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Merge pull request #110 from TREX-CoE/no_hl

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Removed dependency on hdf5_hl library
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Anthony Scemama 2023-01-19 01:31:34 +01:00 committed by GitHub
commit 986f5d8bf8
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5 changed files with 127 additions and 57 deletions
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1
ChangeLog
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@ -4,6 +4,7 @@ CHANGES
2.3
---
- Removed dependency to hdf5_hl
- Fixed Fortran interface on 32-bit (e.g. i386) architectures
- Changed the structure of the state group
- Sparse data type is patched to work with different dimensions

23
README.md
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@ -5,7 +5,7 @@
[![build](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml/badge.svg)](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml)
![GitHub release (latest by date)](https://img.shields.io/github/v/release/TREX-CoE/trexio)
TREX library for efficient I/O.
TREX library for efficient I/O.
## Minimal requirements (for users):
@ -37,6 +37,8 @@ TREX library for efficient I/O.
- Emacs (>= 26.0)
- SWIG (>= 4.0) [required for the Python API]
**Note:** The source code is auto-generated from the Emacs org-mode (`.org`) files following the literate programming approach. This is why the `src` directory is initially empty.
## Installation procedure from the GitHub repo clone (for developers):
1. `git clone https://github.com/TREX-CoE/trexio.git`
@ -83,13 +85,10 @@ The official releases of TREXIO `>=2.0.0` can be installed using the
[GNU Guix](https://guix.gnu.org) functional package manager.
The [trexio.scm](https://github.com/TREX-CoE/trexio/blob/master/tools/trexio.scm)
Schema file contains the manifest specification for the `trexio` package.
It can be installed within the selected `$GUIX_PROFILE` as follows:
It can be installed as follows:
```
guix package \
--profile=$GUIX_PROFILE \
--cores=<n_cores> \
--install-from-file=trexio.scm
guix package --cores=<n_cores> --install-from-file=trexio.scm
```
## Installation procedure for Spack users
@ -104,6 +103,18 @@ It can be installed as follows
spack install --jobs <n_cores> trexio
```
## Installation procedure for Debian/Ubuntu users
The official release of TREXIO `2.2.0` is available as a Debian (`.deb`) package thanks to the [Debichem Team](https://wiki.debian.org/Debichem).
The source code is hosted [here](https://salsa.debian.org/debichem-team/libtrexio) and
the pre-built binary files are available via the [Debian package registry](https://packages.debian.org/bookworm/libtrexio-dev).
TREXIO is also available on [Ubuntu 23.04 (Lunar Lobster)](https://packages.ubuntu.com/lunar/libtrexio-dev) and newer and can be installed as follows:
```
sudo apt-get update && sudo apt-get install libtrexio-dev
```
## Compilation without the HDF5 library
By default, the configuration step proceeds to search for the [HDF5 library](https://portal.hdfgroup.org/display/HDF5/HDF5).

78
configure.ac
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@ -95,7 +95,7 @@ AC_RUN_IFELSE(
execl("/bin/sh", "sh", "-c", "mkdir tmpdir1 && \
touch tmpdir1/test_file && \
$CP_PROG -r -n tmpdir1 tmpdir2 && \
exec ls tmpdir2/test_file", NULL);
