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

Re: [mpich-discuss] installing mpich-1.2.6 to create libmpich.so.1.0
by Pavan Balaji 25 Jun '13

25 Jun '13

Any compiler is fine. But use the latest version of mpich. You don't need all the configure flags that Jeff sent. In fact, I'd recommend that you not use them. For example, --enable-g is only for developers. My recommendation is just this: ./configure --prefix=<where_to_install> CC=pgcc CXX=pgCC F77=pgf77 FC=pgfc -- Pavan On 06/25/2013 02:54 PM, Andre Pattantyus wrote: > Jeff, > > Are you saying that this file will only build with a gnu compiler? or > can I build with pgf compiler with mpich 3.0.4? > > -Andre > > > On Tue, Jun 25, 2013 at 2:19 AM, Jeff Hammond <jhammond(a)alcf.anl.gov > <mailto:[email protected]>> wrote: > > Try MPICH 3.0.4. MPICH 1.2.6 is ancient and not supported. > > This is how I build MPICH 3.0.4. You will have to edit the prefix > option appropriately. > > wget http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz > tar -xzf mpich-3.0.4.tar.gz > cd mpich-3.0.4 > mkdir build-gcc > cd build-gcc/ > ../configure CC=gcc CXX=g++ FC=gfortran F77=gfortran --enable-fc > --enable-f77 --enable-threads --enable-g=dbg > --with-device=ch3:nemesis --with-pm=hydra --prefix=. > > Jeff > > ----- Original Message ----- > From: "Andre Pattantyus" <akp4221(a)hawaii.edu > <mailto:[email protected]>> > To: discuss(a)mpich.org <mailto:[email protected]> > Sent: Tuesday, June 25, 2013 3:15:55 AM > Subject: [mpich-discuss] installing mpich-1.2.6 to create > libmpich.so.1.0 > > > > > Hello, > > I am not familiar with installing mpich and am having problems with > installation. I have found from searching online that mpich-1.2.6 > produces libmpich.so.1.0 which I require run a certain program in > parallel. I am unable to follow the installation documentation I > have found online for this version because when i configure for > ch_p4mpd I get an error when I run make. Therefore I just run > ./configure and make but this does not produce my required > libmpich.so.1.0. What do I need to specify prior to either configure > or make in order to build this? I am building on a linux86-64 with > pgi/10.2 compiler. > > > > -- > Andre Pattantyus > Graduate Student Research Assistant > Department of Meteorology > University of Hawaii at Manoa > 2525 Correa Rd, HIG 350 > Honolulu, HI 96822 > Phone: (845) 264-3582 > > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > > > -- > Andre Pattantyus > Graduate Student Research Assistant > Department of Meteorology > University of Hawaii at Manoa > 2525 Correa Rd, HIG 350 > Honolulu, HI 96822 > Phone: (845) 264-3582 > > > _______________________________________________ > 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

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Re: [mpich-discuss] installing mpich-1.2.6 to create libmpich.so.1.0
by Andre Pattantyus 25 Jun '13

25 Jun '13

Jeff, Are you saying that this file will only build with a gnu compiler? or can I build with pgf compiler with mpich 3.0.4? -Andre On Tue, Jun 25, 2013 at 2:19 AM, Jeff Hammond <jhammond(a)alcf.anl.gov> wrote: > Try MPICH 3.0.4. MPICH 1.2.6 is ancient and not supported. > > This is how I build MPICH 3.0.4. You will have to edit the prefix option > appropriately. > > wget http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz > tar -xzf mpich-3.0.4.tar.gz > cd mpich-3.0.4 > mkdir build-gcc > cd build-gcc/ > ../configure CC=gcc CXX=g++ FC=gfortran F77=gfortran --enable-fc > --enable-f77 --enable-threads --enable-g=dbg --with-device=ch3:nemesis > --with-pm=hydra --prefix=. > > Jeff > > ----- Original Message ----- > From: "Andre Pattantyus" <akp4221(a)hawaii.edu> > To: discuss(a)mpich.org > Sent: Tuesday, June 25, 2013 3:15:55 AM > Subject: [mpich-discuss] installing mpich-1.2.6 to create libmpich.so.1.0 > > > > > Hello, > > I am not familiar with installing mpich and am having problems with > installation. I have found from searching online that mpich-1.2.6 produces > libmpich.so.1.0 which I require run a certain program in parallel. I am > unable to follow the installation documentation I have found online for > this version because when i configure for ch_p4mpd I get an error when I > run make. Therefore I just run ./configure and make but this does not > produce my required libmpich.so.1.0. What do I need to specify prior to > either configure or make in order to build this? I am building on a > linux86-64 with pgi/10.2 compiler. > > > > -- > Andre Pattantyus > Graduate Student Research Assistant > Department of Meteorology > University of Hawaii at Manoa > 2525 Correa Rd, HIG 350 > Honolulu, HI 96822 > Phone: (845) 264-3582 > > _______________________________________________ > 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 > -- Andre Pattantyus Graduate Student Research Assistant Department of Meteorology University of Hawaii at Manoa 2525 Correa Rd, HIG 350 Honolulu, HI 96822 Phone: (845) 264-3582

