April 2014 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] Running mpi from bash script
by Reuti 22 Apr '14

22 Apr '14

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(a)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(a)mpich.org >>>>> To manage subscription options or unsubscribe: >>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>>> >>> -- >>> ----------- >>> 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(a)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(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> >> > > -- > ----------- > 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(a)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(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

1 0

Re: [mpich-discuss] Running mpi from bash script
by Francisco Pastor 22 Apr '14

22 Apr '14

Hi and sorry for the delay in answering. I was out on holidays since Friday. I recompiled the appication, just changing mpich2 path. MPI_PATH=/usr/bin PAR_INCS=-I/usr/local/include PAR_LIBS=-L/usr/local/lib/ -lmpich PAR_DEFS=-DRAMS_MPI Thanks El 17/04/2014 17:58, Reuti escribiï¿½: > 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 escribiï¿½: >>> 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(a)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 informaciï¿½n 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 reenvï¿½o a su direcciï¿½n electrï¿½nica; no deberï¿½ copiar el mensaje ni divulgar su contenido a ninguna persona. >>>> >>>> Su direcciï¿½n de correo electrï¿½nico junto a sus datos personales forman parte de un fichero titularidad de la Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgï¿½nica 15/1999, usted puede ejercitar sus derechos de acceso, rectificaciï¿½n, cancelaciï¿½n y, en su caso, oposiciï¿½n enviando una solicitud por escrito, acompaï¿½ada de una fotocopia de su DNI dirigida a: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.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 Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - 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: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.46980 PATERNA (Valencia). >>>> >>>> >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >>> >> -- >> ----------- >> 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(a)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 informaciï¿½n 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 reenvï¿½o a su direcciï¿½n electrï¿½nica; no deberï¿½ copiar el mensaje ni divulgar su contenido a ninguna persona. >> >> Su direcciï¿½n de correo electrï¿½nico junto a sus datos personales forman parte de un fichero titularidad de la Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgï¿½nica 15/1999, usted puede ejercitar sus derechos de acceso, rectificaciï¿½n, cancelaciï¿½n y, en su caso, oposiciï¿½n enviando una solicitud por escrito, acompaï¿½ada de una fotocopia de su DNI dirigida a: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.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 Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - 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: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.46980 PATERNA (Valencia). >> >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > -- ----------- 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(a)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 informaciï¿½n 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 reenvï¿½o a su direcciï¿½n electrï¿½nica; no deberï¿½ copiar el mensaje ni divulgar su contenido a ninguna persona. Su direcciï¿½n de correo electrï¿½nico junto a sus datos personales forman parte de un fichero titularidad de la Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgï¿½nica 15/1999, usted puede ejercitar sus derechos de acceso, rectificaciï¿½n, cancelaciï¿½n y, en su caso, oposiciï¿½n enviando una solicitud por escrito, acompaï¿½ada de una fotocopia de su DNI dirigida a: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.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 Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - 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: Fundaciï¿½n de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterrï¿½neo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnolï¿½gico.46980 PATERNA (Valencia).

1 0

Re: [mpich-discuss] MPICH (v3.1) Performing slow on 10G Ethernet
by Muhammad Ansar Javed 21 Apr '14

