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psing51
Beginner
295 Views

Issue while spawning processes across multiple nodes (EXIT CODE: 9)

Hi all,
I am using intel parallel studio 2015 on Intel(R) Xeon(R) CPU E5-2680 v3 (RHEL-6.5) and currently facing issues with an mpi based application(Nas Parallel Benchmark-BT). Though the issue seems application specific, I would like to have your opinions on methodology to debug/fix issues like these .

I was successful in testing the mpi setup as :-
 

[puneets@host01 bin]$ cat hosts.txt 
host02
host03

[puneets@host01 bin]$ mpirun -np 4 -ppn 2 -hostfile hosts.txt ./hello 
host02
host02
host03
host03

But when i try to run the application, I end up with:-

[puneets@host01 bin]$ mpirun -np 4 -ppn 2 -hostfile hosts.txt ./bt.E.4.mpi_io_full 

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 25799 RUNNING AT host03
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)

I have attached verbose log of the error (VERBOSE.txt). 

​[puneets@host01 bin]$ mpirun -genv I_MPI_HYDRA_DEBUG=1 -hostfile hosts.txt -genv I_MPI_DEBUG=5 -np 4 -ppn 2 ./bt.E.4.mpi_io_full 

Whereas, on single node, i am able to run the application as:-

[puneets@host01 bin]$ mpirun -np 4  ./bt.E.4.mpi_io_full 


 NAS Parallel Benchmarks 3.3 -- BT Benchmark 

 No input file inputbt.data. Using compiled defaults
 Size: 1020x1020x1020
 Iterations:  250    dt:   0.0000040
 Number of active processes:     4

 BTIO -- FULL MPI-IO write interval:   5



I am attaching the make.def and compilation log for your reference.
Any help/Hint will be very useful. Eagerly awaiting your replies.
 

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1 Reply
psing51
Beginner
295 Views

Hi all,
I tried running this benchmark on compute nodes via PBS, I again end up with similar error. 
Here is my job submission script:
 

#!/bin/bash
#PBS -N NPB_N4_TPP24
#PBS -l select=2:ncpus=24:mpiprocs=2
#PBS -q test
#PBS -o output1.txt
#PBS -e error1.txt
#PBS -P cc
cd $PBS_O_WORKDIR


export OMP_NUM_THREADS=12
module load suite/intel/parallelStudio
mpirun -np 4 -hostfile $PBS_NODEFILE -genv I_MPI_HYDRA_DEBUG=1   -genv OMP_NUM_THREADS=12 -genv I_MPI_DEBUG=5 -ppn 2 ./bt.E.4.mpi_io_full

.

This seems to be an issue with NPB's class E problems.
I recompiled NPB for class D , and i was able to run the benchmark on multiple nodes.

Do let me know if you are able to identify bug with class E problem(each compute nodes in my setup has 64GB RAM).

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