5MultiBlockReadWrite.o: H5MultiBlockReadWrite.c -H5MultiBlockReadWriteF.o: H5MultiBlockReadWriteF.c - -# ----------- Build Parallel H5Part Stuff ------------ +.c.o: + $(CC) $(CFLAGS) $(INCLUDES) -c $< libpH5Part.a: libH5Part.a - ${RM} $@ + $(RM) $@ ln -s $^ $@ libpH5PartF.a: libH5PartF.a - ${RM} $@ + $(RM) $@ ln -s $^ $@ -clean: - rm -f *~ *.o *.a *.so - -distclean: clean - rm -f *.a - rm -rf .deps - rm -rf .libs - rm -f Underscore.h - rm -f H5Part_py_wrap.c - rm -f H5Part.py - rm -f Makefile diff --git a/src/generate-attr.py b/src/generate-attr.py new file mode 100755 index 0000000..1a2946e --- /dev/null +++ b/src/generate-attr.py @@ -0,0 +1,218 @@ +#!/usr/bin/python + +c_head = """ +#include +#include + +#include +#include "H5Part.h" +#include "H5PartErrors.h" +#include "H5PartPrivate.h" + +""" + +h_head = """ +#ifndef _H5PART_ATTRIB_H_ +#define _H5PART_ATTRIB_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +""" + +h_tail = """ + +#ifdef __cplusplus +} +#endif + +#endif +""" + +fc_head = """ +#include "H5Part.h" +#include "H5PartPrivate.h" +#include "Underscore.h" + +#if defined(F77_SINGLE_UNDERSCORE) +#define F77NAME(a,b) a +#elif defined(F77_CRAY_UNDERSCORE) +#define F77NAME(a,b) b +#elif defined(F77_NO_UNDERSCORE) +#else +#error Error, no way to determine how to construct fortran bindings +#endif +""" + +write_attr_h = """ +h5part_int64_t +H5PartWrite#LEVEL#Attrib#TYPE_ABV# ( + H5PartFile *f, + const char *name, + const h5part_#TYPE_H5P#_t data + ); +""" + +write_attr_c = """ +/*! + \\ingroup h5part_attrib + + Writes a \\c value of type #TYPE_FULL# + to the root ("/") of the file + as attribute \\c name. + + \\return \\c H5PART_SUCCESS or error code +*/ +h5part_int64_t +H5PartWrite#LEVEL#Attrib#TYPE_ABV# ( + H5PartFile *f, /*!< IN: file handle */ + const char *name, /*!< IN: attribute name */ + const h5part_#TYPE_H5P#_t value /*!< IN: attribute value */ + ) { + + SET_FNAME ( "H5PartWrite#LEVEL#Attrib#TYPE_ABV#" ); + + CHECK_FILEHANDLE ( f ); + CHECK_WRITABLE_MODE( f ); + + h5part_int64_t herr = _H5Part_write_#LEVELLC#_attrib ( + f, + name, + #TYPE_HDF5#, + (void*)&value, + 1 ); + if ( herr < 0 ) return herr; + + return H5PART_SUCCESS; +} +""" + +write_attr_fi = """ +!< \\ingroup h5partf_attrib +!! See \\ref H5PartWrite#LEVELLC#Attrib#TYPE_ABV# +!! \\return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV# ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + #TYPE_F90#, INTENT(IN) :: data(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: nelem !< the number of elements in the array +END FUNCTION +""" + +write_attr_fc = """ +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV# F77NAME ( \\ + h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV#_, \\ + H5PT_WRITE#LEVELUC#ATTRIB_#TYPE_F90_ABVC# ) +#endif + +h5part_int64_t +h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV# ( + h5part_int64_t *f, + const char *name, + const h5part_#TYPE_H5P#_t *data, + const h5part_#TYPE_H5P#_t *nelem, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartWrite#LEVEL#Attrib ( + filehandle, name2, #TYPE_ATTRIB#, data, *nelem); + + free ( name2 ); + return herr; +} +""" + +read_attr_fi = """ +!< \\ingroup h5partf_attrib +!! Read the attribute \c name into the buffer \c data. +!! \\return 0 on success or error code +!> +INTEGER*8 FUNCTION h5pt_read#LEVELLC#attrib_#TYPE_F90_ABV# ( filehandle, name, data ) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the attribute + #TYPE_F90#, INTENT(OUT) :: data(*) !< buffer to read value into +END FUNCTION +""" + +read_attr_fc = """ +#if ! defined(F77_NO_UNDERSCORE) +#define h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV# F77NAME ( \\ + h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV#_, \\ + H5PT_WRITE#LEVELUC#ATTRIB_#TYPE_F90_ABVC# ) +#endif + +h5part_int64_t +h5pt_read#LEVELLC#attrib_#TYPE_F90_ABV# ( + h5part_int64_t *f, + const char *name, + const h5part_#TYPE_H5P#_t *data, + const int l_name + ) { + + H5PartFile *filehandle = (H5PartFile*)(size_t)*f; + + char *name2 =_H5Part_strdupfor2c ( name, l_name ); + + h5part_int64_t herr = H5PartRead#LEVEL#Attrib ( + filehandle, name2, (void*)data); + + free ( name2 ); + return herr; +} +""" + + +levels = ["File", "Step"] +types = [ + ["floating points (64-bit)", "Float64", "float64", "H5T_NATIVE_DOUBLE", "REAL*8", "r8", "R8", "H5PART_FLOAT64"], + ["floating points (32-bit)", "Float32", "float32", "H5T_NATIVE_FLOAT", "REAL*4", "r4", "R4", "H5PART_FLOAT32"], + ["integers (64-bit)", "Int64", "int64", "H5T_NATIVE_INT64", "INTEGER*8", "i8", "I8", "H5PART_INT64"], + ["integers (32-bit)", "Int32", "int32", "H5T_NATIVE_INT32", "INTEGER*4", "i4", "I4", "H5PART_INT32"] +] + +def create_call(template, type, level): + fcn = template + fcn = fcn.replace('#LEVEL#',level)\ + .replace('#LEVELLC#',level.lower())\ + .replace('#LEVELUC#',level.upper())\ + .replace('#TYPE_FULL#',type[0])\ + .replace('#TYPE_ABV#',type[1])\ + .replace('#TYPE_H5P#',type[2])\ + .replace('#TYPE_HDF5#',type[3])\ + .replace('#TYPE_F90#',type[4])\ + .replace('#TYPE_F90_ABV#',type[5])\ + .replace('#TYPE_F90_ABVC#',type[6])\ + .replace('#TYPE_ATTRIB#',type[7]) + return fcn + +def write_calls(): + cfile = file('H5PartAttrib.c','w') + cfile.write(c_head) + hfile = file('H5PartAttrib.h','w') + hfile.write(h_head) + fcfile = file('H5PartAttribF.c','w') + fcfile.write(fc_head) + fifile = file('H5PartAttrib.f90','w') + for level in levels: + for type in types: + cfile.write(create_call(write_attr_c,type,level)); + hfile.write(create_call(write_attr_h,type,level)); + fifile.write(create_call(write_attr_fi,type,level)); + fcfile.write(create_call(write_attr_fc,type,level)); + fifile.write(create_call(read_attr_fi,type,level)); + fcfile.write(create_call(read_attr_fc,type,level)); + cfile.close() + hfile.write(h_tail) + hfile.close() + fcfile.close() + fifile.close() + +write_calls() + diff --git a/src/generate-h5bl-readwrite.py b/src/generate-h5bl-readwrite.py index 7cdf06f..ab4f797 100755 --- a/src/generate-h5bl-readwrite.py +++ b/src/generate-h5bl-readwrite.py @@ -16,8 +16,8 @@ c_head = """ """ h_head = """ -#ifndef __H5BLOCKREADWRITE_H -#define __H5BLOCKREADWRITE_H +#ifndef _H5BLOCK_READWRITE_H_ +#define _H5BLOCK_READWRITE_H_ #ifdef __cplusplus extern "C" { @@ -51,14 +51,6 @@ fc_head = """ #endif """ -fi_head = """ -INTERFACE -""" - -fi_tail = """ -END INTERFACE -""" - write_scalar_h = """ h5part_int64_t H5Block#DIM#dWriteScalarField#TYPE_ABV# ( @@ -79,7 +71,7 @@ H5Block#DIM#dReadScalarField#TYPE_ABV# ( write_scalar_c = """ /*! - \\ingroup h5block_write + \\ingroup h5block_data Write a 3-dimensional field \\c name from the buffer starting at \\c data to the current time-step using the defined field layout. Values are @@ -117,7 +109,7 @@ H5Block#DIM#dWriteScalarField#TYPE_ABV# ( read_scalar_c = """ /*! - \\ingroup h5block_read + \\ingroup h5block_data Read a 3-dimensional field \\c name into the buffer starting at \\c data from the current time-step using the defined field layout. Values are @@ -153,18 +145,26 @@ H5Block#DIM#dReadScalarField#TYPE_ABV# ( """ write_scalar_fi = """ +!> \\ingroup h5blockf_data +!! See \\ref H5Block#DIM#dWriteScalarField#TYPE_ABV# +!! \\return 0 on success or error code +!< INTEGER*8 FUNCTION h5bl_#DIM#d_write_scalar_field_#TYPE_F90_ABV# ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - #TYPE_F90#, INTENT(IN) :: data(*) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + #TYPE_F90#, INTENT(IN) :: data(*) !< the array of data END FUNCTION """ read_scalar_fi = """ +!> \\ingroup h5blockf_data +!! See \\ref H5Block#DIM#dReadScalarField#TYPE_ABV# +!! \\return 0 on success or error code +!< INTEGER*8 FUNCTION h5bl_#DIM#d_read_scalar_field_#TYPE_F90_ABV# ( filehandle, name, data ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - #TYPE_F90#, INTENT(OUT) :: data(*) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + #TYPE_F90#, INTENT(OUT) :: data(*) !< buffer to read the data into END FUNCTION """ @@ -246,7 +246,7 @@ H5Block#DIM#dRead3dVectorField#TYPE_ABV# ( write_vector_c = """ /*! - \\ingroup h5block_write + \\ingroup h5block_data */ /*! Write a 3-dimensional field \\c name with 3-dimensional vectors as values @@ -292,7 +292,7 @@ H5Block#DIM#dWrite3dVectorField#TYPE_ABV# ( read_vector_c = """ /*! - \\ingroup h5block_read + \\ingroup h5block_data */ /*! Read a 3-dimensional field \\c name with 3-dimensional vectors as values @@ -335,23 +335,31 @@ H5Block#DIM#dRead3dVectorField#TYPE_ABV# ( } """ -write_vector_fi = """ +write_vector_fi = """ +!> \\ingroup h5blockf_data +!! See \\ref H5Block#DIM#dWrite3dVectorField#TYPE_ABV# +!! \\return 0 on success or error code +!