topic Hi Anatoly, in Intel® MPI Library

Running executable compiled with MPI without using mpirun

Dierker__Steve — Wed, 13 Mar 2019 16:40:32 GMT

Hello,

I'm having trouble running the abinit (8.10.2) executable (electronic structure program; www.abinit.org) after compiling with the Intel 19 Update 3 compilers and with MPI enabled (64 bit intel linux).

If I compile with either the gnu tools or the Intel tools (icc, ifort), and without MPI enabled, I can directly run the abinit executable with no errors.

If I compile with the gnu tools and MPI enabled (using openmpi), I can still run the abinit executable direclty (without using mpirun) without errors.

If I compile with the Intel tools (mpiicc, mpiifort) and MPI enabled (using intel MPI), and then try to run the abinit executable directly (without mpirun), then it fails with the following error when trying to read in the input file (t01.input):

abinit < t01.input > OUT-traceback
forrtl: severe (24): end-of-file during read, unit 5, file /proc/26824/fd/0
Image      PC                 Routine        Line      Source
libifcoremt.so.5 00007F0847FAC7B6 for__io_return Unknown Unknown
libifcoremt.so.5 00007F0847FEAC00 for_read_seq_fmt   Unknown Unknown
abinit       000000000187BC1F m_dtfil_mp_iofn1_   1363        m_dtfil.F90
abinit       0000000000407C49 MAIN__ 251          abinit.F90
abinit       0000000000407942 Unknown    Unknown Unknown
libc-2.27.so    00007F08459E4B97 __libc_start_main Unknown Unknown
abinit     000000000040782A Unknown    Unknown Unknown

If I compile with the Intel tools and MPI enabled and run the abinit executable with "mpirun -np 1 abinit < t01.input > OUT-traceback" then reading the input file succeeds.

Running the MPI enabled executable without mpirun succeeds when compiled with the gnu tools, but not when compiled with the intel tools.

A colleague of mine compiled abinit with MPI enabled using the Intel 17 compiler and IS able to run the abinit executable without mpirun.

I am using Intel Parallel Studio XE Cluster Edition Update 3 and source psxevars.sh to set the environment before compiling/running with intel. The output of mpiifort -V is:

mpiifort -V
Intel(R) Fortran Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 19.0.3.199 Build 20190206
Copyright (C) 1985-2019 Intel Corporation. All rights reserved.

Any ideas on what is causing this forrtl crash?

Thanks for any suggestions.

I came across this change in

Jakub_Benda — Thu, 25 Apr 2019 18:33:00 GMT

I came across this change in behaviour in Intel MPI 2019, too, though in different context. It seems that when you want to access the standard input after the call to MPI_Init, you need to launch the application using mpiexec/mpirun.

For example, "echo 1 | ./test_out" will work with this code:

program test_out

    read (5, *) n
    write (6, *) n

    call MPI_Init(ierr)
    call MPI_Finalize(ierr)

end program test_out

but "echo 1 | ./test_in" will not work with this code:

program test_in

    call MPI_Init(ierr)

    read (5, *) n
    write (6, *) n

    call MPI_Finalize(ierr)

end program test_in

unless you execute it as "echo 1 | mpiexec -n 1 ./test_in".

Hello,

Anatoliy_R_Intel — Tue, 02 Jul 2019 12:24:11 GMT

Hello,

Thank you for finding this issue. It will be fixed in one of Intel MPI 2020 updates.

Best regards, Anatoliy.

Hi Steve, Jacub,

Anatoliy_R_Intel — Mon, 16 Sep 2019 07:46:00 GMT

Hi Steve, Jacub,

Could you check 2019 Update 5? That issue should be fixed there.

Best regards, Anatoliy.

I also ran into a similar

ARaoo — Tue, 24 Sep 2019 23:55:48 GMT

I also ran into a similar issue and I do not think it is resolved in update 5 (2019.5.281), I had to use a lower version for this purpose (not performance measurement)!

Regards,

Amir

Hi Anatoly,

Dierker__Steve — Thu, 26 Sep 2019 01:21:15 GMT

Hi Anatoly,

Thanks for following up on this.

Unfortunately, 2019 Update 5 does not fix this problem. The behavior is the same as before, both for the abinit application and for the simple test code that Jakub posted, which succinctly illustrates the issue.

To repeat, with test_in.f given by:

    program test_in
   call MPI_Init(ierr)
   read (5,*)n
   write (6,*) n
   call MPI_Finalize(ierr)
   end program test_in

Running "echo 1 | ./test_in" results in:

forrtl: severe (24): end-of-file during read, unit 5, file /proc/15219/fd/0
Image              PC                Routine            Line        Source
test_in            000000000042A8EB Unknown               Unknown Unknown
test_in            00000000004095E8 Unknown               Unknown Unknown
test_in            0000000000402CD6 MAIN__                      3 test_in.f
test_in            0000000000402C42 Unknown               Unknown Unknown
libc-2.27.so       00001469FDC92B97 __libc_start_main     Unknown Unknown
test_in            0000000000402B2A Unknown               Unknown Unknown

I've tried this code with 2018 Update 4 and it worked fine. It stopped working with 2019 and is still not working with all updates since then, including Update 5.

steve

Hi,

Anatoliy_R_Intel — Thu, 26 Sep 2019 08:13:08 GMT

Hi,

I'm sorry, it's my mistake. The fix for this issue was not included to 2019 Update 5. This fix will be available in 2019 Update 6.

Best regards, Anatoliy.

Hi,

Dierker__Steve — Sat, 30 Nov 2019 17:40:00 GMT

Hi,

I see that 2019 Update 6 (for the MPI library, not the entire PSXE suite) was released on Nov 6. I tested it and it does indeed fix the problem I reported above.

Thank you to Intel for being so responsive in addressing this issue.

Best Regards,

steve