new trunk merged from old trunk, Roman's master thesis and my changes in the sandbox
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tools/h5hutcc
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@@ -0,0 +1,10 @@
|
||||
|
||||
Andreas Adelmann (PSI)
|
||||
Achim Gsell (PSI)
|
||||
Benedikt Oswald (PSI)
|
||||
|
||||
Wes Bethel (NERSC/LBNL)
|
||||
John Shalf (NERSC/LBNL)
|
||||
Cristina Siegerist (NERSC/LBNL)
|
||||
|
||||
Please use h5part@lists.psi.ch for communication.
|
||||
@@ -0,0 +1,71 @@
|
||||
*** Copyright Notice ***
|
||||
|
||||
H5hut Copyright (c) 2006-2010, The Regents of the University of California,
|
||||
through Lawrence Berkeley National Laboratory (subject to receipt of any
|
||||
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
|
||||
Institut (Switzerland). All rights reserved.
|
||||
|
||||
If you have questions about your rights to use or distribute this
|
||||
software, please contact Berkeley Lab's Technology Transfer Department
|
||||
at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
|
||||
|
||||
NOTICE. This software was developed under partial funding from the U.S.
|
||||
Department of Energy. As such, the U.S. Government has been granted for
|
||||
itself and others acting on its behalf a paid-up, nonexclusive,
|
||||
irrevocable, worldwide license in the Software to reproduce, prepare
|
||||
derivative works, and perform publicly and display publicly. Beginning
|
||||
five (5) years after the date permission to assert copyright is obtained
|
||||
from the U.S. Department of Energy, and subject to any subsequent five
|
||||
(5) year renewals, the U.S. Government is granted for itself and others
|
||||
acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide
|
||||
license in the Software to reproduce, prepare derivative works,
|
||||
distribute copies to the public, perform publicly and display publicly,
|
||||
and to permit others to do so.
|
||||
|
||||
|
||||
*** License agreement ***
|
||||
|
||||
H5Part Copyright (c) 2006-2009, The Regents of the University of California,
|
||||
through Lawrence Berkeley National Laboratory (subject to receipt of any
|
||||
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
|
||||
Institut (Switzerland). All rights reserved.
|
||||
|
||||
Redistribution and use in source and binary forms, with or without
|
||||
modification, are permitted provided that the following conditions are met:
|
||||
|
||||
(1) Redistributions of source code must retain the above copyright
|
||||
notice, this list of conditions and the following disclaimer.
|
||||
|
||||
(2) Redistributions in binary form must reproduce the above copyright
|
||||
notice, this list of conditions and the following disclaimer in the
|
||||
documentation and/or other materials provided with the distribution.
|
||||
|
||||
(3) Neither the name of the University of California, Lawrence Berkeley
|
||||
National Laboratory, U.S. Dept. of Energy, Paul Scherrer Institut
|
||||
(Switzerland) nor the names of its contributors may be used to endorse
|
||||
or promote products derived from this software without specific prior
|
||||
written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
|
||||
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
|
||||
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
|
||||
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
|
||||
OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
|
||||
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
||||
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
|
||||
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
|
||||
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
|
||||
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
You are under no obligation whatsoever to provide any bug fixes,
|
||||
patches, or upgrades to the features, functionality or performance of
|
||||
the source code ("Enhancements") to anyone; however, if you choose to
|
||||
make your Enhancements available either publicly, or directly to
|
||||
Lawrence Berkeley National Laboratory, without imposing a separate
|
||||
written license agreement for such Enhancements, then you hereby grant
|
||||
the following license: a non-exclusive, royalty-free perpetual license
|
||||
to install, use, modify, prepare derivative works, incorporate into
|
||||
other computer software, distribute, and sublicense such enhancements or
|
||||
derivative works thereof, in binary and source code form.
|
||||
|
||||
+13
@@ -0,0 +1,13 @@
|
||||
ACLOCAL_AMFLAGS = -I m4
|
||||
|
||||
SUBDIRS = \
|
||||
src \
|
||||
test \
|
||||
tools
|
||||
|
||||
MAINTAINERCLEANFILES = \
|
||||
config.h \
|
||||
config.log \
|
||||
config.status \
|
||||
stamp-h.in \
|
||||
stamp-h1
|
||||
@@ -0,0 +1,376 @@
|
||||
#### H5PART 1.99 ############################################################
|
||||
|
||||
Renamed type:
|
||||
H5PartFile -> h5_file_t
|
||||
h5part_int64_t -> h5_int64_t
|
||||
|
||||
Renamed functions:
|
||||
|
||||
|
||||
#### H5PART 1.6.6 ############################################################
|
||||
|
||||
Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
|
||||
interface.
|
||||
|
||||
Added missing type normalization for int32 type.
|
||||
|
||||
Rewrite of h5pAttrib tool.
|
||||
|
||||
#### H5PART 1.6.5 ############################################################
|
||||
|
||||
Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
|
||||
|
||||
#### H5PART 1.6.4 ############################################################
|
||||
|
||||
Fixed bug where H5PartSetViewIndices was not setting an empty view when the
|
||||
number of elements is 0.
|
||||
|
||||
Set a threshold on the HDF5 alignment parameter so that small metadata writes
|
||||
are not aligned, which causes large gaps in the file.
|
||||
|
||||
#### H5PART 1.6.3 ############################################################
|
||||
|
||||
New build system uses libtool and can build shared libraries.
|
||||
|
||||
Fixed a bug that incorrectly identifies the number of selected points in a view
|
||||
when using H5PartSetViewIndices.
|
||||
|
||||
Fixed bug in Fortran test reported by several people, as well as several
|
||||
incorrect views set in the C test that were causing segfaults.
|
||||
|
||||
Fixed name mismatches in the Fortran interface, and an off-by-one indexing
|
||||
problem.
|
||||
|
||||
#### H5PART 1.6.2 ############################################################
|
||||
|
||||
Removed H5PartSetViewEmpty
|
||||
--------------------------
|
||||
|
||||
An empty view can now be selected with:
|
||||
H5PartSetNumParticles(file, 0);
|
||||
|
||||
Bug Fixes to Attribute Calls in Fortran API
|
||||
-------------------------------------------
|
||||
|
||||
Fixed a problem where attribute values were reverting to zero.
|
||||
|
||||
#### H5PART 1.6.1 ############################################################
|
||||
|
||||
Chunking in the H5Part API
|
||||
--------------------------
|
||||
|
||||
There is now an H5Part equivalent H5PartSetChunkSize to the existing
|
||||
H5BlockDefine3DChunkDims call. Both of these calls enable the chunking
|
||||
mechanism in the underlying HDF5 layer. Chunking is used in combination
|
||||
with the aligned open calls to pad datasets to alignment multiples
|
||||
on disk.
|
||||
|
||||
All Steps Available on Write
|
||||
----------------------------
|
||||
|
||||
Previously, existing steps in a file were only accessible in read-only mode.
|
||||
Now, all steps are available in all modes, including write-truncate and
|
||||
write-append. Thus, it is now possible to overwrite existing data in write
|
||||
mode. To help alert the user to this possibility, a warning is issued every
|
||||
time an existing dataset is written to. Warnings can be printed by setting
|
||||
the verbosity to H5PART_VERB_WARN or higher.
|
||||
|
||||
New Throttling Routine
|
||||
----------------------
|
||||
|
||||
Previously, a throttle factor of N meant that for P processors, the total
|
||||
number of P writes were divided into N batches of P/N writes.
|
||||
|
||||
To better accommodate round-robin lustre striping, the new policy is to
|
||||
execute P/N batches of N writes. Thus, matching N to the number of stripes
|
||||
results in the desirable 1-1 matching of writers to stripes.
|
||||
|
||||
Other Fixes
|
||||
-----------
|
||||
|
||||
* The configure script should correctly detect PGI compilers now.
|
||||
* There was a small memory leak in the Fortran file open calls.
|
||||
* There was a compile error with HDF5 1.6.x due to a missing assignment.
|
||||
|
||||
#### H5PART 1.6 ##############################################################
|
||||
|
||||
Updated Documentation
|
||||
---------------------
|
||||
|
||||
The Fortran API has been added to the doxygen documentation. Most entries have
|
||||
a reference to their respective C API call.
|
||||
|
||||
Regression Test Suite
|
||||
---------------------
|
||||
|
||||
The test subdirectory has been reorganized to include a systematic series
|
||||
of regression tests of common use cases for the API. The goal is to have both
|
||||
complete coverage of the API (every call is exercised) and testing of some
|
||||
unlikely or unsuspected values and cases.
|
||||
|
||||
Currently, the C test covers the entire H5Part API and the Fortran test is
|
||||
still in development.
|
||||
|
||||
Benchmark Utilities
|
||||
-------------------
|
||||
|
||||
Two benchmarking utilities, H5PartBench and H5BlockBench, have been added to
|
||||
the tools collection. Both require the parallel library and have functionality
|
||||
and syntax similar to the IOR benchmark:
|
||||
|
||||
http://sourceforge.net/projects/ior-sio/
|
||||
|
||||
File Mode Flags
|
||||
---------------
|
||||
|
||||
Previously, the only flags used were H5PART_READ, H5PART_WRITE, and
|
||||
H5PART_APPEND, and these were mutually exclusive. Additional flags have been
|
||||
added to select the underlying virtual file driver (VFD) that HDF5 uses in
|
||||
parallel mode and to accommodate the lustre filesystem:
|
||||
|
||||
H5PART_VFD_MPIPOSIX (use the MPI-POSIX driver, which bypasses MPI-IO)
|
||||
H5PART_VFD_MPIIO_IND (use MPI-IO in independent mode)
|
||||
H5PART_FS_LUSTRE (activate H5P tunings for the lustre stripe size)
|
||||
|
||||
These flags can be specified using the typical bitwise OR method, e.g.