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Re: [mpich-discuss] Problem with ADIOI_Info_get (MPI_Info_get) from the ADIO layer
by Matthieu Dorier 25 Jun '13

25 Jun '13

Hi, I found the solution by investigating the code so I'll post it here in case it can be useful to someone else: When opening a file, ADIOI_xxx_SetInfo is called to copy the info structure. Unless overwritten by the ADIO backend, it's ADIO_GEN_SetInfo (in src/mpi/romio/adio/common/ad_hints.c) that ends up being called and this function only copies the hints that it knows (e.g. cb_buffer_size). So the solution consists in changing ADIO_GEN_SetInfo or (more appropriately) provide an implementation of ADIOI_xxx_SetInfo that copies custom parameters and the called ADIO_GEN_SetInfo. Matthieu ----- Mail original ----- > De: "Matthieu Dorier" <matthieu.dorier(a)irisa.fr> > À: discuss(a)mpich.org > Envoyé: Lundi 24 Juin 2013 15:46:21 > Objet: [mpich-discuss] Problem with ADIOI_Info_get (MPI_Info_get) > from the ADIO layer > Hi, > I'm implementing an ADIO backend and I'm having problems retrieving > values from the MPI_Info attached to the file. > On the application side, I have something like this: > MPI_Info_create(&info); > MPI_Info_set(info,"cb_buffer_size","64"); > MPI_Info_set(info,"xyz","3"); > MPI_File_open(comm, "file", > MPI_MODE_WRONLY | MPI_MODE_CREATE, info, &fh); > then a call to a MPI_File_write, which ends up calling my > implementation of ADIOI_xxx_WriteContig. In this function, I try to > read back these info: > int info_flag; > char* value = (char *) > ADIOI_Malloc((MPI_MAX_INFO_VAL+1)*sizeof(char)); > ADIOI_Info_get(fd->info, "xyz", MPI_MAX_INFO_VAL, value,&info_flag); > if(info_flag) fprintf(stderr,"xyz = %d\n",atoi(value)); > ADIOI_Info_get(fd->info, "cb_buffer_size", MPI_MAX_INFO_VAL, > value,&info_flag); > if(info_flag) fprintf(stderr,"cb_buffer_size = %d\n",atoi(value)); > I can get the 64 associated to the cb_buffer_size key (which is a > reserved hint), but I don't get the second value. > Where does the problem come from? > I tried everything: re-ordering the calls, changing the name of the > key, calling MPI_Info_get in the application to check that the > values are properly set (they are)... > 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

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Re: [mpich-discuss] installing mpich-1.2.6 to create libmpich.so.1.0
by Wesley Bland 25 Jun '13

25 Jun '13

Alternatively, if you have access to a package manager on your machine, you can just do something like apt-get install mpich2. The version available from most package managers is a little old, but it does simplify the installation process. If you do need to build from source, make sure you read through the README file in the top level directory of MPICH. It has lots of instructions for installation and will show you the best way to report issues to this mailing list so we can help you most efficiently. Let us know if you're still having trouble after you try those things. Wesley On Jun 25, 2013, at 7:19 AM, Jeff Hammond <jhammond(a)alcf.anl.gov> wrote: > Try MPICH 3.0.4. MPICH 1.2.6 is ancient and not supported. > > This is how I build MPICH 3.0.4. You will have to edit the prefix option appropriately. > > wget http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz > tar -xzf mpich-3.0.4.tar.gz > cd mpich-3.0.4 > mkdir build-gcc > cd build-gcc/ > ../configure CC=gcc CXX=g++ FC=gfortran F77=gfortran --enable-fc --enable-f77 --enable-threads --enable-g=dbg --with-device=ch3:nemesis --with-pm=hydra --prefix=. > > Jeff > > ----- Original Message ----- > From: "Andre Pattantyus" <akp4221(a)hawaii.edu> > To: discuss(a)mpich.org > Sent: Tuesday, June 25, 2013 3:15:55 AM > Subject: [mpich-discuss] installing mpich-1.2.6 to create libmpich.so.1.0 > > > > > Hello, > > I am not familiar with installing mpich and am having problems with installation. I have found from searching online that mpich-1.2.6 produces libmpich.so.1.0 which I require run a certain program in parallel. I am unable to follow the installation documentation I have found online for this version because when i configure for ch_p4mpd I get an error when I run make. Therefore I just run ./configure and make but this does not produce my required libmpich.so.1.0. What do I need to specify prior to either configure or make in order to build this? I am building on a linux86-64 with pgi/10.2 compiler. > > > > -- > Andre Pattantyus > Graduate Student Research Assistant > Department of Meteorology > University of Hawaii at Manoa > 2525 Correa Rd, HIG 350 > Honolulu, HI 96822 > Phone: (845) 264-3582 > > _______________________________________________ > 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