< INTEGER*8 FUNCTION h5bl_#DIM#d_write_3dvector_field_#TYPE_F90_ABV# ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - #TYPE_F90#, INTENT(IN) :: x(*) - #TYPE_F90#, INTENT(IN) :: y(*) - #TYPE_F90#, INTENT(IN) :: z(*) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + #TYPE_F90#, INTENT(IN) :: x(*) !< the array of x data to write + #TYPE_F90#, INTENT(IN) :: y(*) !< the array of y data to write + #TYPE_F90#, INTENT(IN) :: z(*) !< the array of z data to write END FUNCTION """ read_vector_fi = """ +!> \\ingroup h5blockf_data +!! See \\ref H5Block#DIM#dRead3dVectorField#TYPE_ABV# +!! \\return 0 on success or error code +!< INTEGER*8 FUNCTION h5bl_#DIM#d_read_3dvector_field_#TYPE_F90_ABV# ( filehandle, name, x, y, z ) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: name - #TYPE_F90#, INTENT(OUT) :: x(*) - #TYPE_F90#, INTENT(OUT) :: y(*) - #TYPE_F90#, INTENT(OUT) :: z(*) + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset + #TYPE_F90#, INTENT(OUT) :: x(*) !< buffer to read the x data into + #TYPE_F90#, INTENT(OUT) :: y(*) !< buffer to read the y data into + #TYPE_F90#, INTENT(OUT) :: z(*) !< buffer to read the z data into END FUNCTION """ @@ -458,12 +466,16 @@ H5BlockWriteFieldAttrib#TYPE_ABV# ( """ write_attr_fi = """ +!> \\ingroup h5blockf_attrib +!! See \\ref H5BlockWriteFieldAttrib#TYPE_ABV# +!! \\return 0 on success or error code +!< INTEGER*8 FUNCTION h5bl_writefieldattrib_#TYPE_F90_ABV# ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem) - INTEGER*8, INTENT(IN) :: filehandle - CHARACTER(LEN=*), INTENT(IN) :: field_name ! The name of the field - CHARACTER(LEN=*), INTENT(IN) :: attrib_name ! The name of the attribute - #TYPE_F90#, INTENT(IN) :: attrib_value(*) ! The array of data to write into the attribute - INTEGER*8, INTENT(IN) :: attrib_nelem ! Number of elements in the attrib array + INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open + CHARACTER(LEN=*), INTENT(IN) :: field_name !< the name of the field + CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute + #TYPE_F90#, INTENT(IN) :: attrib_value(*) !< the array of data to write into the attribute + INTEGER*8, INTENT(IN) :: attrib_nelem !< the number of elements in the array END FUNCTION """ @@ -528,8 +540,7 @@ def write_calls(): hfile.write(h_head) fcfile = file('H5BlockReadWriteF.c','w') fcfile.write(fc_head) - fifile = file('H5BlockReadWriteF90.inc','w') - fifile.write(fi_head) + fifile = file('H5BlockReadWrite.f90','w') for dim in dims: for type in types: cfile.write(create_call(write_scalar_c,type,dim)); @@ -557,7 +568,6 @@ def write_calls(): hfile.write(h_tail) hfile.close() fcfile.close() - fifile.write(fi_tail) fifile.close() write_calls() diff --git a/src/generate-h5multi-readwrite.py b/src/generate-h5multi-readwrite.py index 530e76a..25dc793 100755 --- a/src/generate-h5multi-readwrite.py +++ b/src/generate-h5multi-readwrite.py @@ -14,8 +14,8 @@ c_head = """ """ h_head = """ -#ifndef __H5MULTIBLOCKREADWRITE_H -#define __H5MULTIBLOCKREADWRITE_H +#ifndef _H5MULTIBLOCK_READWRITE_H_ +#define _H5MULTIBLOCK_READWRITE_H_ #ifdef __cplusplus extern "C" { @@ -49,14 +49,6 @@ fc_head = """ #endif """ -fi_head = """ -INTERFACE -""" - -fi_tail = """ -END INTERFACE -""" - write_h = """ h5part_int64_t H5MultiBlock#DIM#dWriteField#TYPE_ABV# ( @@ -77,7 +69,7 @@ H5MultiBlock#DIM#dReadField#TYPE_ABV# ( write_c = """ /*! - \\ingroup h5multiblock_write + \\ingroup h5multiblock_data Write a multiblock field \\c name from the buffer starting at \\c data to the current time-step using the defined block decomposition and dimensions. @@ -107,7 +99,7 @@ H5MultiBlock#DIM#dWriteField#TYPE_ABV# ( read_c = """ /*! - \\ingroup h5multiblock_read + \\ingroup h5multiblock_data Allocate a buffer to hold a block from a multiblock field and place the pointer in \\c data, then read the block into the buffer. Uses the block diff --git a/test/Makefile.am b/test/Makefile.am index 80e02a9..9f7ff88 100644 --- a/test/Makefile.am +++ b/test/Makefile.am @@ -1,171 +1,30 @@ # test level Makefile.am -# PATH SETTING -HDF5ROOT = @HDF5ROOT@ +OBJEXT=o -# COMPILER SETTING -CXX = @CXX@ -FC = @FC@ -MPIFC = @MPIFC@ -MPICXX = @MPICXX@ -MPICC = @MPICC@ +HDFLIB = -L@HDF5ROOT@/lib -lhdf5 -lz @SZLIB@ +LIBS = -L@H5P_LIB_LOC@ -lH5PartF -lH5Part $(HDFLIB) -lm -# COMPILER FLAG SETTING -CFLAGS = @CFLAGS@ -FFLAGS = @FFLAGS@ @MPIINC@ +INCLUDES = -I@H5P_LIB_LOC@ -I@HDF5ROOT@/include @MPIINC@ -# LIBRARIES -SZLIB = @SZLIB@ -HDFLIB = -L$(HDF5ROOT)/lib -lhdf5 -lz $(SZLIB) @LDFLAGS@ -MPILIB = @MPILIB@ -H5LIB = -L@H5P_LIB_LOC@ -lH5Part +noinst_PROGRAMS = @TTARGET@ -LIBS = ${H5LIB} $(HDFLIB) $(MPILIB) -lm @STDCXX@ +TESTS_ENVIRONMENT = env LD_LIBRARY_PATH=@HDF5ROOT@/lib:$(LD_LIBRARY_PATH) +TESTS = @TTARGET@ -# H5Part compiled library location -# H5PLIB = -L@prefix@/lib +EXTRA_PROGRAMS = test testf -# INCLUDES -HDFINC = -I$(HDF5ROOT)/include -MPIINC = @MPIINC@ -H5INC = -I@H5P_LIB_LOC@ +test_SOURCES = test.c \ + testframe.c \ + write.c \ + read.c \ + testframe.h -INC = $(HDFINC) $(MPIINC) $(H5INC) - - -# What to build... make install will place these files in the $(prefix)/bin directory. -bin_PROGRAMS = @TTARGET@ - -# Some useful scripts that I wish to place in the $(prefix)/bin directory. -bin_SCRIPTS = -#bin_SCRIPTS = JAC_H5PartTestP_script.scr JAC_H5testFpar_script.scr JAC_RUN_ALL_script.scr - - -# Listing of all programs that maybe built. (Has to know statically...) -EXTRA_PROGRAMS = - -# Extra files that I wish to include in the dist tar ball. -EXTRA_DIST = Bench.c \ - H5ParallelTest.cc \ - H5PartTest.cc H5PartTestParallel.cc \ - H5PartAndreasTest.cc \ - H5test.cc H5testF.f \ - H5testFpar.F90 \ - H5BlockParTestScalarField.c H5BlockParTestScalarFieldF.F90 \ - H5BlockTestAttributes.c H5BlockTestAttributesF.F90 \ - H5PartBench.c H5BlockBench.c \ - $(bin_SCRIPTS) - -# Specific building instruction (What compilers to use...) -# ------------ Build Tests ------------ - -Bench: Bench.c - $(CC) $(CFLAGS) $(INC) -o $@ $< $(H5PLIB) -lH5Part $(LIBS) - -H5PartBench: H5PartBench.c - $(CC) $(CFLAGS) $(INC) -o $@ $< $(H5PLIB) -lpH5Part $(LIBS) - -H5BlockBench: H5BlockBench.c - $(CC) $(CFLAGS) $(INC) -o $@ $< $(H5PLIB) -lpH5Part $(LIBS) - -############################################################################### - -H5PartTest: H5PartTest.o - $(CXX) -o $@ $< $(H5PLIB) -lH5Part $(LIBS) - -H5PartTest.o: H5PartTest.cc - $(CXX) $(CFLAGS) $(INC) -DREGRESSIONTEST -g -c $< - -############################################################################### - -H5PartTestP: H5PartTestP.o - $(CXX) $(INC) -o $@ $< $(H5LIB) -lH5Part $(LIBS) - -H5PartTestP.o: H5PartTest.cc - $(CXX) $(CFLAGS) $(INC) -DREGRESSIONTEST -c $< -o $@ - -############################################################################### - -H5PartTestParallel: H5PartTestParallel.o - $(CXX) -o $@ $< $(H5LIB) -lH5Part $(LIBS) - -H5PartTestParallel.o: H5PartTestParallel.cc - $(CXX) $(CFLAGS) $(INC) -c $< - -############################################################################### - -H5PartAndreasTest: H5PartAndreasTest.o - $(CXX) -o $@ $< $(H5LIB) -lpH5Part $(LIBS) - -H5PartAndreasTest.o: H5PartAndreasTest.cc - $(CXX) $(CFLAGS) $(INC) -c $< - -############################################################################### - -H5testF: H5testF.o - $(FC) -o $@ $< $(H5LIB) -lH5PartF -lH5Part $(LIBS) - -H5testF.o: H5testF.f - $(FC) $(FFLAGS) -c $(H5INC) $< - -############################################################################### - -H5testFpar: H5testFpar.o - $(MPIFC) -o $@ $< $(H5LIB) -lpH5PartF -lpH5Part $(LIBS) - -H5testFpar.o: H5testFpar.F90 - $(MPIFC) $(FFLAGS) -c $(H5INC) $< - -############################################################################### - -H5test: H5test.o - $(CXX) -o $@ $< $(H5LIB) $(LIBS) - -H5test.o: H5test.cc - $(CXX) $(CFLAGS) $(INC) -DREGRESSIONTEST -g -c $< - -############################################################################### -% : %.o - $(CC) -o $@ $< $(H5LIB) $(LIBS) - -%.o : %.c - $(CC) $(CFLAGS) $(INC) -g -c $< - -%.o : %.F90 - ${FC} $(FFLAGS) -c $(H5INC) $< - -H5BlockTestAttributes.o: H5BlockTestAttributes.c - -H5BlockTestAttributes: H5BlockTestAttributes.o - -H5BlockTestAttributesF.o: H5BlockTestAttributesF.F90 - -H5BlockTestAttributesF: H5BlockTestAttributesF.o - $(FC) -o $@ $< $(H5LIB) -lH5PartF -lH5Part $(LIBS) - -H5BlockParTestScalarField.o: H5BlockParTestScalarField.c - -H5BlockParTestScalarField: H5BlockParTestScalarField.o - -H5BlockParTestScalarFieldF.o: H5BlockParTestScalarFieldF.F90 - -H5BlockParTestScalarFieldF: H5BlockParTestScalarFieldF.o - $(FC) -o $@ $< $(H5LIB) -lH5PartF -lH5Part $(LIBS) - -H5BlockDissolveGhosts.o: H5BlockDissolveGhosts.c - -H5BlockDissolveGhosts: H5BlockDissolveGhosts.o - - -############################################################################### -clean: - ${RM} -f *~ *.o ${bin_PROGRAMS} - -distclean: clean - ${RM} -rf .deps - ${RM} -rf .libs - ${RM} -f parttest.h5 - ${RM} -rf config.status config.log config.h Makefile +testf_SOURCES = testf.F90 +.c.o: + $(CC) $(CFLAGS) $(INCLUDES) -c $< +clean: clean-am + rm -f *.h5 diff --git a/test/params.h b/test/params.h new file mode 100644 index 0000000..854f2de --- /dev/null +++ b/test/params.h @@ -0,0 +1,22 @@ +#ifndef _H5PART_TEST_PARAMS_H_ +#define _H5PART_TEST_PARAMS_H_ + +#define FILENAME "test.h5" +#define LONGSTEPNAME "thisisaverylongstepnamethatshouldexceedthelimitof64charcausingawarningtoprint" +#define NTIMESTEPS 10 + +/* do not decrease this value below 99, or it will break assumptions + * made in the read tests! */ +#define NPARTICLES 99 + +/* do not increase this value past 32! */ +#define MAX_MPI_TASKS 32 + +#define ATTR_NAME_SIZE 16 +#define ATTR_STR_VAL "test" +#define ATTR_INT32_VAL -2147483648 +#define ATTR_INT64_VAL 2147483648 +#define ATTR_FLOAT_VAL 3.14159265F + +#endif + diff --git a/test/test.c b/test/test.c new file mode 100644 index 0000000..4552a5e --- /dev/null +++ b/test/test.c @@ -0,0 +1,70 @@ +#include +#include + +#include "testframe.h" +#include "params.h" + +/* from write.c */ +void test_write1(void); +void test_write2(void); +void test_write3(void); +void test_write4(void); + +/* from read.c */ +void test_read1(void); +void test_read2(void); +void test_read3(void); +void test_read4(void); + +int main(int argc, char **argv) +{ +#ifdef PARALLEL_IO + MPI_Init(&argc, &argv); + int procs; + MPI_Comm_size(MPI_COMM_WORLD, &procs); + if (procs > MAX_MPI_TASKS) { + fprintf(stderr, "ERROR: please use <= %d MPI tasks for the test.", + MAX_MPI_TASKS); + MPI_Abort(MPI_COMM_WORLD, -1); + } +#endif + + /* Initialize testing framework */ + TestInit(argv[0], NULL, NULL); + + /* Tests are generally arranged from least to most complexity... */ + AddTest("write1", test_write1, NULL, "Write 32-bit data", NULL); + AddTest("read1", test_read1, NULL, "Read 32-bit data", NULL); + AddTest("write2", test_write2, NULL, "Write 32-bit strided data", NULL); + AddTest("read2", test_read2, NULL, "Read 32-bit strided data", NULL); + AddTest("write3", test_write3, NULL, "Write 64-bit strided data", NULL); + AddTest("read3", test_read3, NULL, "Read 64-bit strided data", NULL); + AddTest("write4", test_write4, NULL, "Write 64-bit data", NULL); + AddTest("read4", test_read4, NULL, "Read 64-bit data", NULL); + + /* Display testing information */ + TestInfo(argv[0]); + + /* Parse command line arguments */ + TestParseCmdLine(argc, argv); + + H5PartSetVerbosityLevel(GetTestVerbosity()); + + /* Perform requested testing */ + PerformTests(); + + /* Display test summary, if requested */ + if (GetTestSummary()) + TestSummary(); + + /* Clean up test files, if allowed */ + //if (GetTestCleanup() && !getenv("HDF5_NOCLEANUP")) + // TestCleanup(); + + //return GetTestNumErrs(); + +#ifdef PARALLEL_IO + return MPI_Finalize(); +#endif +} + diff --git a/test/testframe.c b/test/testframe.c new file mode 100644 index 0000000..41f6fcc --- /dev/null +++ b/test/testframe.c @@ -0,0 +1,651 @@ +/* Test framework borrowed from HDF5 1.8.3: + * test/testframe.c + */ + +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Programmer: Quincey Koziol + * Tuesday, January 6, 2004 + * + * Purpose: Provides support functions for the testing framework. + * + */ + +#include +#include +#include +#include +#include +#include "testframe.h" + +/* + * Definitions for the testing structure. + */ +#define MAXNUMOFTESTS 64 +#define MAXTESTNAME 16 +#define MAXTESTDESC 64 + +typedef struct TestStruct { + int NumErrors; + char Description[MAXTESTDESC]; + int SkipFlag; + char Name[MAXTESTNAME]; + void (*Call)(void); + void (*Cleanup)(void); + const void *Parameters; +} TestStruct; + + +/* + * Variables used by testing framework. + */ +static int num_errs = 0; /* Total number of errors during testing */ +static int Verbosity = VERBO_DEF; /* Default Verbosity is Low */ +static int Summary = 0; /* Show test summary. Default is no. */ +static int CleanUp = 1; /* Do cleanup or not. Default is yes. */ +static int TestExpress = -1; /* Do TestExpress or not. -1 means not set yet. */ +static TestStruct Test[MAXNUMOFTESTS]; +static int Index = 0; +static const void *Test_parameters = NULL; +static const char *TestProgName = NULL; +static void (*TestPrivateUsage)(void) = NULL; +static int (*TestPrivateParser)(int ac, char *av[]) = NULL; + + +/* + * Setup a test function and add it to the list of tests. + * It must have no parameters and returns void. + * TheName--short test name. + * If the name starts with '-', do not run it by default. + * TheCall--the test routine. + * Cleanup--the cleanup routine for the test. + * TheDescr--Long description of the test. + * Parameters--pointer to extra parameters. Use NULL if none used. + * Since only the pointer is copied, the contents should not change. + */ +void +AddTest(const char *TheName, void (*TheCall) (void), void (*Cleanup) (void), const char *TheDescr, const void *Parameters) +{ + /* Sanity checking */ + if (Index >= MAXNUMOFTESTS) { + printf("Too many tests added, increase MAXNUMOFTEST(%d).\n", + MAXNUMOFTESTS); + exit(-1); + } /* end if */ + if (strlen(TheDescr) >= MAXTESTDESC) { + printf("Test description too long, increase MAXTESTDESC(%d).\n", + MAXTESTDESC); + exit(-1); + } /* end if */ + if (strlen(TheName) >= MAXTESTNAME) { + printf("Test name too long, increase MAXTESTNAME(%d).\n", + MAXTESTNAME); + exit(-1); + } /* end if */ + + /* Set up test function */ + strcpy(Test[Index].Description, TheDescr); + if (*TheName != '-'){ + strcpy(Test[Index].Name, TheName); + Test[Index].SkipFlag = 0; + } + else { /* skip test by default */ + strcpy(Test[Index].Name, TheName+1); + Test[Index].SkipFlag = 1; + } + Test[Index].Call = TheCall; + Test[Index].Cleanup = Cleanup; + Test[Index].NumErrors = -1; + Test[Index].Parameters = Parameters; + + /* Increment test count */ + Index++; +} + + +/* + * Initialize testing framework + * + * ProgName: Name of test program. + * private_usage: Optional routine provided by test program to print the + * private portion of usage page. Default to NULL which means none is + * provided. + * private_parser: Optional routine provided by test program to parse the + * private options. Default to NULL which means none is provided. + * + * Modifications: + * Albert Cheng 2004/08/17 + * Added the ProgName, private_usage and private_parser arguments. + */ +void TestInit(const char *ProgName, void (*private_usage)(void), int (*private_parser)(int ac, char *av[])) +{ +#if !(defined MAC || defined SYMANTEC_C) + /* Un-buffer the stdout and stderr */ + setbuf(stderr, NULL); + setbuf(stdout, NULL); +#endif + + /* + * Turn off automatic error reporting since we do it ourselves. Besides, + * half the functions this test calls are private, so automatic error + * reporting wouldn't do much good since it's triggered at the API layer. + */ + //H5Eset_auto2(H5E_DEFAULT, NULL, NULL); + + /* + * Record the program name and private routines if provided. + */ + TestProgName = ProgName; + if (NULL != private_usage) + TestPrivateUsage = private_usage; + if (NULL != private_parser) + TestPrivateParser = private_parser; +} + + +/* + * Print test usage. + * First print the common test options, then the extra options if provided. + * + * Modification: + * 2004/08/18 Albert Cheng. Add TestPrivateUsage feature. + */ +void TestUsage(void) +{ + int i; + + printf("Usage: %s [-v[erbose] (l[ow]|m[edium]|h[igh]|0-9)] %s\n", + TestProgName, (TestPrivateUsage ? "" : "")); + printf(" [-[e]x[clude] name+] \n"); + printf(" [-o[nly] name+] \n"); + printf(" [-b[egin] name] \n"); + printf(" [-s[ummary]] \n"); + printf(" [-c[leanoff]] \n"); + printf(" [-h[elp]] \n"); + printf("\n\n"); + printf("verbose controls the amount of information displayed\n"); + printf("exclude to exclude tests by name\n"); + printf("only to name tests which should be run\n"); + printf("begin start at the name of the test givin\n"); + printf("summary prints a summary of test results at the end\n"); + printf("cleanoff does not delete *.hdf files after execution of tests\n"); + printf("help print out this information\n"); + if (TestPrivateUsage){ + printf("\nExtra options\n"); + TestPrivateUsage(); + } + printf("\n\n"); + printf("This program currently tests the following: \n\n"); + printf("%16s %s\n", "Name", "Description"); + printf("%16s %s\n", "----", "-----------"); + + for (i = 0; i < Index; i++) + printf("%16s %s\n", Test[i].Name, Test[i].Description); + + printf("\n\n"); +} + + +/* + * Print test info. + */ +void TestInfo(const char *ProgName) +{ + unsigned major, minor, release; + + H5get_libversion(&major, &minor, &release); + + printf("\nFor help use: %s -help\n",ProgName); + printf("Linked with hdf5 version %u.