|
||||
|
||||
char flag = H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE;
|
||||
|
||||
will select write mode with these two additional options.
|
||||
|
||||
The parallel library now defaults to using the MPI-IO collective mode driver
|
||||
(previously it used independent mode). The collective buffering algorithm in
|
||||
the Cray XT4/5 environment has been substantially improved in the last year,
|
||||
and defaulting to collective mode allows us to take advantage of these
|
||||
improvements automatically.
|
||||
|
||||
There are also new open calls H5PartOpenAlign and H5PartOpenParallelAlign that
|
||||
take an additional 'alignment' value. This value is passed to HDF5 and used to
|
||||
pad out objects so that they align to filesystem boundaries. For instance, it
|
||||
would make sense to use the stripe size as the alignment value when writing to
|
||||
a lustre filesystem.
|
||||
|
||||
Unified 'View' Model
|
||||
--------------------
|
||||
|
||||
Views are now supported in both read and write mode (previously only supported
|
||||
in read mode). It is possible to specify non-sensical views: you could for
|
||||
instance specify a read view that is larger than the dataset on disk. Or you
|
||||
could create a write view that is larger than the data in memory. In those
|
||||
cases, you will encounter an error when you try to perform a read or write
|
||||
operation on a dataset.
|
||||
|
||||
There are two new methods for selecting views. H5PartSetNumParticlesStrided
|
||||
selects a view with $n$ particles per processor, but such that the data in
|
||||
memory is expected to have a 'stride' factor. For instance, if you have
|
||||
particle data with fields $x$ and $y$ and a single array with entries
|
||||
$x1,y1,x2,y2...$, then the stride factor is 2. Striding works for both reads
|
||||
and writes and only affects the view of memory: individual fields are still
|
||||
stored as individual arrays on disk.
|
||||
|
||||
The second new method is H5PartSetViewIndices, which allows for point
|
||||
selections of datasets. You can pass a list of indices for the points you
|
||||
want to select. This is useful, for instance, when interfacing with FastBit
|
||||
to perform queries that select a small subset of non-contiguous particles.
|
||||
|
||||
Because views are now supported on write, it is possible to write a dataset
|
||||
using multiple 'passes' or to leave some values unwritten.
|
||||
|
||||
Also, all views are now *inclusive*, so that a view of (0,9) corresponds
|
||||
to the 10 items 0, 1, 2, ... 9.
|
||||
|
||||
Internal Handling of Dataspaces
|
||||
-------------------------------
|
||||
|
||||
H5PartSetNumParticles and H5PartSetNumParticlesStrided now share the same
|
||||
HDF5 dataspace state in the H5PartFile struct with the calls that modify
|
||||
the view (H5PartSetView etc.). Previously, the memory and disk dataspaces
|
||||
were regenerated from the view on every read access, which was unnecessary.
|
||||
|
||||
Autogeneration of API Calls
|
||||
---------------------------
|
||||
|
||||
Python scripts have been added to automatically generate read/write call
|
||||
variants for different data types.
|
||||
|
||||
Renamed Fortran Include
|
||||
-----------------------
|
||||
|
||||
The automake system no longer greps the *F90.inc files to generate an include
|
||||
called 'H5Part.inc'. Instead, the *F90.inc files have been renamed to *.f90,
|
||||
and awk is used to generate an 'H5PartF.h' file (the same naming convention
|
||||
as in MPI's 'mpif.h').
|
||||
|
||||
The change to *.f90 was necessary to facilitate integration of the Fortran
|
||||
API into doxygen. Note that the *.f90 files will not compile, nor can they
|
||||
be included directly. Simply use
|
||||
|
||||
include 'H5PartF.h'
|
||||
|
||||
in your Fortran code to include all the definitions for Fortran H5Part/H5Block
|
||||
calls.
|
||||
|
||||
64 Char Limit on Dataset Names
|
||||
------------------------------
|
||||
|
||||
Previously, a user could overrun internal buffers for dataset names. Now, a
|
||||
fixed limit of 64 chars is imposed. Dataset names that are longer than this are
|
||||
truncated and a warning is printed. We expect that most users are using
|
||||
short canonical names like x, px, id, etc.
|
||||
|
||||
Changes to Existing API
|
||||
-----------------------
|
||||
|
||||
The H5BlockGetFieldInfo and H5BlockGetFieldInfoByName calls now both include
|
||||
a parameter for the 'type' of the field.
|
||||
|
||||
|
||||
#### H5PART 1.4 ##############################################################
|
||||
|
||||
Error Handling
|
||||
--------------
|
||||
Now all functions, in which an error could occure, are returning a
|
||||
value. This value is either a 64bit integer or a pointer.
|
||||
|
||||
A negative 64bit integer as result indicates an error. Values >= 0
|
||||
indicates successfull execution. This is similiar to the convention
|
||||
used in UNIX system calls, but we do not return -1 but the error
|
||||
number (which is always negative).
|
||||
|
||||
For functions returning a pointer the NULL-pointer is used to indicate
|
||||
an error. You can call the function H5PartGetErrno() to get the error
|
||||
number. For the time being there is no strerror(3) or perror(3)
|
||||
equivalent.
|
||||
|
||||
|
||||
API Changes
|
||||
-----------
|
||||
There are several changes in the API of H5Part. The biggest change is
|
||||
a side-effect of the implementation of strict error handling. The
|
||||
impact to the existing C/C++ code is very small. But now you *can*
|
||||
and *should* implement some kind of error handling. The simplest
|
||||
error handling is to set an error handler which aborts the program as
|
||||
soon as an error occured.
|
||||
|
||||
The next "biggest" change is the use of H5Part types instead of "long
|
||||
long" and "double". The replacement of "long long" is "h5part_int64_t"
|
||||
and for "double" "h5part_float64_t". This change has now effect in
|
||||
Fortran.
|
||||
|
||||
In some functions the argument type changed from "int" to
|
||||
"h5part_int64_t". Since on most systems "int" is a 32bit integer,
|
||||
calls to these functions must be adapted to the new API. In C/C++ the
|
||||
compiler will complain about it. But in Fortran you will *not* get an
|
||||
error message.So, you must check your Fortran code carefully.
|
||||
|
||||
Changes in detail (not listed are functions where only the return
|
||||
type changed from any to "h5part_int64_t"):
|
||||
|
||||
New API Changes to old API
|
||||
|
||||
h5part_int64_t void
|
||||
H5PartSetNumParticles (
|
||||
H5PartFile *f,
|
||||
h5part_int64_t nparticles long long
|
||||
);
|
||||
|
||||
h5part_int64_t int
|
||||
H5PartWriteDataFloat64 (
|
||||
H5PartFile *f,
|
||||
char *name,
|
||||
h5part_float64_t *dta double
|
||||
);
|
||||
|
||||
h5part_int64_t int
|
||||
H5PartWriteDataInt64 (
|
||||
H5PartFile *f,
|
||||
char *name,
|
||||
h5part_int64_t *dta long long
|
||||
);
|
||||
|
||||
h5part_int64_t void
|
||||
H5PartSetStep (
|
||||
H5PartFile *f,
|
||||
h5part_int64_t step int
|
||||
);
|
||||
|
||||
h5part_int64_t void
|
||||
H5PartSetView (
|
||||
H5PartFile *f,
|
||||
h5part_int64_t start, long long
|
||||
h5part_int64_t end long long
|
||||
);
|
||||
|
||||
h5part_int64_t int
|
||||
H5PartGetView (
|
||||
H5PartFile *f,
|
||||
h5part_int64_t *start, long long
|
||||
h5part_int64_t *end long long
|
||||
);
|
||||
|
||||
h5part_int64_t int
|
||||
H5PartReadDataFloat64 (
|
||||
H5PartFile *f,
|
||||
char *name,
|
||||
h5part_float64_t *dta double
|
||||
);
|
||||
|
||||
h5part_int64_t int
|
||||
H5PartReadDataInt64 (
|
||||
H5PartFile *f,
|
||||
char *name,
|
||||
h5part_int64_t *dta long long
|
||||
);
|
||||
|
||||
h5part_int64_t void
|
||||
H5PartReadParticleStep (
|
||||
H5PartFile *f,
|
||||
h5part_int64_t step, int
|
||||
h5part_float64_t *x, double
|
||||
h5part_float64_t *y, double
|
||||
h5part_float64_t *z, double
|
||||
h5part_float64_t *px, double
|
||||
h5part_float64_t *py, double
|
||||
h5part_float64_t *pz, double
|
||||
h5part_int64_t *id long long
|
||||
);
|
||||
|
||||
New functions:
|
||||
|
||||
h5part_int64_t
|
||||
H5PartSetVerbosityLevel (
|
||||
unsigned int
|
||||
);
|
||||
|
||||
h5part_int64_t
|
||||
H5PartSetErrorHandler (
|
||||
h5part_error_handler handler
|
||||
);
|
||||
|
||||
h5part_int64_t
|
||||
H5PartGetErrno (
|
||||
void
|
||||
);
|
||||
|
||||
h5part_int64_t
|
||||
H5PartDefaultErrorHandler (
|
||||
const char *funcname,
|
||||
const h5part_int64_t eno,
|
||||
const char *fmt,
|
||||
...
