November 2012 - discuss - mailman3.cels.anl.gov

MPICH2 for Win: Topology functions
by Alejandro Allievi 27 Nov '12

27 Nov '12

Hi, I'm setting up a grid topology and associated communicator using the function Setup_grid below. It works fine for process zero but throws: Fatal error in PMPI_Comm_rank: Invalid communicator, error stack: PMPI_Comm_rank(109): MPI_Comm_rank(MPI_COMM_NULL, rank=000000000022FE4C) failed PMPI_Comm_rank(66).: Null communicator Does MPICH2 for Win7 support topology functions??? Thanks for any help. Alejandro ************CODE BELOW*************************** void Setup_grid(GRID_INFO_T* grid /* out */) { int old_rank; int dimensions[2]; int wrap_around[2]; int coordinates[2]; int free_coords[2]; /* Set up Global Grid Information */ MPI_Comm_size(MPI_COMM_WORLD, &(grid->p)); MPI_Comm_rank(MPI_COMM_WORLD, &old_rank); printf("Process %d of %d inside Setup_Grid\n", old_rank, grid->p); /* We assume p is a perfect square */ grid->q = (int) sqrt((double) grid->p); dimensions[0] = dimensions[1] = grid->q; /* We want a circular shift in second dimension. */ /* Don't care about first */ wrap_around[0] = wrap_around[1] = 1; MPI_Cart_create(MPI_COMM_WORLD, 2, dimensions, wrap_around, 1, &(grid->comm)); MPI_Comm_rank(grid->comm, &(grid->my_rank)); MPI_Cart_coords(grid->comm, grid->my_rank, 2, coordinates); grid->my_row = coordinates[0]; grid->my_col = coordinates[1]; /* Set up row communicators */ free_coords[0] = 0; free_coords[1] = 1; MPI_Cart_sub(grid->comm, free_coords, &(grid->row_comm)); /* Set up column communicators */ free_coords[0] = 1; free_coords[1] = 0; MPI_Cart_sub(grid->comm, free_coords, &(grid->col_comm)); printf("Process %d leaving Setup_Grid\n", old_rank); } /* Setup_grid */ -- Alejandro Allievi http://www.ace-net.ca/wiki/Alejandro_Allievi "Tenez, mon ami, si vous y pensez bien, vous trouverez qu'en tout, notre véritable sentiment n'est pas celui dans lequel nous n'avons jamais vacillé; mais celui auquel nous sommes le plus habituellement revenus". Denis Diderot. Este e-mail esta consignado sólo para el destinatario designado en el mismo y puede contener información confidencial y privilegiada. Su distribución o copiado está prohibido. Si Usted no fuera el destinatario designado, por favor notifíquenos de inmediato y destruya este e-mail en forma permanente así como todas las copias del mismo. Ce courriel peut renfermer des renseignements confidentiels et privilégiés et s'adresse au destinataire désigné seulement. La distribution ou la copie de ce courriel est interdit. Si vous n'êtes pas le destinataire désigné, veuillez nous en aviser immédiatement et détruire de façon permanente ce courriel ainsi que toute copie de celui-ci. This e-mail may contain confidential information, and is intended only for the named recipient and may be privileged. Distribution or copying of this email is prohibited. If you are not the named recipient, please notify us immediately and permanently destroy this email and all copies of it.

1 0

Re: [mpich-discuss] Mpich2's behavior when too many messages are sent
by Jeff Hammond 27 Nov '12

