topic Re: Re:MPI-IO issue on devCloud in Intel® MPI Library

MPI-IO issue on devCloud

Matthew_Grismer — Wed, 17 Nov 2021 21:58:30 GMT

The latest Intel MPI on the devCloud appears to have an issue with MPI-IO that is related somehow to reading overlapped data with MPI_FILE_READ_ALL. I'm getting the following segmentation fault when running the attached program on 9 or more processors:

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image PC Routine Line Source

a.out 00000000004064EA Unknown Unknown Unknown

libpthread-2.31.s 00007FDCC59923C0 Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC4772850 Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC45AE6B9 Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC481CBEF Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC490D7C9 Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC490613D Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC426B023 Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC482974A PMPI_Waitall Unknown Unknown

libmpi.so.12.0.0 00007FDCC4115803 Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC411443D Unknown Unknown Unknown

libmpi.so.12.0.0 00007FDCC4B69324 PMPI_File_read_al Unknown Unknown

libmpifort.so.12. 00007FDCC626F458 pmpi_file_read_al Unknown Unknown

a.out 000000000040535C Unknown Unknown Unknown

a.out 0000000000404922 Unknown Unknown Unknown

libc-2.31.so 00007FDCC57B20B3 __libc_start_main Unknown Unknown

a.out 000000000040482E Unknown Unknown Unknown

The program simply writes a data file with integers and double precision reals, and then reads it back in again. This mimics what the actual code I am trying to use on the devCloud is doing. During both the write and the read some of the processors are overlapping data to/from the file.

Compile with:

ifx test_mpiio3.f90 -lmpifort

run with:

mpirun -np 9 ./a.out

Matt

Re: MPI-IO issue on devCloud

ArunJ_Intel — Sat, 05 Mar 2022 12:16:43 GMT

Hi Matt,

Thanks for reaching out to us.

I was able to reproduce the issue from my side on certain nodes on devcloud. Could you please try on the e-2176g (coffelake) nodes on devcloud where I could observe the command works without issues. Please find the below command to request a coffelake node.

qsub -l nodes=1:e-2176g:ppn=2 -d . -I

Thanks

Arun

Re:MPI-IO issue on devCloud

ArunJ_Intel — Mon, 22 Nov 2021 03:52:23 GMT

Hi Matt,

Have you tried running the application on a coffelake machine?

Thanks

Arun

Re: Re:MPI-IO issue on devCloud

Matthew_Grismer — Mon, 22 Nov 2021 17:45:03 GMT

Arun,

Yes, I verified my test program works on coffeelake too. Unfortunately, the code I am actually trying to run still does not work on coffeelake. So my example is does not capture all the issues apparently. What I can tell you is I am able to get the main code working by adjusting the MPI_FILE_READ_ALL statements. The original code looks like this:

CALL MPI_FILE_SET_VIEW ( fid, rstdisp, MPI_RP, reading_type(1), 'NATIVE', MPI_INFO_NULL, ierr )

CALL MPI_FILE_READ_ALL ( fid, x, 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, y, 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, z, 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, varg, nvar, reading_type(2), MPI_STATUS_IGNORE, ierr )

IF ( itimeint >= 2 ) CALL MPI_FILE_READ_ALL ( fid, qold, nvar, reading_type(2), MPI_STATUS_IGNORE, ierr )

The first three READ_ALL statements work fine where "1" element of the 3-dimensional datatype is read, the issue occurs in the fourth statement where "nvar" elements of the 3-dimensional datatype are read into a 4D array. I am able to make it work by replacing the fourth (and fifth) READ_ALL with individual statements for each 3D entry:

CALL MPI_FILE_SET_VIEW ( fid, rstdisp, MPI_RP, reading_type(1), 'NATIVE', MPI_INFO_NULL, ierr )

CALL MPI_FILE_READ_ALL ( fid, x, 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, y, 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, z, 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, varg(:,:,:,1), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, varg(:,:,:,2), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, varg(:,:,:,3), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, varg(:,:,:,4), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, varg(:,:,:,5), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

IF ( itimeint >= 2 ) then

CALL MPI_FILE_READ_ALL ( fid, qold(:,:,:,1), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, qold(:,:,:,2), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, qold(:,:,:,3), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, qold(:,:,:,4), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

CALL MPI_FILE_READ_ALL ( fid, qold(:,:,:,5), 1, reading_type(2), MPI_STATUS_IGNORE, ierr )

END IF

It may be that my example code is not generating a large enough dataset to exhibit the error on coffeelake, it may not have enough overlap in the data. But, hopefully it is still useful for tracking down the issue.

Matt

Re:MPI-IO issue on devCloud

SantoshY_Intel — Fri, 26 Nov 2021 07:26:36 GMT

Hi,

We have reported this issue to the concerned development team. They are looking into this issue.

Thanks & Regards,

Santosh

Re: MPI-IO issue on devCloud

SantoshY_Intel — Mon, 21 Feb 2022 10:26:48 GMT

Hi,

Your issue will be fixed soon in the Intel OneAPI future release. For the time being, I_MPI_FABRICS=ofi can be used as a workaround.

Use the below command for running your program:

I_MPI_FABRICS=ofi mpirun -np 9 ./a.out

If this resolves your issue, make sure to accept this as a solution. This would help others with similar issues. Thank you!

Best Regards,

Santosh

Re:MPI-IO issue on devCloud

SantoshY_Intel — Wed, 02 Mar 2022 05:53:52 GMT

Hi,

I assume that your issue is resolved. If you need any additional information, please post a new question as this thread will no longer be monitored by Intel.

Thanks & Regards,

Santosh