[gpaw-users] Fwd: can't using gpaw-python

[謝其軒]

I've compile gpaw without any reference to mkl library.
I export $PATH and $LD_LIBRARY_PATH myself and I got gpaw well compiled.
Then I gpaw-test it in the node with 8 cores. All tests passed but with
some parallel part acting strange:
===================

[z955018 at node05 test]$ mpiexec -np 4 gpaw-python `which gpaw-test` 2>&1 |
tee testgpaw.log

--------------------------------------------------------------------------
An MPI process has executed an operation involving a call to the
"fork()" system call to create a child process.  Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your MPI job may hang, crash, or produce silent
data corruption.  The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.

The process that invoked fork was:

  Local host:          node05 (PID 7485)
  MPI_COMM_WORLD rank: 3

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
python 2.7.5 GCC 4.1.2 20080704 (Red Hat 4.1.2-52) 64bit ELF on Linux
x86_64 redhat 5.8 Final
Running tests in /tmp/gpaw-test-ujm_vy
Jobs: 1, Cores: 4, debug-mode: False
=============================================================================
gemm_complex.py                         0.014  OK
mpicomm.py                              0.010  OK
ase3k_version.py                        0.007  OK

....................


integral4.py                            0.025  OK
parallel/ut_parallel.py            [node05:07477] 3 more processes have
sent help message help-mpi-runtime.txt / mpi_init:warn-fork
[node05:07477] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
     1.074  OK
transformations.py                      0.017  OK
parallel/parallel_eigh.py               0.010  OK
spectrum.py                             0.037  OK
xc.py                                       0.064  OK
......................

parallel/realspace_blacs.py             0.018  OK
AA_exx_enthalpy.py                    139.244  OK
cmrtest/cmr_test.py                     0.023  SKIPPED
cmrtest/cmr_test3.py                    0.012  SKIPPED
cmrtest/cmr_test4.py                    0.018  SKIPPED
cmrtest/cmr_append.py                   0.015  SKIPPED
cmrtest/Li2_atomize.py                  0.015  SKIPPED
=============================================================================
Ran 223 tests out of 230 in 2511.9 seconds
Tests skipped: 7
All tests passed!
=============================================================================
The ground state calculation of parallel version is fine.

But when I run the DF calculations, it seems that something familiar
emerges up:

python2.7: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
(this is run with serial version.....and it pissed me off)

===============================================================================
--------------------------------------------------------------------------
An MPI process has executed an operation involving a call to the
"fork()" system call to create a child process.  Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your MPI job may hang, crash, or produce silent
data corruption.  The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.

The process that invoked fork was:

  Local host:          node03 (PID 24987)
  MPI_COMM_WORLD rank: 3

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
[node03:24983] 7 more processes have sent help message help-mpi-runtime.txt
/ mpi_init:warn-fork
[node03:24983] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
--------------------------------------------------------------------------
mpirun has exited due to process rank 6 with PID 24990 on
node node03 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------

=============================================================================

And this is the parallel version.

I think right now I might try to build with mkl library or I'd like to kill
myself....

BR,

chi-hsuan
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