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Subject: [OMPI users] Error when using more than 88 processors for a specific executable -Abyss
From: Ashwani Kumar Mishra (ashwanimishra_at_[hidden])
Date: 2011-10-14 14:07:49


Hello,
When i try to run the following command i receive the following error when i
try to submit this job on the cluster having 40 nodes with each node having
8 processor & 8 GB RAM:

Both the command work well, as long as i use only upto 88 processors in the
cluster, but the moment i allocate more than 88 processors it gives me the
below 2 errors:

I tried to set the ulimit to unlimited & setting mca parameter
opal_set_max_sys_limits to 1 but still the problem wont go.

$ mpirun=/*opt*/psc/ompi/bin/mpirun abyss-pe np=100 name=cattle k=50 n=10
in=s_1_1_sequence.txt

/opt/mpi/openmpi/1.3.3/intel/
bin/mpirun -np 100 ABYSS-P -k50 -q3 --coverage-hist=coverage.hist -s
cattle-bubbles.fa -o cattle-1.fa s_1_1_sequence.txt
[coe:19807 <http://coe.iitd.ac.in:19807/>] [[62863,0],0] ORTE_ERROR_LOG: The
system limit on number of pipes a process can open was reached in file
base/iof_base_setup.c at line 107
[coe.:19807 <http://coe.iitd.ac.in:19807/>] [[62863,0],0] ORTE_ERROR_LOG:
The system limit on number of pipes a process can open was reached in file
odls_default_module.c at line 203
[coe.:19807 <http://coe.iitd.ac.in:19807/>] [[62863,0],0] ORTE_ERROR_LOG:
The system limit on number of network connections a process can open was
reached in file oob_tcp.c at line 447
--------------------------------------------------------------------------
Error: system limit exceeded on number of network connections that can be
open

This can be resolved by setting the mca parameter opal_set_max_sys_limits to
1,
increasing your limit descriptor setting (using limit or ulimit commands),
or asking the system administrator to increase the system limit.
--------------------------------------------------------------------------
make: *** [cattle-1.fa] Error 1

*
When i submit the same job through qsub, i receive the following error:*
$ qsub -cwd -pe orte 100 -o qsub.out -e qsub.err -b y -N abyss `which
mpirun` /home/genome/abyss/bin/ABYSS-P -k 50 s_1_1_sequence.txt -o av

[compute-0-19.local][[28273,1]
,125][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
connect() to 173.16.255.231 failed: Connection refused (111)
[compute-0-19.local][[28273,1],127][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
connect() to 173.16.255.231 failed: Connection refused (111)
[compute-0-23.local][[28273,1],135][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
connect() to 173.16.255.228 failed: Connection refused (111)
[compute-0-23.local][[28273,1],133][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
connect() to 173.16.255.228 failed: Connection refused (111)
[compute-0-4.local][[28273,1],113][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
connect() to 173.16.255.231 failed: Connection refused (111)

Best Regards,
Ashwani