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Subject: [OMPI users] OpenMPI job initializing problem
From: Beichuan Yan (beichuan.yan_at_[hidden])
Date: 2014-02-28 12:20:20


Hi there,

I am running jobs on clusters with Infiniband connection. They installed OpenMPI v1.5.4 via REDHAT 6 yum package). My problem is that although my jobs gets queued and started by PBS PRO quickly, most of the time they don't really run (occasionally they really run) and give error info like this (even though there are a lot of CPU/IB resource available):

[r2i6n7][[25564,1],0][btl_tcp_endpoint.c:638:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.159.156 failed: Connection refused (111)

And even though when a job gets started and runs well, it prompts this error:
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.
  Local host: r1i2n6
  Local device: mlx4_0
--------------------------------------------------------------------------

1. Here is the info from one of the compute nodes:
-bash-4.1$ /sbin/ifconfig
eth0 Link encap:Ethernet HWaddr 8C:89:A5:E3:D2:96
          inet addr:192.168.159.205 Bcast:192.168.159.255 Mask:255.255.255.0
          inet6 addr: fe80::8e89:a5ff:fee3:d296/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
          RX packets:48879864 errors:0 dropped:0 overruns:17 frame:0
          TX packets:39286060 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:54771093645 (51.0 GiB) TX bytes:37512462596 (34.9 GiB)
          Memory:dfc00000-dfc20000

Ifconfig uses the ioctl access method to get the full address information, which limits hardware addresses to 8 bytes.
Because Infiniband address has 20 bytes, only the first 8 bytes are displayed correctly.
Ifconfig is obsolete! For replacement check ip.
ib0 Link encap:InfiniBand HWaddr 80:00:00:48:FE:C0:00:00:00:00:00:00:00:00:00:00:00:00:00:00
          inet addr:10.148.0.114 Bcast:10.148.255.255 Mask:255.255.0.0
          inet6 addr: fe80::202:c903:fb:3489/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST MTU:65520 Metric:1
          RX packets:43807414 errors:0 dropped:0 overruns:0 frame:0
          TX packets:10534050 errors:0 dropped:24 overruns:0 carrier:0
          collisions:0 txqueuelen:256
          RX bytes:47824448125 (44.5 GiB) TX bytes:44764010514 (41.6 GiB)

lo Link encap:Local Loopback
          inet addr:127.0.0.1 Mask:255.0.0.0
          inet6 addr: ::1/128 Scope:Host
          UP LOOPBACK RUNNING MTU:16436 Metric:1
          RX packets:17292 errors:0 dropped:0 overruns:0 frame:0
          TX packets:17292 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0
          RX bytes:1492453 (1.4 MiB) TX bytes:1492453 (1.4 MiB)

-bash-4.1$ chkconfig --list iptables
iptables 0:off 1:off 2:on 3:on 4:on 5:on 6:off

2. I tried various parameters below but none of them can assure my jobs get initialized and run:
#TCP="--mca btl ^tcp"
#TCP="--mca btl self,openib"
#TCP="--mca btl_tcp_if_exclude lo"
#TCP="--mca btl_tcp_if_include eth0"
#TCP="--mca btl_tcp_if_include eth0, ib0"
#TCP="--mca btl_tcp_if_exclude 192.168.0.0/24,127.0.0.1/8 --mca oob_tcp_if_exclude 192.168.0.0/24,127.0.0.1/8"
#TCP="--mca btl_tcp_if_include 10.148.0.0/16"
mpirun $TCP -hostfile $PBS_NODEFILE -np 8 ./paraEllip3d input.txt

3. Then I turned to Intel MPI, which surprisingly starts and runs my job correctly each time (though it is a little slower than OpenMPI, maybe 15% slower, but it works each time).

Can you please advise? Many thanks.

Sincerely,
Beichuan Yan