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Re: [mpich-discuss] discuss Digest, Vol 8, Issue 40
by Wesley Bland 25 Jun '13

25 Jun '13

The problem is that all of the processes other than rank 0 are not seeing the data that is entered on the command line. They're falling directly through to your receive call and therefore their per_process_data is 0 and they aren't allocating a buffer for the data that needs to be received. The usual way of getting input from a user is not via command line input in a parallel program, but via a file in the filesystem. If the file is shared among all of the MPI processes (such as with a shared file system like NFS), then they can all read it directly. If not, then rank 0 could read the file and send all the data to the other ranks individually, which I believe is more like what you're trying to do. The problem is that you need to tell the other ranks how much data will be sent first so they can allocate an appropriate buffer. By the way, in the future when you see the error Segmentation fault, you can usually debug things your self very simply by using 'gdb' or 'ddd'. Often your program will generate a core file (something like 1234.core) that you can pass into 'gdb' or 'ddd' to discover where the problems are. If you aren't familiar with those debugging programs, there should be plenty of tutorials on the web that can help you familiarize yourself. Thanks, Wesley On Jun 25, 2013, at 3:33 AM, pradnya dixit <pradnya.dixit123(a)gmail.com> wrote: > > Hello, > > I am trying to send chunk of data using send and recv funcions in mpi.. but facing so many problem or errors like > > > Elements of rank 1 are: > [pradnya-Lenovo-G570:04553] *** Process received signal *** > [pradnya-Lenovo-G570:04553] Signal: Segmentation fault (11) > [pradnya-Lenovo-G570:04553] Signal code: Address not mapped (1) > [pradnya-Lenovo-G570:04553] Failing at address: 0x8be8950 > [pradnya-Lenovo-G570:04554] *** Process received signal *** > [pradnya-Lenovo-G570:04554] Signal: Segmentation fault (11) > [pradnya-Lenovo-G570:04554] Signal code: Address not mapped (1) > [pradnya-Lenovo-G570:04554] Failing at address: 0x8be8960 > [pradnya-Lenovo-G570:04552] *** Process received signal *** > [pradnya-Lenovo-G570:04552] Signal: Segmentation fault (11) > [pradnya-Lenovo-G570:04552] Signal code: Address not mapped (1) > [pradnya-Lenovo-G570:04552] Failing at address: 0x8be86f8 > [pradnya-Lenovo-G570:04553] [ 0] [0xff440c] > [pradnya-Lenovo-G570:04553] [ 1] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0xc66e37] > [pradnya-Lenovo-G570:04553] [ 2] lst() [0x8048871] > [pradnya-Lenovo-G570:04553] *** End of error message *** > [pradnya-Lenovo-G570:04552] [ 0] [0x57c40c] > [pradnya-Lenovo-G570:04552] [ 1] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x126e37] > [pradnya-Lenovo-G570:04552] [ 2] lst() [0x8048871] > [pradnya-Lenovo-G570:04552] *** End of error message *** > [pradnya-Lenovo-G570:04554] [ 0] [0xd0740c] > [pradnya-Lenovo-G570:04554] [ 1] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x27de37] > [pradnya-Lenovo-G570:04554] [ 2] lst() [0x8048871] > [pradnya-Lenovo-G570:04554] *** End of error message *** > -------------------------------------------------------------------------- > mpirun noticed that process rank 2 with PID 4553 on node pradnya-Lenovo-G570 exited on signal 11 (Segmentation fault) > > > so plz guide me. > check given attachment. > > thank you. > <last.c>_______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] installing mpich-1.2.6 to create libmpich.so.1.0
by Jeff Hammond 25 Jun '13

25 Jun '13

Try MPICH 3.0.4. MPICH 1.2.6 is ancient and not supported. This is how I build MPICH 3.0.4. You will have to edit the prefix option appropriately. wget http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz tar -xzf mpich-3.0.4.tar.gz cd mpich-3.0.4 mkdir build-gcc cd build-gcc/ ../configure CC=gcc CXX=g++ FC=gfortran F77=gfortran --enable-fc --enable-f77 --enable-threads --enable-g=dbg --with-device=ch3:nemesis --with-pm=hydra --prefix=. Jeff ----- Original Message ----- From: "Andre Pattantyus" <akp4221(a)hawaii.edu> To: discuss(a)mpich.org Sent: Tuesday, June 25, 2013 3:15:55 AM Subject: [mpich-discuss] installing mpich-1.2.6 to create libmpich.so.1.0 Hello, I am not familiar with installing mpich and am having problems with installation. I have found from searching online that mpich-1.2.6 produces libmpich.so.1.0 which I require run a certain program in parallel. I am unable to follow the installation documentation I have found online for this version because when i configure for ch_p4mpd I get an error when I run make. Therefore I just run ./configure and make but this does not produce my required libmpich.so.1.0. What do I need to specify prior to either configure or make in order to build this? I am building on a linux86-64 with pgi/10.2 compiler. -- Andre Pattantyus Graduate Student Research Assistant Department of Meteorology University of Hawaii at Manoa 2525 Correa Rd, HIG 350 Honolulu, HI 96822 Phone: (845) 264-3582 _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] discuss Digest, Vol 8, Issue 40
by pradnya dixit 25 Jun '13