27 Nov '12

This is a quality of implementation issue that lies outside the MPI standard. There is no requirement that an arbitrarily large number of nonblocking messages be allowed to be outstanding at one time since this is not possible with finite resources, but obviously a high-quality implementation will strive to make the allowed number as large as possible. I suspect that MPICH will let you enqueue nonblocking sends and receives until you reach resource exhaustion, i.e. run out of memory for internal state. I ran a simple test (see below) that shows you can post at least 1M messages (true for MPICH 3.0rc1 on my Macbook Pro) without any problems (although at 1M it gets a bit slow). Best, Jeff $ mpichversion MPICH Version: 3.0rc1 MPICH Release date: Mon Nov 12 10:31:40 CST 2012 MPICH Device: ch3:nemesis MPICH configure: --prefix=/opt/local --disable-dependency-tracking --disable-f77 --disable-fc --disable-silent-rules --enable-base-cache --enable-cache --enable-cxx --enable-fast=O2 --enable-shared --enable-smpcoll --includedir=/opt/local/include/mpich --with-device=ch3:nemesis --with-pm=hydra --with-thread-package=posix F90FLAGS= F90= MPICHLIB_CPPFLAGS=-I/opt/local/include --enable-timer-type=mach_absolute_time MPICH CC: /usr/bin/clang -pipe -arch x86_64 MPICH CXX: /usr/bin/clang++ -pipe -arch x86_64 -O2 MPICH F77: -pipe -m64 MPICH FC: -pipe -m64 compile with: mpicc -g -O2 -Wall outstanding.c -o outstanding.x execute with: mpiexec -n 2 ./outstanding.x 1000000 $ cat outstanding.c =========================== #include <stdio.h> #include <stdlib.h> #include <mpi.h> int main(int argc, char* argv[]) { int rank, size; MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &size); if (size<2) { printf("run on 2 or more ranks! \n"); MPI_Abort(MPI_COMM_WORLD, 1); } int n = (argc>1) ? atoi(argv[1]) : 1e6; if (rank==0) printf("attempting to call MPI_I{send,recv} %d times before completing any of them \n", n); MPI_Request * reqs = (MPI_Request*) malloc(n*sizeof(MPI_Request)); if (reqs==NULL) { printf("malloc of %ld bytes failed! \n", (long)n*sizeof(MPI_Request)); MPI_Abort(MPI_COMM_WORLD, 1); } if (rank==0) for (int i=0; i<n; i++) MPI_Irecv(NULL, 0, MPI_BYTE, 1, i, MPI_COMM_WORLD, &(reqs[i]) ); else if (rank==1) for (int i=0; i<n; i++) MPI_Isend(NULL, 0, MPI_BYTE, 0, i, MPI_COMM_WORLD, &(reqs[i]) ); if (rank==0) printf("all MPI_I{send,recv} have been posted \n"); MPI_Barrier(MPI_COMM_WORLD); MPI_Waitall(n, reqs, MPI_STATUSES_IGNORE); if (rank==0) printf("all MPI_I{send,recv} have been completed \n"); free(reqs); if (rank==0) printf("SUCCESS \n"); MPI_Finalize(); return 0; } =========================== $ mpiexec -n 2 ./outstanding.x 100 attempting to call MPI_I{send,recv} 100 times before completing any of them all MPI_I{send,recv} have been posted all MPI_I{send,recv} have been completed SUCCESS $ mpiexec -n 2 ./outstanding.x 1000 attempting to call MPI_I{send,recv} 1000 times before completing any of them all MPI_I{send,recv} have been posted all MPI_I{send,recv} have been completed SUCCESS $ mpiexec -n 2 ./outstanding.x 10000 attempting to call MPI_I{send,recv} 10000 times before completing any of them all MPI_I{send,recv} have been posted all MPI_I{send,recv} have been completed SUCCESS $ mpiexec -n 2 ./outstanding.x 100000 attempting to call MPI_I{send,recv} 100000 times before completing any of them all MPI_I{send,recv} have been posted all MPI_I{send,recv} have been completed SUCCESS $ mpiexec -n 2 ./outstanding.x 1000000 attempting to call MPI_I{send,recv} 1000000 times before completing any of them all MPI_I{send,recv} have been posted all MPI_I{send,recv} have been completed SUCCESS On Tue, Nov 27, 2012 at 3:50 AM, Matthieu Dorier <matthieu.dorier(a)irisa.fr> wrote: > Hello, > > I have a program that include two processes, one is doing a lot of > MPI_Isend, the other one loops, receives the messages using MPI_Irecv and > treats them. > I'd like to know what the MPI-2 standard says, and what Mpich2 does, if the > first process is too fast and the second process cannot keep up with the > number of messages sent. Is the first process supposed to eventually block, > waiting for the messages to be received, or will the application crashes? > > Thanks > > Matthieu Dorier > PhD student at ENS Cachan Brittany and IRISA > http://people.irisa.fr/Matthieu.Dorier > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

