[mpich-discuss] Error Running MPICH for Photochemical Modeling

Sun Sep 14 11:15:50 CDT 2014

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

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