%u release %u\n", major, minor, release); + printf("Linked with H5Part version %s\n", H5PART_VER_STRING); +} + + +/* + * Parse command line information. + * argc, argv: the usual command line argument count and strings + * + * Modification: + * 2004/08/18 Albert Cheng. Add extra_parse feature. + */ +void TestParseCmdLine(int argc, char *argv[]) +{ + int ret_code; + + while (argv++, --argc > 0){ + if ((strcmp(*argv, "-verbose") == 0) || + (strcmp(*argv, "-v") == 0)) { + if (argc > 0){ + --argc; ++argv; + ParseTestVerbosity(*argv); + }else{ + TestUsage(); + exit(1); + } + } + else if (((strcmp(*argv, "-exclude") == 0) || + (strcmp(*argv, "-x") == 0))) { + if (argc > 0){ + --argc; ++argv; + SetTest(*argv, SKIPTEST); + }else{ + TestUsage(); + exit(1); + } + } + else if (((strcmp(*argv, "-begin") == 0) || + (strcmp(*argv, "-b") == 0))) { + if (argc > 0){ + --argc; ++argv; + SetTest(*argv, BEGINTEST); + }else{ + TestUsage(); + exit(1); + } + } + else if (((strcmp(*argv, "-only") == 0) || + (strcmp(*argv, "-o") == 0))) { + if (argc > 0){ + int Loop; + --argc; ++argv; + /* Skip all tests, then activate only one. */ + for (Loop = 0; Loop < Index; Loop++) + Test[Loop].SkipFlag = 1; + SetTest(*argv, ONLYTEST); + }else{ + TestUsage(); + exit(1); + } + } + else if ((strcmp(*argv, "-summary") == 0) || (strcmp(*argv, "-s") == 0)) + Summary = 1; + else if ((strcmp(*argv, "-help") == 0) || (strcmp(*argv, "-h") == 0)) { + TestUsage(); + exit(0); + } + else if ((strcmp(*argv, "-cleanoff") == 0) || (strcmp(*argv, "-c") == 0)) + SetTestNoCleanup(); + else { + /* non-standard option. Break out. */ + break; + } + + } + + /* Call extra parsing function if provided. */ + if (NULL != TestPrivateParser){ + ret_code=TestPrivateParser(argc+1, argv-1); + if (ret_code != 0) + exit(-1); + } +} + + +/* + * Perform Tests. + */ +void PerformTests(void) +{ + int Loop; + + for (Loop = 0; Loop < Index; Loop++) + if (Test[Loop].SkipFlag) { + MESSAGE(2, ("Skipping -- %s (%s) \n", Test[Loop].Description, Test[Loop].Name)); + } else { + MESSAGE(2, ("Testing -- %s (%s) \n", Test[Loop].Description, Test[Loop].Name)); + MESSAGE(5, ("===============================================\n")); + Test[Loop].NumErrors = num_errs; + Test_parameters = Test[Loop].Parameters; + //ALARM_ON; + Test[Loop].Call(); + //ALARM_OFF; + Test[Loop].NumErrors = num_errs - Test[Loop].NumErrors; + MESSAGE(5, ("===============================================\n")); + MESSAGE(5, ("There were %d errors detected.\n\n", (int)Test[Loop].NumErrors)); + } + + Test_parameters = NULL; /* clear it. */ + MESSAGE(2, ("\n\n")); + + if (num_errs) + printf("!!! %d Error(s) were detected !!!\n\n", (int) num_errs); + else + printf("All tests were successful. \n\n"); +} + + +/* + * Display test summary. + */ +void TestSummary(void) +{ + int Loop; + + printf("Summary of Test Results:\n"); + printf("Name of Test Errors Description of Test\n"); + printf("---------------- ------ --------------------------------------\n"); + + for (Loop = 0; Loop < Index; Loop++) { + if (Test[Loop].NumErrors == -1) + printf("%16s %6s %s\n", Test[Loop].Name, "N/A", Test[Loop].Description); + else + printf("%16s %6d %s\n", Test[Loop].Name, (int)Test[Loop].NumErrors, Test[Loop].Description); + } + + printf("\n\n"); +} + + +/* + * Cleanup files from testing + */ +void TestCleanup(void) +{ + int Loop; + + MESSAGE(2, ("\nCleaning Up temp files...\n\n")); + + /* call individual cleanup routines in each source module */ + for (Loop = 0; Loop < Index; Loop++) + if (!Test[Loop].SkipFlag && Test[Loop].Cleanup!=NULL) + Test[Loop].Cleanup(); +} + + +/* + * Retrieve the verbosity level for the testing framework + */ +int GetTestVerbosity(void) +{ + return(Verbosity); +} + +/* + * Set the verbosity level for the testing framework. + * Return previous verbosity level. + */ +int SetTestVerbosity(int newval) +{ + int oldval; + + oldval = Verbosity; + Verbosity = newval; + return(oldval); +} + +/* + * Retrieve the TestExpress mode for the testing framework + Values: + 0: Exhaustive run + Tests should take as long as necessary + 1: Full run. Default if HDF5TestExpress is not defined + Tests should take no more than 30 minutes + 2: Quick run + Tests should take no more than 10 minutes + 3: Smoke test. Default if HDF5TestExpress is set to a value other than 0-3 + Tests should take less than 1 minute + + Design: + If the environment variable $HDF5TestExpress is defined, + then test programs should skip some tests so that they + complete sooner. + + Terms: + A "test" is a single executable, even if it contains multiple + sub-tests. + The standard system for test times is a Linux machine running in + NFS space (to catch tests that involve a great deal of disk I/O). + + Implementation: + I think this can be easily implemented in the test library (libh5test.a) + so that all tests can just call it to check the status of $HDF5TestExpress. + */ +int GetTestExpress(void) +{ + char * env_val; + + /* set it here for now. Should be done in something like h5test_init(). */ + if(TestExpress==-1) + { + env_val = getenv("HDF5TestExpress"); + + if(env_val == NULL) + SetTestExpress(1); + else if(strcmp(env_val, "0") == 0) + SetTestExpress(0); + else if(strcmp(env_val, "1") == 0) + SetTestExpress(1); + else if(strcmp(env_val, "2") == 0) + SetTestExpress(2); + else + SetTestExpress(3); + } + + return(TestExpress); +} + +/* + * Set the TestExpress mode for the testing framework. + * Return previous TestExpress mode. + * Values: non-zero means TestExpress mode is on, 0 means off. + */ +int SetTestExpress(int newval) +{ + int oldval; + + oldval = TestExpress; + TestExpress = newval; + return(oldval); +} + +/* + * Retrieve Summary request value. + * 0 means no summary, 1 means yes. + */ +int GetTestSummary(void) +{ + return(Summary); +} + +/* + * Retrieve Cleanup request value. + * 0 means no Cleanup, 1 means yes. + */ +int GetTestCleanup(void) +{ + return(CleanUp); +} + +/* + * Set cleanup to no. + * Return previous cleanup value. + */ +int SetTestNoCleanup(void) +{ + int oldval; + + oldval = CleanUp; + CleanUp = 0; + return(oldval); +} + +/* + * Parse an argument string for verbosity level and set it. + */ +void ParseTestVerbosity(char *argv) +{ + if (*argv == 'l') + SetTestVerbosity(VERBO_LO); + else if (*argv == 'm') + SetTestVerbosity(VERBO_MED); + else if (*argv == 'h') + SetTestVerbosity(VERBO_HI); + else + SetTestVerbosity(atoi(argv)); +} + + +/* + * Retrieve the number of testing errors for the testing framework + */ +int GetTestNumErrs(void) +{ + return(num_errs); +} + + +/* + * Increment the number of testing errors + */ +void IncTestNumErrs(void) +{ + num_errs++; +} + + +/* + * Retrieve the current Test Parameters pointer. + */ +const void *GetTestParameters(void) +{ + return(Test_parameters); +} + +int +TestPrintf(const char *format, ...) +{ + va_list arglist; + int ret_value; + +#if PARALLEL_IO + int nproc; + MPI_Comm_rank(MPI_COMM_WORLD, &nproc); + if ( nproc == 0 || VERBOSE_HI ) { + char *format2 = malloc(strlen(format)+8); + sprintf(format2, "[%d] %s", nproc, format); + va_start(arglist, format); + ret_value = vprintf(format2, arglist); + va_end(arglist); + } +#else + va_start(arglist, format); + ret_value = vprintf(format, arglist); + va_end(arglist); +#endif + + /* Return the length of the string produced (like printf() does) */ + return ret_value; +} + + +/* + * This routine is designed to provide equivalent functionality to 'printf' + * and also increment the error count for the testing framework. + */ +int +TestErrPrintf(const char *format, ...) +{ + va_list arglist; + int ret_value; + + /* Increment the error count */ + num_errs++; + +#if PARALLEL_IO + int nproc; + MPI_Comm_rank(MPI_COMM_WORLD, &nproc); + if ( nproc == 0 || VERBOSE_HI ) { + char *format2 = malloc(strlen(format)+8); + sprintf(format2, "[%d] %s", nproc, format); + va_start(arglist, format); + ret_value = vfprintf(stderr, format2, arglist); + va_end(arglist); + } +#else + va_start(arglist, format); + ret_value = vfprintf(stderr, format, arglist); + va_end(arglist); +#endif + + /* Return the length of the string produced (like printf() does) */ + return ret_value; +} + + +/* + * Set (control) which test will be tested. + * SKIPTEST: skip this test + * ONLYTEST: do only this test + * BEGINETEST: skip all tests before this test + * + */ +void SetTest(const char *testname, int action) +{ + int Loop; + switch (action){ + case SKIPTEST: + for (Loop = 0; Loop < Index; Loop++) + if (strcmp(testname, Test[Loop].Name) == 0){ + Test[Loop].SkipFlag = 1; + break; + } + break; + case BEGINTEST: + for (Loop = 0; Loop < Index; Loop++) { + if (strcmp(testname, Test[Loop].Name) != 0) + Test[Loop].SkipFlag = 1; + else{ + /* Found it. Set it to run. Done. */ + Test[Loop].SkipFlag = 0; + break; + } + } + break; + case ONLYTEST: + for (Loop = 0; Loop < Index; Loop++) { + if (strcmp(testname, Test[Loop].Name) != 0) + Test[Loop].SkipFlag = 1; + else { + /* Found it. Set it to run. Break to skip the rest. */ + Test[Loop].SkipFlag = 0; + break; + } + } + /* skip the rest */ + while (++Loop < Index) + Test[Loop].SkipFlag = 1; + break; + default: + /* error */ + printf("*** ERROR: Unknown action (%d) for SetTest\n", action); + break; + } +} + +void +get_attr_name(char *name, char *tag, int id) +{ + sprintf(name, "Attr%d%s", id, tag); +} + +void +test_is_valid(H5PartFile *file) +{ + h5part_int64_t status = H5PartFileIsValid(file); + RETURN(status, H5PART_SUCCESS, "H5PartFileIsValid"); +} + diff --git a/test/testframe.h b/test/testframe.h new file mode 100644 index 0000000..858c4c4 --- /dev/null +++ b/test/testframe.h @@ -0,0 +1,188 @@ +/* Test framework borrowed from HDF5 1.8.3: + * test/h5test.h + * test/testhdf5.h + */ + +#ifndef _H5PART_TESTFRAME_H_ +#define _H5PART_TESTFRAME_H_ + +#ifdef PARALLEL_IO +#define OPEN(file,mode) \ + H5PartOpenFileParallel(file,mode,MPI_COMM_WORLD) +#define OPENALIGN(file,mode,align) \ + H5PartOpenFileParallelAlign(file,mode,MPI_COMM_WORLD,align) +#else +#define OPEN(file,mode) H5PartOpenFile(file,mode) +#define OPENALIGN(file,mode,align) H5PartOpenFileAlign(file,mode,align) +#endif + +/* + * Predefined test verbosity levels. + * + * Convention: + * + * The higher the verbosity value, the more information printed. + * So, output for higher verbosity also include output of all lower + * verbosity. + * + * Value Description + * 0 None: No informational message. + * 1 "All tests passed" + * 2 Header of overall test + * 3 Default: header and results of individual test + * 4 + * 5 Low: Major category of tests. + * 6 + * 7 Medium: Minor category of tests such as functions called. + * 8 + * 9 High: Highest level. All information. + */ +#define VERBO_DEF 0 /* Default */ +#define VERBO_LO 2 /* Low */ +#define VERBO_MED 3 /* Medium */ +#define VERBO_HI 4 /* High */ + +/* + * Verbose queries + * Only None needs an exact match. The rest are at least as much. + */ +#define VERBOSE_DEF (GetTestVerbosity()>=VERBO_DEF) +#define VERBOSE_LO (GetTestVerbosity()>=VERBO_LO) +#define VERBOSE_MED (GetTestVerbosity()>=VERBO_MED) +#define VERBOSE_HI (GetTestVerbosity()>=VERBO_HI) + +#define SKIPTEST 1 +#define ONLYTEST 2 +#define BEGINTEST 3 + +/* + * Print the current location on the standard output stream. + */ +#define AT() TestPrintf (" at %s:%d in %s()...\n", \ + __FILE__, __LINE__, __FUNCTION__); + +/* + * The name of the test is printed by saying TESTING("something") which will + * result in the string `Testing something' being flushed to standard output. + * If a test passes, fails, or is skipped then the PASSED(), H5_FAILED(), or + * SKIPPED() macro should be called. After H5_FAILED() or SKIPPED() the caller + * should print additional information to stdout indented by at least four + * spaces. If the h5_errors() is used for automatic error handling then + * the H5_FAILED() macro is invoked automatically when an API function fails. + */ +#define TESTING(WHAT) {TestPrintf("Testing %-62s",WHAT); fflush(stdout);} +#define TESTING_2(WHAT) {TestPrintf(" Testing %-62s",WHAT); fflush(stdout);} +#define PASSED() {TestPrintf(" PASSED");fflush(stdout);} +#define H5_FAILED() {TestPrintf("*FAILED*");fflush(stdout);} +#define H5_WARNING() {TestPrintf("*WARNING*");fflush(stdout);} +#define SKIPPED() {TestPrintf(" -SKIP-");fflush(stdout);} +#define TEST_ERROR {H5_FAILED(); AT(); goto error;} +//#define STACK_ERROR {H5Eprint2(H5E_DEFAULT, stdout); goto error;} +//#define FAIL_STACK_ERROR {H5_FAILED(); AT(); H5Eprint2(H5E_DEFAULT, stdout); \ +// goto error;} +#define FAIL_PUTS_ERROR(s) {H5_FAILED(); AT(); TestPrintf(s); goto error;} + +/* Use %ld to print the value because long should cover most cases. */ +/* Used to make certain a return value _is_not_ a value */ +#define RETURN(ret, val, where) do { \ + if (VERBOSE_HI) TestPrintf( " Call to routine %15s at line %4d " \ + "in %s returned %ld \n", \ + where, (int)__LINE__, __FILE__, \ + (long)(ret)); \ + if ((ret) != (val)) { \ + TestErrPrintf("*** UNEXPECTED RETURN from %s is %ld at line %4d " \ + "in %s\n", where, (long)(ret), (int)__LINE__, __FILE__); \ + } \ +} while(0) + +#define VALUE(val, expected, what) do { \ + if ((val) != (expected)) { \ + TestErrPrintf( "*** INCORRECT VALUE of %s at line " \ + "%d in %s\n", what, (int)__LINE__, \ + __FILE__); \ + } \ +} while(0) + +#define IVALUE(val, expected, what) do { \ + if (VERBOSE_HI) TestPrintf( " Value of int %15s at line %4d " \ + "in %s is %ld =? %ld\n", what, \ + (int)__LINE__, __FILE__, \ + (long)(val), (long)(expected)); \ + VALUE(val, expected, what); \ +} while(0) + +#define FVALUE(val, expected, what) do { \ + if (VERBOSE_HI) TestPrintf( " Value of float %15s at line %4d " \ + "in %s is %g =? %g\n", what, \ + (int)__LINE__, __FILE__, \ + (val), (expected)); \ + VALUE(val, expected, what); \ +} while(0) + +#define CVALUE(val, expected, what) do { \ + if (VERBOSE_HI) TestPrintf( " Value of char %15s at line %4d " \ + "in %s is %c =? %c\n", what, \ + (int)__LINE__, __FILE__, \ + (val), (expected)); \ + VALUE(val, expected, what); \ +} while(0) + + +#define SVALUE(val, expected, what) do { \ + if (VERBOSE_HI) TestPrintf( " Value of string %15s at line %4d " \ + "in %s is %s =? %s\n", what, \ + (int)__LINE__, __FILE__, \ + (val), (expected)); \ + if (strcmp(val,expected) != 0) { \ + TestErrPrintf( "*** INCORRECT VALUE of %d at line " \ + "%4d in %s\n", what, (int)__LINE__, \ + __FILE__); \ + } \ +} while(0) + +/* Used to document process through a test */ +#define MESSAGE(V,A) do { \ + if (V) TestPrintf A; \ +} while(0) + +#define TEST(WHAT) MESSAGE(VERBOSE_DEF,(WHAT "\n")) + +/* definitions for command strings */ +#define VERBOSITY_STR "Verbosity" +#define SKIP_STR "Skip" +#define TEST_STR "Test" +#define CLEAN_STR "Cleanup" + +void TestUsage(void); +void AddTest(const char *TheName, void (*TheCall) (void), + void (*Cleanup) (void), const char *TheDescr, + const void *Parameters); +void TestInfo(const char *ProgName); +void TestParseCmdLine(int argc, char *argv[]); +void PerformTests(void); +void TestSummary(void); +void TestCleanup(void); +void TestInit(const char *ProgName, void (*private_usage)(void), int (*private_parser)(int ac, char *av[])); +int GetTestVerbosity(void); +int SetTestVerbosity(int newval); +int GetTestSummary(void); +int GetTestCleanup(void); +int SetTestNoCleanup(void); +int GetTestExpress(void); +int SetTestExpress(int newval); +void ParseTestVerbosity(char *argv); +int GetTestNumErrs(void); +void IncTestNumErrs(void); +const void *GetTestParameters(void); +int TestPrintf(const char *format, ...); +int TestErrPrintf(const char *format, ...); +void SetTest(const char *testname, int action); + +void +get_attr_name(char *name, char *tag, int id); + +void +test_is_valid(H5PartFile *file); + +#endif + diff --git a/test/write.c b/test/write.c new file mode 100644 index 0000000..41334bb --- /dev/null +++ b/test/write.c @@ -0,0 +1,418 @@ +#include + +#include "testframe.h" +#include "params.h" + +static void +test_write_file_attribs(H5PartFile *file, int position) +{ + h5part_int64_t status; + char name[ATTR_NAME_SIZE]; + + TEST("Writing file attributes"); + + get_attr_name(name, "str", position); + status = H5PartWriteFileAttribString(file, name, ATTR_STR_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteFileAttribString"); + + get_attr_name(name, "i32", position); + status = H5PartWriteFileAttribInt32(file, name, ATTR_INT32_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteFileAttribInt32"); + + get_attr_name(name, "i64", position); + status = H5PartWriteFileAttribInt64(file, name, ATTR_INT64_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteFileAttribInt64"); + + get_attr_name(name, "f32", position); + status = H5PartWriteFileAttribFloat32(file, name, ATTR_FLOAT_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteFileAttribFloat32"); + + get_attr_name(name, "f64", position); + status = H5PartWriteFileAttribFloat64(file, name, ATTR_FLOAT_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteFileAttribFloat64"); +} + +static void +test_write_step_attribs(H5PartFile *file, int position) +{ + h5part_int64_t status; + char name[ATTR_NAME_SIZE]; + + TEST("Writing