21 Apr '14

I am able to achieve around 90% ( maximum 9340 Mbps) bandwidth on 10GE. There were configuration issues disabling Intel Speedstep and Interrupt coalescing helped in achieving expected network bandwidth. Thanks for support. On Mon, Apr 21, 2014 at 4:40 PM, Atchley, Scott <atchleyes(a)ornl.gov> wrote: > From the netperf manual: > > -r <sizespec> > > This option sets the request (first value) and/or response (second value) > sizes for an _RR test. By default the units are bytes, but a suffix of “G,” > “M,” or “K” will specify the units to be 2^30 (GB), 2^20 (MB) or 2^10 (KB) > respectively. A suffix of “g,” “m” or “k” will specify units of 10^9, 10^6 > or 10^3 bytes respectively. For example: > > -r 128,16K > > Will set the request size to 128 bytes and the response size to 16 KB or > 16384 bytes. [Default: 1 - a single-byte request and response ] > > > I thought OSU had a streaming benchmark, but I have not used it in a long > time. > > > On Apr 17, 2014, at 7:47 AM, Muhammad Ansar Javed < > muhammad.ansar(a)seecs.edu.pk> wrote: > > > > > I am running bandwidth test from OSU-Micro-Benchmarks and a simple > Ping-Pong program implemented using MPI Send and Recv methods. I have also > tested bandwidth with NetPipe MPI implementation as well but no > improvements in results. > > > > Interrupt coalescing was ON by default and disabling it makes latency > consistent at 37 us through out messages of 1 byte to 2 MB data size. I > have done following vendor recommended optimizations for network buffer. > Latency is not increasing with the message size may be because of these > settings. > > net.core.rmem_max = 16777216 > > net.core.wmem_max = 16777216 > > net.ipv4.tcp_rmem = 4096 87380 16777216 > > net.ipv4.tcp_wmem = 4096 65536 16777216 > > net.core.netdev_max_backlog = 250000 > > > > > > I have not run streaming benchmark. I found a Streaming MPI benchmark ( > http://www.cs.virginia.edu/stream/) but its C implementation is not > available. Can you please suggest me any Streaming MPI-C benchmark? > > > > Latency test with netperf TCP_RR gives 37 us for message size 1 Bytes. > Moreover, according to Netperf docs, _RR test support only 1 bytes message > size. Please correct me if I am wrong. > > > > Thanks, > > > > > > > > On Wed, Apr 16, 2014 at 5:36 PM, Atchley, Scott <atchleyes(a)ornl.gov> > wrote: > > On Apr 16, 2014, at 8:35 AM, Scott Atchley <atchleyes(a)ornl.gov> wrote: > > > > > Keep in mind that iperf is a streaming test. What MPI application are > you running? IMB pingpong? > > > > > > You should review you NIC vendor's tuning FAQ. Is interrupt coalescing > turned on? Normally it is, but it increases small message latency. > > > > > > As for bandwidth, have you tried a streaming MPI benchmark? > > > > Or run Netperf's TCP_RR for each message size to see how it compares to > pingpong. > > > > > > > > Scott > > > > > > On Apr 15, 2014, at 4:29 PM, Muhammad Ansar Javed < > muhammad.ansar(a)seecs.edu.pk> wrote: > > > > > >> Hi Antonio, > > >> Thanks for response. > > >> Here is output of iperf bandwidth test. > > >> . > > >> Client connecting to 10g2, TCP port 5001 > > >> TCP window size: 1.41 MByte (default) > > >> ------------------------------------------------------------ > > >> [ 5] local 192.168.1.33 port 34543 connected with 192.168.1.34 port > 5001 > > >> [ 4] local 192.168.1.33 port 5001 connected with 192.168.1.34 port > 48531 > > >> [ ID] Interval Transfer Bandwidth > > >> [ 5] 0.0-10.0 sec 11.2 GBytes 9.61 Gbits/sec > > >> [ 4] 0.0-10.0 sec 11.2 GBytes 9.59 Gbits/sec > > >> > > >> > > >> > > >> On Tue, Apr 15, 2014 at 7:17 PM, "Antonio J. Peña" < > apenya(a)mcs.anl.gov> wrote: > > >> > > >> Hi Ansar, > > >> > > >> The bandwidth numbers seem a little low. I'd expect something around > 7,000 Mbps. To discard