[OMPI users] mpirun noticed that process rank 5 with PID 0 on node localhost exited on signal 9 (Killed).

Discussion:

Zeinab Salah

2018-09-28 16:47:50 UTC

Hi everyone,
I use openmpi-3.0.2 and I want to run chimere model with 8 processors, but
in the step of parallel mode, the run stopped with the following error
message,
Please could you help me?
Thank you in advance
Zeinab

+++ CHIMERE RUNNING IN PARALLEL MODE +++
MPI SUB-DOMAINS :
rank izstart izend nzcount imstart imend nmcount i j
--------------------------------------------------------------------
1 1 14 14 1 22 22 1 1
2 15 27 13 1 22 22 2 1
3 28 40 13 1 22 22 3 1
4 41 53 13 1 22 22 4 1
5 1 14 14 23 43 21 1 2
6 15 27 13 23 43 21 2 2
7 28 40 13 23 43 21 3 2
8 41 53 13 23 43 21 4 2
Sub domain dimensions: 14 22

boundary conditions:
/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.list
3 boundary conditions file(s) found
Opening
/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-gas
Opening
/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-aer
Opening
/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-dust
Opening
/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-gas
Opening
/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-aer
Opening
/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-dust
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 5 with PID 0 on node localhost exited on
signal 9 (Killed).
--------------------------------------------------------------------------

real 3m51.733s
user 0m5.044s
sys 1m8.617s
Abnormal termination of step2.sh

Ralph H Castain

2018-09-28 16:55:32 UTC

Permalink

Ummm…looks like you have a problem in your input deck to that application. Not sure what we can say about it…

Post by Zeinab Salah
Hi everyone,
I use openmpi-3.0.2 and I want to run chimere model with 8 processors, but in the step of parallel mode, the run stopped with the following error message,
Please could you help me?
Thank you in advance
Zeinab
+++ CHIMERE RUNNING IN PARALLEL MODE +++
rank izstart izend nzcount imstart imend nmcount i j
--------------------------------------------------------------------
1 1 14 14 1 22 22 1 1
2 15 27 13 1 22 22 2 1
3 28 40 13 1 22 22 3 1
4 41 53 13 1 22 22 4 1
5 1 14 14 23 43 21 1 2
6 15 27 13 23 43 21 2 2
7 28 40 13 23 43 21 3 2
8 41 53 13 23 43 21 4 2
Sub domain dimensions: 14 22
boundary conditions: /home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.list
3 boundary conditions file(s) found
Opening /home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-gas
Opening /home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-aer
Opening /home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-dust
Opening /home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-gas
Opening /home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-aer
Opening /home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-dust
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 5 with PID 0 on node localhost exited on signal 9 (Killed).
--------------------------------------------------------------------------
real 3m51.733s
user 0m5.044s
sys 1m8.617s
Abnormal termination of step2.sh
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Zeinab Salah

2018-09-28 18:19:55 UTC

Permalink

Thank you for your response.
I attached the results of using :valgrind --tool=memcheck --leak-check=yes
-v

valgrind --tool=memcheck --leak-check=yes -v mpirun -np 8 -mca btl
vader,self,tcp -mca btl_tcp_eager_limit 4095 -x
LD_LIBRARY_PATH ./chimere.e

â«ÙÙ Ø§ÙØ¬ÙØ¹Ø©Ø 28 Ø³ØšØªÙØšØ± 2018 ÙÙ 7:03 Ù ØªÙØª ÙØªØ§ØšØ© ÙØ§ ÙÙÙ ØšÙØ§Ø³Ø·Ø© âªRalph H

UmmmâŠlooks like you have a problem in your input deck to that application.
Not sure what we can say about itâŠ

Post by Zeinab Salah
Hi everyone,
I use openmpi-3.0.2 and I want to run chimere model with 8 processors,

but in the step of parallel mode, the run stopped with the following error
message,

Post by Zeinab Salah
Please could you help me?
Thank you in advance
Zeinab
+++ CHIMERE RUNNING IN PARALLEL MODE +++
rank izstart izend nzcount imstart imend nmcount i j
--------------------------------------------------------------------
1 1 14 14 1 22 22 1 1
2 15 27 13 1 22 22 2 1
3 28 40 13 1 22 22 3 1
4 41 53 13 1 22 22 4 1
5 1 14 14 23 43 21 1 2
6 15 27 13 23 43 21 2 2
7 28 40 13 23 43 21 3 2
8 41 53 13 23 43 21 4 2
Sub domain dimensions: 14 22

/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.list

Post by Zeinab Salah
3 boundary conditions file(s) found
Opening

/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-gas

Post by Zeinab Salah
Opening

/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-aer

Post by Zeinab Salah
Opening

/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-dust

Post by Zeinab Salah
Opening

/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-gas

Post by Zeinab Salah
Opening

/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-aer

Post by Zeinab Salah
Opening

/home/dream/CHIMERE/chimere2017r4/../BIGFILES/OUTPUTS/Test/../INIBOUN.10/BOUN_CONCS.2009030700_2009030900_Test.nc-dust

Post by Zeinab Salah
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------

--------------------------------------------------------------------------

Post by Zeinab Salah
mpirun noticed that process rank 5 with PID 0 on node localhost exited

on signal 9 (Killed).
--------------------------------------------------------------------------

Post by Zeinab Salah
real 3m51.733s
user 0m5.044s
sys 1m8.617s
Abnormal termination of step2.sh
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users