[mpich-discuss] MPI_Init hangs under Slurm

[Zhou, Hui]

Hi Kurt,

We have fixed the bug when launching using PMI1 and mpiexec -- https://github.com/pmodels/mpich/issues/5835. Could you checkout the latest main​ branch on github and test? Let us know if you need instructions on building from git checkouts. We are working on the remaining scenarios.

--
Hui Zhou
[https://opengraph.githubassets.com/625f481fa04d88c26174a96205e1a5fc12fb0eb785bcb64a3ac06060ed8e554f/pmodels/mpich/issues/5835]<https://github.com/pmodels/mpich/issues/5835>
MPI_Comm_spawn in Slurm environment · Issue #5835 · pmodels/mpich<https://github.com/pmodels/mpich/issues/5835>
Originated from user email https://lists.mpich.org/pipermail/discuss/2022-January/006360.html. 1. MPICH + Hydra + PMI1 (crashes) Fixed in #5838 2. MPICH + Hydra + PMI2 (works but ignores "host...
github.com

________________________________
From: Mccall, Kurt E. (MSFC-EV41) via discuss <discuss at mpich.org>
Sent: Thursday, February 17, 2022 2:38 PM
To: discuss at mpich.org <discuss at mpich.org>
Cc: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov>
Subject: Re: [mpich-discuss] MPI_Init hangs under Slurm


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>
Sent: Thursday, February 17, 2022 2:36 PM
To: discuss at mpich.org
Cc: Mccall, Kurt E. (MSFC-EV41) <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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