[mpich-discuss] Error Running MPICH for Photochemical Modeling
Abhishek Bhat
abhat at trinityconsultants.com
Mon Sep 15 10:58:11 CDT 2014
Sangmin,
Please see attached the logs from demsg. I apologies but I am not a computer expert so it's all Greek to me.. Can you please see if you can find any error or reason for the failure?
Thank You
Abhishek
................................................................................................................
Abhishek Bhat, PhD, EPI,
Senior Consultant
From: Seo, Sangmin [mailto:sseo at anl.gov]
Sent: Monday, September 15, 2014 9:21 AM
To: Abhishek Bhat
Cc: <discuss at mpich.org>
Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
Can you run dmesg on the node of rank 1, which is killed by signal 9, after you execute your application? You can find the reason that the process is killed at the end of dmesg output, e.g., out of memory.
- Sangmin
On Sep 14, 2014, at 12:37 PM, Abhishek Bhat <abhat at trinityconsultants.com<mailto:abhat at trinityconsultants.com>> wrote:
Because the application works when less intensive runs and fails for more intensive runs, it is likely that the application is requesting too many resources. When\where should I run ulimit -a and dmesg, after I get the error? If that is true, is there any way to change the environment in MPI to increase the capacity so that the increased resources can be accommodated?
If I run it in new terminal - here is what I get
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 250598
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 10240
cpu time (seconds, -t) unlimited
max user processes (-u) 1024
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
in my job, I try to set the stack size to - unlimited but I guess it is not working.
Let me know. Thank you for all the help.
Abhishek
................................................................................................................
Abhishek Bhat, PhD, EPI,
Senior Consultant
From: Seo, Sangmin [mailto:sseo at anl.gov]
Sent: Sunday, September 14, 2014 11:16 AM
To: <discuss at mpich.org<mailto:discuss at mpich.org>>
Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
Abhishek,
Signal 9 is caused by many reasons, e.g., CPU time, out of memory, etc., but it is mostly because the application requests too many resources. You can check the environment settings with ulimit -a. And, you may find some information about your error from dmesg.
Thanks,
Sangmin
On Sep 12, 2014, at 5:51 PM, Abhishek Bhat <abhat at trinityconsultants.com<mailto:abhat at trinityconsultants.com>> wrote:
Sangmin.
I updated to mpich3 and getting the following error
Fatal error in MPI_Recv: A process has failed, error stack:
MPI_Recv(187).............: MPI_Recv(buf=0x7fff93840c30, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff94444f20) failed
dequeue_and_set_error(865): Communication error with rank 1
rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks
exit status of rank 1: killed by signal 9
Same situation, successful runs for smaller resource runs and for up to 7 processes. Error at more than 7. Here is the mpich command I am using to run from my job file...
cat << ieof > nodes
dfw-camx:1
dfw-camx-n1:1
dfw-camx-n2:1
dfw-camx-n3:1
dfw-camx-n4:1
dfw-camx-n5:1
dfw-camx-n6:1
dfw-camx-n7:1
ieof
set NUMPROCS = 8
set RING = `wc -l nodes | awk '{print $1}'`
mpdboot -n $RING -f nodes -verbose
if( ! { mpiexec -machinefile nodes -np $NUMPROCS $EXEC } ) then
mpdallexit
exit
endif
For a successful run the NUMPROCS has to be < = 7.
Any help is much appreciated.
Thank You
Abhishek
................................................................................................................
Abhishek Bhat, PhD, EPI,
Senior Consultant
From: Seo, Sangmin [mailto:sseo at anl.gov]
Sent: Friday, September 12, 2014 1:11 PM
To: <discuss at mpich.org<mailto:discuss at mpich.org>>
Subject: Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling
Hi Abhishek,
Can you try with the recent MPICH release to see if the same error happens? You can download the recent release, 3.1.2, from http://www.mpich.org/downloads/.
Thanks,
Sangmin
On Sep 12, 2014, at 12:59 PM, Abhishek Bhat <abhat at trinityconsultants.com<mailto:abhat at trinityconsultants.com>> wrote:
I am running a photochemical modeling on Linux cluster (CentOS_64 bit) with 1 master and 8 slave nodes with quad core (intel i7) on each node. I have two scenarios, in first scenario, I am running less data intensive run on all 8 nodes (NUMPROCS = 9) and the run will go fine. When running same configuration for a more intense run, I am getting following error.
Fatal error in MPI_Recv: Other MPI error, error stack:
MPI_Recv(187).....................: MPI_Recv(buf=0x7fff989d53b0, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff995d96a0) failed
MPIDI_CH3I_Progress(150)..........:
MPID_nem_mpich2_blocking_recv(948):
MPID_nem_tcp_connpoll(1720).......:
state_commrdy_handler(1556).......:
MPID_nem_tcp_recv_handler(1446)...: socket closed
rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks
exit status of rank 1: killed by signal 9
If I run the program with smaller nodes (smaller than 7 NUMPROCS) the run goes fine.
It appears that the rank 1 (my first node) is collectively causing all the ranks, but I could identify why. I tried following solutions -
1. Increased master memory to 32 gb
2. Increased all nodes memory to 32 gb
3. Exchanged the rank 1 to different node in the parallel.
In all situations, I am getting this error. Surprisingly, when I am running smaller (less data intensive runs), I am not getting this error even if I increase the NUMPROCS to 32 processes.
Any help will be highly appreciated.
I am running mpich 1.4
Thank You
Abhishek
................................................................................................................
Abhishek Bhat, PhD, EPI,
Senior Consultant
Trinity Consultants
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