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<div dir="auto">Is there a way to get mpich to output more debug information, or to get it to do more retries or similar?<br>
<br>
Is it using certain ports for the sockets, and can those be changed?<br>
<br>
When used with LSF, how does it get the host names? Does it only use $LSB_HOSTS? Because I have identified an issue with another app that is fixed by using IPs instead of Hostnames, so I have a shim that re-sets LSB_HOSTS to IPs, but it doesn’t seem to help
with mpich.<br>
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<div class="matchFont">Cheers,
<div>Sendu</div>
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<div name="messageReplySection">On 18 Feb 2021, 01:34 +0000, Zhou, Hui <zhouh@anl.gov>, wrote:<br>
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<p class="MsoNormal">Not sure, but looks like it is not able to hold or establish stable socket connection between nodes.</p>
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<p class="MsoNormal">-- <br>
Hui Zhou</p>
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<p class="MsoNormal"> </p>
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<b><span style="font-size:12.0pt;color:black">From:</span></b> <span style="font-size:12.0pt;color:black">
Sendu Bala via discuss <discuss@mpich.org><br>
<b>Date:</b> Wednesday, February 17, 2021 at 9:14 AM<br>
<b>To:</b> discuss@mpich.org <discuss@mpich.org><br>
<b>Cc:</b> Sendu Bala <sb10@sanger.ac.uk><br>
<b>Subject:</b> [mpich-discuss] Failure to do anything under LSF</span></p>
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<p class="MsoNormal" style="margin-left:.5in">Hi,<br>
<br>
We had an mpi app running under LSF that worked fine tiled across 64 hosts.<br>
<br>
Since moving to a new platform (LSF, but inside an OpenStack cluster*), the app is unreliable when tiled across more than 2 hosts.<br>
The likelyhood of failure increases until when tiled across 16 hosts, it almost never works (but still can). It always works when using 16 cores of a single host.<br>
<br>
The symptoms of failure are that our app doesn’t really start up (it logs nothing), the -outfile-pattern output files don’t get created, and it kills itself after 5mins of apparently doing nothing. (When it works, the -outfile-pattern files are created ~immediately
and the app produces output.)<br>
<br>
When failing, the mpirun process spawns a hydra_pmi_proxy process which spawns the app as well as 15 blaunch processes, which correspond to processes on the 15 other hosts, which have spawned a process for the app each.<br>
<br>
strace says the mpirun and app processes are doing nothing during the 5mins wait, with the app processes stuck on reading from a socket.<br>
<br>
After the 5 mins, the mpirun process exits with:<br>
strace -p 2526<br>
strace: Process 2526 attached<br>
restart_syscall(<... resuming interrupted poll ...>) = ? ERESTART_RESTARTBLOCK (Interrupted by signal)<br>
--- SIGINT {si_signo=SIGINT, si_code=SI_USER, si_pid=2498, si_uid=0} ---<br>
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=2530, si_uid=0, si_status=255, si_utime=1, si_stime=0} ---<br>
fstat(1, {st_mode=S_IFREG|0640, st_size=0, ...}) = 0<br>
write(1, "[mpiexec@node-name] ", 21) = 21<br>
write(1, "Sending Ctrl-C to processes as r"..., 41) = 41<br>
write(1, "[mpiexec@node-name] ", 21) = 21<br>
write(1, "Press Ctrl-C again to force abor"..., 34) = 34<br>
write(4, "\1\0\0\0\2\0\0\0", 8) = 8<br>
rt_sigreturn({mask=[]}) = -1 EINTR (Interrupted system call)<br>
poll([{fd=3, events=POLLIN}, {fd=5, events=POLLIN}, {fd=8, events=POLLIN}, {fd=10, events=POLLIN}, {fd=7, events=POLLIN}, {fd=11, events=POLLIN}, {fd=9, events=POLLIN}, {fd=13, events=POLLIN}, {fd=12, events=POLLIN}, {fd=15, events=POLLIN}, {fd=14, events=POLLIN},
{fd=17, events=POLLIN}, {fd=16, events=POLLIN}, {fd=19, events=POLLIN}, {fd=18, events=POLLIN}, {fd=21, events=POLLIN}, {fd=20, events=POLLIN}, {fd=23, events=POLLIN}, {fd=22, events=POLLIN}, {fd=25, events=POLLIN}, {fd=24, events=POLLIN}, {fd=27, events=POLLIN},
{fd=26, events=POLLIN}, {fd=29, events=POLLIN}, {fd=28, events=POLLIN}, {fd=31, events=POLLIN}, {fd=30, events=POLLIN}, {fd=33, events=POLLIN}, {fd=32, events=POLLIN}, {fd=35, events=POLLIN}, {fd=34, events=POLLIN}, {fd=37, events=POLLIN}, ...], 47, -1) =
6 ([{fd=3, revents=POLLIN}, {fd=15, revents=POLLIN}, {fd=19, revents=POLLIN}, {fd=21, revents=POLLIN}, {fd=25, revents=POLLIN}, {fd=31, revents=POLLIN}])<br>
read(3, "\1\0\0\0\2\0\0\0", 8) = 8<br>
write(6, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(48, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(46, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(38, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(43, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(40, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(45, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(42, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(47, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(50, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(44, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(41, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = 32<br>