25 Jun '13

Hello, I am trying to send chunk of data using send and recv funcions in mpi.. but facing so many problem or errors like Elements of rank 1 are: [pradnya-Lenovo-G570:04553] *** Process received signal *** [pradnya-Lenovo-G570:04553] Signal: Segmentation fault (11) [pradnya-Lenovo-G570:04553] Signal code: Address not mapped (1) [pradnya-Lenovo-G570:04553] Failing at address: 0x8be8950 [pradnya-Lenovo-G570:04554] *** Process received signal *** [pradnya-Lenovo-G570:04554] Signal: Segmentation fault (11) [pradnya-Lenovo-G570:04554] Signal code: Address not mapped (1) [pradnya-Lenovo-G570:04554] Failing at address: 0x8be8960 [pradnya-Lenovo-G570:04552] *** Process received signal *** [pradnya-Lenovo-G570:04552] Signal: Segmentation fault (11) [pradnya-Lenovo-G570:04552] Signal code: Address not mapped (1) [pradnya-Lenovo-G570:04552] Failing at address: 0x8be86f8 [pradnya-Lenovo-G570:04553] [ 0] [0xff440c] [pradnya-Lenovo-G570:04553] [ 1] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0xc66e37] [pradnya-Lenovo-G570:04553] [ 2] lst() [0x8048871] [pradnya-Lenovo-G570:04553] *** End of error message *** [pradnya-Lenovo-G570:04552] [ 0] [0x57c40c] [pradnya-Lenovo-G570:04552] [ 1] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x126e37] [pradnya-Lenovo-G570:04552] [ 2] lst() [0x8048871] [pradnya-Lenovo-G570:04552] *** End of error message *** [pradnya-Lenovo-G570:04554] [ 0] [0xd0740c] [pradnya-Lenovo-G570:04554] [ 1] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x27de37] [pradnya-Lenovo-G570:04554] [ 2] lst() [0x8048871] [pradnya-Lenovo-G570:04554] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 2 with PID 4553 on node pradnya-Lenovo-G570 exited on signal 11 (Segmentation fault) so plz guide me. check given attachment. thank you.

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installing mpich-1.2.6 to create libmpich.so.1.0
by Andre Pattantyus 25 Jun '13

25 Jun '13

Hello, I am not familiar with installing mpich and am having problems with installation. I have found from searching online that mpich-1.2.6 produces libmpich.so.1.0 which I require run a certain program in parallel. I am unable to follow the installation documentation I have found online for this version because when i configure for ch_p4mpd I get an error when I run make. Therefore I just run ./configure and make but this does not produce my required libmpich.so.1.0. What do I need to specify prior to either configure or make in order to build this? I am building on a linux86-64 with pgi/10.2 compiler. -- Andre Pattantyus Graduate Student Research Assistant Department of Meteorology University of Hawaii at Manoa 2525 Correa Rd, HIG 350 Honolulu, HI 96822 Phone: (845) 264-3582

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Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39
by Antonio J. Peña 24 Jun '13