|
||||
);
|
||||
|
||||
h5part_int64_t
|
||||
H5PartAbortErrorHandler (
|
||||
const char *funcname,
|
||||
const h5part_int64_t eno,
|
||||
const char *fmt,
|
||||
...
|
||||
);
|
||||
|
||||
Removed functions:
|
||||
|
||||
int
|
||||
H5PartFileIsValid (
|
||||
H5PartFile *f
|
||||
);
|
||||
Executable
+48
@@ -0,0 +1,48 @@
|
||||
#!/bin/sh
|
||||
# Run this to generate all the initial makefiles, etc.
|
||||
|
||||
ACLOCAL_FLAGS="-I m4 $ACLOCAL_FLAGS"
|
||||
LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
|
||||
AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
|
||||
|
||||
LIBTOOLIZE=`which libtoolize`
|
||||
if [ "$LIBTOOLIZE" = "" ]; then
|
||||
LIBTOOLIZE=`which glibtoolize`
|
||||
fi
|
||||
if [ "$LIBTOOLIZE" = "" ]; then
|
||||
echo "libtoolize not found" 1>&2
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "+ making misc files ..."
|
||||
touch NEWS README AUTHORS ChangeLog
|
||||
echo
|
||||
$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
|
||||
echo "libtoolize failed"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo "+ running aclocal ..."
|
||||
aclocal $ACLOCAL_FLAGS || {
|
||||
echo "aclocal failed - check that all needed development files are present on system"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo "+ running autoheader ... "
|
||||
autoheader || {
|
||||
echo "autoheader failed"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo "+ running autoconf ... "
|
||||
autoconf || {
|
||||
echo "autoconf failed"
|
||||
exit 1
|
||||
}
|
||||
echo
|
||||
echo "+ running automake ... "
|
||||
automake $AUTOMAKE_FLAGS || {
|
||||
echo "automake failed"
|
||||
exit 1
|
||||
}
|
||||
|
||||
+412
@@ -0,0 +1,412 @@
|
||||
AC_INIT([H5hut], [1.99.10], [h5part@lists.psi.ch], H5hut)
|
||||
AC_PREREQ(2.60)
|
||||
AC_CONFIG_HEADERS(config.h)
|
||||
AC_CONFIG_MACRO_DIR([m4])
|
||||
AM_INIT_AUTOMAKE
|
||||
|
||||
BUILD_LIBS='libH5hut'
|
||||
|
||||
ENABLE_DEBUG='no'
|
||||
ENABLE_C='yes'
|
||||
ENABLE_FORTRAN='no'
|
||||
ENABLE_PARALLEL='no'
|
||||
|
||||
###############################################################################
|
||||
# --enable-xxx and --with-xxx Arguments
|
||||
AC_ARG_ENABLE(
|
||||
[debug],
|
||||
[AS_HELP_STRING([--enable-debug], [Compile with debug flags [default=no]])],
|
||||
[ENABLE_DEBUG=$enableval])
|
||||
AM_CONDITIONAL([ENABLE_DEBUG], [test "$ENABLE_DEBUG" = "yes"])
|
||||
|
||||
AC_ARG_ENABLE(
|
||||
[c],
|
||||
[AS_HELP_STRING([--enable-c],
|
||||
[Compile the C interface [default=yes]])],
|
||||
[ENABLE_C=$enableval])
|
||||
AM_CONDITIONAL([ENABLE_C], [test "$ENABLE_C" = "yes"])
|
||||
|
||||
AC_ARG_ENABLE(
|
||||
[fortran],
|
||||
[AS_HELP_STRING([--enable-fortran],
|
||||
[Compile the Fortran interface [default=no]])],
|
||||
[ENABLE_FORTRAN=$enableval])
|
||||
AM_CONDITIONAL([ENABLE_FORTRAN], [test "$ENABLE_FORTRAN" = "yes"])
|
||||
|
||||
AC_ARG_ENABLE(
|
||||
[parallel],
|
||||
[AS_HELP_STRING([--enable-parallel],
|
||||
[Compile the MPI/IO interface [default=no]])],
|
||||
[ENABLE_PARALLEL=$enableval])
|
||||
AM_CONDITIONAL([ENABLE_PARALLEL], [test "$ENABLE_PARALLEL" = "yes"])
|
||||
|
||||
AC_ARG_ENABLE(
|
||||
[large-indices],
|
||||
[AC_HELP_STRING([--enable-large-indices],
|
||||
[Compile with 64bit local IDs and indices [default=no]])],
|
||||
[USE_LARGE_INDICES=$enableval])
|
||||
|
||||
AC_ARG_ENABLE(
|
||||
[experimental],
|
||||
[AS_HELP_STRING([--enable-experimental],
|
||||
[Compile experimental code [default=no]])],
|
||||
[ENABLE_EXPERIMENTAL=$enableval])
|
||||
AM_CONDITIONAL([ENABLE_EXPERIMENTAL], [test "$ENABLE_EXPERIMENTAL" = "yes"])
|
||||
|
||||
AC_ARG_ENABLE(
|
||||
[vtkconverter],
|
||||
[AS_HELP_STRING([--enable-vtkconverter],
|
||||
[Compile the vtk to H5hut converter for grids [default=no]])],
|
||||
[ENABLE_VTKCONVERTER=$enableval])
|
||||
AM_CONDITIONAL([ENABLE_VTKCONVERTER], [test "$ENABLE_VTKCONVERTER" = "yes"])
|
||||
|
||||
AC_ARG_WITH(
|
||||
[hdf5],
|
||||
[AS_HELP_STRING([--with-hdf5],
|
||||
[path to HDF5 installation [default=""]])],
|
||||
[HDF5_PREFIX=$withval], [HDF5_PREFIX=""])
|
||||
|
||||
AC_ARG_WITH(
|
||||
[mpi],
|
||||
[AS_HELP_STRING([--with-mpi],
|
||||
[path to MPI installation [default=""]])],
|
||||
[PATH=$MPI_PREFIX/bin:$PATH])
|
||||
|
||||
AC_ARG_WITH(
|
||||
[lustre],
|
||||
[AS_HELP_STRING([--with-lustre],
|
||||
[path to lustre user API [default=""]])],
|
||||
[LUSTREPATH=$withval], [LUSTREPATH=""])
|
||||
|
||||
AC_ARG_WITH(
|
||||
[parmetis],
|
||||
[AC_HELP_STRING([--with-parmetis],
|
||||
[path to ParMETIS API [default=""]])],
|
||||
[PARMETISPATH=$withval], [PARMETISPATH=""])
|
||||
|
||||
|
||||
###############################################################################
|
||||
############### PATH SERACH FUNCTION - to be used later... ####################
|
||||
###############################################################################
|
||||
# /*@@
|
||||
# @routine CCTK_Search
|
||||
# @date Wed Jul 21 11:16:35 1999
|
||||
# @author Tom Goodale
|
||||
# @desc
|
||||
# Used to search for something in various directories
|
||||
# @enddesc
|
||||
#@@*/
|
||||
|
||||
PATH_Search() {
|
||||
eval $1=""
|
||||
if test $# -lt 4 ; then
|
||||
h5part_basedir=""
|
||||
else
|
||||
h5part_basedir="$4/"
|
||||
fi
|
||||
for h5part_place in $2; do
|
||||
AC_MSG_CHECKING([looking in $h5part_place ... ])
|
||||
if test -r "$h5part_basedir$h5part_place/$3" ; then
|
||||
AC_MSG_RESULT([found])
|
||||
eval $1="$h5part_place"
|
||||
break
|
||||
fi
|
||||
AC_MSG_RESULT([no])
|
||||
done
|
||||
return
|
||||
}
|
||||
|
||||
###############################################################################
|
||||
# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING
|
||||
|
||||
# Compute the canonical host-system type variable, host, and its three
|
||||
# individual parts host_cpu, host_vendor, and host_os.
|
||||
AC_CANONICAL_HOST
|
||||
AC_PROG_MAKE_SET
|
||||
|
||||
# debug enabled?
|
||||
AC_MSG_CHECKING([if debug is enabled])
|
||||
if test "X$ENABLE_DEBUG" = "Xyes"; then
|
||||
AC_MSG_RESULT([yes])
|
||||
CFLAGS="$CFLAGS -g -Wall"
|
||||
CXXFLAGS="$CFLAGS -g -Wall"
|
||||
FFLAGS="$FFLAGS -g"
|
||||
else
|
||||
AC_MSG_RESULT([no])
|
||||
fi
|
||||
|
||||
# Determine a C/C++ compiler to use.
|
||||
# If CC is not already set in the environment, check for other C compilers.
|
||||
# Set output variable CC to the name of the compiler found.
|
||||
if test "x$ENABLE_PARALLEL" = "xyes"; then
|
||||
CCOMPILERS="mpicc"
|
||||
CXXCOMPILERS="mpic++"
|
||||
else
|
||||
CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
|
||||
CXXCOMPILERS="pgcc pathcc icc g++ cc_r c++"
|
||||
fi
|
||||
|
||||
AC_PROG_CC($CCOMPILERS)
|
||||
CC=`which $CC`
|
||||
AC_PROG_CXX($CXXCOMPILERS)
|
||||
CXX=`which $CXX`
|
||||
|
||||
# Use macro to set C99 mode instead of checking for gcc, which breaks with
|
||||
# parallel builds.
|
||||
AC_PROG_CC_C99
|
||||
if test "x$ac_cv_prog_cc_c99" = "xno"; then
|
||||
AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# Set output variable INSTALL to the path of a BSD-compatible install program,
