[gpaw-users] Fwd: can't using gpaw-python
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Tue Oct 22 14:46:36 CEST 2013
On 10/22/2013 01:35 PM, 謝其軒 wrote:
> Dear Marcin,
> Although I may realize what the problem is, I still don't know how to
> solve it.
> Could you demonstrate step by step?
make sure it's the gpaw-python which is linked to libmkl_intel_thread.so:
ldd `which gpaw-python`
and in order to get rid of that library please try to build new
gpaw-python using the customize.py
https://wiki.fysik.dtu.dk/gpaw/install/Linux/SUNCAT/SUNCAT.html#mkl-10-2-notes
(or something very similar to)
without reference to threading libraries, as described at
https://wiki.fysik.dtu.dk/gpaw/devel/developer_installation.html#developer-installation
cd gpaw
rm -rf build
....
Best regards,
Marcin
>
> BR,
>
> chi-hsuan
>
>
> 2013/10/19 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk
> <mailto:Marcin.Dulak at fysik.dtu.dk>>
>
> 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 <tel:%28%2B45%29%204525%203157>
> Fax.:(+45) 4593 2399 <tel:%28%2B45%29%204593%202399>
> email:Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>
>
> ***********************************
>
>
--
***********************************
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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