24 Jun '13

Thanks Jeff, it looks trivial now you explained it. On Monday, June 24, 2013 04:30:57 PM Jeff Hammond wrote: > N threads calling MPI_Barrier corresponds to N different, unrelated > barriers. A thread calling MPI_Barrier will only synchronize with > other processes, not any other threads. > > MPI_Barrier only acts between processes. It has no effect on threads. > Just use comm=MPI_COMM_SELF and think about the behavior of > MPI_Barrier. That is the one-process limit of the multithreaded > problem. > > Jeff > > On Mon, Jun 24, 2013 at 4:22 PM, Antonio J. Peña <apenya(a)mcs.anl.gov> wrote: > > Hi Jeff, > > > > Please correct me where I'm wrong: if only one thread calls MPI_Barrier, > > that one will get locked while others will go ahead. On the other hand, > > if every thread calls MPI_Barrier, all will get locked in that call until > > the barrier completes. That doesn't mean this will be a replacement for > > thread-wise synchronization mechanisms, but will be effective for all of > > them waiting for the barrier. > > > > Antonio > > > > On Monday, June 24, 2013 04:14:20 PM Jeff Hammond wrote: > >> MPI_Barrier will not sync threads. If N threads call MPI_Barrier, you > >> will > >> get at best the same result as if you call MPI_Barrier N times from the > >> main thread. > >> > >> If you want to sync threads, you need to sync them with the appropriate > >> thread API. OpenMP and Pthreads both have barrier calls. If you want a > >> fast Pthread barrier, you should not use pthread_barrier though. The > >> Internet has details. > >> > >> Jeff > >> > >> ----- Original Message ----- > >> From: "Antonio J. Peña" <apenya(a)mcs.anl.gov> > >> To: discuss(a)mpich.org > >> Sent: Monday, June 24, 2013 3:49:08 PM > >> Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39 > >> > >> > >> > >> > >> > >> > >> Sufeng, > >> > >> > >> > >> I'd say you're OK syncing your threads by all of them calling > >> MPI_Barrier, > >> as it's a thread-safe function. > >> > >> > >> > >> Antonio > >> > >> > >> > >> > >> > >> On Monday, June 24, 2013 11:41:44 AM Sufeng Niu wrote: > >> > >> > >> Hi, Antonio > >> > >> > >> > >> Thanks a lot! Now I make sense. Let's say if I am running MPI and > >> multithreads program. If I called MPI_Barrier in each threads > >> > >> > >> what gonna happen? Will threads be synced by MPI_Barrier? or I should use > >> thread level sync? > >> > >> > >> > >> Thank you! > >> > >> > >> Sufeng > >> > >> > >> > >> > >> > >> > >> On Sun, Jun 23, 2013 at 6:54 PM, < discuss-request(a)mpich.org > wrote: > >> > >> > >> Send discuss mailing list submissions to > >> discuss(a)mpich.org > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://lists.mpich.org/mailman/listinfo/discuss > >> or, via email, send a message with subject or body 'help' to > >> discuss-request(a)mpich.org > >> > >> You can reach the person managing the list at > >> discuss-owner(a)mpich.org > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of discuss digest..." > >> > >> > >> Today's Topics: > >> > >> 1. Re: Error with MPI_Spawn (Jeff Hammond) > >> 2. Re: discuss Digest, Vol 8, Issue 37 (Antonio J. Pe?a) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sun, 23 Jun 2013 17:03:09 -0500 > >> From: Jeff Hammond < jeff.science(a)gmail.com > > >> To: " discuss(a)mpich.org " < discuss(a)mpich.org > > >> Subject: Re: [mpich-discuss] Error with MPI_Spawn > >> Message-ID: <-1578386667793986954@unknownmsgid> > >> Content-Type: text/plain; charset=ISO-8859-1 > >> > >> This is the wrong way to use PETSc and to parallelize a code with a > >> parallel library in general. > >> > >> Write the PETSc user list and they will explain to you how to > >> parallelize your code properly with PETSc. > >> > >> Jeff > >> > >> Sent from my iPhone > >> > >> On Jun 23, 2013, at 4:59 PM, Nitel Muhtaroglu < muhtaroglu.n(a)gmail.com > > > > > wrote: > >> > Hello, > >> > > >> > I am trying to integrate PETSc library to a serial program. The idea is > >> > that the serial program creates a linear equation system and then calls > >> > PETSc solver by MPI_Spawn and then solves this system in parallel. But > >> > when I execute MPI_Spawn the following error message occurs and the > >> > solver is not called. I couldn't find a solution to this error. Does > >> > anyone have an idea about it? > >> > > >> > Kind Regards, > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Sun, 23 Jun 2013 18:54:38 -0500 > >> From: Antonio J. Pe?a < apenya(a)mcs.anl.gov > > >> To: discuss(a)mpich.org > >> Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 37 > >> Message-ID: <8872211.IGCl89YM8r(a)localhost.localdomain> > >> Content-Type: text/plain; charset="iso-8859-1" > >> > >> > >> Sufeng, > >> > >> The correct way is