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Subject: Re: [OMPI users] OpenMPI job initializing problem
From: Ralph Castain (rhc_at_[hidden])
Date: 2014-02-28 12:36:54

Almost certainly, the redhat package wasn't built with matching infiniband support and so we aren't picking it up. I'd suggest downloading the latest 1.7.4 or 1.7.5 nightly tarball, or even the latest 1.6 tarball if you want the stable release, and build it yourself so you *know* it was built for your system.

On Feb 28, 2014, at 9:20 AM, Beichuan Yan <beichuan.yan_at_[hidden]> wrote:

> 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 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: Bcast: Mask:
> inet6 addr: fe80::8e89:a5ff:fee3:d296/64 Scope:Link
> 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 Ifconfig is obsolete!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: Bcast: Mask:
> inet6 addr: fe80::202:c903:fb:3489/64 Scope:Link
> 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: Mask:
> inet6 addr: ::1/128 Scope:Host
> 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, --mca oob_tcp_if_exclude,"
> #TCP="--mca btl_tcp_if_include"
> 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
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