Merge branch '1.99' of gitorious.psi.ch:h5hut/src into 1.99

.gitignore

@@ -1,3 +1,11 @@
+*.o
+*.lo
+*.la
+*~
+*.h5
+*.vtk
+.deps
+.libs
 /H5hut
 /INSTALL
 /Makefile
@@ -5,6 +13,7 @@
 /aclocal.m4
 /autom4te.cache
 /build
+/compile
 /config.guess
 /config.h
 /config.h.in

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([H5hut], [1.99.11], [h5part@lists.psi.ch], H5hut)
+AC_INIT([H5hut], [1.99.13], [h5part@lists.psi.ch], H5hut)
 AC_PREREQ(2.60)
 AC_CONFIG_HEADERS(config.h)
 AC_CONFIG_MACRO_DIR([m4])
@@ -62,7 +62,7 @@ AC_ARG_WITH(
 	[hdf5],
 	[AS_HELP_STRING([--with-hdf5],
 	[path to HDF5 installation [default=""]])],
-	[HDF5_PREFIX=$withval], [HDF5_PREFIX=""])
+	[HDF5_PREFIX=$withval], [])
 
 AC_ARG_WITH(
 	[mpi],
@@ -259,13 +259,13 @@ fi
 AC_MSG_CHECKING([if parallel interface enabled])
 if test "X$ENABLE_PARALLEL" = "Xyes"; then
 	AC_MSG_RESULT([yes])
-	AM_CPPFLAGS="${AM_CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
+	CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
 
         if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
         	AC_MSG_CHECKING([for ParMETIS])
                 if test "X$PARMETISPATH" != "X"; then
-                        AM_CPPFLAGS="$AM_CPPFLAGS -I$PARMETISPATH/include"
-	                AM_LDFLAGS="$AM_LDFLAGS -L$PARMETISPATH/lib"
+                        CPPFLAGS="$CPPFLAGS -I$PARMETISPATH/include"
+	                LDFLAGS="$LDFLAGS -L$PARMETISPATH/lib"
 	        fi
 
                 LIBS="$LIBS -lparmetis -lmetis"
@@ -284,9 +284,15 @@ fi
 
 ###############################################################################
 # LIBRARY PATHS
-if test -n "${HDF5_PREFIX}" ; then
-        AM_CPPFLAGS="$AM_CPPFLAGS -I$HDF5_PREFIX/include"
-        AM_LDFLAGS="$AM_LDFLAGS -L$HDF5_PREFIX/lib"
+if test -z "${HDF5_PREFIX}"; then
+	# alternatives to HDF5_PREFIX
+	if test -n "${HDF5_DIR}"; then
+		HDF5_PREFIX=${HDF5_DIR}
+	fi
+fi
+if test -n "${HDF5_PREFIX}"; then
+        CPPFLAGS="$CPPFLAGS -I$HDF5_PREFIX/include"
+        LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
 fi
 AC_CHECK_LIB([z], [compress2])
 AC_CHECK_LIB([hdf5], [H5open])
@@ -317,8 +323,8 @@ if test -z "$LUSTREROOT"; then
 	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
 else
         CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
-        AM_CPPFLAGS="$AM_CPPFLAGS -I$LUSTREROOT/usr/include"
-        AM_LDFLAGS="$AM_LDFLAGS -L$LUSTREROOT/usr/lib"
+        CPPFLAGS="$CPPFLAGS -I$LUSTREROOT/usr/include"
+        LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
         LIBS="$LIBS -llustreapi"
 fi
 
@@ -336,6 +342,9 @@ fi
 
 ###############################################################################
 # EXPORTING VARIABLES & CREATING OUTPUT FILES
+AM_CPPFLAGS=$CPPFLAGS
+AM_LDFLAGS=$LDFLAGS
+
 AC_SUBST(HDF5_PREFIX)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)

tools/vtk2h5grid/Makefile.am

@@ -1,10 +1,10 @@
-AM_CPPFLAGS = -I${abs_top_builddir}/src/include -Wno-deprecated
+AM_CPPFLAGS = -I${abs_top_srcdir}/src/include -Wno-deprecated
 FFLAGS += -cpp $(AM_CPPFLAGS)
 LDFLAGS += -L${abs_top_builddir}/src/lib
 
 LDADD = 
 
-LDADD += -lH5hut -lvtkIO -lvtkFiltering -lvtkCommon -lvtksys
+LDADD += -lH5hut -lvtkIO -lvtkFiltering -lvtkCommon -lvtksys -lpthread -ldl
 
 
 bin_PROGRAMS = 

tools/vtk2h5grid/vtk2h5grid.cc

@@ -14,9 +14,21 @@
 
 #include "H5hut.h"
 
+#if !defined (PARALLEL_IO)
+#define MPI_Init(argc, argv)
+#define MPI_Comm_size(comm, nprocs) { *nprocs = 1; }
+#define MPI_Comm_rank(comm, myproc) { *myproc = 0; }
+#define MPI_Finalize()
+#define MPI_COMM_WORLD (0)
+#endif
+
 const char* version = "0.1.0";
 int convert_boundary = 1;
 int convert_volume = 0;
+double x_shift = 0.0;
+double y_shift = 0.0;
+double z_shift = 0.0;
+
 const struct option longopts[] = {
         {"version",     no_argument, 0,                 'v'},
         {"help",        no_argument, 0,                 'h'},
@@ -24,6 +36,7 @@ const struct option longopts[] = {
         {"volume",      no_argument, &convert_volume,   1},
         {"no-boundary", no_argument, &convert_boundary, 0},
         {"no-volume",   no_argument, &convert_volume,   0},
+        {"shift",       required_argument,  0,          's'},
         {0,0,0,0},
 };
 
@@ -40,6 +53,7 @@ usage (
         std::cout << "                    default is yes" << std::endl;
         std::cout << "  --(no-)volume     do (not) convert volume mesh." << std::endl;
         std::cout << "                    default is no" << std::endl;
+        std::cout << "  --shift x,y,z     shift all points by x,y,z" << std::endl;
         std::cout << std::endl;
         exit (1);
 }
@@ -75,6 +89,10 @@ init (
                 case 'v':
                         print_version (argv[0]);
                         break;
+                case 's':
+                        sscanf (optarg, "%lf,%lf,%lf", &x_shift, &y_shift, &z_shift);
+                        cout << "shift = (" << x_shift << ", " << y_shift << ", " << z_shift << ")" << endl;
+                        break;
                 }
         }
         return argc - optind;
@@ -106,6 +124,9 @@ convert_vtk2h5grid (
                                 // add point to H5hut mesh
                                 double pt[3];
                                 vtk_grid->GetPoint (pts[i], pt);
+                                pt[0] += x_shift;
+                                pt[1] += y_shift;
+                                pt[2] += z_shift;
                                 H5FedStoreVertex (h5_grid, -1, pt);
                                 // map pt index in vtk file to pt index in H5hut file
                                 idmap.insert (IdMap::value_type (pts[i], h5_vertex_idx));
@@ -145,6 +166,10 @@ main (
         int argc,
         char* argv[]
         ) {
+        MPI_Init (&argc, &argv);
+        MPI_Comm comm = MPI_COMM_WORLD;
+        int comm_size;
+        MPI_Comm_size (comm,&comm_size);
 
         argc = init (argc, argv);
         if (argc == 0) {
@@ -200,5 +225,6 @@ main (
                 }
                 H5CloseFile (f);
         }
+        MPI_Finalize ();
         return 0;
 }