August 2013 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] regarding parallel programming
by Pavan Balaji 17 Aug '13

17 Aug '13

Urmila, Please send all future emails to discuss(a)mpich.org instead of to individual developers. There could be a number of problems here, including possibly a firewall between the two nodes. Did you try disabling that? Another possibility is that the /etc/hosts file on one or both the nodes is messed up. Did you check that? There should be more information on the mpich FAQ page, which I can't seem to reach right now. http://wiki.mpich.org/mpich/index.php/Frequently_Asked_Questions -- Pavan On 08/17/2013 02:09 PM, urmila pol wrote: > Dear sir, > I try to do parallel programming but I have problems with Hydra > process manager errors . parsing error,token error, file not found etc. > I install mpich-3.0.4 on two machines and I create cluster of two machines. > program should be run on single node but it will not execute on other node. > I use ssh for communication. > please guide me. waiting for reply. > With regards, > > Dr.Urmila R. Pol > Assistant Professor, > Department of computer Science, > Shivaji University, Kolhapur. > Maharashtra-India. -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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abusing MPI_2DOUBLE_PRECISION to fake MPI_DOUBLE_LONG
by Jeff Hammond 13 Aug '13

13 Aug '13

Does MPICH preserve the ability of doubles to hold integers up to 2^53 properly when doing MPI_{MAX,MIN}LOC over Fortran MPI_2DOUBLE_PRECISION? I see no evidence in http://www.mpi-forum.org/docs/mpi-11-html/node79.html that this isn't possible, but I guess implementations might fall back to the C implementation for MPI_DOUBLE_INT under the assumption that the Fortran programmer only needs half of the bits in the second double of MPI_2DOUBLE_PRECISION. The motivation is that, until https://svn.mpi-forum.org/trac/mpi-forum-web/ticket/319 is part of the standard, there's no way to have loc be more than a 32b int, at least from C. This hideous hack via Fortran seems like the only viable option for the time being. Thanks, Jeff -- Jeff Hammond jeff.science(a)gmail.com

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Re: [mpich-discuss] MPI_File_open fails on the cluster (2 node)
by Wesley Bland 13 Aug '13

13 Aug '13

Can you update to a recent version of MPICH? 1.4.1p is very old at this point. The most recent stable version is 3.0.4. Wesley On Tuesday, August 13, 2013 at 9:43 AM, 정재용 wrote: > I set up 2 node cluster and installed mpich by using intel compiler. OS is CentOS 6.4 > > Each node is connected by ethernet. They shared directories where the compiler and mpich are installed, by using nfs. > > SSH co nnection can be done without password. > > By way of experiment, I compiled simple example of MPI_File_open with mpicc and executed by mpiexec on the nfs directory. > > The code is > > #include "mpi.h" > #include > > > int main( int argc, char *argv[] ) > { > MPI_Fint handleA, handleB; > int rc; > int errs = 0; > int rank; > MPI_File cFile; > > > MPI_Init( &argc, &argv ); > MPI_Comm_rank( MPI_COMM_WORLD, &rank ); > rc = MPI_File_open( MPI_COMM_WORLD, "temp", MPI_MODE_RDWR | MPI_MODE_DELETE_ON_CLOSE | MPI_MODE_CREATE, MPI_INFO_NULL, &cFile ); > if (rc) { > printf( "Unable to open file \"temp\"\n" );fflush(stdout); > } > else { > MPI_File_close( &cFile ); > } > MPI_Finalize(); > return 0; > } > > > > > > > This example just opens the file and closes it in parallel. > > On the single machine, it worked well. > > However, it didn't work when 2 machines' processor executed the code in parallel. > > The error message: > > Internal Error: invalid error code 209e0e (Ring ids do not match) in MPIR_Bcast_intra:1119 > Fatal error in PMPI_Bcast: Other MPI error, error stack: > PMPI_Bcast(1478)......: MPI_Bcast(b uf=0x1deb980, count=1, MPI_CHAR, root=0, comm=0x84000004) failed > MPIR_Bcast_impl(1321).: > MPIR_Bcast_intra(1119): > > When I added the prefix nfs: to the filename, as "nfs:temp", it worked well. > > However, I don't want to add that because I should execute very big code on the cluster. > > It is very hard to modify the code. Would you let me know what the problem is and how the problem is solved? > > The nfs options are > (client) > mount -t nfs -o noac,nfsvers=3 "server_directory" "mount_directory" > (server, /etc/exports) > sync,rw,no_root_squash > > I shared /opt and /home/username > > mpich configuration is > MPICH2 Version: 1.4.1p1 > MPICH2 Release date: Thu Sep 1 13:53:02 CDT 2011 > MPICH2 Device: ch3:nemesis > MPICH2 configure: --prefix=/home/master/lib/mpich/mpich2-1.4.1p1 CC=icc F77=ifort CXX=icpc FC=ifort --enable-romio --with-file-system=nfs+ufs --with-pm=hydra > MPICH2 CC: icc -O2 > MPICH2 CXX: icpc -O2 > MPICH2 F77: ifort -O2 > MPICH2 FC: ifort -O2 > > ------------------------------------------------------ > Jaeyong Jeong > Department of Mechanical Engineering > Pohang University of Science and Technology > > > > > > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org (mailto:[email protected]) > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > >

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MPI_File_open fails on the cluster (2 node)
by 정재용 13 Aug '13

13 Aug '13

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Re: [mpich-discuss] wrong SSH user using mpdboot
by Marcelo Soares Souza 13 Aug '13

13 Aug '13

You can use MPICH 3.0.4 on Debian Wheezy. MPICH2 1.2.1p1 is a little old :) I made available a repository for Debian and Ubuntu package for stable (and updated) releases of MPICH (3.0.4) For Debian Wheezy deb http://cebacad.net/repos/debian wheezy main For Ubuntu Quantal deb http://cebacad.net/repos/ubuntu quantal main - Mini-HowTo * Edit sources.list (/etc/apt/sources.list) nano /etc/apt/sources.list * Put in the final deb http://cebacad.net/repos/debian wheezy main Or for Ubuntu deb http://cebacad.net/repos/ubuntu quantal main * update the package list apt-get update * install mpich apt-get install mpich Em 13-08-2013 02:21, vahid shahabi escreveu: > Hi > I compiled MPICH2 1.2.1p1 on debian 6. I'm using VMware 9. > My master hostname is "debian1" and slave one is "debian2". > username on master is bb1 and bb2 on slave system. > when I run "mpdboot -n 3 -f ~/mpd.hosts||" it tries to ssh as > "bb1@debian2" and asks for password. But doesn't accept it and some > error about port problem. > I'm new in MPI and I don't know what is the problem. I appreciate if you > can help me. > <http://www.mpich.org/static/downloads/1.2.1p1/> > > -- > > > Live free() or die() > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Abraï¿½os Marcelo Soares Souza https://marcelo.juntadados.org Diaspora* https://diaspora.juntadados.org/u/marcelo Friendica http://friendica.ambientedigital.org/profile/marcelo

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wrong SSH user using mpdboot
by vahid shahabi 13 Aug '13

13 Aug '13

Hi I compiled MPICH2 1.2.1p1 on debian 6. I'm using VMware 9. My master hostname is "debian1" and slave one is "debian2". username on master is bb1 and bb2 on slave system. when I run "mpdboot -n 3 -f ~/mpd.hosts" it tries to ssh as "bb1@debian2" and asks for password. But doesn't accept it and some error about port problem. I'm new in MPI and I don't know what is the problem. I appreciate if you can help me. <http://www.mpich.org/static/downloads/1.2.1p1/> -- Live free() or die()

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Re: [mpich-discuss] MPICH 3.1b1 packages for Ubuntu, Debian and Slackware (x86 and amd64)
by Pavan Balaji 09 Aug '13

