[easybuild] Re: Missing features in ABINIT/8.10.3-intel-2018b
Hi Jean-Michel,
Our user requiring ABINIT with XML has now hit a new error:
--- !ERROR
src_file: m_pspheads.F90
src_line: 226
mpi_rank: 0
message: |
XML norm-conserving pseudopotential has been input, but abinit is
not compiled with libPSML support. Reconfigure and recompile.
...
Question: How do I build ABINIT with libpsml support?
I noticed that EB includes an old libpsml version:
$ eb -S libpsml
CFGS1=/home/modules/software/EasyBuild/3.9.4/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.4-py2.7.egg/easybuild/easyconfigs/l/libpsml
* $CFGS1/libpsml-1.1.7-foss-2016b.eb
* $CFGS1/libpsml-1.1.7-foss-2017a.eb
Maybe such a module could be used?
Thanks,
Ole
On 8/27/19 12:47 PM, Ole Holm Nielsen wrote:
Hi Jean-Michel,
On 8/27/19 11:24 AM, Jean-Michel Beuken wrote:
it seems a problem of dependency...
you need to install ( for CentOS )
libxml2-2.9.1-6.el7_2.3.x86_64
libxml2-devel-2.9.1-6.el7_2.3.x86_64
and add this two environment variables in the config file
configopts += 'CFLAGS_EXTRA="-I/usr/include/libxml2" '
configopts += 'FC_LIBS_EXTRA="-lxml2 -lz -lm -ldl" '
Actually we already have the libxml2 EB module installed, so I changed
ABINIT-8.10.3-intel-2018b.eb to contain an extra line for a libxml2
dependency and added your suggested configopts lines:
...
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'),
('libxml2', '2.9.8'),
]
# ensure mpi and intel toolchain
configopts = '--enable-mpi '
# xml support
configopts += '--enable-xml '
configopts += 'FC_LIBS_EXTRA="-lxml2 -lz -lm -ldl" '
# openmp support
configopts += '--enable-openmp '
...
Now ABINIT builds successfully! Do you think it is a good idea to add
the XML support to the ABINIT .eb file in EasyBuild?
Thanks a lot for your support!
Best regards,
Ole
Re: [easybuild] Autoconf run in ./src rather than .
Hi Åke,
Ah, thanks for the information. The change must have happened
post 3.2.6, as I have a working easyconfig for that version.
I would in fact be happy to install an older version, but an apparently
bumpy transition from Sourceforge to Github seems to have broken all the
archived source packages :-(
Cheers,
Loris
Åke Sandgren writes:
> You're not doing anything wrong, but since MrBayes changed layout
> between some 3.2 version and 3.2.7 the easyblock need to be updated.
>
> (Don't have time to look at this myself)
>
> On 8/27/19 1:23 PM, Loris Bennett wrote:
>> Hi,
>>
>> With EasyBuild 3.9.4 and the following easyconfig:
>>
>> name = 'MrBayes'
>> version = '3.2.7'
>>
>> homepage = 'http://nbisweden.github.io'
>> description = "MrBayes is a program for the Bayesian estimation of
>> phylogeny."
>>
>> toolchain = {'name': 'foss', 'version': '2018b'}
>> toolchainopts = {'usempi': True}
>>
>> source_urls = ['https://github.com/NBISweden/MrBayes/archive']
>> sources = ['v%(version)s.tar.gz']
>>
>> dependencies = [
>> ('beagle-lib', '3.0.2'),
>> ('libreadline', '7.0'),
>> ]
>>
>> builddependencies = [
>> ('Autotools', '20180311'),
>> ]
>>
>> moduleclass = 'bio'
>>
>> I have the following error for a
>>
>> == 2019-08-27 13:12:36,748 run.py:173 DEBUG run_cmd: running cmd autoconf
>> (in
>> /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/src)
>> == 2019-08-27 13:12:36,748 run.py:192 INFO running cmd: autoconf
>> == 2019-08-27 13:12:36,960 build_log.py:163 ERROR EasyBuild crashed with an
>> error (at
>> easybuild/software/EasyBuild/3.9.4/lib/python2.7/site-packages/vsc_base-2.8.4-py2.7.egg/vsc/utils/exceptions.py:124
>> in __init__): cmd "autoconf" exited with exit code 1 and output:
>> autoconf: error: no input file
>>
>> As the unpacked tarball has the structure
>>
>> /trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/
>> ├── aclocal.m4
>> ├── am-aux
>> ├── am-macros
>> ├── configure
>> ├── configure.ac
>> ├── COPYING
>> ├── doc
>> ├── examples
>> ├── INSTALL
>> ├── Makefile.am
>> ├── Makefile.in
>> ├── NEWS
>> ├── README
>> ├── src
>> └── TODO
>>
>> autoconf should be run in .../MrBayes-3.2.7, rather than
>> .../MrBayes-3.2.7/src
>>
>> What am I doing wrong?