step attributes"); + + get_attr_name(name, "str", position); + status = H5PartWriteStepAttribString(file, name, ATTR_STR_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteStepAttribString"); + + get_attr_name(name, "i32", position); + status = H5PartWriteStepAttribInt32(file, name, ATTR_INT32_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteStepAttribInt32"); + + get_attr_name(name, "i64", position); + status = H5PartWriteStepAttribInt64(file, name, ATTR_INT64_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteStepAttribInt64"); + + get_attr_name(name, "f32", position); + status = H5PartWriteStepAttribFloat32(file, name, ATTR_FLOAT_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteStepAttribFloat32"); + + get_attr_name(name, "f64", position); + status = H5PartWriteStepAttribFloat64(file, name, ATTR_FLOAT_VAL); + RETURN(status, H5PART_SUCCESS, "H5PartWriteStepAttribFloat64"); +} + +static void +test_write_data64(H5PartFile *file, int nparticles, int step) +{ + int i,t; + h5part_int64_t status; + + double *x,*y,*z; + double *px,*py,*pz; + h5part_int64_t *id; + + x=(double*)malloc(nparticles*sizeof(double)); + y=(double*)malloc(nparticles*sizeof(double)); + z=(double*)malloc(nparticles*sizeof(double)); + px=(double*)malloc(nparticles*sizeof(double)); + py=(double*)malloc(nparticles*sizeof(double)); + pz=(double*)malloc(nparticles*sizeof(double)); + id=(h5part_int64_t*)malloc(nparticles*sizeof(h5part_int64_t)); + + /* invalid stride will produce a warning */ + status = H5PartSetNumParticlesStrided(file, nparticles, -1); + RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticlesStrided"); + +#if PARALLEL_IO + TEST("Setting throttle"); + status = H5PartSetThrottle(file, 2); + RETURN(status, H5PART_SUCCESS, "H5PartSetThrottle"); +#endif + + TEST("Writing 64-bit data"); + + for (t=step; t +#include +#include +#include +#include +#include +#include + +#define VERBOSITY_LOW 1 +#define VERBOSITY_MEDIUM 3 +#define VERBOSITY_HIGH 5 + +#define ONE_MEGABYTE 1048576.0 + +#ifdef PARALLEL_IO + +/* Parameters ***********************************************************/ +struct Params { +int rank; // MPI +int procs; // MPI +int segments; // number of segments (i.e. time steps) +int repetitions; // number of times to repeat the test +int read; // enable read test +int write; // enable write test +int nofillvals; // disable fill values in HDF5 +int verbosity; // verbosity level +char* filename; // path to the test file +char flags; // file open flags +double aggregate_size; // aggregate size in MB +h5part_int64_t alignment; // HDF5 alignment in bytes +h5part_int64_t block_size; // size of the block data +h5part_int64_t bdims[3]; // block dimensions +h5part_int64_t cdims[3]; // chunk dimensions +h5part_int64_t layout[6]; // H5Block layout +}; +typedef struct Params Params; + + +/************************************************************************/ +/* Argument helper functions */ +/************************************************************************/ + +void print_usage () +{ + printf ("Usage:\n"); + printf (" -a\talignment in bytes [1048576]\n"); + printf (" -b\tblock dimensions [64 64 64]\n"); + printf (" -c\tchunk dimentions [0 0 0]\n"); + printf (" -i\trepetitions [1]\n"); + printf (" -n\tHDF5 no fill [0]\n"); + printf (" -o\toutput dir [output]\n"); + printf (" -r\tperform read test [0]\n"); + printf (" -s\tsegments [1]\n"); + printf (" -v\tverbosity level [1]\n"); + printf (" -w\tpreform write test [0]\n"); + printf (" -lustre\tenable lustre-specific tuning\n"); + printf (" -posix\tuse the MPI-POSIX VFD\n"); +} + +void parse_args (int argc, char** argv, Params* p) +{ + int i; + + if (argc < 2) { + if (p->rank == 0) print_usage(); + MPI_Finalize(); + exit (EXIT_SUCCESS); + } + + // default values + p->bdims[0] = 64; + p->bdims[1] = 64; + p->bdims[2] = 64; + p->cdims[0] = 0; + p->cdims[1] = 0; + p->cdims[2] = 0; + p->segments = 1; + p->repetitions = 1; + p->read = 0; + p->write = 0; + p->alignment = 1048576; + p->nofillvals = 0; + p->verbosity = VERBOSITY_MEDIUM; + p->filename = "output"; + p->flags = H5PART_WRITE; + + i = 1; + while (i < argc) + { + // block dimensions + if (strcmp(argv[i],"-b") == 0) + { + i++; + p->bdims[0] = atoi (argv[i]); + i++; + p->bdims[1] = atoi (argv[i]); + i++; + p->bdims[2] = atoi (argv[i]); + } + // chunk dimensions + else if (strcmp(argv[i],"-c") == 0) + { + i++; + p->cdims[0] = atoi (argv[i]); + i++; + p->cdims[1] = atoi (argv[i]); + i++; + p->cdims[2] = atoi (argv[i]); + } + // segments + else if (strcmp(argv[i],"-s") == 0) + { + i++; + p->segments = atoi (argv[i]); + } + // repetitions + else if (strcmp(argv[i],"-i") == 0) + { + i++; + p->repetitions = atoi (argv[i]); + } + // read + else if (strcmp(argv[i],"-r") == 0) + { + p->read = 1; + } + // write + else if (strcmp(argv[i],"-w") == 0) + { + p->write = 1; + } + // alignment + else if (strcmp(argv[i],"-a") == 0) + { + i++; + p->alignment = atoi (argv[i]); + } + // nofillvals + else if (strcmp(argv[i],"-n") == 0) + { + p->nofillvals = 1; + } + // verbosity level + else if (strcmp(argv[i],"-v") == 0) + { + i++; + p->verbosity = atoi (argv[i]); + } + // filename + else if (strcmp(argv[i],"-o") == 0) + { + i++; + p->filename = (char*) malloc (strlen (argv[i]) + 1); + strcpy (p->filename, argv[i]); + } + else if (strcmp(argv[i],"-lustre") == 0) + { + p->flags |= H5PART_FS_LUSTRE; + } + else if (strcmp(argv[i],"-posix") == 0) + { + p->flags |= H5PART_VFD_MPIPOSIX; + } + // print usage + else if (strcmp(argv[i],"--help") == 0) + { + if (p->rank == 0) print_usage(); + MPI_Finalize(); + exit (EXIT_SUCCESS); + } + else + { + if (p->rank == 0) { + fprintf (stderr, "%s: unrecognized argument %s \n", + argv[0], argv[i]); + print_usage(); + } + MPI_Finalize(); + exit (EXIT_FAILURE); + } + i++; + } +} + + +/************************************************************************/ +/* Layout functions */ +/************************************************************************/ + +int nth_root_int_divisor (const int m, const int n) +{ + int i, root; + double p; + + p = 1.0 / (double) n; + root = (int) ceil ( pow ((double) m, p) ); + for (i=root; i<=m; i++) + { + if (m % i == 0) return i; + } + + return i; +} + +void set_layout (Params* p) +{ + int i, j, k; + int x, y, z; + + x = nth_root_int_divisor (p->procs, 3); + y = nth_root_int_divisor (p->procs / x, 2); + z = p->procs / x / y; + + if (p->verbosity >= VERBOSITY_HIGH && p->rank == 0) { + printf ("creating (%d,%d,%d) layout\n", x, y, z); + } + + i = p->rank % x; + j = (p->rank / x) % y; + k = p->rank / (x * y); + + p->layout[0] = i * p->bdims[0]; + p->layout[1] = (i + 1) * p->bdims[0] - 1; + p->layout[2] = j * p->bdims[1]; + p->layout[3] = (j + 1) * p->bdims[1] - 1; + p->layout[4] = k * p->bdims[2]; + p->layout[5] = (k + 1) * p->bdims[2] - 1; + + if (p->verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: (%d,%d,%d) [%lld,%lld]x[%lld,%lld]x[%lld,%lld]\n", + p->rank, i, j, k, + (long long)p->layout[0], (long long)p->layout[1], + (long long)p->layout[2], (long long)p->layout[3], + (long long)p->layout[4], (long long)p->layout[5]); + } +} + +void check_cdims (Params* p) +{ + int i; + + for (i=0; i<3; i++) { + if (p->bdims[i] % p->cdims[i] != 0) { + if (p->rank == 0) { + fprintf (stderr, + "Chunk dim %d does not divide block dim %d!\n", + i, i); + } + MPI_Barrier (MPI_COMM_WORLD); + exit (EXIT_FAILURE); + } + } +} + + +/************************************************************************/ +/* Data functions */ +/************************************************************************/ + +void create_data (float* data, Params* p) +{ + int i; + + if (p->verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: creating random data\n", p->rank); + } + + for (i=0; iblock_size; i++) { + data[i] = (float) random(); + } +} + +double write_data (float* data, int iter, Params* p) +{ + int i; + double start_time; + double open_time; + double write_time; + double close_time; + double total_time; + double sum_time; + double open_mean; + double write_mean; + double close_mean; + double bandwidth; + float* segment; + char* filename; + H5PartFile* file; + h5part_int64_t status; + + if (p->verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: writing data\n", p->rank); + } + + start_time = MPI_Wtime(); + + filename = (char*) malloc (strlen (p->filename) + 64); + sprintf (filename, "%s/%d.h5", p->filename, iter); + + file = H5PartOpenFileParallelAlign (filename, + p->flags, MPI_COMM_WORLD, p->alignment); + if (!file) { + fprintf (stderr, + "rank %d: could not open H5Part file!