[gpaw-users] GPAW installation issue

Krishnakanta Mondal krishnakanta1987 at gmail.com
Wed Jun 10 22:04:56 CEST 2020 

Dear Michael,
Thanks a lot for the suggestion.
I could overcome the mpi related issue. However, now I have libxc related
issues, (i guess). see the following error messages:
I have linked the libxc- lib and include directories in the siteconfig.py
file
siteconfig.py:
LIBXCDIR='/cineca/prod/opt/libraries/libxc/4.3.2/intel--pe-xe-2018--binary/'
library_dirs += [LIBXCDIR + 'lib']
include_dirs += [LIBXCDIR + 'include']
include_dirs +=
['/cineca/prod/opt/libraries/numpy/1.15.2/python--3.6.4/lib/python3.6/site-packages/numpy-1.15.2-py3.6-linux-x86_64.egg/numpy/core/include']

Is there any other reason apart from the linking issue?

/galileo/home/userexternal/kmondal0/source/gpaw-develop/gpaw/c/xc/tpss.c:547:
undefined reference to `xc_func_end'
/galileo/home/userexternal/kmondal0/source/gpaw-develop/gpaw/c/xc/tpss.c:548:
undefined reference to `xc_func_end'
build/temp.linux-x86_64-3.6/c/xc/tpss.o: In function `tpss_init':
/galileo/home/userexternal/kmondal0/source/gpaw-develop/gpaw/c/xc/tpss.c:534:
undefined reference to `xc_func_init'
/galileo/home/userexternal/kmondal0/source/gpaw-develop/gpaw/c/xc/tpss.c:538:
undefined reference to `xc_func_init'
/galileo/home/userexternal/kmondal0/source/gpaw-develop/gpaw/c/xc/tpss.c:539:
undefined reference to `xc_func_init'
build/temp.linux-x86_64-3.6/c/xc/xc.o: In function `NewXCFunctionalObject':
/galileo/home/userexternal/kmondal0/source/gpaw-develop/gpaw/c/xc/xc.c:297:
undefined reference to `_intel_fast_memcpy'
collect2: error: ld returned 1 exit status
Traceback (most recent call last):
  File "setup.py", line 246, in <module>
    'Topic :: Scientific/Engineering :: Physics'])
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/core.py",
line 148, in setup
    dist.run_commands()
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/dist.py",
line 955, in run_commands
    self.run_command(cmd)
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/dist.py",
line 974, in run_command
    cmd_obj.run()
  File "setup.py", line 193, in run
    _install.run(self)
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/site-packages/setuptools/command/install.py",
line 65, in run
    orig.install.run(self)
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/command/install.py",
line 545, in run
    self.run_command('build')
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/cmd.py",
line 313, in run_command
    self.distribution.run_command(command)
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/dist.py",
line 974, in run_command
    cmd_obj.run()
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/command/build.py",
line 135, in run
    self.run_command(cmd_name)
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/cmd.py",
line 313, in run_command
    self.distribution.run_command(command)
  File
"/cineca/prod/opt/compilers/python/3.6.4/none/lib/python3.6/distutils/dist.py",
line 974, in run_command
    cmd_obj.run()
  File "setup.py", line 188, in run
    assert error == 0
AssertionError


Regards,
Krishna


On Tue, Jun 9, 2020 at 7:31 PM Michael Walter <
Michael.Walter at fmf.uni-freiburg.de> wrote:

> Dear Krishna,
>
> it seems your compiler does not find mpi libraries. Load the module or set
> INCLUDEPATH accordingly.
>
> Best regards,
> Michael
>
> Am Mo., 8. Juni 2020 um 12:10 Uhr schrieb Krishnakanta Mondal via
> gpaw-users <gpaw-users at listserv.fysik.dtu.dk>:
>
>> Dear all,
>> I have some issues with installing GPAW (latest version)
>> The error message is:
>>
>> [kmondal0 at r033c01s04 gpaw]$ python setup.py install --prefix=$PWD/install
>> Reading configuration from siteconfig.py
>> running install
>> running build
>> running build_py
>> running build_ext
>> building '_gpaw' extension
>> icc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
>> -Wstrict-prototypes -fPIC -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_C
>> BLACS=1 -DGPAW_NO_UNDERSCORE_CSCALAPACK=1
>> -DGPAW_GITHASH=3b0afef7805b8f6540dea15dad6c0142f1213afd
>> -DGPAW_NO_UNDERSCORE_CBLACS=1 -DGPAW_NO_UNDE
>> RSCORE_CSCALAPACK=1 -DGPAW_ASYNC=1 -DGPAW_MPI2=1 -DPARALLEL=1
>> -DGPAW_WITH_SL=1 -UNDEBUG
>> -I/galileo/home/userexternal/kmondal0/source/libxc/ins
>> tall/include
>> -I/cineca/prod/opt/compilers/python/3.6.4/none/include/python3.6m
>> -I/cineca/prod/opt/libraries/numpy/1.15.2/python--3.6.4/lib/pyt
>> hon3.6/site-packages/numpy-1.15.2-py3.6-linux-x86_64.egg/numpy/core/include
>> -c c/_gpaw.c -o build/temp.linux-x86_64-3.6/c/_gpaw.o -Wall -Wno-u
>> nknown-pragmas -std=c99
>> icc: command line warning #10006: ignoring unknown option
>> '-Wno-unused-result'
>> c/_gpaw.c(10): catastrophic error: cannot open source file "mpi.h"
>>   #include <mpi.h>
>>                   ^
>>
>> compilation aborted for c/_gpaw.c (code 4)
>> error: command 'icc' failed with exit status 4
>>
>> It will be highly appreciated if someone can help me to solve this.
>>
>> Regards,
>> Krishnakanta
>>
>> --
>> Dr. Krishnakanta Mondal
>> DST-INSPIRE Faculty (Asst. Prof.)
>> Department of Physical Sciences,
>> Central University of Punjab
>> Bathinda, Punjab-151001
>> Phone: +91 9424540649
>> email: krishnakanta1987 at gmail.com <krishnakanta at iiserpune.ac.in>
>> Google Scholar ID:
>> http://scholar.google.co.in/citations?hl=en&user=iptbu_0AAAAJ
>> _______________________________________________
>> gpaw-users mailing list
>> gpaw-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
>
>
> --
> ------------------------------------------
> PD Dr Michael Walter
> Addresses:
> - Fraunhofer IWM, Wöhlerstrasse 11, D-79108 Freiburg i. Br., Germany
>   Tel.: +49 761 5142 296
> - FIT Freiburg Centre for Interactive Materials and Bioinspired
> Technologies, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
>   Tel: +49 761 203 95072
> email: Michael.Walter at fmf.uni-freiburg.de
> www:
> http://www.functional-nanosystems.uni-freiburg.de/People/PDWalter/group
> publications: http://scholar.google.com/citations?user=vlmryKEAAAAJ&hl=en
>


-- 
Dr. Krishnakanta Mondal
DST-INSPIRE Faculty (Asst. Prof.)
Department of Physical Sciences,
Central University of Punjab
Bathinda, Punjab-151001
Phone: +91 9424540649
email: krishnakanta1987 at gmail.com <krishnakanta at iiserpune.ac.in>
Google Scholar ID:
http://scholar.google.co.in/citations?hl=en&user=iptbu_0AAAAJ
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