Configure abinit-8.10.1 in order to read psml files  [SOLVED]

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Alex
Posts: 2
Joined: Tue Jan 01, 2019 11:58 pm

Configure abinit-8.10.1 in order to read psml files

Post by Alex » Wed Jan 02, 2019 12:24 am

Dear abinit community,

I am trying to compile abinit-8.10.1 in order to read psml files but failed. I got the following command's output text:

root@Ragnar:~/lib/abinit-8.10.1/Gfortran/tests# ../../tests/runtests.py -j4 psml
Running on Ragnar -- system Linux -- ncpus 4 -- Python 2.7.12 -- runtests.py-0.6.0
Regenerating database...
Saving database to /root/lib/abinit-8.10.1/tests/test_suite.cpkl
Test_suite directory already exists. Files will be removed
Running 14 test(s) with MPI_procs=1, py_threads=4...
Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t02/t02.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t02/t02.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t02/t02.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t04/t04.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t04/t04.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t04/t04.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t01/t01.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t01/t01.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t01/t01.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t03/t03.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t03/t03.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t03/t03.stderr
returned exit_code: 127

[psml][t02][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t02/t02.out [file=t02.out]
[psml][t02][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t02][np=1]
[psml][t04][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t04/t04.out [file=t04.out]
[psml][t04][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t04][np=1]
[psml][t03][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t03/t03.out [file=t03.out]
[psml][t03][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

[psml][t01][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t01/t01.out [file=t01.out]
[psml][t01][np=1]Test was not expected to fail but subprocesses returned 127
No YAML Error found in [psml][t03][np=1]
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t01][np=1]
Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t05/t05.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t05/t05.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t05/t05.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t08/t08.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t08/t08.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t08/t08.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t06/t06.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t06/t06.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t06/t06.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t07/t07.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t07/t07.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t07/t07.stderr
returned exit_code: 127
[psml][t05][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t05/t05.out [file=t05.out]
[psml][t05][np=1]Test was not expected to fail but subprocesses returned 127

/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t05][np=1]
[psml][t08][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t08/t08.out [file=t08.out]
[psml][t08][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

[psml][t06][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t06/t06.out [file=t06.out]
[psml][t06][np=1]Test was not expected to fail but subprocesses returned 127
No YAML Error found in [psml][t08][np=1]
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t06][np=1]
[psml][t07][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t07/t07.out [file=t07.out]
[psml][t07][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t07][np=1]
Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t09/t09.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t09/t09.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t09/t09.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t10/t10.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t10/t10.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t10/t10.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t11/t11.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t11/t11.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t11/t11.stderr
returned exit_code: 127
Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t12/t12.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t12/t12.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t12/t12.stderr
returned exit_code: 127


[psml][t09][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t09/t09.out [file=t09.out]
[psml][t09][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t09][np=1]
[psml][t10][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t10/t10.out [file=t10.out]
[psml][t10][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t10][np=1]
[psml][t12][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t12/t12.out [file=t12.out]
[psml][t12][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t12][np=1]
[psml][t11][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t11/t11.out [file=t11.out]
[psml][t11][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t11][np=1]
Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t13/t13.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t13/t13.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t13/t13.stderr
returned exit_code: 127

Command /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit < /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t14/t14.stdin > /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t14/t14.stdout 2> /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t14/t14.stderr
returned exit_code: 127

[psml][t13][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t13/t13.out [file=t13.out]
[psml][t13][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t13][np=1]
[psml][t14][np=1]: fldiff.pl fatal error:
Unable to open input file /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t14/t14.out [file=t14.out]
[psml][t14][np=1]Test was not expected to fail but subprocesses returned 127
/root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit: error while loading shared libraries: libpsml.so.0: cannot open shared object file: No such file or directory

No YAML Error found in [psml][t14][np=1]
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t01/t01.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t01/t01.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t02/t02.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t02/t02.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t03/t03.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t03/t03.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t04/t04.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t04/t04.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t05/t05.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t05/t05.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t06/t06.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t06/t06.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t07/t07.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t07/t07.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t08/t08.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t08/t08.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t09/t09.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t09/t09.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t10/t10.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t10/t10.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t11/t11.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t11/t11.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t12/t12.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t12/t12.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t13/t13.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t13/t13.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))
/root/lib/abinit-8.10.1/tests/pymods/testsuite.py:3339: UserWarning: exception while adding /root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t14/t14.out to tarball:
[Errno 2] No such file or directory: '/root/lib/abinit-8.10.1/Gfortran/tests/Test_suite/psml_t14/t14.out'
warnings.warn("exception while adding %s to tarball:\n%s" % (p, exc))

Suite failed passed succeeded skipped disabled run_etime tot_etime
psml 14 0 0 0 0 0.09 0.26

Any suggestion will be appreciated.

Regards,

Alex
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jbeuken
Posts: 365
Joined: Tue Aug 18, 2009 9:24 pm
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Re: Configure abinit-8.10.1 in order to read psml files  [SOLVED]

Post by jbeuken » Thu Jan 03, 2019 10:58 pm

Hi,

LD_LIBRARY_PATH is the key !

export LD_LIBRARY_PATH=/path/where/libpsml/is/installed/lib:$LD_LIBRARY_PATH

what is the result of this cmd :

Code: Select all

ldd /root/lib/abinit-8.10.1/Gfortran/src/98_main/abinit
------
Jean-Michel Beuken
Computer Scientist
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Alex
Posts: 2
Joined: Tue Jan 01, 2019 11:58 pm

Re: Configure abinit-8.10.1 in order to read psml files

Post by Alex » Fri Jan 04, 2019 6:48 am

Dear Jean-Michel,

Problem solved! Thank you very much! :)

Alex
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