[gmx-users] Parallel run error

[M.Naser]

Hi Itamar !

Thanks for your response. It is still crashing.

Please give me some hint about likley problems.

With regards,

Abu

> try mpirun -np 2 mdrun ... -np2
>
>
> On Nov 25, 2004, at 1:27 AM, David wrote:
>
>> On Wed, 2004-11-24 at 20:07 +0000, M.Naser wrote:
>>> Hi Itamar,
>>>
>>> Thanks for your response. The followings are the commands I have been
>>> using:
>>> grompp -f md.mdp -c confout.gro -o pro.tpr -p pro.top -np 2
>>> mpirun -c 2  mdrun -s pro.tpr -o pro.trr -v
>>>
>> does it run fine on one processor?
>>> Thanking you again,
>>>
>>> Abu
>>>
>>>
>>>> can you send the complete commands you used, how you run grompp and
>>>> mdrun?  It will help.
>>>>
>>>> M.Naser wrote:
>>>>
>>>>> Hi All Users,
>>>>>
>>>>> I have been trying to run a molecular simulation on 2 nodes. I have
>>>>> been
>>>>> getting the following error message:
>>>>>
>>>>> One of the processes started by mpirun has exited with a nonzero
>>>>> exit
>>>>> code.  This typically indicates that the process finished in error.
>>>>> If your process did not finish in error, be sure to include a
>>>>> "return
>>>>> 0" or "exit(0)" in your C code before exiting the application.
>>>>>
>>>>> PID 30006 failed on node n1 (10.10.10.2) due to signal 11.
>>>>>
>>>>> Cloud anyone  give me a clue what went wrong?
>>>>>
>>>>>
>>>>>
>>>>> ________________________________________________________________
>>>>>
>>>>> DISCLAIMER:
>>>>>
>>>>> This e-mail and any files transmitted with it are confidential
>>>>> and intended solely for the use of the individual or entity to
>>>>> whom it is addressed.  If you are not the intended recipient
>>>>> you are prohibited from using any of the information contained
>>>>> in this e-mail.  In such a case, please destroy all copies in
>>>>> your possession and notify the sender by reply e-mail.  Heriot
>>>>> Watt University does not accept liability or responsibility
>>>>> for changes made to this e-mail after it was sent, or for
>>>>> viruses transmitted through this e-mail.  Opinions, comments,
>>>>> conclusions and other information in this e-mail that do not
>>>>> relate to the official business of Heriot Watt University are
>>>>> not endorsed by it.
>>>>> ________________________________________________________________
>>>>> _______________________________________________
>>>>> gmx-users mailing list
>>>>> gmx-users at gromacs.org
>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>> _______________________________________________
>>>> gmx-users mailing list
>>>> gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>
>>>
>>>
>>>
>>> ________________________________________________________________
>>>
>>> DISCLAIMER:
>>>
>>> This e-mail and any files transmitted with it are confidential
>>> and intended solely for the use of the individual or entity to
>>> whom it is addressed.  If you are not the intended recipient
>>> you are prohibited from using any of the information contained
>>> in this e-mail.  In such a case, please destroy all copies in
>>> your possession and notify the sender by reply e-mail.  Heriot
>>> Watt University does not accept liability or responsibility
>>> for changes made to this e-mail after it was sent, or for
>>> viruses transmitted through this e-mail.  Opinions, comments,
>>> conclusions and other information in this e-mail that do not
>>> relate to the official business of Heriot Watt University are
>>> not endorsed by it.
>>> ________________________________________________________________
>>> _______________________________________________
>>> gmx-users mailing list
>>> gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>> --
>> David.
>> _______________________________________________________________________
>> _
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> phone:  46 18 471 4205          fax: 46 18 511 755
>> spoel at xray.bmc.uu.se    spoel at gromacs.org
>> http://xray.bmc.uu.se/~spoel
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> +
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>>
>
>
>
> ********************************************
> Computers are like airconditioners... They don't work well with Windows
> open.
> ********************************************
>
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585146
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
> | Homepage:
> http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> ============================================
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



________________________________________________________________

DISCLAIMER:

This e-mail and any files transmitted with it are confidential
and intended solely for the use of the individual or entity to
whom it is addressed.  If you are not the intended recipient
you are prohibited from using any of the information contained
in this e-mail.  In such a case, please destroy all copies in
your possession and notify the sender by reply e-mail.  Heriot
Watt University does not accept liability or responsibility
for changes made to this e-mail after it was sent, or for
viruses transmitted through this e-mail.  Opinions, comments,
conclusions and other information in this e-mail that do not
relate to the official business of Heriot Watt University are
not endorsed by it.
________________________________________________________________