to use the MPI_Init_thread function with > >> MPI_THREAD_MULTIPLE. This will tell the MPI implementation to be thread > >> safe. It supports OpenMP and Posix Threads (OpenMP primitives in most > >> systems are likely to be implemented on top of PThreads). > >> > >> Antonio > >> > >> > >> On Sunday, June 23, 2013 11:13:31 AM Sufeng Niu wrote: > >> > >> > >> Hi, Antonio > >> > >> > >> Thanks a lot for your reply, I just figure out that is the firewall > >> issue. > >> after I set the firewall. it works now. Thanks again. > >> > >> > >> But I still got a few questions on MPI and multithreads mixed > >> programming. > >> Currently, I try to run each process on each server, and each process > >> using thread pool to run multiple threads (pthread lib). I am not sure > >> whether it is the correct way or not. I wrote it as: > >> > >> > >> MPI_Init() > >> .... > >> ... > >> /* create thread pool and initial */ > >> ...... > >> /* fetch job into thread pool */ > >> ...... > >> > >> > >> MPI_Finalize(); > >> > >> > >> When I check the book and notes, I found people use > >> > >> > >> MPI_Init_thread() with MPI_THREAD_MULTIPLE > >> > >> > >> but the some docs said it supported OpenMP, is that possible to use it > >> with pthread library? > >> I am new guy to this hybrid programming. I am not sure which is the > >> proper > >> way to do it. Any suggestions are appreciate. Thank you! > >> > >> > >> Sufeng > >> > >> > >> > >> > >> On Sat, Jun 22, 2013 at 12:12 PM, < discuss-request(a)mpich.org [1]> wrote: > >> > >> > >> Send discuss mailing list submissions to discuss(a)mpich.org [2] > >> https://lists.mpich.org/mailman/listinfo/discuss[3] > >> discuss-request(a)mpich.org [1] > >> discuss-owner(a)mpich.org [4] > >> sniu(a)hawk.iit.edu [5]>To: discuss(a)mpich.org [2] > >> CAFNNHkwpqdGfZXctL0Uz3hpeL25mZZMtB93qGXjc_+tjnV4csA(a)mail.gmail.c > >> om[6]>Content-Type: text/plain; charset="iso-8859-1" > >> > >> Hi, > >> > >> Sorry to bother you guys on this stupid question. last time I re-install > >> OSfor all blades to keep them the same version. after I mount, set > >> keylessssh, the terimnal gives the error below: > >> > >> [ proxy:0:[email protected] [7]] > >> HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from > >> " iocfccd3.aps.anl.gov [8]" to" iocfccd1.aps.anl.gov [9]" (No route to > >> host) [ proxy:0:[email protected] [7]] main > >> (./pm/pmiserv/pmip.c:189): unable toconnect to server > >> iocfccd1.aps.anl.gov [9] at port 38242 (check for firewalls!) > >> > >> I can ssh from iocfccd1 to iocfccd3 without password. Should I shut > >> downall > >> firewalls on each server? I cannot find out where is the problem. > >> Thankyou > >> > >> --Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of > >> TechnologyTel: 312-731-7219[10] > >> http://lists.mpich.org/pipermail/discuss/attachments/20130621/5503b1bc/a > >> ttachment-0001.html[11] > > >> > >> ------------------------------ > >> > >> Message: 2Date: Fri, 21 Jun 2013 10:58:26 -0500From: Antonio J. Pe?a > >> < apenya(a)mcs.anl.gov [12]>To: discuss(a)mpich.org [2] > >> iocfccd1.aps.anl.gov [9]" from iocfccd3?[1] > >> > >> Antonio > >> > >> > >> On Friday, June 21, 2013 10:51:50 AM Sufeng Niu wrote: > >> > >> > >> Hi, > >> > >> > >> Sorry to bother you guys on this stupid question. last time I re-install > >> OS > >> forall blades to keep them the same version. after I mount, set keyless > >> ssh,the terimnal gives the error below: > >> > >> > >> proxy:0:[email protected] [7][2]] > >> HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from > >> " iocfccd3.aps.anl.gov [8][3]"to " iocfccd1.aps.anl.gov [9][1]" (No route > >> to host)[ proxy:0:[email protected] [7][2]] main > >> (./pm/pmiserv/pmip.c:189):unable to connect to server > >> iocfccd1.aps.anl.gov [9][1] at port 38242 (checkfor firewalls!) > >> > >> > >> > >> I can ssh from iocfccd1 to iocfccd3 without password. Should I shut > >> downall > >> firewalls on each server? I cannot find out where is the problem. > >> Thankyou > >> > >> > >> > >> > >> -- Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute > >> of > >> TechnologyTel: 312-731-7219[4] > >> > >> > >> --------[1] _ http://iocfccd1.aps.anl.gov_ > >> proxy%3A0%3A1(a)iocfccd3.aps.anl.gov [13] > >> http://iocfccd3.aps.anl.gov [8] > >> 312-731-7219[10] > >> http://lists.mpich.org/pipermail/discuss/attachments/20130621/01b37902/ > >> attachment-0001.html[14] > > >> > >> ------------------------------ > >> > >> Message: 3Date: Sat, 22 Jun 2013 12:49:10 -0400From: Jiri Simsa > >> < jsimsa(a)cs.cmu.edu [15]>To: discuss(a)mpich.org [2] > >> CAHs9ut-_6W6SOHTJ_rD+shQ76bo4cTCuFVAy1f9x- > >> J0gioakHg(a)mail.gmail.com [16]>Content-Type: text/plain; > >> charset="iso-8859-1" > >> > >> Hi, > >>

