[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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