date:20171012

[OMPI users] Hybrid MPI+OpenMP benchmarks (looking for)

2017-10-12 Thread Sasso, John (GE Digital, consultant)

Thank you Peter.  I downloaded and built, and think it will suit our needs.  

-Original Message-
From: Peter Kjellström [mailto:c...@nsc.liu.se] 
Sent: Tuesday, October 10, 2017 5:38 AM
To: Sasso, John (GE Digital, consultant) 
Cc: Open MPI Users 
Subject: EXT: Re: [OMPI users] Hybrid MPI+OpenMP benchmarks (looking for)

HPGMG-FV is easy to build and to run both serial, mpi, openmp and
mpi+openmp.

/Peter

On Mon, 9 Oct 2017 17:54:02 +
"Sasso, John (GE Digital, consultant)"  wrote:

> I am looking for a decent hybrid MPI+OpenMP benchmark utility which I 
> can easily build and run with OpenMPI 1.6.5 (at least) and OpenMP 
> under Linux, using GCC build of OpenMPI as well as the Intel Compiler 
> suite.  I have looked at CP2K but that is much too complex a build for 
> its own good (I managed to build all the prerequisite libraries, only 
> to have the build of cp2k itself just fail).  Also looked at HOMB 1.0.
> 
> I am wondering what others have used.  The build should be simple and 
> not require a large # of prereq libraries to build beforehand.
> Thanks!
> 
> --john

___
users mailing list
users@lists.open-mpi.org
https://lists.open-mpi.org/mailman/listinfo/users

[OMPI users] Missing data with MPI I/O and NFS

2017-10-12 Thread Stephen Guzik

Hi,

I'm having trouble with parallel I/O to a file system mounted with NFS
over an infiniband network.  In my test code, I'm simply writing 1 byte
per process to the same file.  When using two nodes, some bytes are not
written (zero bits in the unwritten bytes).  Usually at least some data
from each node is written---it appears to be all data from one node and
partial from the other.

This used to work fine but broke when the cluster was upgraded from
Debian 8 to Debian 9.  I suspect an issue with NFS and not with
OpenMPI.  However, if anyone can suggest a work-around or ways to get
more information, I would appreciate it.  In the sole case where the
file system is exported with 'sync' and mounted with 'hard,intr', I get
the error:
[node1:14823] mca_sharedfp_individual_file_open: Error during datafile
file open
MPI_ERR_FILE: invalid file
[node2:14593] (same)

--

Some additional info:
- tested versions 1.8.8, 2.1.1, and 3.0.0 self-compiled and packaged and
vendor-supplied versions.  All have same behavior.
- all write methods (individual or collective) fail similarly.
- exporting the file system to two workstations across ethernet and
running the job across the two workstations seems to work fine.
- on a single node, everything works as expected in all cases.  In the
case described above where I get an error, the error is only observed
with processes on two nodes.
- code follows.

Thanks,
Stephen Guzik

--

#include 

#include 

int main(int argc, const char* argv[])
{
  MPI_File fh;
  MPI_Status status;

  int mpierr;
  char mpistr[MPI_MAX_ERROR_STRING];
  int mpilen;
  int numProc;
  int procID;
  MPI_Init(&argc, const_cast(&argv));
  MPI_Comm_size(MPI_COMM_WORLD, &numProc);
  MPI_Comm_rank(MPI_COMM_WORLD, &procID);

  const int filesize = numProc;
  const int bufsize = filesize/numProc;
  char *buf = new char[bufsize];
  buf[0] = (char)(48 + procID);
  int numChars = bufsize/sizeof(char);

  mpierr = MPI_File_open(MPI_COMM_WORLD, "dataio",
 MPI_MODE_CREATE | MPI_MODE_WRONLY,
MPI_INFO_NULL, &fh);
  if (mpierr != MPI_SUCCESS)
    {
  MPI_Error_string(mpierr, mpistr, &mpilen);
  std::cout << "Error: " << mpistr << std::endl;
    }
  mpierr = MPI_File_write_at_all(fh, (MPI_Offset)(procID*bufsize), buf,
 numChars, MPI_CHAR, &status);
  if (mpierr != MPI_SUCCESS)
    {
  MPI_Error_string(mpierr, mpistr, &mpilen);
  std::cout << "Error: " << mpistr << std::endl;
    }
  mpierr = MPI_File_close(&fh);
  if (mpierr != MPI_SUCCESS)
    {
  MPI_Error_string(mpierr, mpistr, &mpilen);
  std::cout << "Error: " << mpistr << std::endl;
    }

