I'll give it a try.
____________________
Steve Dale
Senior Platform Analyst
Health Canada
Phone: (613)-948-4910
E-mail: steven_dale@hc-sc.gc.ca
Ralph Castain <rhc@open-mpi.org> Sent by: users-bounces@open-mpi.org
07/17/2009 10:35 AM
Please respond to
Open MPI Users <users@open-mpi.org>
To
Open MPI Users <users@open-mpi.org>
cc
Subject
Re: [OMPI users] Possible openmpi bug?
Okay, just checking the obvious. :-)
We regularly run with the exact same configuration here
(i.e., slurm + 16cpus/node) without problem on jobs that are both short
and long, so it seems doubtful that it would be an OMPI bug. However, it
is possible as the difference could be due to configuration and/or parameter
settings. We have seen some site-specific problems that are easily resolved
with parameter changes.
You might take a look at our (LANL's) platform files for
our slurm-based system and see if they help. You will find them in the
tarball at
contrib/platform/lanl/tlcc
Specifically, since you probably aren't running panasas
(?), look at the optimized-nopanasas and optimized-nopanasas.conf (they
are a pair) files to see how we configure the system for build, and the
mca params we use to execute applications. If you can, I would suggest
giving them a try (adjusting as required for your setup - e.g., you may
want not want the -m64 flags) and see if it resolves the problem.
Ralph
On Jul 17, 2009, at 7:15 AM, Steven Dale wrote:
I think it unlikely that its a time limit thing. Firstly, slurm is set
up with no time limit on jobs, and we get the same behaviour whether or
not slurm is in the picture.
In addition, we've run several other much larger jobs with a greater number
of permutations and they complete fine.
This job takes about 5-10 minutes to run. We've run jobs that take a week
or more and the indivdual R process can be seen to run for days at a time
and they run fine.
In addition, I'd find it hard to believe (although I concede the possibility)
that jobs entirely self-contained within the same box run slower that jobs
which span 2 boxes over the network. (14 cpus vs 17 cpus for example).
____________________
Steve Dale
Senior Platform Analyst
Health Canada
Phone: (613)-948-4910
E-mail: steven_dale@hc-sc.gc.ca
>From what I can see, it looks like your job is being terminated - something
is killing mpirun. Is it possible that the job runs slowly enough on 14
or less cpus that it simply isn't completing within your specified time
limit?
The lifeline message simply indicates that a process self-aborted because
it lost contact with its local daemon - in this case, mpirun (as that is
always daemon 0) - which means that the daemon was terminated for some
reason.
On Jul 16, 2009, at 11:15 AM, Steven Dale wrote:
Here is my situation:
2 Dell R900's with 16 cpus each and 64 GB RAM
OS: SuSE SLES 10 SP2 patched up to date
R version 2.9.1
Rmpi version 0.5-7
snow version 0.3-3
maanova library version 1.14.0
openmpi version 1.3.3
slurm version 2.0.3
With a given set of R code, we get abnormal exits when using 14 or less
cpus. When using 15 or more, the job completes normally.
error is a variation on:
[pdp-dev-r01:22618] [[15549,1],0] routed:binomial: Connection to lifeline
[[15549,0],0] lost
during the array permutations.
Increasing the number of permutations above 200 also produces similar results.
The R code is executed with a typical command line for 14 cpus being:
Config.log, ompi_info, Rscript.txt and slurm outputs are attached. Network
is GB Ethernet copper tcp/ip.
I think this to be an openmpi error/bug due to the routed:binomial message.
This also had the same results with openmpi-1.3.2, R 2.9.0, maanova 1.12
and slurm 2.0.1.