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

Marcin Dulak Marcin.Dulak at fysik.dtu.dk
Sat Oct 19 10:32:39 CEST 2013


Hi,

On 10/18/2013 11:28 AM, 謝其軒 wrote:
> Dear everyone,
> I am one step close to compile the parallel version!
> here's my question.
> when I start the test :
> ----
> mpiexec -np 4 gpaw-python `which gpaw-test` 2>&1 | tee testgpaw.log
> ----
> and here's the file : testgpaw.log
you can find my suggestion here: 
http://listserv.fysik.dtu.dk/pipermail/gpaw-users/2013-October/002408.html

Best regards,

Marcin
> ----
> --------------------------------------------------------------------------
> 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:          node04 (PID 26324)
>   MPI_COMM_WORLD rank: 0
>
> 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 5.7 Final
> Running tests in /tmp/gpaw-test-4xzJUA
> Jobs: 1, Cores: 4, debug-mode: False
> =============================================================================
> gemm_complex.py                         0.011  OK
> mpicomm.py                              0.011  OK
> ase3k_version.py                        0.009  OK
> numpy_core_multiarray_dot.py            0.008  OK
> eigh.py                                 0.011  OK
> lapack.py                               0.012  OK
> dot.py                                  0.012  OK
> lxc_fxc.py                              0.011  OK
> blas.py                                 0.013  OK
> erf.py                                  0.011  OK
> gp2.py                                  0.014  OK
> kptpar.py                               4.205  OK
> non_periodic.py                         0.040  OK
> parallel/blacsdist.py                   0.014  OK
> gradient.py                             0.017  OK
> cg2.py                                  0.022  OK
> kpt.py                                  0.028  OK
> lf.py                                   0.032  OK
> gd.py                                   0.013  OK
> parallel/compare.py                     0.046  OK
> pbe_pw91.py                             0.012  OK
> fsbt.py                                 0.014  OK
> derivatives.py                          0.018  OK
> Gauss.py                                0.024  OK
> second_derivative.py                    0.022  OK
> integral4.py                            0.038  OK
> parallel/ut_parallel.py            [node04:26319] 3 more processes 
> have sent help message help-mpi-runtime.txt / mpi_init:warn-fork
> [node04:26319] Set MCA parameter "orte_base_help_aggregate" to 0 to 
> see all help / error messages
>      1.080  OK
> transformations.py                      0.023  OK
> parallel/parallel_eigh.py               0.010  OK
> spectrum.py                             0.080  OK
> xc.py                                   0.047  OK
> zher.py                                 0.046  OK
> pbc.py                                  0.041  OK
> lebedev.py                              0.030  OK
> parallel/ut_hsblacs.py                  0.065  OK
> occupations.py                          0.070  OK
> dump_chi0.py                            0.046  OK
> cluster.py                              0.128  OK
> pw/interpol.py                          0.013  OK
> poisson.py                              0.054  OK
> pw/lfc.py                          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
> --------------------------------------------------------------------------
> mpiexec has exited due to process rank 0 with PID 26324 on
> node node04 exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpiexec (as reported here).
> --------------------------------------------------------------------------
>
> what happened?
>
>
>
>
> 2013/10/11 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk 
> <mailto:Marcin.Dulak at fysik.dtu.dk>>
>
>     On 10/11/2013 12:13 PM, 謝其軒 wrote:
>>
>>
>>     ---------- Forwarded message ----------
>>     From: *謝其軒* <z955018 at gmail.com <mailto:z955018 at gmail.com>>
>>     Date: 2013/10/11
>>     Subject: Re: [gpaw-users] can't using gpaw-python
>>     To: Marcin Dulak <Marcin.Dulak at fysik.dtu.dk
>>     <mailto:Marcin.Dulak at fysik.dtu.dk>>
>>
>>
>>     Hi again,
>>     Is Mr. Marcin there?
>>     I've tried to compile all the package myself and failed.
>>     I recover the system to the original one that numpy and scipy and
>>     others belongs to Canopy.
>>     And of course, the error remain. I doubt that the numpy
>>     gpaw-python uses is not the one in Canopy but in the root's
>>     directory.
>>     But how can I change that for serial version works fine?
>     please attach the customize.py and all the steps you perform.
>     After your last email it looked like we were close to get the
>     working a gpaw-python,
>     you just need to replace the intel threading libraries as
>     described in the link i sent.
>
>     Best regards,
>
>     Marcin
>
>


-- 
***********************************
  
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk

***********************************

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