November 2016 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] Hybrid HPC system
by Kenneth Raffenetti 16 Nov '16

16 Nov '16

Have you disabled any and all firewalls on both nodes? It sounds like they are unable to communicate in initialization. Ken On 11/16/2016 07:34 AM, Doha Ehab wrote: > Yes, I built MPICH-3 on both systems and I tried the code on each node > separately and it worked, I tried each node with other nodes that has > the same operating system and it worked as well. > When I try the code on the 2 nodes that have different operating systems > no result or error message appear. > > Regards > Doha > > On Mon, Nov 14, 2016 at 6:25 PM, Kenneth Raffenetti > <raffenet(a)mcs.anl.gov <mailto:[email protected]>> wrote: > > It may be possible to run in such a setup, but it would not be > recommended. Did you build MPICH on both systems you are trying to > run on? What exactly happened when the code didn't work? > > Ken > > > On 11/13/2016 12:36 AM, Doha Ehab wrote: > > Hello, > I tried to run a parallel (Hello World) C code on a cluster > that has 2 > nodes, the nodes have different operating system so the code did not > work and no results were printed. > How to make such a cluster work? is there is extra steps that > should be > done? > > Regards, > Doha > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > <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 > <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

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Re: [mpich-discuss] Hybrid HPC system
by Doha Ehab 16 Nov '16

16 Nov '16

Yes, I built MPICH-3 on both systems and I tried the code on each node separately and it worked, I tried each node with other nodes that has the same operating system and it worked as well. When I try the code on the 2 nodes that have different operating systems no result or error message appear. Regards Doha On Mon, Nov 14, 2016 at 6:25 PM, Kenneth Raffenetti <raffenet(a)mcs.anl.gov> wrote: > It may be possible to run in such a setup, but it would not be > recommended. Did you build MPICH on both systems you are trying to run on? > What exactly happened when the code didn't work? > > Ken > > > On 11/13/2016 12:36 AM, Doha Ehab wrote: > >> Hello, >> I tried to run a parallel (Hello World) C code on a cluster that has 2 >> nodes, the nodes have different operating system so the code did not >> work and no results were printed. >> How to make such a cluster work? is there is extra steps that should be >> done? >> >> Regards, >> Doha >> >> >> _______________________________________________ >> 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

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Re: [mpich-discuss] Hybrid HPC system
by Kenneth Raffenetti 14 Nov '16

14 Nov '16

It may be possible to run in such a setup, but it would not be recommended. Did you build MPICH on both systems you are trying to run on? What exactly happened when the code didn't work? Ken On 11/13/2016 12:36 AM, Doha Ehab wrote: > Hello, > I tried to run a parallel (Hello World) C code on a cluster that has 2 > nodes, the nodes have different operating system so the code did not > work and no results were printed. > How to make such a cluster work? is there is extra steps that should be > done? > > Regards, > Doha > > > _______________________________________________ > 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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Hybrid HPC system
by Doha Ehab 13 Nov '16

13 Nov '16

Hello, I tried to run a parallel (Hello World) C code on a cluster that has 2 nodes, the nodes have different operating system so the code did not work and no results were printed. How to make such a cluster work? is there is extra steps that should be done? Regards, Doha _______________________________________________ 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] Size of a type created with MPI_Type_create_darray
by Rob Latham 11 Nov '16

11 Nov '16

On 11/11/2016 07:36 AM, Dorier, Matthieu wrote: > Hi, > > I have a trace of an MPI program in which parameters of every MPI calls > have been recorded. Some communication functions are using a > user-defined type created with MPI_Type_create_darray. > > I would like to know what is the size of this type as a function of the > parameters passed to MPI_Type_create_darray (again, I'm working on a > trace, so I can't just call MPI_Type_size). We can assume, for > simplicity, that the oldtype parameter is MPI_BYTE. I'm having troubles > understanding, from the standard and from online documentation, how this > function works and how I can compute this size. Could you help? the romio flatten.c and ad_darray.c code might be helpful? I'd be tempted to make your trace program a singleton MPI program just so you *can* call MPI_Type_size. Or, make two passes over your trace and generate a darray lookup table? ==rob > > Thanks, > > Matthieu > > > _______________________________________________ > 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] Size of a type created with MPI_Type_create_darray
by Dorier, Matthieu 11 Nov '16

11 Nov '16

Yes but I have no control over what was used since it's in the trace of an already-executed program. Thanks, Matthieu ________________________________ From: Jeff Hammond [jeff.science(a)gmail.com] Sent: Friday, November 11, 2016 9:20 AM To: MPICH Subject: Re: [mpich-discuss] Size of a type created with MPI_Type_create_darray I've always found darray types to be profoundly confusing. You might try to use MPI_Type_create_subarray instead. Jeff On Fri, Nov 11, 2016 at 5:36 AM, Dorier, Matthieu <mdorier(a)anl.gov<mailto:[email protected]>> wrote: Hi, I have a trace of an MPI program in which parameters of every MPI calls have been recorded. Some communication functions are using a user-defined type created with MPI_Type_create_darray. I would like to know what is the size of this type as a function of the parameters passed to MPI_Type_create_darray (again, I'm working on a trace, so I can't just call MPI_Type_size). We can assume, for simplicity, that the oldtype parameter is MPI_BYTE. I'm having troubles understanding, from the standard and from online documentation, how this function works and how I can compute this size. Could you help? Thanks, Matthieu _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond jeff.science(a)gmail.com<mailto:[email protected]> http://jeffhammond.github.io/ _______________________________________________ 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] Size of a type created with MPI_Type_create_darray
by Jeff Hammond 11 Nov '16

11 Nov '16

I've always found darray types to be profoundly confusing. You might try to use MPI_Type_create_subarray instead. Jeff On Fri, Nov 11, 2016 at 5:36 AM, Dorier, Matthieu <mdorier(a)anl.gov> wrote: > Hi, > > I have a trace of an MPI program in which parameters of every MPI calls > have been recorded. Some communication functions are using a user-defined > type created with MPI_Type_create_darray. > > I would like to know what is the size of this type as a function of the > parameters passed to MPI_Type_create_darray (again, I'm working on a trace, > so I can't just call MPI_Type_size). We can assume, for simplicity, that > the oldtype parameter is MPI_BYTE. I'm having troubles understanding, from > the standard and from online documentation, how this function works and how > I can compute this size. Could you help? > > Thanks, > > Matthieu > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Jeff Hammond jeff.science(a)gmail.com http://jeffhammond.github.io/ _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Size of a type created with MPI_Type_create_darray
by Dorier, Matthieu 11 Nov '16

11 Nov '16

Hi, I have a trace of an MPI program in which parameters of every MPI calls have been recorded. Some communication functions are using a user-defined type created with MPI_Type_create_darray. I would like to know what is the size of this type as a function of the parameters passed to MPI_Type_create_darray (again, I'm working on a trace, so I can't just call MPI_Type_size). We can assume, for simplicity, that the oldtype parameter is MPI_BYTE. I'm having troubles understanding, from the standard and from online documentation, how this function works and how I can compute this size. Could you help? Thanks, Matthieu _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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[mpich-devel] Meet Us at SC '16
by Kenneth Raffenetti 10 Nov '16

10 Nov '16

The link below shows events where the MPICH team will be present at SC '16. https://www.mpich.org/2016/10/25/meet-us-at-sc-16/ Come and say hi! _______________________________________________ To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/devel

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Re: [mpich-discuss] ADIOI_Set_lock error
by Luke Van Roekel 03 Nov '16

03 Nov '16

setting the driver as outlined by rob, fixed the issue with the program. Thanks! Luke On Tue, Nov 1, 2016 at 11:52 AM, Rob Latham <robl(a)mcs.anl.gov> wrote: > > > On 11/01/2016 11:10 AM, Wei-keng Liao wrote: > >> Hi, Luke >> >> Could you try the attached program and run by adding "lustre:" prefix to >> the filename? >> I.e. mpiexec -n 2 a.out lustre:/path/to/Lustre/testfile >> >> This checks whether the Intel MPI calls the Lustre driver correctly. >> >> > Intel's MPI does driver selection a little differently. Does prefixing > the file name work? > > http://press3.mcs.anl.gov/romio/2014/06/12/romio-and-intel-mpi/ > > You request a file system with the I_MPI_EXTRA_FILESYSTEM and > I_MPI_EXTRA_FILESYSTEM_LIST environment variables. > > ==rob > > Wei-keng >> >> >> >> On Nov 1, 2016, at 10:00 AM, Luke Van Roekel wrote: >> >> Thanks Rob, no luck with the mpi_info object and our computing folks are >>> not willing to set the necessary option. Do you know why this is specific >>> to intel-mpi? Openmpi has no issue. Our HPC people thought the >>> MPI_File_write_at_all always requires a file lock, but openmpi seems to be >>> fine. >>> >>> On Tue, Nov 1, 2016 at 8:42 AM, Rob Latham <robl(a)mcs.anl.gov> wrote: >>> >>> >>> On 10/31/2016 11:47 PM, Luke Van Roekel wrote: >>> Hello, >>> >>> I've been trying to compile and run a very simple mpi test on our >>> cluster with intel-mpi and openmpi. The test program is below. When I >>> run with openmpi everything is fine. When I run with intel-mpi, I >>> receive the following error >>> >>> This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. >>> Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 6,cmd >>> F_SETLKW/7,type F_WRLCK/1,whence 0) with return value FFFFFFFF and errno >>> 26. >>> >>> >>> - If the file system is NFS, you need to use NFS version 3, ensure that >>> the lockd daemon is running on all the machines, and mount the directory >>> with the 'noac' option (no attribute caching). >>> >>> - If the file system is LUSTRE, ensure that the directory is mounted >>> with the 'flock' option. >>> >>> ADIOI_Set_lock:: Function not implemented >>> >>> ADIOI_Set_lock:offset 0, length 4 >>> >>> >>> your site administrator needs to enable fcntl locking with the 'flock' >>> mount option . >>> >>> You can try disabling data sieving: you would create an MPI_Info object >>> and add the key "romio_ds_write" with the value "disable" >>> >>> ==rob >>> >>> >>> >>> Any thoughts on how to proceed? The size/format of the file read in >>> seems to make no difference. >>> >>> Regards, >>> Luke >>> >>> >>> #include <stdio.h> >>> >>> #include <stdlib.h> >>> >>> #include <mpi.h> >>> >>> >>> >>> int main(int argc, char **argv) { >>> >>> int buf, err; >>> >>> MPI_File fh; >>> >>> MPI_Status status; >>> >>> >>> MPI_Init(&argc, &argv); >>> >>> if (argc != 2) { >>> >>> printf("Usage: %s filename\n", argv[0]); >>> >>> MPI_Finalize(); >>> >>> return 1; >>> >>> } >>> >>> err = MPI_File_open(MPI_COMM_WORLD, argv[1], MPI_MODE_CREATE | >>> >>> MPI_MODE_RDWR, MPI_INFO_NULL, &fh); >>> >>> if (err != MPI_SUCCESS) printf("Error: MPI_File_open()\n"); >>> >>> >>> err = MPI_File_write_all(fh, &buf, 1, MPI_INT, &status); >>> >>> if (err != MPI_SUCCESS) printf("Error: MPI_File_write_all()\n"); >>> >>> >>> MPI_File_close(&fh); >>> >>> MPI_Finalize(); >>> >>> return 0; >>> >>> } >>> >>> >>> >>> _______________________________________________ >>> 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 >> > _______________________________________________ > 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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