issues with MPI, you can try generic benchmarking > tools such as those described here> > > >> > > >> > http://linuxaria.com/article/tool-command-line-bandwidth-linux?lang=en > > >> > > >> If you get similar numbers, you'll have to check your setup. > Otherwise, let us know and we'll try to see if there's any performance > issue with MPICH. > > >> > > >> Best, > > >> Antonio > > >> > > >> > > >> > > >> On 04/15/2014 06:35 AM, Muhammad Ansar Javed wrote: > > >>> Hi, > > >>> I am running benchmarks for MPICH v3.1 performance evaluation on 10G > Ethernet connection between two hosts. The performance results are less > than expected. Here is complete set of numbers for Latency and Bandwidth > tests. > > >>> > > >>> mpj@host3:~/code/benchmarks$ mpiexec -n 2 -f machines ./latency.out > > >>> Latency: MPICH-C > > >>> Size ______ Time (us) > > >>> 1 _________ 37.91 > > >>> 2 _________ 37.76 > > >>> 4 _________ 37.75 > > >>> 8 _________ 39.02 > > >>> 16 ________ 52.71 > > >>> 32 ________ 39.08 > > >>> 64 ________ 37.75 > > >>> 128 _______ 37.77 > > >>> 256 _______ 57.47 > > >>> 512 _______ 37.86 > > >>> 1024 ______ 37.76 > > >>> 2048 ______ 37.88 > > >>> > > >>> mpj@host3:~/code/benchmarks$ mpiexec -n 2 -f machines > ./bandwidth.out > > >>> Bandwidth: MPICH-C > > >>> Size(Bytes) Bandwidth (Mbps) > > >>> 2048 ______ 412.32 > > >>> 4096 ______ 820.06 > > >>> 8192 ______ 827.77 > > >>> 16384 _____ 1644.36 > > >>> 32768 _____ 2207.52 > > >>> 65536 _____ 4368.76 > > >>> 131072 ____ 2942.93 > > >>> 262144 ____ 4281.17 > > >>> 524288 ____ 4773.78 > > >>> 1048576 ___ 5310.85 > > >>> 2097152 ___ 5382.94 > > >>> 4194304 ___ 5518.97 > > >>> 8388608 ___ 5508.87 > > >>> 16777216 __ 5498.93 > > >>> > > >>> My environments consists of two hosts having point-to-point > (switch-less) 10Gbps Ethernet connection. Environment (OS, user, directory > structure etc) on both hosts is exactly same. There is no NAS or shared > file system between hosts. I have attached output of script > > >>> mpiexec -all. > > >>> > > >>> Are these numbers okay? If not then please suggest performance > improvement methodology... > > >>> > > >>> Thanks > > >>> > > >>> -- > > >>> Regards > > >>> > > >>> Ansar Javed > > >>> HPC Lab > > >>> SEECS NUST > > >>> Contact: +92 334 438 9394 > > >>> Email: muhammad.ansar(a)seecs.edu.pk > > >>> > > >>> > > >>> _______________________________________________ > > >>> discuss mailing list > > >>> discuss(a)mpich.org > > >>> > > >>> To manage subscription options or unsubscribe: > > >>> > > >>> https://lists.mpich.org/mailman/listinfo/discuss > > >> > > >> > > >> -- > > >> Antonio J. Peña > > >> Postdoctoral Appointee > > >> Mathematics and Computer Science Division > > >> Argonne National Laboratory > > >> 9700 South Cass Avenue, Bldg. 240, Of. 3148 > > >> Argonne, IL 60439-4847 > > >> > > >> apenya(a)mcs.anl.gov > > >> www.mcs.anl.gov/~apenya > > >> > > >> _______________________________________________ > > >> discuss mailing list discuss(a)mpich.org > > >> To manage subscription options or unsubscribe: > > >> https://lists.mpich.org/mailman/listinfo/discuss > > >> > > >> > > >> > > >> -- > > >> Regards > > >> > > >> Ansar Javed > > >> HPC Lab > > >> SEECS NUST > > >> Contact: +92 334 438 9394 > > >> Email: muhammad.ansar(a)seecs.edu.pk > > >> _______________________________________________ > > >> discuss mailing list discuss(a)mpich.org > > >> To manage subscription options or unsubscribe: > > >> https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > > -- > > Regards > > > > Ansar Javed > > HPC Lab > > SEECS NUST > > Contact: +92 334 438 9394 > > Email: muhammad.ansar(a)seecs.edu.pk > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Regards Ansar Javed HPC Lab SEECS NUST Contact: +92 334 438 9394 Email: muhammad.ansar(a)seecs.edu.pk

1 0

Re: [mpich-discuss] MPICH (v3.1) Performing slow on 10G Ethernet
by Atchley, Scott 21 Apr '14

21 Apr '14

>From the netperf manual: -r <sizespec> This option sets the request (first value) and/or response (second value) sizes for an _RR test. By default the units are bytes, but a suffix of “G,” “M,” or “K” will specify the units to be 2^30 (GB), 2^20 (MB) or 2^10 (KB) respectively. A suffix of “g,” “m” or “k” will specify units of 10^9, 10^6 or 10^3 bytes respectively. For example: -r 128,16K Will set the request size to 128 bytes and the response size to 16 KB or 16384 bytes. [Default: 1 - a single-byte request and response ] I thought OSU had a streaming benchmark, but I have not used it in a long time. On Apr 17, 2014, at 7:47 AM, Muhammad Ansar Javed <muhammad.ansar(a)seecs.edu.pk> wrote: > > I am running bandwidth test from OSU-Micro-Benchmarks and a simple Ping-Pong program implemented using MPI Send and Recv methods. I have also tested bandwidth with NetPipe MPI implementation as well but no improvements in results. > > Interrupt coalescing was ON by default and disabling it makes latency consistent at 37 us through out messages of 1 byte to 2 MB data size. I have done following vendor recommended optimizations for network buffer. Latency is not increasing with the message size may be because of these settings. > net.core.rmem_max = 16777216 > net.core.wmem_max = 16777216 > net.ipv4.tcp_rmem = 4096 87380 16777216 > net.ipv4.tcp_wmem = 4096 65536 16777216 > net.core.netdev_max_backlog = 250000 > > > I have not run streaming benchmark. I found a Streaming MPI benchmark (http://www.cs.virginia.edu/stream/) but its C implementation is not available. Can you please suggest me any Streaming MPI-C benchmark? > > Latency test with netperf TCP_RR gives 37 us for message size 1 Bytes. Moreover, according to Netperf docs, _RR test support only 1 bytes message size. Please correct me if I am wrong. > > Thanks, > > > > On Wed, Apr 16, 2014 at 5:36 PM, Atchley, Scott <atchleyes(a)ornl.gov> wrote: > On Apr 16, 2014, at 8:35 AM, Scott Atchley <atchleyes(a)ornl.gov> wrote: > > > Keep in mind that iperf is a streaming test. What MPI application are you running? IMB pingpong? > > > > You should review you NIC vendor's tuning FAQ. Is interrupt coalescing turned on? Normally it is, but it increases small message latency. > > > > As for bandwidth, have you tried a streaming MPI benchmark? > > Or run Netperf's TCP_RR for each message size to see how it compares to pingpong. > > > > > Scott > > > > On Apr 15, 2014, at 4:29 PM, Muhammad Ansar Javed <muhammad.ansar(a)seecs.edu.pk> wrote: > > > >> Hi Antonio, > >> Thanks for response. > >> Here is output of iperf bandwidth test. > >> . > >> Client connecting to 10g2, TCP port 5001 > >> TCP window size: 1.41 MByte (default) > >> ------------------------------------------------------------ > >> [ 5] local 192.168.1.33 port 34543 connected with 192.168.1.34 port 5001 > >> [ 4] local 192.168.1.33 port 5001 connected with 192.168.1.34 port 48531 > >> [ ID] Interval Transfer Bandwidth > >> [ 5] 0.0-10.0 sec 11.2 GBytes 9.61 Gbits/sec > >> [ 4] 0.0-10.0 sec 11.2 GBytes 9.59 Gbits/sec > >> > >> > >> > >> On Tue, Apr 15, 2014 at 7:17 PM, "Antonio J. Peña" <apenya(a)mcs.anl.gov> wrote: > >> > >> Hi Ansar, > >> > >> The