|
||||
# if one is found in the current PATH.
|
||||
# Otherwise, set INSTALL to `dir/install-sh -c`
|
||||
AC_PROG_INSTALL
|
||||
AC_PROG_AWK
|
||||
|
||||
# Disable shared libraries by default: can be enabled with --enable-shared
|
||||
LT_INIT([disable-shared])
|
||||
AC_PROG_LIBTOOL
|
||||
|
||||
# Default prefix for bindir, etc... (eg >> ./build/bin)
|
||||
AC_PREFIX_DEFAULT(`pwd`/build)
|
||||
|
||||
# Checks for header files.
|
||||
AC_CHECK_HEADERS([fcntl.h limits.h stdint.h stdlib.h string.h sys/ioctl.h unistd.h])
|
||||
|
||||
# Checks for typedefs, structures, and compiler characteristics.
|
||||
AC_HEADER_STDBOOL
|
||||
AC_C_INLINE
|
||||
AC_TYPE_INT16_T
|
||||
AC_TYPE_INT32_T
|
||||
AC_TYPE_INT64_T
|
||||
AC_TYPE_SIZE_T
|
||||
AC_TYPE_SSIZE_T
|
||||
AC_TYPE_UINT16_T
|
||||
AC_TYPE_UINT32_T
|
||||
AC_TYPE_UINT64_T
|
||||
AC_CHECK_TYPES([ptrdiff_t])
|
||||
|
||||
# Checks for library functions.
|
||||
AC_FUNC_MALLOC
|
||||
AC_FUNC_REALLOC
|
||||
AC_CHECK_FUNCS([memmove memset pow strchr strdup strerror strstr])
|
||||
|
||||
# AC_DEFINE_UNQUOTED (variable, value, [description])
|
||||
# Define the C preprocessor variable variable to value
|
||||
# Use this macro instead of AC_DEFINE when variable or value is a shell variable.
|
||||
AC_DEFINE_UNQUOTED(MY_BUILD_VENDOR, "$host_vendor", "")
|
||||
AC_DEFINE_UNQUOTED(MY_BUILD_CPU, "$host_cpu", "")
|
||||
AC_DEFINE_UNQUOTED(MY_BUILD_OS, "$host_os", "")
|
||||
AC_DEFINE_UNQUOTED(MY_GNUNAME, "${host_cpu}-${host_vendor}-${host_os}", "")
|
||||
AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
|
||||
|
||||
|
||||
###############################################################################
|
||||
# PROCESS ARGUMENTS
|
||||
|
||||
# C enabled?
|
||||
AC_MSG_CHECKING([if C interface enabled])
|
||||
if test "X$ENABLE_C" = "Xyes"; then
|
||||
AC_MSG_RESULT([yes])
|
||||
BINDINGS="$BINDINGS C"
|
||||
BUILD_LIBS="$BUILD_LIBS"
|
||||
BUILD_TESTS="$BUILD_TESTS h5u_test h5b_test"
|
||||
BUILD_TOOLS="$BUILD_TOOLS h5hutcc"
|
||||
else
|
||||
AC_MSG_RESULT([no])
|
||||
fi
|
||||
|
||||
# fortran enabled?
|
||||
AC_MSG_CHECKING([if fortran interface enabled])
|
||||
if test "X$ENABLE_FORTRAN" = "Xyes"; then
|
||||
AC_MSG_RESULT([yes])
|
||||
BINDINGS="$BINDINGS Fortran"
|
||||
LIB_FORTRAN="libH5hutF.la"
|
||||
BUILD_LIBS="$BUILD_LIBS libH5hutF"
|
||||
|
||||
if test "X$ENABLE_PARALLEL" = "Xyes"; then
|
||||
AC_PROG_FC(mpif90 mpif77)
|
||||
else
|
||||
AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
|
||||
fi
|
||||
FC=`which $FC`
|
||||
if test -z "$FC" ; then
|
||||
AC_MSG_ERROR([Cannot find a Fortran compiler!])
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if test $FC = "g90"; then
|
||||
FFLAGS="${FFLAGS} -fno-second-underscore"
|
||||
fi
|
||||
|
||||
if test $FC = "g95"; then
|
||||
FFLAGS="${FFLAGS} -fno-second-underscore"
|
||||
fi
|
||||
|
||||
AC_MSG_CHECKING([symbol convention in object files])
|
||||
`cd src/Fortran && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
|
||||
`cd src/Fortran && ${FC} ${FFLAGS} -c TestUnderscore.f`
|
||||
`cd src/Fortran && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
|
||||
`cd src/Fortran && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
|
||||
|
||||
if test -f src/Fortran/TestUnderscore ; then
|
||||
UNDERSCORE_H=Underscore.h
|
||||
`cd src/Fortran && ./TestUnderscore > Underscore.h`
|
||||
AC_MSG_RESULT([ok])
|
||||
else
|
||||
AC_MSG_RESULT([nok])
|
||||
AC_MSG_ERROR([Cannot determine the symbol convention for Fortran object files!])
|
||||
exit 1
|
||||
fi
|
||||
|
||||
else
|
||||
AC_MSG_RESULT([no])
|
||||
fi
|
||||
|
||||
######################## large indices enabled ###########################
|
||||
AC_MSG_CHECKING([if large indices are enabled])
|
||||
if test "X$USE_LARGE_INDICES" = "Xyes"; then
|
||||
AC_MSG_RESULT([yes])
|
||||
CFLAGS="${CFLAGS} -DUSE_LARGE_INDICES"
|
||||
else
|
||||
AC_MSG_RESULT([no])
|
||||
fi
|
||||
|
||||
######################## parallel interface enabled ###########################
|
||||
AC_MSG_CHECKING([if parallel interface enabled])
|
||||
if test "X$ENABLE_PARALLEL" = "Xyes"; then
|
||||
AC_MSG_RESULT([yes])
|
||||
AM_CPPFLAGS="${AM_CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
|
||||
|
||||
if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
|
||||
AC_MSG_CHECKING([for ParMETIS])
|
||||
if test "X$PARMETISPATH" != "X"; then
|
||||
AM_CPPFLAGS="$AM_CPPFLAGS -I$PARMETISPATH/include"
|
||||
LDFLAGS="$LDFLAGS -L$PARMETISPATH/lib"
|
||||
fi
|
||||
|
||||
LIBS="$LIBS -lparmetis -lmetis"
|
||||
AC_TRY_LINK([#include <parmetis.h>], [
|
||||
ParMETIS_V3_PartGeom (NULL, NULL, NULL, NULL, NULL);],
|
||||
[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
|
||||
|
||||
if test "X$r" = "Xno"; then
|
||||
AC_MSG_ERROR([ParMETIS])
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
else # --enable-parallel=no
|
||||
AC_MSG_RESULT([no])
|
||||
fi
|
||||
|
||||
###############################################################################
|
||||
# LIBRARY PATHS
|
||||
if test -n "${HDF5_PREFIX}" ; then
|
||||
AM_CPPFLAGS="$AM_CPPFLAGS -I$HDF5_PREFIX/include"
|
||||
LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
|
||||
fi
|
||||
AC_CHECK_LIB([z], [compress2])
|
||||
AC_CHECK_LIB([hdf5], [H5open])
|
||||
AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes],
|
||||
[AC_MSG_ERROR([Cannot compile and link a HDF5 program]);
|
||||
exit 1])
|
||||
|
||||
|
||||
AC_MSG_CHECKING([for lustre API ])
|
||||
AC_MSG_RESULT([])
|
||||
if test -n "${LUSTREPATH}"; then
|
||||
P=${LUSTREPATH}
|
||||
elif test -n "${LUSTREROOT}" ; then
|
||||
P=${LUSTREROOT}
|
||||
elif test -n "${LUSTREHOME}" ; then
|
||||
P=${LUSTREHOME}
|
||||
elif test -n "${LUSTRE_DIR}" ; then
|
||||
P=${LUSTRE_DIR}
|
||||
else
|
||||
P=''
|
||||
P="$P /usr"
|
||||
P="$P /usr/local"
|
||||
P="$P /usr/local/lustre"
|
||||
P="$P /opt/lustre"
|
||||
fi
|
||||
PATH_Search LUSTREROOT "$P" usr/include/lustre/liblustreapi.h
|
||||
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"
|
||||
LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
|
||||
LIBS="$LIBS -llustreapi"
|
||||
fi
|
||||
|
||||
LIBS="$LIBS -lm"
|
||||
|
||||
###############################################################################
|
||||
# TOOLS
|
||||
AC_MSG_CHECKING([if we have to compile the VTK to H5hut grid converter])
|
||||
if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
|
||||
AC_MSG_RESULT([yes])
|
||||
# :TODO: add test whether we can compile/link a prog with vtk
|
||||
else
|
||||
AC_MSG_RESULT([no])
|
||||
fi
|
||||
|
||||
###############################################################################
|
||||
# EXPORTING VARIABLES & CREATING OUTPUT FILES
|
||||
AC_SUBST(HDF5_PREFIX)
|
||||
AC_SUBST(LUSTREROOT)
|
||||
AC_SUBST(CFLAGS)
|
||||
AC_SUBST(FFLAGS)
|
||||
AC_SUBST(AM_CPPFLAGS)
|
||||
AC_SUBST(LDFLAGS)
|
||||
AC_SUBST(LIBS)
|
||||
AC_SUBST(UNDERSCORE_H)
|
||||
AC_SUBST(LIB_FORTRAN)
|
||||
AC_SUBST(BINDINGS)
|
||||
AC_SUBST(BUILD_TESTS)
|
||||
AC_SUBST(BUILD_TOOLS)
|
||||
|
||||
AC_CONFIG_FILES([
|
||||
Makefile
|
||||
src/Makefile
|
||||
src/h5core/Makefile
|
||||
src/include/Makefile
|
||||
src/C/Makefile
|
||||
src/Fortran/Makefile
|
||||
test/Makefile
|
||||
doc/Makefile
|
||||
examples/H5/Makefile
|
||||
examples/H5Part/Makefile
|
||||
examples/H5Block/Makefile
|
||||
examples/H5Fed/Makefile
|
||||
tools/Makefile
|
||||
tools/h5hutcc
|
||||
tools/vtk2h5grid/Makefile
|
||||
])
|
||||
|
||||
AC_OUTPUT
|
||||
|
||||
###############################################################################
|
||||
# PRINTING SUMMARY
|
||||
AC_MSG_RESULT([ ])
|
||||
AC_MSG_RESULT([Summary:])
|
||||
AC_MSG_RESULT([ ])
|
||||
AC_MSG_RESULT([Host OS: $host_os])
|
||||
AC_MSG_RESULT([Host CPU: $host_cpu])
|
||||
AC_MSG_RESULT([Host vendor: $host_vendor])
|
||||
AC_MSG_RESULT([Build libraries: $BUILD_LIBS])
|
||||
AC_MSG_RESULT([Build test programs: $BUILD_TESTS])