exec ls tmpdir2/test_file > /dev/null", NULL);
])],
[ rm -rf tmpdir1 tmpdir2
CP_COMMAND="\"$CP_PROG\", \"-r\", \"-n\""
@ -122,7 +122,9 @@ AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd
### ----
HDF5_LIBS=""
HDF5_LDFLAGS=""
HDF5_CFLAGS=""
HDF5_CPPFLAGS=""
AC_ARG_WITH([hdf5],
AS_HELP_STRING([--with-hdf5=PATH], [Path to HDF5 library and headers]), [
with_hdf5="$withval"], [with_hdf5="yes"])
@ -130,29 +132,87 @@ AC_ARG_WITH([hdf5],
AS_IF([test "x$with_hdf5" == "xno"], [
AC_DEFINE([HAVE_HDF5], 0, [Define to 1 if HDF5 is available]) ],
[test "x$with_hdf5" != "xyes"], [
HDF5_LIBS="-lhdf5"
HDF5_PATH="$with_hdf5"
HDF5_LIBS="-L$HDF5_PATH/lib -lhdf5 -lhdf5_hl"
HDF5_CFLAGS="-I$HDF5_PATH/include"
HDF5_LDFLAGS="-L$HDF5_PATH/lib"
HDF5_CPPFLAGS="-I$HDF5_PATH/include"
AC_DEFINE([HAVE_HDF5], 1, [Define to 1 if HDF5 is available]) ],
[
PKG_CHECK_MODULES([HDF5], [hdf5 >= 1.8])
AS_IF([ test "${HDF5_LIBS}" == "" ], [
AC_CHECK_LIB([hdf5], [H5Fcreate], [ HDF5_LIBS="-lhdf5" ])
AC_CHECK_HEADER([hdf5.h], [HDF5_CFLAGS=""], [AC_MSG_ERROR([HDF5 header not found]) ])
AC_CHECK_HEADER([hdf5_hl.h], [HDF5_CFLAGS=""], [AC_MSG_ERROR([HDF5 header not found]) ])
PKG_CHECK_EXISTS([hdf5], [
PKG_CHECK_MODULES([HDF5], [hdf5 >= 1.8])
],
[ AC_PATH_PROG([H5CC],[h5cc],[not_found])
AS_IF([test "$H5CC" != "not_found"], [
HDF5_LIBS="-lhdf5"
AC_REQUIRE([AC_PROG_SED])
AC_REQUIRE([AC_PROG_AWK])
AC_REQUIRE([AC_PROG_GREP])
# Look for "HDF5 Version: X.Y.Z"
HDF5_VERSION=$(eval $H5CC -showconfig | $GREP 'HDF5 Version:' \
| $AWK '{print $[]3}')
# A ideal situation would be where everything we needed was
# in the AM_* variables. However most systems are not like this
# and seem to have the values in the non-AM variables.
#
# We try the following to find the flags:
# (1) Look for "NAME:" tags
# (2) Look for "H5_NAME:" tags
# (3) Look for "AM_NAME:" tags
#
HDF5_tmp_flags=$(eval $H5CC -showconfig \
| $GREP 'FLAGS\|Extra libraries:' \
| $AWK -F: '{printf("%s "), $[]2}' )
dnl Find the installation directory and append include/
HDF5_tmp_inst=$(eval $H5CC -showconfig \
| $GREP 'Installation point:' \
| $AWK '{print $[]NF}' )
dnl Add this to the CPPFLAGS
HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
HDF5_SHOW=$(eval $H5CC -show)
dnl Now sort the flags out based upon their prefixes
for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
case "$arg" in
-I*) echo $HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_CPPFLAGS="$HDF5_CPPFLAGS $arg"
;;
-L*) echo $HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_LDFLAGS="$HDF5_LDFLAGS $arg"
;;
-l*) echo $HDF5_LIBS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_LIBS="$HDF5_LIBS $arg"
;;
esac
done
])
])
AC_DEFINE([HAVE_HDF5], 1, [Define to 1 if HDF5 is available])
HDF5_LIBS="$HDF5_LIBS -lhdf5_hl"
])
AM_CONDITIONAL([HAVE_HDF5],[test "x$with_hdf5" != "xno"])
AC_SUBST([HDF5_LDFLAGS])
AC_SUBST([HDF5_LIBS])
AC_SUBST([HDF5_CFLAGS])
AC_SUBST([HDF5_CPPFLAGS])
CPPFLAGS="${HDF5_CPPFLAGS} ${CPPFLAGS}"
CFLAGS="${HDF5_CFLAGS} ${CFLAGS}"
LDFLAGS="${HDF5_LDFLAGS} ${LDFLAGS}"
LIBS="${HDF5_LIBS} ${LIBS}"
AS_IF([test "x$with_hdf5" != "xno"], [
OLD_LIBS=$LIBS
AC_CHECK_LIB([hdf5], [H5Fcreate], [], [
AC_MSG_ERROR([-lhdf5 fails, use ./configure --with-hdf5=...]) ])
LIBS=$OLD_LIBS
AC_CHECK_HEADER([hdf5.h], [], [
AC_MSG_ERROR([hdf5.h not found, use ./configure --with-hdf5=...]) ])
])