bandwidth numbers seem a little low. I'd expect something around 7,000 Mbps. To discard issues with MPI, you can try generic benchmarking tools such as those described here> > >> > >> http://linuxaria.com/article/tool-command-line-bandwidth-linux?lang=en > >> > >> If you get similar numbers, you'll have to check your setup. Otherwise, let us know and we'll try to see if there's any performance issue with MPICH. > >> > >> Best, > >> Antonio > >> > >> > >> > >> On 04/15/2014 06:35 AM, Muhammad Ansar Javed wrote: > >>> Hi, > >>> I am running benchmarks for MPICH v3.1 performance evaluation on 10G Ethernet connection between two hosts. The performance results are less than expected. Here is complete set of numbers for Latency and Bandwidth tests. > >>> > >>> mpj@host3:~/code/benchmarks$ mpiexec -n 2 -f machines ./latency.out > >>> Latency: MPICH-C > >>> Size ______ Time (us) > >>> 1 _________ 37.91 > >>> 2 _________ 37.76 > >>> 4 _________ 37.75 > >>> 8 _________ 39.02 > >>> 16 ________ 52.71 > >>> 32 ________ 39.08 > >>> 64 ________ 37.75 > >>> 128 _______ 37.77 > >>> 256 _______ 57.47 > >>> 512 _______ 37.86 > >>> 1024 ______ 37.76 > >>> 2048 ______ 37.88 > >>> > >>> mpj@host3:~/code/benchmarks$ mpiexec -n 2 -f machines ./bandwidth.out > >>> Bandwidth: MPICH-C > >>> Size(Bytes) Bandwidth (Mbps) > >>> 2048 ______ 412.32 > >>> 4096 ______ 820.06 > >>> 8192 ______ 827.77 > >>> 16384 _____ 1644.36 > >>> 32768 _____ 2207.52 > >>> 65536 _____ 4368.76 > >>> 131072 ____ 2942.93 > >>> 262144 ____ 4281.17 > >>> 524288 ____ 4773.78 > >>> 1048576 ___ 5310.85 > >>> 2097152 ___ 5382.94 > >>> 4194304 ___ 5518.97 > >>> 8388608 ___ 5508.87 > >>> 16777216 __ 5498.93 > >>> > >>> My environments consists of two hosts having point-to-point (switch-less) 10Gbps Ethernet connection. Environment (OS, user, directory structure etc) on both hosts is exactly same. There is no NAS or shared file system between hosts. I have attached output of script > >>> mpiexec -all. > >>> > >>> Are these numbers okay? If not then please suggest performance improvement methodology... > >>> > >>> Thanks > >>> > >>> -- > >>> Regards > >>> > >>> Ansar Javed > >>> HPC Lab > >>> SEECS NUST > >>> Contact: +92 334 438 9394 > >>> Email: muhammad.ansar(a)seecs.edu.pk > >>> > >>> > >>> _______________________________________________ > >>> discuss mailing list > >>> discuss(a)mpich.org > >>> > >>> To manage subscription options or unsubscribe: > >>> > >>> https://lists.mpich.org/mailman/listinfo/discuss > >> > >> > >> -- > >> Antonio J. Peña > >> Postdoctoral Appointee > >> Mathematics and Computer Science Division > >> Argonne National Laboratory > >> 9700 South Cass Avenue, Bldg. 240, Of. 3148 > >> Argonne, IL 60439-4847 > >> > >> apenya(a)mcs.anl.gov > >> www.mcs.anl.gov/~apenya > >> > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > >> > >> > >> > >> -- > >> Regards > >> > >> Ansar Javed > >> HPC Lab > >> SEECS NUST > >> Contact: +92 334 438 9394 > >> Email: muhammad.ansar(a)seecs.edu.pk > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > > -- > Regards > > Ansar Javed > HPC Lab > SEECS NUST > Contact: +92 334 438 9394 > Email: muhammad.ansar(a)seecs.edu.pk > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] Problem met when installing mpich on a linux server
by Fenglei Qi 20 Apr '14