>>
>> Cheers,
>>
>> Loris
>>
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
[easybuild] Autoconf run in ./src rather than .
Hi,
With EasyBuild 3.9.4 and the following easyconfig:
name = 'MrBayes'
version = '3.2.7'
homepage = 'http://nbisweden.github.io'
description = "MrBayes is a program for the Bayesian estimation of phylogeny."
toolchain = {'name': 'foss', 'version': '2018b'}
toolchainopts = {'usempi': True}
source_urls = ['https://github.com/NBISweden/MrBayes/archive']
sources = ['v%(version)s.tar.gz']
dependencies = [
('beagle-lib', '3.0.2'),
('libreadline', '7.0'),
]
builddependencies = [
('Autotools', '20180311'),
]
moduleclass = 'bio'
I have the following error for a
== 2019-08-27 13:12:36,748 run.py:173 DEBUG run_cmd: running cmd autoconf (in
/trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/src)
== 2019-08-27 13:12:36,748 run.py:192 INFO running cmd: autoconf
== 2019-08-27 13:12:36,960 build_log.py:163 ERROR EasyBuild crashed with an
error (at
easybuild/software/EasyBuild/3.9.4/lib/python2.7/site-packages/vsc_base-2.8.4-py2.7.egg/vsc/utils/exceptions.py:124
in __init__): cmd "autoconf" exited with exit code 1 and output:
autoconf: error: no input file
As the unpacked tarball has the structure
/trinity/shared/easybuild/build/MrBayes/3.2.7/foss-2018b/MrBayes-3.2.7/
├── aclocal.m4
├── am-aux
├── am-macros
├── configure
├── configure.ac
├── COPYING
├── doc
├── examples
├── INSTALL
├── Makefile.am
├── Makefile.in
├── NEWS
├── README
├── src
└── TODO
autoconf should be run in .../MrBayes-3.2.7, rather than
.../MrBayes-3.2.7/src
What am I doing wrong?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
[easybuild] Re: Missing features in ABINIT/8.10.3-intel-2018b
Hi Jean-Michel,
On 8/27/19 11:24 AM, Jean-Michel Beuken wrote:
it seems a problem of dependency...
you need to install ( for CentOS )
libxml2-2.9.1-6.el7_2.3.x86_64
libxml2-devel-2.9.1-6.el7_2.3.x86_64
and add this two environment variables in the config file
configopts += 'CFLAGS_EXTRA="-I/usr/include/libxml2" '
configopts += 'FC_LIBS_EXTRA="-lxml2 -lz -lm -ldl" '
Actually we already have the libxml2 EB module installed, so I changed
ABINIT-8.10.3-intel-2018b.eb to contain an extra line for a libxml2
dependency and added your suggested configopts lines:
...
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'),
('libxml2', '2.9.8'),
]
# ensure mpi and intel toolchain
configopts = '--enable-mpi '
# xml support
configopts += '--enable-xml '
configopts += 'FC_LIBS_EXTRA="-lxml2 -lz -lm -ldl" '
# openmp support
configopts += '--enable-openmp '
...
Now ABINIT builds successfully! Do you think it is a good idea to add
the XML support to the ABINIT .eb file in EasyBuild?
Thanks a lot for your support!
Best regards,
Ole
--
Ole Holm Nielsen
PhD, Senior HPC Officer
Department of Physics, Technical University of Denmark
[easybuild] Re: Missing features in ABINIT/8.10.3-intel-2018b
Hi Jean-Michel, Thanks very much for your fine analysis of our user's attempts to configure ABINIT (incorrectly, as it turned out)! I have made a copy of the ABINIT-8.10.3-intel-2018b.eb file and added the two configopts which you recommend below. Unfortunately it seems that I miss something because the build fails due to a missing source file "libxml/parser.h". Error messages in the log file are: 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_mathfuncs.o m_mathfuncs.F90 effpot_xml.c(29): catastrophic error: cannot open source file "libxml/parser.h" #include ^ compilation aborted for effpot_xml.c (code 4) Can you help adding the missing file to the build somehow? Thanks a lot, Ole On 8/26/19 6:45 PM, Jean-Michel Beuken wrote: Add blue lines in ABINIT/8.10.3-intel-2018b config - # ensure mpi and intel toolchain configopts = '--enable-mpi ' *# xml support* *configopts += '--enable-xml '* * * *# openmp support* *configopts += '--enable-openmp '* # linalg & fft -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark