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Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39
by Jeff Hammond 24 Jun '13

24 Jun '13

N threads calling MPI_Barrier corresponds to N different, unrelated barriers. A thread calling MPI_Barrier will only synchronize with other processes, not any other threads. MPI_Barrier only acts between processes. It has no effect on threads. Just use comm=MPI_COMM_SELF and think about the behavior of MPI_Barrier. That is the one-process limit of the multithreaded problem. Jeff On Mon, Jun 24, 2013 at 4:22 PM, Antonio J. Peña <apenya(a)mcs.anl.gov> wrote: > > Hi Jeff, > > Please correct me where I'm wrong: if only one thread calls MPI_Barrier, that > one will get locked while others will go ahead. On the other hand, if every > thread calls MPI_Barrier, all will get locked in that call until the barrier > completes. That doesn't mean this will be a replacement for thread-wise > synchronization mechanisms, but will be effective for all of them waiting for > the barrier. > > Antonio > > > On Monday, June 24, 2013 04:14:20 PM Jeff Hammond wrote: >> MPI_Barrier will not sync threads. If N threads call MPI_Barrier, you will >> get at best the same result as if you call MPI_Barrier N times from the >> main thread. >> >> If you want to sync threads, you need to sync them with the appropriate >> thread API. OpenMP and Pthreads both have barrier calls. If you want a >> fast Pthread barrier, you should not use pthread_barrier though. The >> Internet has details. >> >> Jeff >> >> ----- Original Message ----- >> From: "Antonio J. Peña" <apenya(a)mcs.anl.gov> >> To: discuss(a)mpich.org >> Sent: Monday, June 24, 2013 3:49:08 PM >> Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 39 >> >> >> >> >> >> >> Sufeng, >> >> >> >> I'd say you're OK syncing your threads by all of them calling MPI_Barrier, >> as it's a thread-safe function. >> >> >> >> Antonio >> >> >> >> >> >> On Monday, June 24, 2013 11:41:44 AM Sufeng Niu wrote: >> >> >> Hi, Antonio >> >> >> >> Thanks a lot! Now I make sense. Let's say if I am running MPI and >> multithreads program. If I called MPI_Barrier in each threads >> >> >> what gonna happen? Will threads be synced by MPI_Barrier? or I should use >> thread level sync? >> >> >> >> Thank you! >> >> >> Sufeng >> >> >> >> >> >> >> On Sun, Jun 23, 2013 at 6:54 PM, < discuss-request(a)mpich.org > wrote: >> >> >> Send discuss mailing list submissions to >> discuss(a)mpich.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.mpich.org/mailman/listinfo/discuss >> or, via email, send a message with subject or body 'help' to >> discuss-request(a)mpich.org >> >> You can reach the person managing the list at >> discuss-owner(a)mpich.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of discuss digest..." >> >> >> Today's Topics: >> >> 1. Re: Error with MPI_Spawn (Jeff Hammond) >> 2. Re: discuss Digest, Vol 8, Issue 37 (Antonio J. Pe?a) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 23 Jun 2013 17:03:09 -0500 >> From: Jeff Hammond < jeff.science(a)gmail.com > >> To: " discuss(a)mpich.org " < discuss(a)mpich.org > >> Subject: Re: [mpich-discuss] Error with MPI_Spawn >> Message-ID: <-1578386667793986954@unknownmsgid> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> This is the wrong way to use PETSc and to parallelize a code with a >> parallel library in general. >> >> Write the PETSc user list and they will explain to you how to >> parallelize your code properly with PETSc. >> >> Jeff >> >> Sent from my iPhone >> >> On Jun 23, 2013, at 4:59 PM, Nitel Muhtaroglu < muhtaroglu.n(a)gmail.com > > wrote: >> > Hello, >> > >> > I am trying to integrate PETSc library to a serial program. The idea is >> > that the serial program creates a linear equation system and then calls >> > PETSc solver by MPI_Spawn and then solves this system in parallel. But >> > when I execute MPI_Spawn the following error message occurs and the >> > solver is not called. I couldn't find a solution to this error. Does >> > anyone have an idea about it? >> > >> > Kind Regards, >> >> ------------------------------ >> >> Message: 2 >> Date: Sun, 23 Jun 2013 18:54:38 -0500 >> From: Antonio J. Pe?a < apenya(a)mcs.anl.gov > >> To: discuss(a)mpich.org >> Subject: Re: [mpich-discuss] discuss Digest, Vol 8, Issue 37 >> Message-ID: <8872211.IGCl89YM8r(a)localhost.localdomain> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Sufeng, >> >> The correct way is to use