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Subject: Re: [OMPI users] Possible openmpi bug?
From: Steven Dale (steven_dale_at_[hidden])
Date: 2009-07-20 11:17:43

Okay, now the plot is just getting weirder.

I implemented most of the changes you recommend below. We are not running
panasas, and our network is GB ethernet only, so I left the openib
parameters out as well. I also recompiled with the switches suggested in
the tlcc directory for the non-panasas file.

Now our test case will run on 10 nodes with 160 permutations, which is a
step forward. It does however still crash with a routed:binomial error on
10 nodes with 1600 permutations after about 14 minutes. With 800
permutations, it runs quite happily as well.

....current openmpi-mca-param.conf is now:

# $sysconf is a directory on a local disk, it is likely that changes
# to this file will need to be propagated to other nodes. If $sysconf
# is a directory that is shared via a networked filesystem, changes to
# this file will be visible to all nodes that share this $sysconf.

# The format is straightforward: one per line, mca_param_name =
# rvalue. Quoting is ignored (so if you use quotes or escape
# characters, they'll be included as part of the value). For example:

# Disable run-time MPI parameter checking
# mpi_param_check = 0

# Note that the value "~/" will be expanded to the current user's home
# directory. For example:

# Change component loading path
# component_path = /usr/local/lib/openmpi:~/my_openmpi_components

# See "ompi_info --param all all" for a full listing of Open MPI MCA
# parameters available and their default values.
orte_abort_timeout = 10
opal_set_max_sys_limits = 1
orte_no_session_dirs = /usr,/users,/home,/hcadmin
orte_tmpdir_base = /tmp
orte_allocation_required = 1
coll_sync_priority = 100
coll_sync_barrier_before = 1000
coll_hierarch_priority = 90
oob_tcp_peer_retries = 10
oob_tcp_disable_family = IPv6
oob_tcp_listen_mode = listen_thread
oob_tcp_sndbuf = 65536
oob_tcp_rcvbuf = 65536
btl = sm,tcp,self
## Setup MPI options
mpi_show_handle_leaks = 0
mpi_warn_on_fork = 1

Current compilation looks like this:


# Takes about 20-25 minutes

PATH=$PATH:/usr/local/bin:;export PATH

# Build and install OpenMPI

cd openmpi/openmpi-1.3.3

sh ./configure --enable-dlopen=no --enable-binaries=yes
--enable-shared=yes --enable-ipv6=no --enable-ft-thread=no
--with-slurm=yes --with-io-romio-flags="--with-file-system=ufs+nfs"
--with-memory-manager=ptmalloc2 --with-wrapper-ldflags="-m64"
--with-wrapper-cxxflags="-m64" --with-wrapper-fcflags="-m64"

make install

Steve Dale
Senior Platform Analyst
Health Canada

Ralph Castain <rhc_at_[hidden]>
Sent by: users-bounces_at_[hidden]
07/17/2009 10:35 AM
Please respond to
Open MPI Users <users_at_[hidden]>

Open MPI Users <users_at_[hidden]>

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


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.


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_at_[hidden]

Ralph Castain <rhc_at_[hidden]>
Sent by: users-bounces_at_[hidden]
07/17/2009 01:13 AM

Please respond to
Open MPI Users <users_at_[hidden]>

Open MPI Users <users_at_[hidden]>

Re: [OMPI users] Possible openmpi bug?

>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

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

The R code is executed with a typical command line for 14 cpus being:

sbatch -n 14 -i ./Rtest.txt --mail-type=ALL
--mail-user=steven_dale_at_[hidden] /usr/local/bin/R --no-save

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.

No non-default MCA parameters are set.


Configuration done with defaults.

Any ideas are welcome.

Steve Dale
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