\n", p->rank); + MPI_Barrier (MPI_COMM_WORLD); + exit (EXIT_FAILURE); + } + + open_time = MPI_Wtime() - start_time; + + if (p->cdims[0] > 0 && p->cdims[1] > 0 && p->cdims[2] > 0) { + status = H5BlockDefine3DChunkDims (file, + p->cdims[0], p->cdims[1], p->cdims[2]); + if (status != H5PART_SUCCESS) { + fprintf (stderr, + "rank %d: H5Block chunk error!", p->rank); + } + } + + status = H5BlockDefine3DFieldLayout (file, + p->layout[0], p->layout[1], + p->layout[2], p->layout[3], + p->layout[4], p->layout[5]); + if (status != H5PART_SUCCESS) { + fprintf (stderr, + "rank %d: H5Block layout error!", p->rank); + } + + segment = data; + + for (i=0; isegments; i++) { + status = H5PartSetStep (file, i); + if (status != H5PART_SUCCESS) { + fprintf (stderr, "rank %d: H5PartSetStep error!", p->rank); + } + + status = H5Block3dWriteScalarFieldFloat32 (file, "test", segment); + if (status != H5PART_SUCCESS) { + fprintf (stderr, "rank %d: H5Block write error!", p->rank); + } + + segment += p->block_size; + } + + write_time = (MPI_Wtime() - start_time) - open_time; + + H5PartCloseFile (file); + + close_time = (MPI_Wtime() - start_time) - write_time - open_time; + + total_time = open_time + write_time + close_time; + + if (p->verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: write\t%.3f\t%.3f\t%.3f\t%.3f\n", p->rank, + open_time, write_time, close_time, total_time); + } + + MPI_Barrier (MPI_COMM_WORLD); + MPI_Reduce (&open_time, &sum_time, 1, MPI_DOUBLE, + MPI_SUM, 0, MPI_COMM_WORLD); + open_mean = sum_time / p->procs; + MPI_Reduce (&write_time, &sum_time, 1, MPI_DOUBLE, + MPI_SUM, 0, MPI_COMM_WORLD); + write_mean = sum_time / p->procs; + MPI_Reduce (&close_time, &sum_time, 1, MPI_DOUBLE, + MPI_SUM, 0, MPI_COMM_WORLD); + close_mean = sum_time / p->procs; + bandwidth = p->aggregate_size / total_time; + + if (p->verbosity >= VERBOSITY_MEDIUM && p->rank == 0) { + printf ("write\t%.1f\t%.3f\t%.3f\t%.3f\t%.3f\n", bandwidth, + open_mean, write_mean, close_mean, total_time); + } + + return bandwidth; +} + + +/************************************************************************/ +/* Main procedure */ +/************************************************************************/ + +int main (int argc, char** argv) +{ + int i; + Params p; + float* data; + double chunk_size; + double data_size; + double bandwidth; + double write_max; + double write_min; + double write_mean; + double read_max; + double read_min; + double read_mean; + time_t rawtime; + struct tm * timeinfo; + + // initialize MPI + MPI_Init (&argc, &argv); + MPI_Comm_rank (MPI_COMM_WORLD, &p.rank); + MPI_Comm_size (MPI_COMM_WORLD, &p.procs); + + parse_args (argc, argv, &p); + //check_cdims (&p); + + H5PartSetVerbosityLevel (p.verbosity); + + if (p.verbosity >= VERBOSITY_MEDIUM && p.rank == 0) { + time (&rawtime); + timeinfo = localtime (&rawtime); + printf ("Started: %s", asctime (timeinfo)); + printf ("Command line:\n"); + for (i=0; i= VERBOSITY_MEDIUM && p.rank == 0) { + printf ("chunk_size\t\t= %.1f MB\n", chunk_size); + printf ("block_size\t\t= %.1f MB\n", + p.block_size * sizeof(float) / 1048576.0); + printf (" x %5d segment(s)\t= %.1f MB per proc\n", + p.segments, data_size); + printf (" x %5d procs\t\t= %.1f MB aggregate\n", + p.procs, p.aggregate_size); + } + + if (p.verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: mallocing block data\n", p.rank); + } + + data = (float*) malloc (p.segments * p.block_size * sizeof(float)); + if (!data) { + fprintf (stderr, + "rank %d: could not malloc block data!\n", p.rank); + MPI_Barrier (MPI_COMM_WORLD); + exit (EXIT_FAILURE); + } + + if (p.verbosity >= VERBOSITY_MEDIUM && p.rank == 0) { + printf ("access\tbw\topen\twr/rd\tclose\ttotal\n"); + printf ("(wr/rd)\t(MB/s)\t(s)\t(s)\t(s)\t(s)\n"); + printf ("------\t--\t----\t-----\t-----\t-----\n"); + } + + write_max = 0.0; + write_min = 10e300; + for (i=0; i write_max) write_max = bandwidth; + if (bandwidth < write_min) write_min = bandwidth; + write_mean += bandwidth; + } + } + write_mean /= p.repetitions; + + if (p.verbosity >= VERBOSITY_LOW && p.rank == 0) { + printf ("********************************\n"); + printf ("** Aggregate Bandwidth (MB/s) **\n"); + printf ("access max min mean \n"); + printf ("------ --- --- ---- \n"); + if (p.write) { + printf ("write\t%.1f\t%.1f\t%.1f\n", + write_max, write_min, write_mean); + } + if (p.read) { + printf ("read\t%.1f\t%.1f\t%.1f\n", + read_max, read_min, read_mean); + } + printf ("********************************\n"); + time (&rawtime); + timeinfo = localtime (&rawtime); + printf ("Finished: %s", asctime (timeinfo)); + } + + if (p.verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: Exiting!\n", p.rank); + } + + MPI_Finalize(); + return (EXIT_SUCCESS); +} + +#else +#error This file only works when PARALLEL_IO is enabled. +#endif diff --git a/tools/H5PartBench.c b/tools/H5PartBench.c new file mode 100644 index 0000000..e9338e8 --- /dev/null +++ b/tools/H5PartBench.c @@ -0,0 +1,412 @@ +/* + * File: H5PartBench.c + * Author: Mark Howison + * Created: 11-29-2008 + * Description: Benchmark application for H5Part, with similar + * functionality to IOR. + */ + +#include +#include +#include +#include +#include +#include + +#define VERBOSITY_LOW 1 +#define VERBOSITY_MEDIUM 3 +#define VERBOSITY_HIGH 5 + +#define ONE_MEGABYTE 1048576.0 + +#ifdef PARALLEL_IO + +/* Parameters ***********************************************************/ +struct Params { +int rank; // MPI +int procs; // MPI +int segments; // number of segments (i.e. time steps) +int repetitions; // number of times to repeat the test +int read; // enable read test +int write; // enable write test +int nofillvals; // disable fill values in HDF5 +int verbosity; // verbosity level +char* filename; // path to the test file +char flags; // file open flags +double aggregate_size; // aggregate size in MB +h5part_int64_t alignment; // HDF5 alignment in bytes +h5part_int64_t particles; // number of particles to write per block +h5part_int64_t blocks; // number of blocks to write per segment +}; +typedef struct Params Params; + + +/************************************************************************/ +/* Argument helper functions */ +/************************************************************************/ + +void print_usage () +{ + printf ("Usage:\n"); + printf (" -a\talignment in bytes\n"); + printf (" -b\tblocks per segment (i.e. chunks per timestep)\n"); + printf (" -i\trepetitions\n"); + printf (" -n\tHDF5 no fill\n"); + printf (" -o\toutput dir\n"); + printf (" -p\tparticles per block\n"); + printf (" -r\tperform read test\n"); + printf (" -s\tsegments (i.e. H5Part timesteps)\n"); + printf (" -v\tverbosity level\n"); + printf (" -w\tpreform write test\n"); + printf (" -lustre\tenable lustre-specific tuning\n"); + printf (" -posix\tuse the MPI-POSIX VFD\n"); +} + +void parse_args (int argc, char** argv, Params* p) +{ + int i; + + if (argc < 2) { + if (p->rank == 0) print_usage(); + MPI_Finalize(); + exit (EXIT_SUCCESS); + } + + // default values + p->blocks = 1; + p->particles = 262144; + p->segments = 1; + p->repetitions = 1; + p->read = 0; + p->write = 0; + p->alignment = 1048576; + p->nofillvals = 0; + p->verbosity = VERBOSITY_MEDIUM; + p->filename = "output"; + p->flags = H5PART_WRITE; + + i = 1; + while (i < argc) + { + // blocks + if (strcmp(argv[i],"-b") == 0) + { + i++; + p->blocks = atoi (argv[i]); + } + // particles + else if (strcmp(argv[i],"-p") == 0) + { + i++; + p->particles = atoi (argv[i]); + } + // segments + else if (strcmp(argv[i],"-s") == 0) + { + i++; + p->segments = atoi (argv[i]); + } + // repetitions + else if (strcmp(argv[i],"-i") == 0) + { + i++; + p->repetitions = atoi (argv[i]); + } + // read + else if (strcmp(argv[i],"-r") == 0) + { + p->read = 1; + } + // write + else if (strcmp(argv[i],"-w") == 0) + { + p->write = 1; + } + // alignment + else if (strcmp(argv[i],"-a") == 0) + { + i++; + p->alignment = atoi (argv[i]); + } + // nofillvals + else if (strcmp(argv[i],"-n") == 0) + { + p->nofillvals = 1; + } + // verbosity level + else if (strcmp(argv[i],"-v") == 0) + { + i++; + p->verbosity = atoi (argv[i]); + } + // filename + else if (strcmp(argv[i],"-o") == 0) + { + i++; + p->filename = (char*) malloc (strlen (argv[i]) + 1); + strcpy (p->filename, argv[i]); + } + else if (strcmp(argv[i],"-lustre") == 0) + { + p->flags |= H5PART_FS_LUSTRE; + } + else if (strcmp(argv[i],"-posix") == 0) + { + p->flags |= H5PART_VFD_MPIPOSIX; + } + // print usage + else if (strcmp(argv[i],"--help") == 0) + { + if (p->rank == 0) print_usage(); + MPI_Finalize(); + exit (EXIT_SUCCESS); + } + else + { + if (p->rank == 0) { + fprintf (stderr, "%s: unrecognized argument %s \n", + argv[0], argv[i]); + print_usage(); + } + MPI_Finalize(); + exit (EXIT_FAILURE); + } + i++; + } +} + + +/************************************************************************/ +/* Data functions */ +/************************************************************************/ + +void create_data (float* data, Params* p) +{ + int i; + + if (p->verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: creating random data\n", p->rank); + } + + for (i=0; i<(p->blocks * p->particles); i++) { + data[i] = (float) random(); + } +} + +double write_data (float* data, int iter, Params* p) +{ + int i,j; + double start_time; + double open_time; + double write_time; + double close_time; + double total_time; + double sum_time; + double open_mean; + double write_mean; + double close_mean; + double bandwidth; + float* segment; + char var_name[64]; + char* filename; + H5PartFile* file; + h5part_int64_t status; + + if (p->verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: writing data\n", p->rank); + } + + start_time = MPI_Wtime(); + + filename = (char*) malloc (strlen (p->filename) + 64); + sprintf (filename, "%s/%d.h5", p->filename, iter); + + file = H5PartOpenFileParallelAlign (filename, + p->flags, MPI_COMM_WORLD, p->alignment); + if (!file) { + fprintf (stderr, + "rank %d: could not open H5Part file!