write(-1, "\3\0\0\0\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\377\2\0\0\0", 32) = -1 EBADF (Bad file descriptor)<br>
write(2, "[mpiexec@node-name] ", 21) = 21<br>
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=2541, si_uid=0, si_status=255, si_utime=0, si_stime=0} ---<br>
write(2, "HYDU_sock_write (utils/sock/sock"..., 41) = 41<br>
write(2, "write error (Bad file descriptor"..., 34) = 34<br>
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=2529, si_uid=0, si_status=255, si_utime=0, si_stime=0} ---<br>
write(2, "[mpiexec@node-name] ", 21) = 21<br>
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=2537, si_uid=0, si_status=255, si_utime=0, si_stime=1} ---<br>
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=2528, si_uid=0, si_status=255, si_utime=0, si_stime=2} ---<br>
write(2, "HYD_pmcd_pmiserv_send_signal (pm"..., 60) = 60<br>
write(2, "unable to write data to proxy\n", 30) = 30<br>
write(2, "[mpiexec@node-name] ", 21) = 21<br>
write(2, "ui_cmd_cb (pm/pmiserv/pmiserv_pm"..., 42) = 42<br>
write(2, "unable to send signal downstream"..., 33) = 33<br>
write(2, "[mpiexec@node-name] ", 21) = 21<br>
write(2, "HYDT_dmxu_poll_wait_for_event (t"..., 61) = 61<br>
write(2, "callback returned error status\n", 31) = 31<br>
write(2, "[mpiexec@node-name] ", 21) = 21<br>
write(2, "HYD_pmci_wait_for_completion (pm"..., 62) = 62<br>
write(2, "error waiting for event\n", 24) = 24<br>
write(2, "[mpiexec@node-name] ", 21) = 21<br>
write(2, "main (ui/mpich/mpiexec.c:326): ", 31) = 31<br>
write(2, "process manager error waiting fo"..., 45) = 45<br>
exit_group(-1) = ?<br>
+++ exited with 255 +++<br>
<br>
The bsub -e file says the corresponding:<br>
[mpiexec@node-name] HYDU_sock_write (utils/sock/sock.c:254): write error (Bad file descriptor)<br>
[mpiexec@node-name] HYD_pmcd_pmiserv_send_signal (pm/pmiserv/pmiserv_cb.c:176): unable to write data to proxy<br>
[mpiexec@node-name] ui_cmd_cb (pm/pmiserv/pmiserv_pmci.c:42): unable to send signal downstream<br>
[mpiexec@node-name] HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status<br>
[mpiexec@node-name] HYD_pmci_wait_for_completion (pm/pmiserv/pmiserv_pmci.c:160): error waiting for event<br>
[mpiexec@node-name] main (ui/mpich/mpiexec.c:326): process manager error waiting for completion<br>
<br>
The issue isn’t specific to our app; I get the same symptoms with:<br>
<br>
bsub -q normal -o bsub.o -e bsub.e -R"span[ptile=1]” -n16 mpirun mpich/examples/cpi<br>
<br>
bsub.e is empty, and bsub.o has this:<br>
[mpiexec@node-name] Sending Ctrl-C to processes as requested<br>
[mpiexec@node-name] Press Ctrl-C again to force abort<br>
[…]<br>
Your job looked like:<br>
<br>
------------------------------------------------------------<br>
# LSBATCH: User input<br>
mpirun mpich/examples/cpi<br>
------------------------------------------------------------<br>
<br>
Exited with exit code 141.<br>
<br>
Resource usage summary:<br>
<br>
CPU time : 0.49 sec.<br>
Max Memory : 85 MB<br>
Average Memory : 70.89 MB<br>
Total Requested Memory : -<br>
Delta Memory : -<br>
Max Swap : -<br>
Max Processes : 63<br>
Max Threads : 80<br>
Run time : 310 sec.<br>
Turnaround time : 317 sec.<br>
<br>
(I did not initiate any Ctrl-C or similar myself.)<br>
<br>
This is with mpich-3.4.1 configured --with-device=ch4:ucx. It’s worth noting I get the exact same symptoms using latest OpenMPI as well, so this is not an mpich-specific issue.<br>
<br>
What can I do to investigate further or try to resolve this, so it works reliably with 16 or ideally 64 hosts again?<br>
<br>
<br>
[*] I know very little about networking, but I’m told we have new nodes in the LSF cluster that use a software-defined network, but also old nodes that use a hardware network like our old system; limiting to the old nodes doesn’t help. But maybe there are some
subtleties here I’ve overlooked.</p>
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<p class="MsoNormal" style="margin-left:.5in"> </p>
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<p class="MsoNormal" style="margin-left:.5in">Cheers,</p>
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<p class="MsoNormal" style="margin-left:.5in">Sendu</p>
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<p class="MsoNormal" style="margin-left:.5in">-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215
Euston Road, London, NW1 2BE.</p>
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--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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