20 Apr '14

Thanks for your guys help. The problem is really caused by time stamps. I just followed Balaji's suggestion and redid it again. Now the soft was smoothly installed. Thank you guys for helping me out of this mess. Have a good weekend. On Sun, Apr 20, 2014 at 10:35 AM, "Antonio J. Peña" <apenya(a)mcs.anl.gov>wrote: > > I know, I was just providing a possible quick fix for the particular issue > of this user, rather than trying to figure out what's wrong in his setup. > > > > On 04/20/2014 10:33 AM, Balaji, Pavan wrote: > >> Users should not have to download autotools. That’s only meant for mpich >> developers. >> >> — Pavan >> >> On Apr 20, 2014, at 10:23 AM, Antonio J. Peña <apenya(a)mcs.anl.gov> wrote: >> >> Hi Fenglei, >>> >>> aclocal is part of automake. You can download and compile the latest >>> version from its website for use it with MPICH. Here you have the link: >>> >>> http://www.gnu.org/software/automake/ >>> >>> Antonio >>> >>> >>> On 04/19/2014 10:49 PM, Fenglei Qi wrote: >>> >>>> Hi all, >>>> >>>> I tried to install mpich on a server with redhat system. I can >>>> configure mpich successfully but I met problems when I tried to build >>>> mpich. It threw out a warning: 'aclocal-1.14' is missing on your system. I >>>> checked the system and I found out that my system only has aclocal-1.11. >>>> Since I don't have privilege to install software so I can't update it. Any >>>> suggestion for further installation? I attached m.txt and c.txt below. >>>> Thanks. >>>> >>>> -- >>>> Fenglei Qi >>>> Research Assistant >>>> Mechanical Engineering >>>> Iowa State University >>>> >>>> >>>> _______________________________________________ >>>> discuss mailing list >>>> discuss(a)mpich.org >>>> >>>> To manage subscription options or unsubscribe: >>>> >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>> >>> -- >>> Antonio J. Peña >>> Postdoctoral Appointee >>> Mathematics and Computer Science Division >>> Argonne National Laboratory >>> 9700 South Cass Avenue, Bldg. 240, Of. 3148 >>> Argonne, IL 60439-4847 >>> >>> apenya(a)mcs.anl.gov >>> www.mcs.anl.gov/~apenya >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > -- > Antonio J. Peña > Postdoctoral Appointee > Mathematics and Computer Science Division > Argonne National Laboratory > 9700 South Cass Avenue, Bldg. 240, Of. 3148 > Argonne, IL 60439-4847 > apenya(a)mcs.anl.gov > www.mcs.anl.gov/~apenya > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- *Fenglei Qi* Research Assistant Mechanical Engineering Iowa State University

1 0

Re: [mpich-discuss] Problem met when installing mpich on a linux server
by "Antonio J. Peña" 20 Apr '14