1 0

Mpich2's behavior when too many messages are sent
by Matthieu Dorier 27 Nov '12

27 Nov '12

Hello, I have a program that include two processes, one is doing a lot of MPI_Isend, the other one loops, receives the messages using MPI_Irecv and treats them. I'd like to know what the MPI-2 standard says, and what Mpich2 does, if the first process is too fast and the second process cannot keep up with the number of messages sent. Is the first process supposed to eventually block, waiting for the messages to be received, or will the application crashes? Thanks Matthieu Dorier PhD student at ENS Cachan Brittany and IRISA http://people.irisa.fr/Matthieu.Dorier

1 0

Re: [mpich-discuss] Fwd: Windows and mpicc
by Jayesh Krishna 26 Nov '12

26 Nov '12

Hi, The LANG setting might be related to the unrecognized characters in the makefile. Looks like the build system is not able to find the definition for sighandler_t (usually found in signal.h). This should have been handled at configure time. You should be able to find MPICH2 configure options in the MPICH2 installers guide (http://www.mpich.org/documentation/guides/) Regards, Jayesh ----- Original Message ----- From: "John Mole" <j.mole(a)imperial.ac.uk> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> Sent: Monday, November 26, 2012 8:54:42 AM Subject: RE: [mpich-discuss] Fwd: Windows and mpicc Hi Jayesh, The LANG environment variable refers to localisation, so is not relevant. On looking closely at the code, I found some bugs in dbxerr.c.in. I made the following changes to get it to compile: Line 406: #define SIG_HANDLER_PROTOTYPE sighandler_t Changed to: #define SIG_HANDLER_PROTOTYPE int Line 409: int sig Changed to: int sig; I am still trying to resolve the Win32 memory issue. Meanwhile, can you let me have a full list of the mpich config options please? Regards, John Mole -----Original Message----- From: Jayesh Krishna [mailto:[email protected]] Sent: 20 November 2012 14:42 To: Mole, John Cc: mpich-discuss(a)mcs.anl.gov Subject: Re: [mpich-discuss] Fwd: Windows and mpicc Hi, A google search suggests that your setting for LANG environment variable may be incorrect. Can you check what it is (Can you set it to say "LANG=C" and see if it works)? Regards, Jayesh ----- Original Message ----- From: "John Mole" <j.mole(a)imperial.ac.uk> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> Sent: Monday, November 19, 2012 9:37:49 AM Subject: RE: [mpich-discuss] Fwd: Windows and mpicc Hi Jayesh, I have checked dbxerr.c in hex and there are no DOS characters - make output attached. I don't want to disable MPE so I need to solve this problem somehow. I will post on the Cygwin forum about the memory issue as you suggested. Regards, John Mole -----Original Message----- From: Jayesh Krishna [mailto:[email protected]] Sent: 12 November 2012 16:32 To: mpich-discuss(a)mcs.anl.gov Cc: Mole, John Subject: Re: [mpich-discuss] Fwd: Windows and mpicc Hi, Looks like you have compile time errors for mpe because of DOS characters. If you are not planning to use MPE you can disable it (Specify "--disable-mpe" during configure time). The error that stopped the build looks like a Cygwin error (Unable to allocate enough memory for the linker). I have seen these errors when packages are updated (A "rebase" sometimes solves the problem). I would recommend posting your issue on a Cygwin forum. Can you try running the build again (after disabling MPE at compile time) after you fix the Cygwin issue? Regards, Jayesh ----- Original Message ----- From: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> To: mpich-discuss(a)mcs.anl.gov Sent: Friday, November 9, 2012 2:58:06 PM Subject: [mpich-discuss] Fwd: Windows and mpicc FYI ----- Forwarded Message ----- From: "John Mole" <j.mole(a)imperial.ac.uk> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> Sent: Friday, November 9, 2012 10:25:19 AM Subject: RE: [mpich-discuss] Windows and mpicc Hi Jayesh, Thanks. I did as you suggested. On the configure stage, I had to convert all the configure-related files to change the end of line characters to UNIX rather than DOS. The Cygwin version of BASH seems to be very picky about this. Eventually I managed to persuade the ./configure to work (output attached). However, the make stage failed with various errors (output attached). I have also included a list of the environmental variables, which may be relevant. Any advice on how to proceed would be much appreciated. Regards, John Mole -----Original Message----- From: Jayesh Krishna [mailto:[email protected]] Sent: 07 November 2012 15:50 To: Mole, John Cc: mpich-discuss(a)mcs.anl.gov Subject: Re: [mpich-discuss] Windows and mpicc Hi, There are two ways to install MPICH2 on Windows - (1) Using the Windows installers (2) Downloading MPICH2 source and compiling it under Cygwin. If you install MPICH2 using the Windows msi installers mpicc is not installed (Users typically compile their programs using Visual Studio, Intel Windows compilers etc). Since you are working in the Cygwin environment please uninstall MPICH2 and download the MPICH2 source from the link below and install (configure/make/make install - like you would install software on a unix-like/cygwin system) it. Regards, Jayesh ----- Original Message ----- From: "John Mole" <j.mole(a)imperial.ac.uk> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> Sent: Wednesday, November 7, 2012 6:49:59 AM Subject: RE: [mpich-discuss] Windows and mpicc Hi Jayesh, I have already downloaded and installed the Windows version but there is no sign of mpicc (or the Fortran equivalent) in the /bin folder hence my original query. Regards, John Mole -----Original Message----- From: Jayesh Krishna [mailto:[email protected]] Sent: 06 November 2012 15:27 To: mpich-discuss(a)mcs.anl.gov Cc: Mole, John Subject: Re: [mpich-discuss] Windows and mpicc Hi, mpicc is the compiler wrapper that is installed with MPICH2 (or an MPI library suite). You can download the source and install MPICH2 from the MPICH2 website (http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downl…) Regards, Jayesh ----- Original Message ----- From: "John Mole" <j.mole(a)imperial.ac.uk> To: mpich-discuss(a)mcs.anl.gov Sent: Monday, November 5, 2012 4:40:58 PM Subject: [mpich-discuss] Windows and mpicc I am currently porting a mathematical modelling application from Ubuntu to Windows. I am fairly new to Linux. I am mostly working in Cygwin which emulates the Linux environment in Windows. I have installed MPICH2 on Windows and have set the necessary paths. In trying to make Parmetis in Cygwin I get the error ‘mpicc not found’. So I am trying to track down mpicc. I don’t know where it comes from. Is it from GNU or MPICH or where? How do I get hold of it? I would be most grateful if someone could provide guidance. Thanks, John Mole _______________________________________________ mpich-discuss mailing list mpich-discuss(a)mcs.anl.gov To manage subscription options or unsubscribe: https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss _______________________________________________ mpich-discuss mailing list mpich-discuss(a)mcs.anl.gov To manage subscription options or unsubscribe: https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss

1 0

Re: [mpich-discuss] FW: MPICH2 matters
by Jayesh Krishna 26 Nov '12

26 Nov '12

Hi, Do you have multiple versions of MPICH2 installed in your (user) system? MPICH2 implementation on Windows does not support installing multiple versions of the suite in the same system. Regards, Jayesh ----- Original Message ----- From: "Robert Bauer" <Robert.Bauer(a)iconplc.com> To: discuss(a)mpich.org Sent: Monday, November 26, 2012 1:20:15 AM Subject: [mpich-discuss] FW: MPICH2 matters Dear sirs: I find that in the windows environment some of the users of our software that uses MPICH2 may have more than one version of MPICH2 installed on their system. Therefore I am not aware of where the smpd.exe that is presently loaded comes from. If my software launches the incorrect mpiexec, then a version mismatch notice is given. Is there a way to enquire which version of smpd.exe is loaded at any time? smpd -version only gives the version that is closest in the PATH environment variable, and is not necessarily the one that is loaded. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: Robert.Bauer(a)iconplc.com Web: www.iconplc.com ICON plc made the following annotations. ------------------------------------------------------------------------------ This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that ICON plc can arrange for proper delivery, and then please delete the message. Thank You, ICON plc South County Business Park Leopardstown Dublin 18 Ireland Registered number: 145835 _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

