[Pw_forum] error in running pw.x command

Mon Jul 20 19:22:44 CEST 2015

Dear all,

Thanks for your comments.
I will check them up.

Regards,
Mohaddeseh

On Mon, Jul 20, 2015 at 12:57 PM, nicola varini <nicola.varini at gmail.com>
wrote:

> Dear all, if you use mkl you can rely on the intel linking advisor for
> proper linking
> https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
> If you open the file $MKL_ROOT/include/mkl.h you see the version number.
> It should be something like
>
> #define __INTEL_MKL__ 11
>
> #define __INTEL_MKL_MINOR__ 2
>
> #define __INTEL_MKL_UPDATE__ 2
>
> In the link above put your version number, OS, and other options.
>
> You should get some options in output which you should use for linking.
>
> HTH
>
>
> Nicola
>
>
>
>
> 2015-07-20 9:57 GMT+02:00 Bahadır salmankurt <bsalmankurt at gmail.com>:
>
>> Dear Mohaddeseh et co,
>>
>> installing one of the old version of mpi could solve the problem.
>>
>> 2015-07-20 10:06 GMT+03:00 Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>:
>>
>>>
>>> Dear Mohaddeseh et co,
>>>
>>>   Just a note: I used to have such problems when I had compiled with
>>> MKL-ScaLAPACK of old version, indeed around 11.1, when I ran with more than
>>> four cores. I think I managed to run when I disabled ScaLAPACK. Of course
>>> this might be fully unrelated to your problem.
>>>
>>>     Greetings from Lappeenranta,
>>>
>>>        apsi
>>>
>>>
>>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>>>   Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi /
>>> http://www.iki.fi/~apsi/
>>>   Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>>>   Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935
>>>
>>>
>>>
>>> On Mon, 20 Jul 2015, Paolo Giannozzi wrote:
>>>
>>>  This is not a QE problem: the fortran code knows nothing about nodes
>>>> and cores. It's the software setup for parallel execution on your machine
>>>> that has a problem.
>>>>
>>>> Paolo
>>>>
>>>> On Thu, Jul 16, 2015 at 2:25 PM, mohaddeseh abbasnejad <
>>>> m.abbasnejad at gmail.com> wrote:
>>>>
>>>>       Dear all,
>>>>
>>>> I have recently installed PWscf (version 5.1) on our cluster (4 nodes,
>>>> 32 cores).
>>>> Ifort & mkl version 11.1 has been installed.
>>>> When I run pw.x command on every node individually, for both the
>>>> following command, it will work properly.
>>>> 1- /opt/exp_soft/espresso-5.1/bin/pw.x -in scf.in
>>>> 2- mpirun -n 4 /opt/exp_soft/espresso-5.1/bin/pw.x -in scf.in
>>>> However, when I use the following command (again for each of them,
>>>> separately),
>>>> 3- mpirun -n 8 /opt/exp_soft/espresso-5.1/bin/pw.x -in scf.in
>>>> it gives me such an error:
>>>>
>>>> [cluster:14752] *** Process received signal ***
>>>> [cluster:14752] Signal: Segmentation fault (11)
>>>> [cluster:14752] Signal code:  (128)
>>>> [cluster:14752] Failing at address: (nil)
>>>> [cluster:14752] [ 0] /lib64/libpthread.so.0() [0x3a78c0f710]
>>>> [cluster:14752] [ 1]
>>>> /opt/intel/Compiler/11.1/064/mkl/lib/em64t/libmkl_mc3.so(mkl_blas_zdotc+0x79)
>>>> [0x2b5e8e37d4f9]
>>>> [cluster:14752] *** End of error message ***
>>>>
>>>> --------------------------------------------------------------------------
>>>> mpirun noticed that process rank 4 with PID 14752 on node
>>>> cluster.khayam.local exited on signal 11 (Segmentation fault).
>>>>
>>>> --------------------------------------------------------------------------
>>>>
>>>> This error also exists when I use all the node with each other in
>>>> parallel mode (using the following command):
>>>> 4- mpirun -n 32 -hostfile testhost /opt/exp_soft/espresso-5.1/bin/pw.x
>>>> -in scf.in
>>>> The error:
>>>>
>>>> [cluster:14838] *** Process received signal ***
>>>> [cluster:14838] Signal: Segmentation fault (11)
>>>> [cluster:14838] Signal code:  (128)
>>>> [cluster:14838] Failing at address: (nil)
>>>> [cluster:14838] [ 0] /lib64/libpthread.so.0() [0x3a78c0f710]
>>>> [cluster:14838] [ 1]
>>>> /opt/intel/Compiler/11.1/064/mkl/lib/em64t/libmkl_mc3.so(mkl_blas_zdotc+0x79)
>>>> [0x2b04082cf4f9]
>>>> [cluster:14838] *** End of error message ***
>>>>
>>>> --------------------------------------------------------------------------
>>>> mpirun noticed that process rank 24 with PID 14838 on node
>>>> cluster.khayam.local exited on signal 11 (Segmentation fault).
>>>>
>>>> --------------------------------------------------------------------------
>>>>
>>>> Any help will be appreciated.
>>>>
>>>> Regards,
>>>> Mohaddeseh
>>>>
>>>> ---------------------------------------------------------
>>>>
>>>> Mohaddeseh Abbasnejad,
>>>> Room No. 323, Department of Physics,
>>>> University of Tehran, North Karegar Ave.,
>>>> Tehran, P.O. Box: 14395-547- IRAN
>>>> Tel. No.: +98 21 6111 8634  & Fax No.: +98 21 8800 4781
>>>> Cellphone: +98 917 731 7514
>>>> E-Mail:     m.abbasnejad at gmail.com
>>>> Website:  http://physics.ut.ac.ir
>>>>
>>>> ---------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
>>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>>> Phone +39-0432-558216, fax +39-0432-558222
>>>>
>>>>
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>>>
>>
>>
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>
>
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-- 
---------------------------------------------------------

Mohaddeseh Abbasnejad,
Room No. 323, Department of Physics,
University of Tehran, North Karegar Ave.,
Tehran, P.O. Box: 14395-547- IRAN
Tel. No.: +98 21 6111 8634  & Fax No.: +98 21 8800 4781
Cellphone: +98 917 731 7514
E-Mail:     m.abbasnejad at gmail.com
Website:  http://physics.ut.ac.ir

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