the MPI_Init_thread function with >> MPI_THREAD_MULTIPLE. This will tell the MPI implementation to be thread >> safe. It supports OpenMP and Posix Threads (OpenMP primitives in most >> systems are likely to be implemented on top of PThreads). >> >> Antonio >> >> >> On Sunday, June 23, 2013 11:13:31 AM Sufeng Niu wrote: >> >> >> Hi, Antonio >> >> >> Thanks a lot for your reply, I just figure out that is the firewall issue. >> after I set the firewall. it works now. Thanks again. >> >> >> But I still got a few questions on MPI and multithreads mixed programming. >> Currently, I try to run each process on each server, and each process >> using thread pool to run multiple threads (pthread lib). I am not sure >> whether it is the correct way or not. I wrote it as: >> >> >> MPI_Init() >> .... >> ... >> /* create thread pool and initial */ >> ...... >> /* fetch job into thread pool */ >> ...... >> >> >> MPI_Finalize(); >> >> >> When I check the book and notes, I found people use >> >> >> MPI_Init_thread() with MPI_THREAD_MULTIPLE >> >> >> but the some docs said it supported OpenMP, is that possible to use it >> with pthread library? >> I am new guy to this hybrid programming. I am not sure which is the proper >> way to do it. Any suggestions are appreciate. Thank you! >> >> >> Sufeng >> >> >> >> >> On Sat, Jun 22, 2013 at 12:12 PM, < discuss-request(a)mpich.org [1]> wrote: >> >> >> Send discuss mailing list submissions to discuss(a)mpich.org [2] >> https://lists.mpich.org/mailman/listinfo/discuss[3] >> discuss-request(a)mpich.org [1] >> discuss-owner(a)mpich.org [4] >> sniu(a)hawk.iit.edu [5]>To: discuss(a)mpich.org [2] >> CAFNNHkwpqdGfZXctL0Uz3hpeL25mZZMtB93qGXjc_+tjnV4csA(a)mail.gmail.c >> om[6]>Content-Type: text/plain; charset="iso-8859-1" >> >> Hi, >> >> Sorry to bother you guys on this stupid question. last time I re-install >> OSfor all blades to keep them the same version. after I mount, set >> keylessssh, the terimnal gives the error below: >> >> [ proxy:0:[email protected] [7]] >> HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from >> " iocfccd3.aps.anl.gov [8]" to" iocfccd1.aps.anl.gov [9]" (No route to host) >> [ proxy:0:[email protected] [7]] main (./pm/pmiserv/pmip.c:189): >> unable toconnect to server iocfccd1.aps.anl.gov [9] at port 38242 (check >> for firewalls!) >> >> I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall >> firewalls on each server? I cannot find out where is the problem. Thankyou >> >> --Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of >> TechnologyTel: 312-731-7219[10] >> http://lists.mpich.org/pipermail/discuss/attachments/20130621/5503b1bc/a >> ttachment-0001.html[11] > >> >> ------------------------------ >> >> Message: 2Date: Fri, 21 Jun 2013 10:58:26 -0500From: Antonio J. Pe?a >> < apenya(a)mcs.anl.gov [12]>To: discuss(a)mpich.org [2] >> iocfccd1.aps.anl.gov [9]" from iocfccd3?[1] >> >> Antonio >> >> >> On Friday, June 21, 2013 10:51:50 AM Sufeng Niu wrote: >> >> >> Hi, >> >> >> Sorry to bother you guys on this stupid question. last time I re-install OS >> forall blades to keep them the same version. after I mount, set keyless >> ssh,the terimnal gives the error below: >> >> >> proxy:0:[email protected] [7][2]] >> HYDU_sock_connect(./utils/sock/sock.c:174): unable to connect from >> " iocfccd3.aps.anl.gov [8][3]"to " iocfccd1.aps.anl.gov [9][1]" (No route to >> host)[ proxy:0:[email protected] [7][2]] main >> (./pm/pmiserv/pmip.c:189):unable to connect to server >> iocfccd1.aps.anl.gov [9][1] at port 38242 (checkfor firewalls!) >> >> >> >> I can ssh from iocfccd1 to iocfccd3 without password. Should I shut downall >> firewalls on each server? I cannot find out where is the problem. Thankyou >> >> >> >> >> -- Best Regards,Sufeng NiuECASP lab, ECE department, Illinois Institute of >> TechnologyTel: 312-731-7219[4] >> >> >> --------[1] _ http://iocfccd1.aps.anl.gov_ >> proxy%3A0%3A1(a)iocfccd3.aps.anl.gov [13] >> http://iocfccd3.aps.anl.gov [8] >> 312-731-7219[10] >> http://lists.mpich.org/pipermail/discuss/attachments/20130621/01b37902/ >> attachment-0001.html[14] > >> >> ------------------------------ >> >> Message: 3Date: Sat, 22 Jun 2013 12:49:10 -0400From: Jiri Simsa >> < jsimsa(a)cs.cmu.edu [15]>To: discuss(a)mpich.org [2] >> CAHs9ut-_6W6SOHTJ_rD+shQ76bo4cTCuFVAy1f9x- >> J0gioakHg(a)mail.gmail.com [16]>Content-Type: text/plain; >> charset="iso-8859-1" >> >> Hi, >>

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