# The block below should only execute if the ax_lib_hdf5.m4 macro failed to find HDF5.
# It is only needed to manually build Python API because setup.py depends on HDF5.

2
python/setup.py
View File

@ -92,7 +92,7 @@ h5_ldflags = h5_ldflags_withl.split(" ")[0] if not do_sdist else ""
pytrexio_module = Extension('pytrexio._pytrexio',
sources = [os.path.join(srcpath, code) for code in c_files],
include_dirs = [h5_cflags, srcpath, numpy_includedir],
libraries = ['hdf5', 'hdf5_hl'],
libraries = ['hdf5' ],
extra_compile_args = [
'-std=c99',
'-Wno-discarded-qualifiers',

80
src/templates_hdf5/templator_hdf5.org
View File

@ -39,7 +39,6 @@
#include <sys/stat.h>
#include "hdf5.h"
#include "hdf5_hl.h"
#+end_src
@ -380,18 +379,21 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
}
FREE(ddims);
/* Read dataset */
herr_t status = H5Dread(dset_id,
H5T_$GROUP_DSET_H5_DTYPE$,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
H5Sclose(dspace_id);
H5Dclose(dset_id);
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
herr_t status = H5LTread_dataset(f->$group$_group,
$GROUP_DSET$_NAME,
H5T_$GROUP_DSET_H5_DTYPE$,
$group_dset$);
if (status < 0) return TREXIO_FAILURE;
return TREXIO_SUCCESS;
}
#+end_src
#+begin_src c :tangle write_dset_data_hdf5.c
@ -411,7 +413,8 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype$*
Consider using HDF5-native h5repack utility after deleting/overwriting big datasets.
,*/
if (H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) == 1 && file->mode == 'u') {
if ((trexio_hdf5_has_$group_dset$(file) == TREXIO_SUCCESS) && (file->mode == 'u')) {
herr_t status_del = H5Ldelete(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (status_del < 0) return TREXIO_FAILURE;
}
@ -454,14 +457,13 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->$group$_group == (hsize_t) 0) return TREXIO_HAS_NOT;
herr_t status = H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME);
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
@ -534,7 +536,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file,
trexio_exit_code rc_write = TREXIO_FAILURE;
/* NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed ! */
if ( H5LTfind_dataset(f->$group$_group, dset_index_name) != 1 ) {
if (trexio_hdf5_has_$group_dset$(file) == TREXIO_HAS_NOT) {
/* If the file does not exist -> create it and write */
/* Create chunked dataset with index_dtype datatype and write indices into it */
@ -657,14 +659,13 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->$group$_group == (hsize_t) 0) return TREXIO_HAS_NOT;
herr_t status = H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME "_values");
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->$group$_group, $GROUP_DSET$_NAME "_values", H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
@ -728,7 +729,7 @@ trexio_exit_code trexio_hdf5_write_$group_dset$(trexio_t* const file,
trexio_exit_code rc_write = TREXIO_FAILURE;
/* NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed ! */
if ( H5LTfind_dataset(f->$group$_group, dset_name) != 1 ) {
if (trexio_hdf5_has_$group_dset$(file) == TREXIO_HAS_NOT) {
/* If the file does not exist -> create it and write */
/* Create chunked dataset with dtype datatype and write indices into it */
@ -793,14 +794,13 @@ trexio_exit_code trexio_hdf5_has_$group_dset$(trexio_t* const file)
const char dset_name[256] = "$group_dset$";
herr_t status = H5LTfind_dataset(f->$group$_group, dset_name);
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->$group$_group, dset_name, H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
#+end_src
@ -936,7 +936,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const char** $group_dset$,
Consider using HDF5-provided h5repack utility after deleting/overwriting big datasets.
,*/
if (H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) == 1 && file->mode == 'u') {
if ( (trexio_hdf5_has_$group_dset$(file) == TREXIO_SUCCESS) && (file->mode == 'u') ) {
herr_t status_del = H5Ldelete(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (status_del < 0) return TREXIO_FAILURE;
}
@ -991,14 +991,13 @@ trexio_hdf5_has_$group_dset$ (trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->$group$_group == (hsize_t) 0) return TREXIO_HAS_NOT;
herr_t status = H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME);
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
@ -1231,7 +1230,7 @@ trexio_exit_code trexio_hdf5_write_determinant_list(trexio_t* const file,
trexio_exit_code rc_write = TREXIO_FAILURE;
/* NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed ! */
if ( H5LTfind_dataset(f->determinant_group, dset_det_name) != 1 ) {
if ( trexio_hdf5_has_determinant_list(file) == TREXIO_HAS_NOT ) {
/* If the file does not exist -> create it and write */
/* Create chunked dataset with det_dtype datatype and write indices into it */
@ -1260,14 +1259,13 @@ trexio_exit_code trexio_hdf5_has_determinant_list(trexio_t* const file)
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
if (f->determinant_group == (hsize_t) 0) return TREXIO_HAS_NOT;
herr_t status = H5LTfind_dataset(f->determinant_group, "determinant_list");
/* H5LTfind_dataset returns 1 if dataset exists, 0 otherwise */
if (status == 1){
htri_t exists = H5Lexists(f->determinant_group, "determinant_list", H5P_DEFAULT);
if (exists > 0) {
return TREXIO_SUCCESS;
} else if (status == 0) {
return TREXIO_HAS_NOT;
} else {
} else if (exists < 0) {
return TREXIO_FAILURE;
} else {
return TREXIO_HAS_NOT;
}
}
#+end_src