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

[Marcin Dulak]

Hi,

On 10/10/2013 03:09 PM, 謝其軒 wrote:
> Hi,
> Marcin
> I'm afraid that I'd confuse you.
> I compiled numpy1.7.0 myself with the recipe in 
>  install_sun_chpc_SUSE10.sh 
> <https://wiki.fysik.dtu.dk/gpaw/install/Linux/sun_chpc.html> and with 
> python2.7 only.
> Then I compiled gpaw with python2.7, too.
> and do the gpaw-python test
>
> ------------
> 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-Htm4W4
> Jobs: 1, Cores: 4, debug-mode: False
> =============================================================================
> gemm_complex.py                         0.049  OK
> mpicomm.py                              0.009  OK
> ase3k_version.py                        0.007  OK
> numpy_core_multiarray_dot.py            0.007  OK
> eigh.py                                 0.075  OK
> lapack.py                               0.014  OK
> ......................
> occupations.py                          0.057  OK
> dump_chi0.py                            0.040  OK
> cluster.py                              0.144  OK
> pw/interpol.py                          0.011  OK
> poisson.py                              0.051  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
please do not link threading libraries, see 
http://listserv.fysik.dtu.dk/pipermail/gpaw-users/2013-October/002398.html
Use example customize.py mentioned there.

Best regards,

Marcin
> --------------------------------------------------------------------------
> mpiexec has exited due to process rank 2 with PID 26226 on
> node breadserver.physics.ntu exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpiexec (as reported here).
> --------------------------------------------------------------------------
>
>
>
> ---------------------------------------------------------------------------------------------------
>
> All sound fine.
> ----------------
> [z955018 at breadserver gpaw-0.9.1.10596]$ gpaw-python
> Python 2.7.5 (default, Aug 13 2013, 16:24:20)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
> --------------
>
> When I start to calculate the ground state, the result works fine.
> However, there's a MPI warning :
>
>
> --------------------------------------------------------------------------
> 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:          node01 (PID 4577)
>   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.
> --------------------------------------------------------------------------
> [node01:04576] 7 more processes have sent help message 
> help-mpi-runtime.txt / mpi_init:warn-fork
> [node01:04576] Set MCA parameter "orte_base_help_aggregate" to 0 to 
> see all help / error messages
> ~
>
> I can't figure out what it is.
>
> ---------------------------------------------------------
>
> By the way, how can I find a BLAS/LAPACK library when compiling Scipy?
>
>
>
>
> chi-hsuan


-- 
***********************************
  
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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