20 Apr '14

I know, I was just providing a possible quick fix for the particular issue of this user, rather than trying to figure out what's wrong in his setup. On 04/20/2014 10:33 AM, Balaji, Pavan wrote: > Users should not have to download autotools. Thatï¿½s only meant for mpich developers. > > ï¿½ Pavan > > On Apr 20, 2014, at 10:23 AM, Antonio J. Peï¿½a <apenya(a)mcs.anl.gov> wrote: > >> Hi Fenglei, >> >> aclocal is part of automake. You can download and compile the latest version from its website for use it with MPICH. Here you have the link: >> >> http://www.gnu.org/software/automake/ >> >> Antonio >> >> >> On 04/19/2014 10:49 PM, Fenglei Qi wrote: >>> Hi all, >>> >>> I tried to install mpich on a server with redhat system. I can configure mpich successfully but I met problems when I tried to build mpich. It threw out a warning: 'aclocal-1.14' is missing on your system. I checked the system and I found out that my system only has aclocal-1.11. Since I don't have privilege to install software so I can't update it. Any suggestion for further installation? I attached m.txt and c.txt below. Thanks. >>> >>> -- >>> Fenglei Qi >>> >>> Research Assistant >>> Mechanical Engineering >>> Iowa State University >>> >>> >>> _______________________________________________ >>> discuss mailing list >>> discuss(a)mpich.org >>> >>> To manage subscription options or unsubscribe: >>> >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> -- >> Antonio J. Peï¿½a >> Postdoctoral Appointee >> Mathematics and Computer Science Division >> Argonne National Laboratory >> 9700 South Cass Avenue, Bldg. 240, Of. 3148 >> Argonne, IL 60439-4847 >> >> apenya(a)mcs.anl.gov >> www.mcs.anl.gov/~apenya >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Antonio J. Peï¿½a Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

1 0

Re: [mpich-discuss] Problem met when installing mpich on a linux server
by Balaji, Pavan 20 Apr '14

20 Apr '14

Users should not have to download autotools. That’s only meant for mpich developers. — Pavan On Apr 20, 2014, at 10:23 AM, Antonio J. Peña <apenya(a)mcs.anl.gov> wrote: > > Hi Fenglei, > > aclocal is part of automake. You can download and compile the latest version from its website for use it with MPICH. Here you have the link: > > http://www.gnu.org/software/automake/ > > Antonio > > > On 04/19/2014 10:49 PM, Fenglei Qi wrote: >> Hi all, >> >> I tried to install mpich on a server with redhat system. I can configure mpich successfully but I met problems when I tried to build mpich. It threw out a warning: 'aclocal-1.14' is missing on your system. I checked the system and I found out that my system only has aclocal-1.11. Since I don't have privilege to install software so I can't update it. Any suggestion for further installation? I attached m.txt and c.txt below. Thanks. >> >> -- >> Fenglei Qi >> >> Research Assistant >> Mechanical Engineering >> Iowa State University >> >> >> _______________________________________________ >> discuss mailing list >> discuss(a)mpich.org >> >> To manage subscription options or unsubscribe: >> >> https://lists.mpich.org/mailman/listinfo/discuss > > > -- > Antonio J. Peña > Postdoctoral Appointee > Mathematics and Computer Science Division > Argonne National Laboratory > 9700 South Cass Avenue, Bldg. 240, Of. 3148 > Argonne, IL 60439-4847 > > apenya(a)mcs.anl.gov > www.mcs.anl.gov/~apenya > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] Problem met when installing mpich on a linux server
by "Antonio J. Peña" 20 Apr '14

20 Apr '14

Hi Fenglei, aclocal is part of automake. You can download and compile the latest version from its website for use it with MPICH. Here you have the link: http://www.gnu.org/software/automake/ Antonio On 04/19/2014 10:49 PM, Fenglei Qi wrote: > Hi all, > > I tried to install mpich on a server with redhat system. I can > configure mpich successfully but I met problems when I tried to build > mpich. It threw out a warning: 'aclocal-1.14' is missing on your > system. I checked the system and I found out that my system only has > aclocal-1.11. Since I don't have privilege to install software so I > can't update it. Any suggestion for further installation? I attached > m.txt and c.txt below. Thanks. > > -- > *Fenglei Qi* > Research Assistant > Mechanical Engineering > Iowa State University > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Antonio J. Peï¿½a Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