\n", p->rank); + MPI_Barrier (MPI_COMM_WORLD); + exit (EXIT_FAILURE); + } + + H5PartSetNumParticles (file, p->particles); + if (p->verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: %ld particles\n", p->rank, p->particles); + } + + open_time = MPI_Wtime() - start_time; + + segment = data; + + for (i=1; i<=p->segments; i++) { + status = H5PartSetStep (file, i); + if (status != H5PART_SUCCESS) { + fprintf (stderr, "rank %d: H5PartSetStep error!", p->rank); + } + for (j=0; jblocks; j++) { + sprintf (var_name, "test%d", j); + status = H5PartWriteDataFloat32 (file, var_name, segment); + if (status != H5PART_SUCCESS) { + fprintf (stderr, + "rank %d: H5PartWriteDataFloat32 error!", p->rank); + } + segment += p->particles; + } + } + + write_time = (MPI_Wtime() - start_time) - open_time; + + H5PartCloseFile (file); + + close_time = (MPI_Wtime() - start_time) - write_time - open_time; + + total_time = open_time + write_time + close_time; + + if (p->verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: write\t%.3f\t%.3f\t%.3f\t%.3f\n", p->rank, + open_time, write_time, close_time, total_time); + } + + MPI_Barrier (MPI_COMM_WORLD); + MPI_Reduce (&open_time, &sum_time, 1, MPI_DOUBLE, + MPI_SUM, 0, MPI_COMM_WORLD); + open_mean = sum_time / p->procs; + MPI_Reduce (&write_time, &sum_time, 1, MPI_DOUBLE, + MPI_SUM, 0, MPI_COMM_WORLD); + write_mean = sum_time / p->procs; + MPI_Reduce (&close_time, &sum_time, 1, MPI_DOUBLE, + MPI_SUM, 0, MPI_COMM_WORLD); + close_mean = sum_time / p->procs; + bandwidth = p->aggregate_size / total_time; + + if (p->verbosity >= VERBOSITY_MEDIUM && p->rank == 0) { + printf ("write\t%.1f\t%.3f\t%.3f\t%.3f\t%.3f\n", bandwidth, + open_mean, write_mean, close_mean, total_time); + } + + free (filename); + + return bandwidth; +} + + +/************************************************************************/ +/* Main procedure */ +/************************************************************************/ + +int main (int argc, char** argv) +{ + int i; + Params p; + float* data; + double block_size; + double data_size; + double bandwidth; + double write_max; + double write_min; + double write_mean; + double read_max; + double read_min; + double read_mean; + time_t rawtime; + struct tm * timeinfo; + + // initialize MPI + MPI_Init (&argc, &argv); + MPI_Comm_rank (MPI_COMM_WORLD, &p.rank); + MPI_Comm_size (MPI_COMM_WORLD, &p.procs); + + parse_args (argc, argv, &p); + + H5PartSetVerbosityLevel (p.verbosity); + + if (p.verbosity >= VERBOSITY_MEDIUM && p.rank == 0) { + time (&rawtime); + timeinfo = localtime (&rawtime); + printf ("Started: %s", asctime (timeinfo)); + printf ("Command line:\n"); + for (i=0; i= VERBOSITY_MEDIUM && p.rank == 0) { + printf ("block_size\t\t= %.1f MB\n", block_size); + printf ("segment_size\t\t= %.1f MB\n", + p.blocks * block_size); + printf (" x %5d segment(s)\t= %.1f MB per proc\n", + p.segments, data_size); + printf (" x %5d procs\t\t= %.1f MB aggregate\n", + p.procs, p.aggregate_size); + } + + if (p.verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: mallocing block data\n", p.rank); + } + + data = (float*) malloc (p.segments * p.blocks * p.particles + * sizeof(float)); + if (!data) { + fprintf (stderr, + "rank %d: could not malloc block data!\n", p.rank); + MPI_Barrier (MPI_COMM_WORLD); + exit (EXIT_FAILURE); + } + + if (p.verbosity >= VERBOSITY_MEDIUM && p.rank == 0) { + printf ("access\tbw\topen\twr/rd\tclose\ttotal\n"); + printf ("(wr/rd)\t(MB/s)\t(s)\t(s)\t(s)\t(s)\n"); + printf ("------\t--\t----\t-----\t-----\t-----\n"); + } + + write_max = 0.0; + write_min = 10e300; + for (i=0; i write_max) write_max = bandwidth; + if (bandwidth < write_min) write_min = bandwidth; + write_mean += bandwidth; + } + } + write_mean /= p.repetitions; + + if (p.verbosity >= VERBOSITY_LOW && p.rank == 0) { + printf ("********************************\n"); + printf ("** Aggregate Bandwidth (MB/s) **\n"); + printf ("access max min mean \n"); + printf ("------ --- --- ---- \n"); + if (p.write) { + printf ("write\t%.1f\t%.1f\t%.1f\n", + write_max, write_min, write_mean); + } + if (p.read) { + printf ("read\t%.1f\t%.1f\t%.1f\n", + read_max, read_min, read_mean); + } + printf ("********************************\n"); + time (&rawtime); + timeinfo = localtime (&rawtime); + printf ("Finished: %s", asctime (timeinfo)); + } + + if (p.verbosity >= VERBOSITY_HIGH) { + printf ("rank %d: Exiting!\n", p.rank); + } + + MPI_Finalize(); + return (EXIT_SUCCESS); +} + +#else +#error This file only works when PARALLEL_IO is enabled. +#endif diff --git a/tools/Makefile.am b/tools/Makefile.am index 9f3c610..ec23bed 100644 --- a/tools/Makefile.am +++ b/tools/Makefile.am @@ -1,83 +1,32 @@ # tools level Makefile.am -# PATH SETTING -HDF5ROOT = @HDF5ROOT@ +OBJEXT=o -# COMPILER SETTING -CXX = @CXX@ -TOOLS_CXX = @TOOLS_CXX@ +HDFLIB = -L@HDF5ROOT@/lib -lhdf5 -lz @SZLIB@ +LIBS = -L@H5P_LIB_LOC@ -lH5Part $(HDFLIB) -lm @STDCXX@ -# COMPILER FLAG SETTING -CFLAGS = @CFLAGS@ - -# # -L$(HDF5ROOT)/lib -lhdf5 - -# LIBRARIES -SZLIB = @SZLIB@ -HDFLIB = @TOOLS_HDFLIB@ -lz $(SZLIB) -LIBS = $(HDFLIB) $(MPILIB) -lm @STDCXX@ @LDFLAGS@ - -# H5Part compiled library location -# H5PLIB = -L@prefix@/lib -H5PLIB = -L@H5P_LIB_LOC@ @TOOLS_H5PART_LIB@ - -# INCLUDES -HDFINC = -I$(HDF5ROOT)/include -INC = $(HDFINC) $(H5PINC) $(MPIINC) - -# H5Part header file location -# H5PINC = -I@prefix@/include -H5PINC = -I@H5P_LIB_LOC@ +INCLUDES = -I@H5P_LIB_LOC@ -I@HDF5ROOT@/include @MPIINC@ # What to build... make install will place these files in the $(prefix)/bin directory. bin_PROGRAMS = @BUILD_TOOLS@ # Listing of all programs that maybe built. (Has to know statically...) -EXTRA_PROGRAMS = h5pAttrib h5pToGNUplot # homdynToH5p - -# Extra files that I wish to include in the dist tar ball. -EXTRA_DIST = h5pAttrib.cc h5pToGNUplot.cc## TO BE TAILORED LATER... +EXTRA_PROGRAMS = h5pAttrib \ + h5pToGNUplot \ + homdynToH5p \ + H5PartBench \ + H5BlockBench # Listing of sources -h5pAttrib_SOURCES = h5pAttrib.cc +h5pAttrib_SOURCES = h5pAttrib.cc +h5pToGNUplot_SOURCES = h5pToGNUplot.cc +homdynToH5p_SOURCES = homdynToH5p.cc +H5PartBench_SOURCES = H5PartBench.c +H5BlockBench_SOURCES = H5BlockBench.c -h5pToGNUplot_SOURCES = h5pToGNUplot.cc +.o.cc: + $(CXX) $(CFLAGS) $(INCLUDES) -c $< -#homdynToH5p_SOURCES = homdynToH5p.cc +.o.c: + $(CC) $(CFLAGS) $(INCLUDES) -c $< -# Specific building instruction (What compilers to use...) -# ------------ Build Tools ------------ - -h5pAttrib: h5pAttrib.o - $(TOOLS_CXX) -o h5pAttrib h5pAttrib.o $(H5PLIB) $(LIBS) - -h5pAttrib.o: h5pAttrib.cc - $(TOOLS_CXX) $(CFLAGS) $(INC) -g -c h5pAttrib.cc - - -h5pToGNUplot: h5pToGNUplot.o - $(TOOLS_CXX) -o h5pToGNUplot h5pToGNUplot.o $(H5PLIB) $(LIBS) - -h5pToGNUplot.o: h5pToGNUplot.cc - $(TOOLS_CXX) $(CFLAGS) $(INC) -g -c $< - -homdynToH5p : homdynToH5p.o - $(TOOLS_CXX) -o $@ $< $(H5PLIB) $(LIBS) - -homdynToH5p.o: homdynToH5p.cc - $(TOOLS_CXX) $(CFLAGS) $(INC) -g -c $< - - -clean: - rm -f *~ *.o h5pAttrib h5pToGNUplot - -distclean: clean - rm -rf .deps - rm -rf Makefile - - -# # bash-3.00$ /usr/bin/mpcc_r -g -O2 -I/scratch/scratchdirs/cristina/hdf5/hdf5_par/include -I/u2/antino/trunk/src -c h5pAttrib.cc -# # bash-3.00$ /usr/bin/mpcc_r -o h5pAttrib h5pAttrib.o -L/u2/antino/trunk/src -lpH5Part -L/scratch/scratchdirs/cristina/hdf5/hdf5_par/lib -lhdf5 -lz -lm - - -#####################################################################################################################