|
||||
AC_MSG_RESULT([Build tools: $BUILD_TOOLS])
|
||||
AC_MSG_RESULT([CC = $CC])
|
||||
AC_MSG_RESULT([CXX = $CXX])
|
||||
AC_MSG_RESULT([FC = $FC])
|
||||
AC_MSG_RESULT([CFLAGS = $CFLAGS])
|
||||
AC_MSG_RESULT([FFLAGS = $FFLAGS])
|
||||
AC_MSG_RESULT([AM_CPPFLAGS = $AM_CPPFLAGS])
|
||||
AC_MSG_RESULT([LDFLAGS = $LDFLAGS])
|
||||
AC_MSG_RESULT([LIBS = $LIBS])
|
||||
AC_MSG_RESULT([HDF5_PREFIX = $HDF5_PREFIX])
|
||||
AC_MSG_RESULT([LUSTREROOT = $LUSTREROOT])
|
||||
AC_MSG_RESULT([ ])
|
||||
+1816
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,188 @@
|
||||
<doxygenlayout version="1.0">
|
||||
<!-- Navigation index tabs for HTML output -->
|
||||
<navindex>
|
||||
<tab type="mainpage" visible="yes" title=""/>
|
||||
<tab type="pages" visible="yes" title="" intro=""/>
|
||||
<tab type="modules" visible="yes" title="" intro=""/>
|
||||
<tab type="namespaces" visible="yes" title="">
|
||||
<tab type="namespacelist" visible="yes" title="" intro=""/>
|
||||
<tab type="namespacemembers" visible="yes" title="" intro=""/>
|
||||
</tab>
|
||||
<tab type="classes" visible="yes" title="">
|
||||
<tab type="classlist" visible="yes" title="" intro=""/>
|
||||
<tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/>
|
||||
<tab type="hierarchy" visible="yes" title="" intro=""/>
|
||||
<tab type="classmembers" visible="yes" title="" intro=""/>
|
||||
</tab>
|
||||
<tab type="files" visible="yes" title="">
|
||||
<tab type="filelist" visible="yes" title="" intro=""/>
|
||||
<tab type="globals" visible="yes" title="" intro=""/>
|
||||
</tab>
|
||||
<tab type="dirs" visible="yes" title="" intro=""/>
|
||||
<tab type="examples" visible="yes" title="" intro=""/>
|
||||
</navindex>
|
||||
|
||||
<!-- Layout definition for a class page -->
|
||||
<class>
|
||||
<briefdescription visible="yes"/>
|
||||
<includes visible="$SHOW_INCLUDE_FILES"/>
|
||||
<inheritancegraph visible="$CLASS_GRAPH"/>
|
||||
<collaborationgraph visible="$COLLABORATION_GRAPH"/>
|
||||
<allmemberslink visible="yes"/>
|
||||
<memberdecl>
|
||||
<nestedclasses visible="yes" title=""/>
|
||||
<publictypes title=""/>
|
||||
<publicslots title=""/>
|
||||
<signals title=""/>
|
||||
<publicmethods title=""/>
|
||||
<publicstaticmethods title=""/>
|
||||
<publicattributes title=""/>
|
||||
<publicstaticattributes title=""/>
|
||||
<protectedtypes title=""/>
|
||||
<protectedslots title=""/>
|
||||
<protectedmethods title=""/>
|
||||
<protectedstaticmethods title=""/>
|
||||
<protectedattributes title=""/>
|
||||
<protectedstaticattributes title=""/>
|
||||
<packagetypes title=""/>
|
||||
<packagemethods title=""/>
|
||||
<packagestaticmethods title=""/>
|
||||
<packageattributes title=""/>
|
||||
<packagestaticattributes title=""/>
|
||||
<properties title=""/>
|
||||
<events title=""/>
|
||||
<privatetypes title=""/>
|
||||
<privateslots title=""/>
|
||||
<privatemethods title=""/>
|
||||
<privatestaticmethods title=""/>
|
||||
<privateattributes title=""/>
|
||||
<privatestaticattributes title=""/>
|
||||
<friends title=""/>
|
||||
<related title="" subtitle=""/>
|
||||
<membergroups visible="yes"/>
|
||||
</memberdecl>
|
||||
<detaileddescription title=""/>
|
||||
<memberdef>
|
||||
<inlineclasses title=""/>
|
||||
<typedefs title=""/>
|
||||
<enums title=""/>
|
||||
<constructors title=""/>
|
||||
<functions title=""/>
|
||||
<related title=""/>
|
||||
<variables title=""/>
|
||||
<properties title=""/>
|
||||
<events title=""/>
|
||||
</memberdef>
|
||||
<usedfiles visible="$SHOW_USED_FILES"/>
|
||||
<authorsection visible="yes"/>
|
||||
</class>
|
||||
|
||||
<!-- Layout definition for a namespace page -->
|
||||
<namespace>
|
||||
<briefdescription visible="yes"/>
|
||||
<memberdecl>
|
||||
<nestednamespaces visible="yes" title=""/>
|
||||
<classes visible="yes" title=""/>
|
||||
<typedefs title=""/>
|
||||
<enums title=""/>
|
||||
<functions title=""/>
|
||||
<variables title=""/>
|
||||
<membergroups visible="yes"/>
|
||||
</memberdecl>
|
||||
<detaileddescription title=""/>
|
||||
<memberdef>
|
||||
<inlineclasses title=""/>
|
||||
<typedefs title=""/>
|
||||
<enums title=""/>
|
||||
<functions title=""/>
|
||||
<variables title=""/>
|
||||
</memberdef>
|
||||
<authorsection visible="yes"/>
|
||||
</namespace>
|
||||
|
||||
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
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|
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28 10 -1 20 3 18 27 26 25 24
|
||||
|
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3,0 3,1 4,2 2,3 16,4
|
||||
|
||||
1 2 -1 3 4
|
||||
|
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1 2 3
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1 3 6
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2 11 1 13 14
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ASCII
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DATASET UNSTRUCTURED_GRID
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POINTS 17 DOUBLE
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-1 0 0
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0 1 0
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CELLS 18 90
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4 6 8 2 10
|
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4 7 9 10 1
|
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4 5 6 7 9
|
||||
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|
||||
4 6 7 9 10
|
||||
4 6 8 9 10
|
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4 0 11 12 13
|
||||
4 11 5 14 15
|
||||
4 12 14 6 16
|
||||
4 13 15 16 7
|
||||
4 11 12 13 15
|
||||
4 11 12 14 15
|
||||
4 12 13 15 16
|
||||
4 12 14 15 16
|
||||
|
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CELL_TYPES 18
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
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10
|
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10
|
||||
10
|
||||
10
|
||||
10
|
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10
|
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10
|
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|
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POINT_DATA 17
|
||||
SCALARS vertex_id int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
CELL_DATA 18
|
||||
SCALARS cell_attribute_data int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
17
|
||||
|
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@@ -0,0 +1,59 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
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ASCII
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DATASET UNSTRUCTURED_GRID
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|
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POINTS 17 DOUBLE
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|
||||
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|
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|
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|
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|
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|
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CELL_TYPES 2
|
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10
|
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10
|
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|
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POINT_DATA 17
|
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SCALARS vertex_id int 1
|
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|
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|
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1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
CELL_DATA 2
|
||||
SCALARS cell_attribute_data int 1
|
||||
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|
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0
|
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|