1 0

Re: [mpich-discuss] illegal ioctl
by Lu, Huiwei 20 Apr '14

20 Apr '14

I would suggest the first place you check is some data structures that expand as the number of MPI processes increases. — Huiwei On Apr 20, 2014, at 10:08 AM, Hans-Joachim Werner <werner(a)theochem.uni-stuttgart.de> wrote: > Thanks. Yes, most likely it runs out of some system resources. It happens independently > of the other memory the job needs. We use Global Arrays with MPI, and the problem happens > in ga_put (one-sided write to a global array). We can also run it with pure MPI, and the > same problem occurs (it’s not SHMMAX). The application is the Molpro quantum chemistry program. > Joachim Werner > --- > Prof. Dr. Hans-Joachim Werner > Institut for Theoretical Chemistry > University of Stuttgart > Pfaffenwaldring 55 > D-70569 Stuttgart > Tel: +49 711 / 685 64400 > Fax: +49 711 / 685 64442 > email: werner(a)theochem.uni-stuttgart.de > > > > Am 20.04.2014 um 16:52 schrieb Lu, Huiwei <huiweilu(a)mcs.anl.gov>: > >> It’s possible your system is running out of memory or other system resources that cause the MPI job to abort. >> >> — >> Huiwei Lu >> Postdoc Appointee >> Mathematics and Computer Science Division, Argonne National Laboratory >> http://www.mcs.anl.gov/~huiweilu/ >> >> On Apr 20, 2014, at 9:49 AM, Balaji, Pavan <balaji(a)anl.gov> wrote: >> >>> >>> This is not an MPICH problem. It means that your application is asking MPICH to kill it using “MPI_Abort”. >>> >>> — Pavan >>> >>> On Apr 20, 2014, at 7:48 AM, Hans-Joachim Werner <werner(a)theochem.uni-stuttgart.de> wrote: >>> >>>> On my system large jobs die with messages like this: >>>> >>>> Last System Error Message from Task 3:: Inappropriate ioctl for device >>>> application called MPI_Abort(comm=0x84000004, 11) - process 3 >>>> >>>> Does anybody know how this can be avoided? Maybe a stack overflow? >>>> >>>> Joachim Werner >>>> >>>> >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] illegal ioctl
by Hans-Joachim Werner 20 Apr '14

20 Apr '14

Thanks. Yes, most likely it runs out of some system resources. It happens independently of the other memory the job needs. We use Global Arrays with MPI, and the problem happens in ga_put (one-sided write to a global array). We can also run it with pure MPI, and the same problem occurs (it’s not SHMMAX). The application is the Molpro quantum chemistry program. Joachim Werner --- Prof. Dr. Hans-Joachim Werner Institut for Theoretical Chemistry University of Stuttgart Pfaffenwaldring 55 D-70569 Stuttgart Tel: +49 711 / 685 64400 Fax: +49 711 / 685 64442 email: werner(a)theochem.uni-stuttgart.de Am 20.04.2014 um 16:52 schrieb Lu, Huiwei <huiweilu(a)mcs.anl.gov>: > It’s possible your system is running out of memory or other system resources that cause the MPI job to abort. > > — > Huiwei Lu > Postdoc Appointee > Mathematics and Computer Science Division, Argonne National Laboratory > http://www.mcs.anl.gov/~huiweilu/ > > On Apr 20, 2014, at 9:49 AM, Balaji, Pavan <balaji(a)anl.gov> wrote: > >> >> This is not an MPICH problem. It means that your application is asking MPICH to kill it using “MPI_Abort”. >> >> — Pavan >> >> On Apr 20, 2014, at 7:48 AM, Hans-Joachim Werner <werner(a)theochem.uni-stuttgart.de> wrote: >> >>> On my system large jobs die with messages like this: >>> >>> Last System Error Message from Task 3:: Inappropriate ioctl for device >>> application called MPI_Abort(comm=0x84000004, 11) - process 3 >>> >>> Does anybody know how this can be avoided? Maybe a stack overflow? >>> >>> Joachim Werner >>> >>> >>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

1 0