  delete[] buf;
  MPI_Finalize();
  return 0;
}

___
users mailing list
users@lists.open-mpi.org
https://lists.open-mpi.org/mailman/listinfo/users

Re: [OMPI users] Missing data with MPI I/O and NFS

2017-10-12 Thread Edgar Gabriel

try for now to switch to the romio314 component with OpenMPI. There is 
an issue with NFS and OMPIO that I am aware of and working on, that 
might trigger this behavior (although it should actually work for 
collective I/O even in that case).


try to set something like

mpirun --mca io romio314 ...

Thanks

Edgar


On 10/12/2017 8:26 PM, Stephen Guzik wrote:

Hi,

I'm having trouble with parallel I/O to a file system mounted with NFS
over an infiniband network.  In my test code, I'm simply writing 1 byte
per process to the same file.  When using two nodes, some bytes are not
written (zero bits in the unwritten bytes).  Usually at least some data
from each node is written---it appears to be all data from one node and
partial from the other.

This used to work fine but broke when the cluster was upgraded from
Debian 8 to Debian 9.  I suspect an issue with NFS and not with
OpenMPI.  However, if anyone can suggest a work-around or ways to get
more information, I would appreciate it.  In the sole case where the
file system is exported with 'sync' and mounted with 'hard,intr', I get
the error:
[node1:14823] mca_sharedfp_individual_file_open: Error during datafile
file open
MPI_ERR_FILE: invalid file
[node2:14593] (same)

--

Some additional info:
- tested versions 1.8.8, 2.1.1, and 3.0.0 self-compiled and packaged and
vendor-supplied versions.  All have same behavior.
- all write methods (individual or collective) fail similarly.
- exporting the file system to two workstations across ethernet and
running the job across the two workstations seems to work fine.
- on a single node, everything works as expected in all cases.  In the
case described above where I get an error, the error is only observed
with processes on two nodes.
- code follows.

Thanks,
Stephen Guzik

--

#include 

#include 

int main(int argc, const char* argv[])
{
   MPI_File fh;
   MPI_Status status;

   int mpierr;
   char mpistr[MPI_MAX_ERROR_STRING];
   int mpilen;
   int numProc;
   int procID;
   MPI_Init(&argc, const_cast(&argv));
   MPI_Comm_size(MPI_COMM_WORLD, &numProc);
   MPI_Comm_rank(MPI_COMM_WORLD, &procID);

   const int filesize = numProc;
   const int bufsize = filesize/numProc;
   char *buf = new char[bufsize];
   buf[0] = (char)(48 + procID);
   int numChars = bufsize/sizeof(char);

   mpierr = MPI_File_open(MPI_COMM_WORLD, "dataio",
  MPI_MODE_CREATE | MPI_MODE_WRONLY,
MPI_INFO_NULL, &fh);
   if (mpierr != MPI_SUCCESS)
 {
   MPI_Error_string(mpierr, mpistr, &mpilen);
   std::cout << "Error: " << mpistr << std::endl;
 }
   mpierr = MPI_File_write_at_all(fh, (MPI_Offset)(procID*bufsize), buf,
  numChars, MPI_CHAR, &status);
   if (mpierr != MPI_SUCCESS)
 {
   MPI_Error_string(mpierr, mpistr, &mpilen);
   std::cout << "Error: " << mpistr << std::endl;
 }
   mpierr = MPI_File_close(&fh);
   if (mpierr != MPI_SUCCESS)
 {
   MPI_Error_string(mpierr, mpistr, &mpilen);
   std::cout << "Error: " << mpistr << std::endl;
 }

   delete[] buf;
   MPI_Finalize();
   return 0;
}

___
users mailing list
users@lists.open-mpi.org
https://lists.open-mpi.org/mailman/listinfo/users


___
users mailing list
users@lists.open-mpi.org
https://lists.open-mpi.org/mailman/listinfo/users

Re: [OMPI users] Missing data with MPI I/O and NFS

2017-10-12 Thread Edgar Gabriel


I opened an issue on this, hope to have the fix available next week.

https://github.com/open-mpi/ompi/issues/4334

Thanks
Edgar

On 10/12/2017 8:36 PM, Edgar Gabriel wrote:

try for now to switch to the romio314 component with OpenMPI. There is
an issue with NFS and OMPIO that I am aware of and working on, that
might trigger this behavior (although it should actually work for
collective I/O even in that case).

try to set something like

mpirun --mca io romio314 ...

Thanks

Edgar


On 10/12/2017 8:26 PM, Stephen Guzik wrote:

Hi,

I'm having trouble with parallel I/O to a file system mounted with NFS
over an infiniband network.  In my test code, I'm simply writing 1 byte
per process to the same file.  When using two nodes, some bytes are not
written (zero bits in the unwritten bytes).  Usually at least some data
from each node is written---it appears to be all data from one node and
partial from the other.

This used to work fine but broke when the cluster was upgraded from
Debian 8 to Debian 9.  I suspect an issue with NFS and not with
OpenMPI.  However, if anyone can suggest a work-around or ways to get
more information, I would appreciate it.  In the sole case where the
file system is exported with 'sync' and mounted with 'hard,intr', I get
the error:
[node1:14823] mca_sharedfp_individual_file_open: Error during datafile
file open
MPI_ERR_FILE: invalid file
[node2:14593] (same)

--

Some additional info:
- tested versions 1.8.8, 2.1.1, and 3.0.0 self-compiled and packaged and
vendor-supplied versions.  All have same behavior.
- all write methods (individual or collective) fail similarly.
- exporting the file system to two workstations across ethernet and
running the job across the two workstations seems to work fine.
- on a single node, everything works as expected in all cases.  In the
case described above where I get an error, the error is only observed
with processes on two nodes.
- code follows.

Thanks,
Stephen Guzik

--

#include 

#include 

int main(int argc, const char* argv[])
{
MPI_File fh;
MPI_Status status;

int mpierr;
char mpistr[MPI_MAX_ERROR_STRING];
int mpilen;
int numProc;
int procID;
MPI_Init(&argc, const_cast(&argv));
MPI_Comm_size(MPI_COMM_WORLD, &numProc);
MPI_Comm_rank(MPI_COMM_WORLD, &procID);

const int filesize = numProc;
const int bufsize = filesize/numProc;
char *buf = new char[bufsize];
buf[0] = (char)(48 + procID);
int numChars = bufsize/sizeof(char);

mpierr = MPI_File_open(MPI_COMM_WORLD, "dataio",
   MPI_MODE_CREATE | MPI_MODE_WRONLY,
MPI_INFO_NULL, &fh);
if (mpierr != MPI_SUCCESS)
  {
MPI_Error_string(mpierr, mpistr, &mpilen);
std::cout << "Error: " << mpistr << std::endl;
  }
mpierr = MPI_File_write_at_all(fh, (MPI_Offset)(procID*bufsize), buf,
   numChars, MPI_CHAR, &status);
if (mpierr != MPI_SUCCESS)
  {
MPI_Error_string(mpierr, mpistr, &mpilen);
std::cout << "Error: " << mpistr << std::endl;
  }
mpierr = MPI_File_close(&fh);
if (mpierr != MPI_SUCCESS)
  {
MPI_Error_string(mpierr, mpistr, &mpilen);
std::cout << "Error: " << mpistr << std::endl;
  }

delete[] buf;
MPI_Finalize();
return 0;
}

___
users mailing list
users@lists.open-mpi.org
https://lists.open-mpi.org/mailman/listinfo/users

___
users mailing list
users@lists.open-mpi.org
https://lists.open-mpi.org/mailman/listinfo/users


___
users mailing list
users@lists.open-mpi.org
https://lists.open-mpi.org/mailman/listinfo/users

[OMPI users] Hybrid MPI+OpenMP benchmarks (looking for)

[OMPI users] Missing data with MPI I/O and NFS

Re: [OMPI users] Missing data with MPI I/O and NFS

Re: [OMPI users] Missing data with MPI I/O and NFS

4 matches

Site Navigation

Mail list logo

Footer information