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|
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|
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VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
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ASCII
|
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DATASET UNSTRUCTURED_GRID
|
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|
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
4 0 4 3 1
|
||||
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|
||||
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|
||||
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|
||||
4 7 9 10 1
|
||||
4 5 6 7 9
|
||||
4 5 6 8 9
|
||||
4 6 7 9 10
|
||||
4 6 8 9 10
|
||||
|
||||
CELL_TYPES 9
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
POINT_DATA 17
|
||||
SCALARS vertex_id int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
CELL_DATA 9
|
||||
SCALARS cell_attribute_data int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
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|
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@@ -0,0 +1,101 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
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ASCII
|
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DATASET UNSTRUCTURED_GRID
|
||||
|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
0.5 0.5 0
|
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
CELLS 16 80
|
||||
4 0 4 3 1
|
||||
4 5 3 8 9
|
||||
4 6 8 2 10
|
||||
4 7 9 10 1
|
||||
4 5 6 7 9
|
||||
4 5 6 8 9
|
||||
4 6 7 9 10
|
||||
4 6 8 9 10
|
||||
4 0 11 12 13
|
||||
4 11 5 14 15
|
||||
4 12 14 6 16
|
||||
4 13 15 16 7
|
||||
4 11 12 13 15
|
||||
4 11 12 14 15
|
||||
4 12 13 15 16
|
||||
4 12 14 15 16
|
||||
|
||||
CELL_TYPES 16
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
POINT_DATA 17
|
||||
SCALARS vertex_id int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
|
||||
CELL_DATA 16
|
||||
SCALARS cell_attribute_data int 1
|
||||
LOOKUP_TABLE default
|
||||
1
|
||||
3
|
||||
4
|
||||
5
|
||||
6
|
||||
7
|
||||
8
|
||||
9
|
||||
10
|
||||
11
|
||||
12
|
||||
13
|
||||
14
|
||||
15
|
||||
16
|
||||
17
|
||||
|
||||
@@ -0,0 +1,13 @@
|
||||
12 14
|
||||
2 11
|
||||
1 3
|
||||
2 4 12
|
||||
3 5
|
||||
4 6
|
||||
5 7 12
|
||||
6 8
|
||||
7 9
|
||||
8 10
|
||||
9 11 12
|
||||
1 10
|
||||
3 6 10
|
||||
@@ -0,0 +1,12 @@
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
@@ -0,0 +1,12 @@
|
||||
1
|
||||
1
|
||||
2
|
||||
2
|
||||
2
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
2
|
||||
@@ -0,0 +1,49 @@
|
||||
24 35
|
||||
%1
|
||||
2 8
|
||||
%2
|
||||
1 9 10
|
||||
%3
|
||||
4 10 11
|
||||
%4
|
||||
3 14 15
|
||||
%5
|
||||
6 13 15
|
||||
%6
|
||||
5 7
|
||||
%7
|
||||
6 21 23
|
||||
%8
|
||||
1 21 22
|
||||
%9
|
||||
2 12 17
|
||||
%10
|
||||
2 3 12
|
||||
%11
|
||||
3 12 19
|
||||
%12
|
||||
9 10 11
|
||||
%13
|
||||
5 16 18
|
||||
%14
|
||||
4 16 19
|
||||
%15
|
||||
4 5 16
|
||||
%16
|
||||
13 14 15
|
||||
%17
|
||||
9 20 22
|
||||
%18
|
||||
13 20 23
|
||||
%19
|
||||
11 14 20
|
||||
%20
|
||||
17 18 19
|
||||
%21
|
||||
7 8 24
|
||||
%22
|
||||
8 17 24
|
||||
%23
|
||||
7 18 24
|
||||
%24
|
||||
21 22 23
|
||||
@@ -0,0 +1,24 @@
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
@@ -0,0 +1,13 @@
|
||||
12 1
|
||||
1 2 3
|
||||
2 3 4
|
||||
3 4 6
|
||||
4 5 6
|
||||
5 6 7
|
||||
6 7 8
|
||||
7 8 11
|
||||
8 10 11
|
||||
8 9 10
|
||||
3 8 9
|
||||
1 3 9
|
||||
3 6 8
|
||||
@@ -0,0 +1,12 @@
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
@@ -0,0 +1,12 @@
|
||||
11 22
|
||||
2 3 9
|
||||
1 3 4
|
||||
1 2 4 6 8 9
|
||||
2 3 6 5
|
||||
4 6 7
|
||||
3 4 5 7 8
|
||||
5 6 8 11
|
||||
6 7 11 10 9 3
|
||||
8 10 3 1
|
||||
8 11 9
|
||||
7 8 10
|
||||
@@ -0,0 +1,11 @@
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
@@ -0,0 +1,41 @@
|
||||
20 43
|
||||
%1
|
||||
2 3 11
|
||||
%2
|
||||
1 3 4
|
||||
%3
|
||||
1 2 14 13 18 20
|
||||
%4
|
||||
2 14 12 6
|
||||
%5
|
||||
12 6 15 17 13
|
||||
%6
|
||||
4 5 7
|
||||
%7
|
||||
6 15 16 9
|
||||
%8
|
||||
9 10 19 18 17 16
|
||||
%9
|
||||
7 8 10
|
||||
%10
|
||||
8 9 11
|
||||
%11
|
||||
1 20 19 10
|
||||
%12
|
||||
4 14 13 5
|
||||
%13
|
||||
3 14 12 5 17 18
|
||||
%14
|
||||
3 13 12 4
|
||||
%15
|
||||
5 17 17 7
|
||||
%16
|
||||
7 8 17 15
|
||||
%17
|
||||
5 15 16 8 18 13
|
||||
%18
|
||||
3 13 17 8 19 20
|
||||
%19
|
||||
8 11 20 18
|
||||
%20
|
||||
3 18 19 11
|
||||
@@ -0,0 +1,20 @@
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
1
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
0
|
||||
1
|
||||
1
|
||||
1
|
||||
+84
@@ -0,0 +1,84 @@
|
||||
/*!
|
||||
\mainpage H5hut: A High-Performance I/O Library for Particle-based Simulations
|
||||
|
||||
Particle-based simulations running on large high-performance computing systems
|
||||
over many time steps can generate an enormous amount of particle- and
|
||||
field-based data for post-processing and analysis. Achieving high-performance
|
||||
I/O for this data, effectively managing it on disk, and interfacing it with
|
||||
analysis and visualization tools can be challenging, especially for domain
|
||||
scientists who do not have I/O and data management expertise. We present the
|
||||
H5hut library, an implementation of several data models for particle-based
|
||||
simulations that encapsulates the complexity of HDF5 and is simple to use, yet
|
||||
does not compromise performance.
|
||||
|
||||
Developers:
|
||||
|
||||
<UL>
|
||||
<LI> Andreas Adelmann (PSI) </LI>
|
||||
<LI> Achim Gsell (PSI) </LI>
|
||||
<LI> Benedikt Oswald (PSI) </LI>
|
||||
<LI> Mark Howison (NERSC/LBNL) </LI>
|
||||
<LI> Prabhat (NERSC/LBNL) </LI>
|
||||
<LI> Wes Bethel (NERSC/LBNL) </LI>
|
||||
</UL>
|
||||
|
||||
Previous developers:
|
||||
|
||||
<UL>
|
||||
<LI> John Shalf (NERSC/LBNL)</LI>
|
||||
<LI> Cristina Siegerist (NERSC/LBNL)</LI>
|
||||
</UL>
|
||||
|
||||
For more information, please contact the
|
||||
<a href="mailto:h5part@lists.psi.ch">h5part</a> mailing list.
|
||||
|
||||
*/
|
||||
|
||||
/*!
|
||||
\defgroup c_api C API
|
||||
@{
|
||||
\defgroup h5hut_c_api H5hut basic functions
|
||||
@{
|
||||
\defgroup h5hut_file file handling
|
||||
\defgroup h5hut_error error handling
|
||||
\defgroup h5hut_model setting up the data model
|
||||
\defgroup h5hut_attrib reading and writing attributes
|
||||
@}
|
||||
\defgroup h5part_c_api H5Part
|
||||
@{
|
||||
\defgroup h5part_model setting up the data model
|
||||
\defgroup h5part_data reading and writing datasets
|
||||
@}
|
||||
\defgroup h5block_c_api H5Block
|
||||
@{
|
||||
\defgroup h5block_model setting up the data model
|
||||
\defgroup h5block_data reading and writing datasets
|
||||
\defgroup h5block_attrib reading and writing attributes
|
||||
@}
|
||||
@}
|
||||
*/
|
||||
|
||||
/*!
|
||||
\defgroup f90_api Fortran90 API
|
||||
@{
|
||||
\defgroup h5hut_f90_api H5hut basic functions
|
||||
@{
|
||||
\defgroup h5hut_file_f file handling
|
||||
\defgroup h5hut_error_f error handling
|
||||
\defgroup h5hut_model_f setting up the data model
|
||||
\defgroup h5hut_attrib_f reading and writing attributes
|
||||
@}
|
||||
\defgroup h5part_f90_api H5Part
|
||||
@{
|
||||
\defgroup h5part_model_f setting up the data model
|
||||
\defgroup h5part_data_f reading and writing datasets
|
||||
@}
|
||||
\defgroup h5block_f90_api H5Block
|
||||
@{
|
||||
\defgroup h5block_model_f setting up the data model
|
||||
\defgroup h5block_data_f reading and writing datasets
|
||||
\defgroup h5block_attrib_f reading and writing attributes
|
||||
@}
|
||||
@}
|
||||
*/
|
||||
|
||||
@@ -0,0 +1,170 @@
|
||||
Proposal for a more general file format used by H5Part/H5Block
|
||||
|
||||
Authors: Achim Gsell
|
||||
Status: Draft
|
||||
|
||||
1. Introduction
|
||||
|
||||
H5X is the file format used by H5Part and H5Block. H5X is designed on
|
||||
top of HDF5: A H5X file is a very special HDF5 file.
