Hi Yann,
Thanks very much for your insightful advice! I've modified
ABINIT-8.10.3-intel-2018b.eb to contain flags pointing to the CentOS
system libxml2 headers:
dependencies = [
('libxc', '3.0.1'),
('netCDF', '4.6.1'),
('netCDF-Fortran', '4.4.4'),
('HDF5', '1.10.2'),
('Wannier90', '2.0.1.1', '-abinit'),
('AtomPAW', '4.1.0.5'),
]
# ensure mpi and intel toolchain
configopts = '--enable-mpi '
# xml support
configopts += '--enable-xml '
configopts += 'CFLAGS_EXTRA="-I/usr/include/libxml2" '
configopts += 'FC_LIBS_EXTRA="-lxml2 -lz -lm -ldl" '
# openmp support
configopts += '--enable-openmp '
...
The RPM packages were already installed on our CentOS 7.6 system:
$ rpm -q libxml2 libxml2-devel
libxml2-2.9.1-6.el7_2.3.x86_64
libxml2-devel-2.9.1-6.el7_2.3.x86_64
Unfortunately, the build now crashes with this error in the log file:
mpiifort -DHAVE_CONFIG_H -I. -I../.. -I../../src/77_ddb
-I../../src/77_ddb -I../../src/32_util -I../../src/32_util
-I../../src/44_abitools -I../../src/44_abitools
-I../../src/27_toolbox_oop -I../../src/27_toolbox_oop
-I../../src/44_abitypes_defs -I../../src/44_abitypes_defs
-I../../src/72_response -I../../src/72_response -I../../src/16_hideleave
-I../../src/16_hideleave -I../../src/42_parser -I../../src/42_parser
-I../../src/55_abiutil -I../../src/55_abiutil -I../../src/41_geometry
-I../../src/41_geometry -I../../src/45_geomoptim
-I../../src/45_geomoptim -I../../src/12_hide_mpi -I../../src/12_hide_mpi
-I../../src/10_defs -I../../src/10_defs -I../../src/14_hidewrite
-I../../src/14_hidewrite -I../../src/57_iovars -I../../src/57_iovars
-I../../src/28_numeric_noabirule -I../../src/28_numeric_noabirule
-I../../src/incs -I../../src/incs
-I/home/modules/software/netCDF/4.6.1-intel-2018b/include
-I/home/modules/software/netCDF-Fortran/4.4.4-intel-2018b/include
-I/home/modules/build/ABINIT/8.10.3/intel-2018b/abinit-8.10.3/fallbacks/exports/include
-free -module
/home/modules/build/ABINIT/8.10.3/intel-2018b/abinit-8.10.3/src/mods
-O2 -xHost -ftz -fp-speculation=safe -fp-model source -fPIC -c -o
m_spin_reciprocal.o m_spin_reciprocal.F90
m_multibinit_dataset.F90(2032): remark #8291: Recommended relationship
between field width 'W' and the number of fractional digits 'D' in this
edit descriptor is 'W>=D+7'.
if(multibinit_dtset%strcpling==2)write(nunit,'(3x,a9,3es8.2)')'delta_df',multibinit_dtset%delta_df
-----------------------------------------------------------^
effpot_xml.c(29): catastrophic error: cannot open source file
"libxml/parser.h"
#include <libxml/parser.h>
^
compilation aborted for effpot_xml.c (code 4)
The missing source file libxml/parser.h is actually installed on the system:
$ rpm -qf /usr/include/libxml2/libxml/parser.h
libxml2-devel-2.9.1-6.el7_2.3.x86_64
Could you kindly suggest some additional configopts to solve this problem?
Thanks a lot,
Ole
On 8/27/19 11:33 PM, Yann Pouillon wrote:
Dear Ole,
If you use the --enable-xml option, the configure script of ABINIT assumes
that you have the development files of LibXML2 installed on your system.
I don't know if there is a specific EasyConfig for LibXML2 or if this should
be marked as "system dependency". In any case, EasyBuild should be informed
that the XML header files are required.
