[mpich-discuss] MPI_Init hangs under Slurm

Fri Feb 18 14:08:22 CST 2022

I’m clueless.  Here is the correct output, running mpiexec inside of sbatch.

Kurt

From: Zhou, Hui <zhouh at anl.gov>
Sent: Friday, February 18, 2022 2:00 PM
To: Raffenetti, Ken <raffenet at anl.gov>; discuss at mpich.org
Cc: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov>
Subject: [EXTERNAL] Re: [mpich-discuss] MPI_Init hangs under Slurm

Hi Kurt,

Did you run mpiexec inside sbatch? It will need sbatch to allocate the nodes.

--
Hui
________________________________
From: Mccall, Kurt E. (MSFC-EV41) via discuss <discuss at mpich.org<mailto:discuss at mpich.org>>
Sent: Friday, February 18, 2022 1:39 PM
To: Raffenetti, Ken <raffenet at anl.gov<mailto:raffenet at anl.gov>>; discuss at mpich.org<mailto:discuss at mpich.org> <discuss at mpich.org<mailto:discuss at mpich.org>>
Cc: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
Subject: Re: [mpich-discuss] MPI_Init hangs under Slurm

Here is the --verbose output.    Is it trying to launch the processes all on the head node rocci.ndc.nasa.gov?

Kurt

-----Original Message-----
From: Raffenetti, Ken <raffenet at anl.gov<mailto:raffenet at anl.gov>>
Sent: Friday, February 18, 2022 1:31 PM
To: discuss at mpich.org<mailto:discuss at mpich.org>
Cc: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
Subject: [EXTERNAL] Re: [mpich-discuss] MPI_Init hangs under Slurm

From the looks of it, using the ssh launcher might not be able to access all the nodes. To confirm, can you try launching a non-MPI program? Something like

      mpiexec -verbose -launcher ssh -print-all-exitcodes -np 20 -ppn1 hostname

Ken

On 2/17/22, 2:39 PM, "Mccall, Kurt E. (MSFC-EV41) via discuss" <discuss at mpich.org<mailto:discuss at mpich.org>> wrote:

    Sorry, my attachment with an .out extension was blocked.  Here is the file with a .txt extension.

    From: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
    Sent: Thursday, February 17, 2022 2:36 PM
    To: discuss at mpich.org<mailto:discuss at mpich.org>
    Cc: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov<mailto:kurt.e.mccall at nasa.gov>>
    Subject: MPI_Init hangs under Slurm

    Things were working fine when I was launching 1 node jobs under Slurm 20.11.8, but when I launched a 20 node job, MPICH hangs in MPI_Init.   The output of “mpiexec -verbose” is attached, and the stack trace at the point where it hangs is below.

    In the “mpiexec -verbose” output, I wonder why variables such as PATH_modshare point to our Intel MPI implementation, which I am no using.    I am using MPICH 4.0 with a patch that Ken Raffenetti provided (which makes MPICH recognize the “host” info key).  My $PATH and $LD_LIBRARY_PATH variables definitely point to the correct MPICH installation.

    I appreciate any help you can give.

    Here is the Slurm sbatch command:

    sbatch --nodes=20 --ntasks=20 --job-name $job_name --exclusive –verbose

    Here is the mpiexec command:

    mpiexec -verbose -launcher ssh -print-all-exitcodes -np 20  -wdir ${work_dir} -env DISPLAY localhost:10.0 --ppn 1 <many more args…>

    Stack trace at MPI_Init:

    #0  0x00007f6d85f499b2 in read () from /lib64/libpthread.so.0
    #1  0x00007f6d87a5753a in PMIU_readline (fd=5, buf=buf at entry=0x7ffd6fb596e0 "", maxlen=maxlen at entry=1024)
        at ../mpich-slurm-patch-4.0/src/pmi/simple/simple_pmiutil.c:134
    #2  0x00007f6d87a57a56 in GetResponse (request=0x7f6d87b48351 "cmd=barrier_in\n",
        expectedCmd=0x7f6d87b48345 "barrier_out", checkRc=0) at ../mpich-slurm-patch-4.0/src/pmi/simple/simple_pmi.c:818
    #3  0x00007f6d87a29915 in MPIDI_PG_SetConnInfo (rank=rank at entry=0,
        connString=connString at entry=0x1bbf5a0 "description#n001$port#33403$ifname#172.16.56.1$")
        at ../mpich-slurm-patch-4.0/src/mpid/ch3/src/mpidi_pg.c:559
    #4  0x00007f6d87a38611 in MPID_nem_init (pg_rank=pg_rank at entry=0, pg_p=pg_p at entry=0x1bbf850, has_parent=<optimized out>)
        at ../mpich-slurm-patch-4.0/src/mpid/ch3/channels/nemesis/src/mpid_nem_init.c:393
    #5  0x00007f6d87a2ad93 in MPIDI_CH3_Init (has_parent=<optimized out>, pg_p=0x1bbf850, pg_rank=0)
        at ../mpich-slurm-patch-4.0/src/mpid/ch3/channels/nemesis/src/ch3_init.c:83
    #6  0x00007f6d87a1b3b7 in init_world () at ../mpich-slurm-patch-4.0/src/mpid/ch3/src/mpid_init.c:190
    #7  MPID_Init (requested=<optimized out>, provided=provided at entry=0x7f6d87e03540 <MPIR_ThreadInfo>)
        at ../mpich-slurm-patch-4.0/src/mpid/ch3/src/mpid_init.c:76
    #8  0x00007f6d879828eb in MPII_Init_thread (argc=argc at entry=0x7ffd6fb5a5cc, argv=argv at entry=0x7ffd6fb5a5c0,
        user_required=0, provided=provided at entry=0x7ffd6fb5a574, p_session_ptr=p_session_ptr at entry=0x0)
        at ../mpich-slurm-patch-4.0/src/mpi/init/mpir_init.c:208
    #9  0x00007f6d879832a5 in MPIR_Init_impl (argc=0x7ffd6fb5a5cc, argv=0x7ffd6fb5a5c0)
        at ../mpich-slurm-patch-4.0/src/mpi/init/mpir_init.c:93
    #10 0x00007f6d8786388e in PMPI_Init (argc=0x7ffd6fb5a5cc, argv=0x7ffd6fb5a5c0)
        at ../mpich-slurm-patch-4.0/src/binding/c/init/init.c:46
    #11 0x000000000040640d in main (argc=23, argv=0x7ffd6fb5ad68) at src/NeedlesMpiManagerMain.cpp:53
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