|
||||
|
||||
+--------------------+
|
||||
| Application |
|
||||
+--------------------+
|
||||
| H5Part/H5Block API |
|
||||
+--------------------+
|
||||
| H5X API |
|
||||
+--------------------+
|
||||
| HDF5 API |
|
||||
+--------------------+
|
||||
| Filesystem of OS |
|
||||
+--------------------+
|
||||
|
||||
|
||||
2. H5X file format specification
|
||||
|
||||
2.1 The root group
|
||||
|
||||
2.1.1 File attributes
|
||||
|
||||
Attributes of the HDF5 root group are called "file attributes". There
|
||||
are no restrictions on file attribute names. Names with "__" as prefix and
|
||||
postfix are intended for internal use. Supported values for file attributes
|
||||
are scalars and arrays of 64bit integer and 64bit floating point number as
|
||||
well as string values. Arrays of strings are not supported.
|
||||
|
||||
2.1.1.1 Predefined file attributes
|
||||
|
||||
__stepname__ (optional)
|
||||
See below.
|
||||
|
||||
__stepnumwidth__ (optional)
|
||||
See below.
|
||||
|
||||
2.1.2 Members of the root group
|
||||
|
||||
Members of the root group are special formated HDF5 groups called
|
||||
"step groups". The name of a step group is "<name>#<number>".
|
||||
Whereby <name> is either defined by the optional file attribute
|
||||
__stepname__ or set to "Step" by default. <number> is an
|
||||
unsigned integer less than 2^63.
|
||||
|
||||
/
|
||||
+- Step#0
|
||||
+- Step#1
|
||||
...
|
||||
+- Step#n
|
||||
+- StepProperties [NEW]
|
||||
+- Mesh [NEW]
|
||||
|
||||
The optional file attribute __stepnumwidth__ defines the minimum width
|
||||
of <number> in the name of the step group. The number is padded with
|
||||
'0'. The minimum width defaults to zero, so that no paddings occurs.
|
||||
Example: With __stepnumwidth__ := 5 the name of the step group with
|
||||
number 42 is "Step#00042", with __stepnumwidth__ := 0 the name is
|
||||
"Step#42".
|
||||
|
||||
Step groups may be unsorted in the HDF5 file und needn't be number
|
||||
consecutively.
|
||||
|
||||
2.1.3 Other members of the root group
|
||||
|
||||
Other sub-groups of the root group are allowed, but the group names are restricted
|
||||
to names not matching "Step#.*".
|
||||
|
||||
2.2 Format of a step group
|
||||
|
||||
2.2.1 Step attributes
|
||||
|
||||
Step attributes are HDF5 attributes asigned to a step group. There
|
||||
are no restrictions on step attribute names. As with file attributes names
|
||||
enclosed in "__" are intended for internal use. Supported values are the same
|
||||
as for file attributes:
|
||||
* 64bit integer value
|
||||
* arrays of 64bit integer values
|
||||
* 64bit floating point number
|
||||
* array of 64bit floating point number
|
||||
* strings
|
||||
Note that array of strings are not supported!
|
||||
|
||||
2.2.2 Predefined step attributes
|
||||
|
||||
No predefined step attributes exists.
|
||||
|
||||
|
||||
2.2.3 Members of a step group
|
||||
|
||||
Members of a step group are HDF5 datasets and optional one HDF5 group
|
||||
with the name "Block". HDF5 datasets in a step group are called "step
|
||||
datasets". The optional block group is called "block data".
|
||||
|
||||
Mesh?!
|
||||
|
||||
2.2.4 Step datasets
|
||||
|
||||
Step datasets are arrays of rank 1. The dataset size must be the same
|
||||
for all datasets inside a step. The size of the dataset may vary
|
||||
from step to step. Array values are 64bit integer or 64bit floating
|
||||
point numbers. No limitations (other than given by HDF5) are given on
|
||||
step dataset names.
|
||||
|
||||
|
||||
2.2.5 Block Data
|
||||
|
||||
The block data group is a container for an arbitrary number of field
|
||||
data. A field is a data structure to store arrays of rank m with
|
||||
n-dimensional vector values. Fields are represented within HDF5
|
||||
groups. The HDF5 group name is the unique identifier for a field in
|
||||
the current step.
|
||||
|
||||
2.2.5.1 m-rank fields with n-dimensional-vector values
|
||||
|
||||
Values are stored per dimension in separate datasets. Thus we have n
|
||||
datasets for a field with n-dimensional vector values. Each dataset
|
||||
corresponse to one dimension. The datasets are numbered from '0' to
|
||||
'n-1'. Arrays are stored in column major order (Fortran indexing
|
||||
scheme).
|
||||
|
||||
/ # HDF5 root group
|
||||
...
|
||||
+- Step#<i> # HDF5 group
|
||||
|
|
||||
+- Block # HDF5 group
|
||||
|
|
||||
+- <field name> # HDF5 group
|
||||
|
|
||||
+- 0 # HDF5 dataset, first dim of vector
|
||||
+- 1 # HDF5 dataset, second dim of vector
|
||||
...
|
||||
+- n-1 # HDF5 dataset, last dim of vector
|
||||
...
|
||||
|
||||
2.2.5.2 m-rank fields with scalar values
|
||||
|
||||
Fields with scalar values are stored as special case of fields with
|
||||
n-dimensional vector values with n := 1.
|
||||
|
||||
/ # HDF5 root group
|
||||
...
|
||||
+- Step#<i> # HDF5 group
|
||||
|
|
||||
+- Block # HDF5 group
|
||||
|
|
||||
+- <field name> # HDF5 group
|
||||
|
|
||||
+- 0 # HDF5 dataset, scalar value
|
||||
...
|
||||
|
||||
|
||||
2.3 Step properties [NEW]
|
||||
|
||||
Why? Much faster than step attributes if you need to access consecutive values
|
||||
|
||||
Group of root group with name "StepProperties"
|
||||
|
||||
Members are datasets
|
||||
|
||||
Supported values are the same as for step attributes
|
||||
|
||||
Mapping of value to step via object index of step group
|
||||
|
||||
@@ -0,0 +1,14 @@
|
||||
EXTRA_DIST = \
|
||||
Doxyfile \
|
||||
H5.dox
|
||||
|
||||
all:
|
||||
|
||||
doc:
|
||||
|
||||
doxydoc:
|
||||
doxygen
|
||||
|
||||
clean-local:
|
||||
$(RM) -r ReferencePages TWiki
|
||||
$(RM) *~
|
||||
@@ -0,0 +1,2 @@
|
||||
|
||||
|
||||
@@ -0,0 +1,4 @@
|
||||
<style type="text/css">
|
||||
h1 { text-align: center; }
|
||||
</style>
|
||||
|
||||
@@ -0,0 +1,2 @@
|
||||
</BODY>
|
||||
</HTML>
|
||||
@@ -0,0 +1,6 @@
|
||||
<HTML>
|
||||
<HEAD>
|
||||
<TITLE>H5/H5Part/H5Block/H5Fed API</TITLE>
|
||||
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
|
||||
</HEAD>
|
||||
<BODY BGCOLOR="#FFFFFF">
|
||||
Executable
+36
@@ -0,0 +1,36 @@
|
||||
#!/bin/bash
|
||||
|
||||
shopt -s nullglob
|
||||
|
||||
function html2twiki() {
|
||||
declare -rx infile=$1
|
||||
declare -rx outdir=$2
|
||||
declare -rx fname=$( sed -n 's/.* member="\([a-zA-Z0-9_.]*\)::\([_a-zA-Z0-9]*\)" .*/\2/p' "${infile}" )
|
||||
declare -rx outfile="${outdir}/${fname}.txt"
|
||||
|
||||
grep -q " member=" "${infile}" || return 0
|
||||
|
||||
sed '/Generated by/,/anchor/d' "${infile}" > "${outfile}"
|
||||
}
|
||||
|
||||
mkdir -p TWiki/h5_core
|
||||
mkdir -p TWiki/H5
|
||||
mkdir -p TWiki/H5Part
|
||||
mkdir -p TWiki/H5Block
|
||||
mkdir -p TWiki/H5Fed
|
||||
|
||||
for f in ReferencePages/group__h5__core_*.html; do
|
||||
html2twiki $f TWiki/h5_core
|
||||
done
|
||||
for f in ReferencePages/group__h5__c__api_*.html; do
|
||||
html2twiki $f TWiki/H5
|
||||
done
|
||||
for f in ReferencePages/group__h5part__c__api_*.html; do
|
||||
html2twiki $f TWiki/H5Part
|
||||
done
|
||||
for f in ReferencePages/group__h5block__c__api_*.html; do
|
||||
html2twiki $f TWiki/H5Block
|
||||
done
|
||||
for f in ReferencePages/group__h5fed__c__api_*.html; do
|
||||
html2twiki $f TWiki/H5Fed
|
||||
done
|
||||
+6982
File diff suppressed because it is too large
Load Diff
Executable
+39
@@ -0,0 +1,39 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
from lxml import etree
|
||||
from lxml.html import builder as E
|
||||
import os
|
||||
import re
|
||||
|
||||
tree = etree.parse('tagfile')
|
||||
tags = tree.xpath ('//member[@kind="function"]')
|
||||
tags_per_files = {}
|
||||
for tag in tags:
|
||||
name = tag.find("name").text
|
||||
anchor = tag.find("anchor").text
|
||||
anchorfile = tag.find("anchorfile").text
|
||||
if anchorfile in tags_per_files:
|
||||
tags_per_files[anchorfile].append([name, anchor])
|
||||
else:
|
||||
tags_per_files[anchorfile] = [[name, anchor]]
|
||||
|
||||
|
||||
prefix = None
|
||||
for line in open("Doxyfile", "r"):
|
||||
if re.search ("^OUTPUT_DIRECTORY", line):
|
||||
prefix = line.split("=")[-1].strip()
|
||||
|
||||
if not prefix:
|
||||
prefix = "."