09 Aug '13

Thanks Marcelo. The downloads page has been updated. On 08/09/2013 01:43 PM, Marcelo Soares Souza wrote: > mpich-3.1b1 packages > > * Ubuntu 13.04 (Raring Ringtail) > > - amd64 > http://www.cebacad.net/files/mpich/ubuntu/mpich-3.1b1/mpich_3.1b1-1ubuntu_a… > > > - x86 > http://www.cebacad.net/files/mpich/ubuntu/mpich-3.1b1/mpich_3.1b1-1ubuntu_i… > > > * Debian 7.1.0 (Wheezy) > > - amd64 > http://www.cebacad.net/files/mpich/debian/mpich-3.1b1/mpich_3.1b1-1debian_a… > > > - x86 > http://www.cebacad.net/files/mpich/debian/mpich-3.1b1/mpich_3.1b1-1debian_i… > > > * Slackware 14.1 > > - amd64 > http://www.cebacad.net/files/mpich/slackware/mpich-3.1b1/mpich-3.1b1-x86_64… > > > - x86 > http://www.cebacad.net/files/mpich/slackware/mpich-3.1b1/mpich-3.1b1-i486-g… > > > Enjoy! ;) > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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MPICH stable (and updated) package repositories for Debian and Ubuntu
by Marcelo Soares Souza 09 Aug '13

09 Aug '13

Hi, I made available a repository for Debian and Ubuntu package for stable (and updated) releases of MPICH For Debian Wheezy deb http://cebacad.net/repos/debian wheezy main For Ubuntu Quantal deb http://cebacad.net/repos/ubuntu quantal main - Mini-HowTo * Edit sources.list (/etc/apt/sources.list) nano /etc/apt/sources.list * Put in the final deb http://cebacad.net/repos/debian wheezy main Or for Ubuntu deb http://cebacad.net/repos/ubuntu quantal main * update the package list apt-get update * install mpich apt-get install mpich -- Marcelo Soares Souza https://marcelo.juntadados.org Diaspora* https://diaspora.juntadados.org/u/marcelo Friendica http://friendica.ambientedigital.org/profile/marcelo

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MPICH 3.1b1 packages for Ubuntu, Debian and Slackware (x86 and amd64)
by Marcelo Soares Souza 09 Aug '13

09 Aug '13

mpich-3.1b1 packages * Ubuntu 13.04 (Raring Ringtail) - amd64 http://www.cebacad.net/files/mpich/ubuntu/mpich-3.1b1/mpich_3.1b1-1ubuntu_a… - x86 http://www.cebacad.net/files/mpich/ubuntu/mpich-3.1b1/mpich_3.1b1-1ubuntu_i… * Debian 7.1.0 (Wheezy) - amd64 http://www.cebacad.net/files/mpich/debian/mpich-3.1b1/mpich_3.1b1-1debian_a… - x86 http://www.cebacad.net/files/mpich/debian/mpich-3.1b1/mpich_3.1b1-1debian_i… * Slackware 14.1 - amd64 http://www.cebacad.net/files/mpich/slackware/mpich-3.1b1/mpich-3.1b1-x86_64… - x86 http://www.cebacad.net/files/mpich/slackware/mpich-3.1b1/mpich-3.1b1-i486-g… Enjoy! ;) -- Marcelo Soares Souza https://marcelo.juntadados.org Diaspora* https://diaspora.juntadados.org/u/marcelo Friendica http://friendica.ambientedigital.org/profile/marcelo

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Re: [mpich-discuss] Incorrect error message for MPID_nem_tcp_bind (1.5, 3.0.4)
by Yauheni Zelenko 08 Aug '13

08 Aug '13

Hi, Wesley! Thank you for quick fix! Eugene. ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] On Behalf Of Wesley Bland [wbland(a)mcs.anl.gov] Sent: Thursday, August 08, 2013 2:57 PM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Incorrect error message for MPID_nem_tcp_bind (1.5, 3.0.4) This has been resolved: https://trac.mpich.org/projects/mpich/ticket/1923 On Wednesday, August 7, 2013 at 10:53 PM, Wesley Bland wrote: Thanks for the report. I've got a patch done now that should be going into the repository soon. Wesley On Wednesday, August 7, 2013 at 4:37 PM, Yauheni Zelenko wrote: Hi! I have a problem on one host when MPID_nem_tcp_bind() failed with "MPID_nem_tcp_bind(580): unable to bind socket to port (port=1,errno=98:Address already in use)". However, MPID_nem_tcp_bind() tried to bind to port 0 (ports ranges was not specified), then failed, and port variable was incremented before final error message recorded. MPICH_PORT_RANGE helped to solve problem on aforementioned host. I tried version 1.5 and 3.0.4. Eugene. _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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