FW: MPICH2 matters
by Bauer, Robert 26 Nov '12

26 Nov '12

Dear sirs: I find that in the windows environment some of the users of our software that uses MPICH2 may have more than one version of MPICH2 installed on their system. Therefore I am not aware of where the smpd.exe that is presently loaded comes from. If my software launches the incorrect mpiexec, then a version mismatch notice is given. Is there a way to enquire which version of smpd.exe is loaded at any time? smpd -version only gives the version that is closest in the PATH environment variable, and is not necessarily the one that is loaded. Robert J. Bauer, Ph.D. Vice President, Pharmacometrics, R&D ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email: Robert.Bauer(a)iconplc.com Web: www.iconplc.com<http://www.iconplc.com/> ICON plc made the following annotations. ------------------------------------------------------------------------------ This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that ICON plc can arrange for proper delivery, and then please delete the message. Thank You, ICON plc South County Business Park Leopardstown Dublin 18 Ireland Registered number: 145835

1 0

Re: [mpich-discuss] FW: MPICH problem
by Pavan Balaji 24 Nov '12

24 Nov '12

Fixed. Thanks for reporting the problem. -- Pavan On 11/24/2012 04:03 PM US Central Time, A.L. Heba Khaled wrote: > I tried to download the MPICH2 but both x86 and x86_64 are page not found. > > http://www.mpich.org/files/tarballs/1.4.1p1/mpich2-1.4.1p1-win-ia32.msi > > http://www.mpich.org/files/tarballs/1.4.1p1/mpich2-1.4.1p1-win-x86-64.msi > > > > where else can I found it ?? > > > > > > Regards, > > */_____________________/* > > *Heba Khaled Ahmed* > > *Assistant Lecturer, > Department of Computer Systems, > Faculty of Computer & Information Sciences, > Ain Shams University, Cairo, Egypt.* > > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] Windows download issue
by Pavan Balaji 24 Nov '12

24 Nov '12

Fixed. Thanks for reporting the problem. -- Pavan On 11/23/2012 05:17 PM US Central Time, Roberto Schiabel wrote: > Hi all, > I receive an error trying to download of MPI windows version > here http://www.mpich.org/downloads/ . > > Where is available another file ? > > Thank you very much > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0

Re: [mpich-discuss] windows binaries for mpich2 - link broken on mpich.org
by Andrew Cohen 24 Nov '12

24 Nov '12

That works! Thanks so much!! -andrew -----Original Message----- From: discuss-bounces(a)mpich.org [mailto:[email protected]] On Behalf Of Rayson Ho Sent: Saturday, November 24, 2012 9:37 PM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] windows binaries for mpich2 - link broken on mpich.org You can try: http://www.mpich.org/static/tarballs/1.4.1p1/ Rayson ================================================== Open Grid Scheduler - The Official Open Source Grid Engine http://gridscheduler.sourceforge.net/ Scalable Grid Engine http://www.scalablelogic.com/scalable-grid-engine-support On Sat, Nov 24, 2012 at 9:27 PM, Andrew Cohen <acohen(a)coe.drexel.edu> wrote: > Hello, > > > > Sorry to bother you, but I'm trying to download mpich binaries for windows. > > > > There is a link to x86 and x86_64 on the downloads page, but both > links are broken. > > > > Are binaries available for Windows platform? > > > > Thanks, > > > > -andrew cohen > > > > > _______________________________________________ > 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] windows binaries for mpich2 - link broken on mpich.org
by Rayson Ho 24 Nov '12

24 Nov '12

You can try: http://www.mpich.org/static/tarballs/1.4.1p1/ Rayson ================================================== Open Grid Scheduler - The Official Open Source Grid Engine http://gridscheduler.sourceforge.net/ Scalable Grid Engine http://www.scalablelogic.com/scalable-grid-engine-support On Sat, Nov 24, 2012 at 9:27 PM, Andrew Cohen <acohen(a)coe.drexel.edu> wrote: > Hello, > > > > Sorry to bother you, but I’m trying to download mpich binaries for windows. > > > > There is a link to x86 and x86_64 on the downloads page, but both links are > broken. > > > > Are binaries available for Windows platform? > > > > Thanks, > > > > -andrew cohen > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

1 0