[mpich-discuss] Running mpi from bash script

Reuti reuti at staff.uni-marburg.de
Tue Apr 22 09:41:26 CDT 2014 

Am 22.04.2014 um 09:18 schrieb Francisco Pastor:

> Hi and sorry for the delay in answering. I was out on holidays since Friday.
> 
> I recompiled the appication, just changing mpich2 path.

Fine.


> MPI_PATH=/usr/bin
> PAR_INCS=-I/usr/local/include
> PAR_LIBS=-L/usr/local/lib/ -lmpich

Is it a C application, or are you using the wrapper during compliation to add also the Fortran interface?


> PAR_DEFS=-DRAMS_MPI

Do you have more than one MPI library at this location? Often it's better to have a dedicated directory where you can check the used path to it instantly.

Is there any output whether the application is now running in parallel, or executing a serial run N times only?

-- Reuti


> Thanks
> 
> El 17/04/2014 17:58, Reuti escribió:
>> Hi,
>> 
>> Am 17.04.2014 um 11:35 schrieb Francisco Pastor:
>> 
>>> The point is that I am using a program, meteorological model RAMS, that was running fine with this mpich2 version. And it runs fine from the command line.
>>> 
>>> If the system works, should I upgrade? Will it work with my program? Can I install two different versions at the same time or should I delete the older one? Is there any chance to run
>> Well, using a new version usually means to recompile the application to gain advantage of it. Did you compile it on your own, or is this a binary you downloaded somewhere?
>> 
>> -- Reuti
>> 
>> 
>>> Thanks
>>> 
>>> El 17/04/2014 11:06, Reuti escribió:
>>>> Hi,
>>>> 
>>>> Am 17.04.2014 um 10:04 schrieb Francisco Pastor:
>>>> 
>>>>> I need to daily run an mpi job from a bash script. I have prepared the script and run from the command line, this works fine. But when I try to execute at a later time with at (at -f my_script now +1 minute) the parallel processes do not start.
>>>>> 
>>>>> These are the significant parts of my script:
>>>>> 
>>>>> # path to mpi executables
>>>>> ruta_mpi=/usr/local/mpich2-1.0.5p4/bin
>>>> This version of MPICH is quite old. Please use a more recent one, where the necessity for starting an MPD beforehand does no longer exist.
>>>> 
>>>> -- Reuti
>>>> 
>>>> 
>>>>> # Function that checks if mpd processes are ok (checks mpdtrace output, five nodes should be up)
>>>>> Comprueba_MPD()
>>>>> {
>>>>>  mpdtrace > log.mpd
>>>>>  wc -l log.mpd > check.mpd
>>>>>  check1=`awk '{ print $1 }' check.mpd`
>>>>>  if [ $check1 -eq 5 ];
>>>>>    then
>>>>>       echo "Salida de mpdtrace correcta, hosts=$check1"
>>>>>    else
>>>>>       echo "Salida de mpdtrace incorrecta, hosts=$check1"
>>>>>       $ruta_mpi/mpdboot -n 5 &
>>>>>       sleep 10
>>>>>       mpdtrace
>>>>>  fi
>>>>> }
>>>>> 
>>>>> 
>>>>> # Run rams60 program with mpirun
>>>>> time $ruta_mpi/mpirun -n 21 ./rams60 -f RAMSIN.operatiu
>>>>> 
>>>>> I am sure missing something but I can't find out what's going on.
>>>>> 
>>>>> Thanks in advance
>>>>> 
>>>>> -- 
>>>>> -----------
>>>>> Dr. Francisco Pastor
>>>>> Meteorology department, Instituto Universitario CEAM-UMH
>>>>> http://www.ceam.es
>>>>> -----------
>>>>> Mendeley profile: http://www.mendeley.com/profiles/francisco-pastor1/
>>>>> Google Scholar: http://scholar.google.com/citations?user=V3mmCdkAAAAJ&hl=es
>>>>> Researcher ID: http://www.researcherid.com/rid/B-8331-2008
>>>>> Cosis profile: http://www.cosis.net/profile/francisco.pastor
>>>>> -----------
>>>>> mail: paco at ceam.es
>>>>> skype: paco.pastor.guzman
>>>>> -----------
>>>>> Parque Tecnologico, C/ Charles R. Darwin, 14
>>>>> 46980 PATERNA (Valencia), Spain
>>>>> Tlf. 96 131 82 27 - Fax. 96 131 81 90
>>>>> 
>>>>> 
>>>>> ---------------------------------------------------------------------
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>>>>> 
>>>>> Su dirección de correo electrónico junto a sus datos personales forman parte de un fichero titularidad de la Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgánica 15/1999, usted puede ejercitar sus derechos de acceso, rectificación, cancelación y, en su caso, oposición enviando una solicitud por escrito, acompañada de una fotocopia de su DNI dirigida a: Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnológico.46980 PATERNA (Valencia).
>>>>> 
>>>>> This message and the attached files are confidential. They contain reserved information belonging to our centre and are not to be broadcast. If you have received this email by mistake, please delete it from your system and alert the sender by returning it to his/her email address. You must not copy or divulge the contents of the message to anyone.
>>>>> 
>>>>> Your email address and personal data are included in a file belonging to the Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM, con CIF: G-46957213. The purpose of this file is to allow us to keep in contact with you. In accordance with Organic Law 15/1999, you are permitted to access, rectify, cancel or oppose the contents of this file by submitting a written request, accompanied by a photocopy of your DNI, to: Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnológico.46980 PATERNA (Valencia).
>>>>> 
>>>>> 
>>>>> 
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>>>>> 
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>>>> 
>>> -- 
>>> -----------
>>> Dr. Francisco Pastor
>>> Meteorology department, Instituto Universitario CEAM-UMH