|
||||
|
||||
parser = etree.HTMLParser()
|
||||
for filename,anchors in tags_per_files.items():
|
||||
print "Processing file: %s/%s" % (prefix, filename)
|
||||
tree = etree.parse ("%s/%s" % (prefix, filename), parser)
|
||||
for name,id in anchors:
|
||||
anchor = tree.xpath ('//a[@id="%s"]' % id)
|
||||
el = E.A(id="%s" % name)
|
||||
anchor[0].addnext (el)
|
||||
|
||||
f = open ("%s/%s" % (prefix, filename), "w")
|
||||
f.write (etree.tostring (tree))
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 8.4 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,10 @@
|
||||
TET no. 0:
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
0.0, 0.0, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
TET no. 1:
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
1.0, 0.0, 0.0
|
||||
@@ -0,0 +1,25 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 5 DOUBLE
|
||||
0.5 0.5 0.0
|
||||
0.0 0.0 1.0
|
||||
0.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
1.0 0.0 0.0
|
||||
|
||||
CELLS 2 10
|
||||
4 0 1 2 3
|
||||
4 0 2 1 4
|
||||
|
||||
CELL_TYPES 2
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 2
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 8.0 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 8.0 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 8.5 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,10 @@
|
||||
TET no. 0:
|
||||
0.0, 0.5, 0.5
|
||||
0.0, 0.0, 0.0
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
TET no. 1:
|
||||
0.0, 0.5, 0.5
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
@@ -0,0 +1,25 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 5 DOUBLE
|
||||
0.0 0.5 0.5
|
||||
0.0 0.0 0.0
|
||||
1.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 1.0
|
||||
|
||||
CELLS 2 10
|
||||
4 0 1 2 3
|
||||
4 0 2 1 4
|
||||
|
||||
CELL_TYPES 2
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 2
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 8.1 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 8.7 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,10 @@
|
||||
TET no. 0:
|
||||
0.5, 0.0, 0.5
|
||||
0.0, 0.0, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
TET no. 1:
|
||||
0.5, 0.0, 0.5
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
1.0, 0.0, 0.0
|
||||
@@ -0,0 +1,25 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 5 DOUBLE
|
||||
0.5 0.0 0.5
|
||||
0.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 1.0
|
||||
1.0 0.0 0.0
|
||||
|
||||
CELLS 2 10
|
||||
4 0 1 2 3
|
||||
4 0 2 1 4
|
||||
|
||||
CELL_TYPES 2
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 2
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 8.9 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 8.3 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,10 @@
|
||||
TET no. 0:
|
||||
0.0, 0.0, 0.5
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 1:
|
||||
0.0, 0.0, 0.5
|
||||
0.0, 1.0, 0.0
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
@@ -0,0 +1,25 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 5 DOUBLE
|
||||
0.0 0.0 0.5
|
||||
1.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 0.0
|
||||
0.0 0.0 1.0
|
||||
|
||||
CELLS 2 10
|
||||
4 0 1 2 3
|
||||
4 0 2 1 4
|
||||
|
||||
CELL_TYPES 2
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 2
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 8.4 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 8.0 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,10 @@
|
||||
TET no. 0:
|
||||
0.5, 0.0, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 1:
|
||||
0.5, 0.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
0.0, 1.0, 0.0
|
||||
1.0, 0.0, 0.0
|
||||
@@ -0,0 +1,25 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 5 DOUBLE
|
||||
0.5 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 1.0
|
||||
0.0 0.0 0.0
|
||||
1.0 0.0 0.0
|
||||
|
||||
CELLS 2 10
|
||||
4 0 1 2 3
|
||||
4 0 2 1 4
|
||||
|
||||
CELL_TYPES 2
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 2
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 7.8 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 9.1 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,10 @@
|
||||
TET no. 0:
|
||||
0.0, 0.5, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 1:
|
||||
0.0, 0.5, 0.0
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
0.0, 1.0, 0.0
|
||||
@@ -0,0 +1,25 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 5 DOUBLE
|
||||
0.0 0.5 0.0
|
||||
0.0 0.0 1.0
|
||||
1.0 0.0 0.0
|
||||
0.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
|
||||
CELLS 2 10
|
||||
4 0 1 2 3
|
||||
4 0 2 1 4
|
||||
|
||||
CELL_TYPES 2
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 2
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 8.7 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 8.8 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,15 @@
|
||||
TET no. 0:
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.5, 0.5
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 1:
|
||||
0.0, 0.5, 0.5
|
||||
1.0, 0.0, 0.0
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 2:
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 0.5, 0.5
|
||||
0.0, 0.0, 1.0
|
||||
0.0, 0.0, 0.0
|
||||
@@ -0,0 +1,29 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 6 DOUBLE
|
||||
0.5 0.5 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.5 0.5
|
||||
0.0 0.0 0.0
|
||||
1.0 0.0 0.0
|
||||
0.0 0.0 1.0
|
||||
|
||||
CELLS 3 15
|
||||
4 0 1 2 3
|
||||
4 2 4 0 3
|
||||
4 4 2 5 3
|
||||
|
||||
CELL_TYPES 3
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 3
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 8.5 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 8.5 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 9.6 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,15 @@
|
||||
TET no. 0:
|
||||
0.5, 0.0, 0.5
|
||||
1.0, 0.0, 0.0
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 1:
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
0.5, 0.0, 0.5
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 2:
|
||||
0.0, 0.0, 1.0
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
@@ -0,0 +1,29 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 6 DOUBLE
|
||||
0.5 0.0 0.5
|
||||
1.0 0.0 0.0
|
||||
0.5 0.5 0.0
|
||||
0.0 0.0 0.0
|
||||
0.0 0.0 1.0
|
||||
0.0 1.0 0.0
|
||||
|
||||
CELLS 3 15
|
||||
4 0 1 2 3
|
||||
4 2 4 0 3
|
||||
4 4 2 5 3
|
||||
|
||||
CELL_TYPES 3
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 3
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 9.2 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 11 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,20 @@
|
||||
TET no. 0:
|
||||
1.0, 0.0, 0.0
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 0.5
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 1:
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.0, 0.5
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 2:
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 0.5
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
TET no. 3:
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 0.0, 0.5
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
@@ -0,0 +1,32 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 6 DOUBLE
|
||||
1.0 0.0 0.0
|
||||
0.5 0.5 0.0
|
||||
0.0 0.0 0.5
|
||||
0.0 0.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 1.0
|
||||
|
||||
CELLS 4 20
|
||||
4 0 1 2 3
|
||||
4 1 4 2 3
|
||||
4 1 2 4 5
|
||||
4 0 2 1 5
|
||||
|
||||
CELL_TYPES 4
|
||||
10
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 4
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 12 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 12 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 10 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,15 @@
|
||||
TET no. 0:
|
||||
0.5, 0.5, 0.0
|
||||
1.0, 0.0, 0.0
|
||||
0.5, 0.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
TET no. 1:
|
||||
0.5, 0.0, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
TET no. 2:
|
||||
0.0, 1.0, 0.0
|
||||
0.5, 0.0, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
@@ -0,0 +1,29 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 6 DOUBLE
|
||||
0.5 0.5 0.0
|
||||
1.0 0.0 0.0
|
||||
0.5 0.0 0.0
|
||||
0.0 0.0 1.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 0.0
|
||||
|
||||
CELLS 3 15
|
||||
4 0 1 2 3
|
||||
4 2 4 0 3
|
||||
4 4 2 5 3
|
||||
|
||||
CELL_TYPES 3
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 3
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 11 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 11 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,15 @@
|
||||
TET no. 0:
|
||||
0.0, 0.5, 0.0
|
||||
0.0, 1.0, 0.0
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
TET no. 1:
|
||||
0.5, 0.5, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
0.0, 0.5, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
TET no. 2:
|
||||
0.0, 0.0, 0.0
|
||||
0.5, 0.5, 0.0
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 0.0, 1.0
|
||||
@@ -0,0 +1,29 @@
|
||||
# vtk DataFile Version 2.0
|
||||
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
|
||||
ASCII
|
||||
DATASET UNSTRUCTURED_GRID
|
||||
|
||||
POINTS 6 DOUBLE
|
||||
0.0 0.5 0.0
|
||||
0.0 1.0 0.0
|
||||
0.5 0.5 0.0
|
||||
0.0 0.0 1.0
|
||||
0.0 0.0 0.0
|
||||
1.0 0.0 0.0
|
||||
|
||||
CELLS 3 15
|
||||
4 0 1 2 3
|
||||
4 2 4 0 3
|
||||
4 4 2 5 3
|
||||
|
||||
CELL_TYPES 3
|
||||
10
|
||||
10
|
||||
10
|
||||
|
||||
CELL_DATA 3
|
||||
SCALARS cell_attribute_data float 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 12 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 9.5 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,15 @@
|
||||
TET no. 0:
|
||||
0.0, 0.5, 0.5
|
||||
0.0, 0.0, 1.0
|
||||
0.5, 0.0, 0.5
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 1:
|
||||
0.5, 0.0, 0.5
|
||||
0.0, 1.0, 0.0
|
||||
0.0, 0.5, 0.5
|
||||
0.0, 0.0, 0.0
|
||||
TET no. 2:
|
||||
0.0, 1.0, 0.0
|
||||
0.5, 0.0, 0.5
|
||||
1.0, 0.0, 0.0
|
||||
0.0, 0.0, 0.0
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user