>>> http://www.ceam.es
>>> -----------
>>> Mendeley profile: http://www.mendeley.com/profiles/francisco-pastor1/
>>> Google Scholar: http://scholar.google.com/citations?user=V3mmCdkAAAAJ&hl=es
>>> Researcher ID: http://www.researcherid.com/rid/B-8331-2008
>>> Cosis profile: http://www.cosis.net/profile/francisco.pastor
>>> -----------
>>> mail: paco at ceam.es
>>> skype: paco.pastor.guzman
>>> -----------
>>> Parque Tecnologico, C/ Charles R. Darwin, 14
>>> 46980 PATERNA (Valencia), Spain
>>> Tlf. 96 131 82 27 - Fax. 96 131 81 90
>>> 
>>> 
>>> ---------------------------------------------------------------------
>>> Este mensaje y los ficheros anexos son confidenciales. Los mismos contienen información reservada de la empresa que no puede ser difundida. Si usted ha recibido este correo por error, tenga la amabilidad de eliminarlo de su sistema y avisar al remitente mediante reenvío a su dirección electrónica; no deberá copiar el mensaje ni divulgar su contenido a ninguna persona.
>>> 
>>> Su dirección de correo electrónico junto a sus datos personales forman parte de un fichero titularidad de la Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgánica 15/1999, usted puede ejercitar sus derechos de acceso, rectificación, cancelación y, en su caso, oposición enviando una solicitud por escrito, acompañada de una fotocopia de su DNI dirigida a: Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnológico.46980 PATERNA (Valencia).
>>> 
>>> This message and the attached files are confidential. They contain reserved information belonging to our centre and are not to be broadcast. If you have received this email by mistake, please delete it from your system and alert the sender by returning it to his/her email address. You must not copy or divulge the contents of the message to anyone.
>>> 
>>> Your email address and personal data are included in a file belonging to the Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM, con CIF: G-46957213. The purpose of this file is to allow us to keep in contact with you. In accordance with Organic Law 15/1999, you are permitted to access, rectify, cancel or oppose the contents of this file by submitting a written request, accompanied by a photocopy of your DNI, to: Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnológico.46980 PATERNA (Valencia).
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> discuss mailing list     discuss at mpich.org
>>> To manage subscription options or unsubscribe:
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>>> 
>> _______________________________________________
>> discuss mailing list     discuss at mpich.org
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>> 
>> 
> 
> -- 
> -----------
> Dr. Francisco Pastor
> Meteorology department, Instituto Universitario CEAM-UMH
> http://www.ceam.es
> -----------
> Mendeley profile: http://www.mendeley.com/profiles/francisco-pastor1/
> Google Scholar: http://scholar.google.com/citations?user=V3mmCdkAAAAJ&hl=es
> Researcher ID: http://www.researcherid.com/rid/B-8331-2008
> Cosis profile: http://www.cosis.net/profile/francisco.pastor
> -----------
> mail: paco at ceam.es
> skype: paco.pastor.guzman
> -----------
> Parque Tecnologico, C/ Charles R. Darwin, 14
> 46980 PATERNA (Valencia), Spain
> Tlf. 96 131 82 27 - Fax. 96 131 81 90
> 
> 
> ---------------------------------------------------------------------
> Este mensaje y los ficheros anexos son confidenciales. Los mismos contienen información reservada de la empresa que no puede ser difundida. Si usted ha recibido este correo por error, tenga la amabilidad de eliminarlo de su sistema y avisar al remitente mediante reenvío a su dirección electrónica; no deberá copiar el mensaje ni divulgar su contenido a ninguna persona.
> 
> Su dirección de correo electrónico junto a sus datos personales forman parte de un fichero titularidad de la Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgánica 15/1999, usted puede ejercitar sus derechos de acceso, rectificación, cancelación y, en su caso, oposición enviando una solicitud por escrito, acompañada de una fotocopia de su DNI dirigida a: Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnológico.46980 PATERNA (Valencia).
> 
> This message and the attached files are confidential. They contain reserved information belonging to our centre and are not to be broadcast. If you have received this email by mistake, please delete it from your system and alert the sender by returning it to his/her email address. You must not copy or divulge the contents of the message to anyone.
> 
> Your email address and personal data are included in a file belonging to the Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM, con CIF: G-46957213. The purpose of this file is to allow us to keep in contact with you. In accordance with Organic Law 15/1999, you are permitted to access, rectify, cancel or oppose the contents of this file by submitting a written request, accompanied by a photocopy of your DNI, to: Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnológico.46980 PATERNA (Valencia).
> 
> 
> 
> _______________________________________________
> discuss mailing list     discuss at mpich.org
> To manage subscription options or unsubscribe:
> https://lists.mpich.org/mailman/listinfo/discuss
>

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