Hi Cristobal
Cristobal Navarro wrote:
On Wed, Jul 28, 2010 at 11:09 AM, Gus Correa <g...@ldeo.columbia.edu
<mailto:g...@ldeo.columbia.edu>> wrote:
Hi Cristobal
In case you are not using full path name for mpiexec/mpirun,
what does "which mpirun" say?
--> $which mpirun
/opt/openmpi-1.4.2
Often times this is a source of confusion, old versions may
be first on the PATH.
Gus
openMPI version problem is now gone, i can confirm that the version is
consistent now :), thanks.
This is good news.
however, i keep getting this kernel crash randomnly when i execute with
-np higher than 5
these are Xeons, with Hyperthreading On, is that a problem??
The problem may be with Hyperthreading, maybe not.
Which Xeons?
If I remember right, the old hyperthreading on old Xeons was problematic.
OTOH, about 1-2 months ago I had trouble with OpenMPI on a relatively
new Xeon Nehalem machine with (the new) Hyperthreading turned on,
and Fedora Core 13.
The machine would hang with the OpenMPI connectivity example.
I reported this to the list, you may find in the archives.
Apparently other people got everything (OpenMPI with HT on Nehalem)
working in more stable distributions (CentOS, RHEL, etc).
That problem was likely to be in the FC13 kernel,
because even turning off HT I still had the machine hanging.
Nothing worked with shared memory turned on,
so I had to switch OpenMPI to use tcp instead,
which is kind of ridiculous in a standalone machine.
im trying to locate the kernel error on logs, but after rebooting a
crash, the error is not in the kern.log (neither kern.log.1).
all i remember is that it starts with "Kernel BUG..."
and somepart it mentions a certain CPU X, where that cpu can be any from
0 to 15 (im testing only in main node). Someone knows where the log of
kernel error could be?
Have you tried to turn off hyperthreading?
In any case, depending on the application, it may not help much
performance to have HT on.
A more radical alternative is to try
-mca btl tcp,self
in the mpirun command line.
That is what worked in the case I mentioned above.
My $0.02
Gus Correa
Cristobal Navarro wrote:
On Tue, Jul 27, 2010 at 7:29 PM, Gus Correa
<g...@ldeo.columbia.edu <mailto:g...@ldeo.columbia.edu>
<mailto:g...@ldeo.columbia.edu <mailto:g...@ldeo.columbia.edu>>>
wrote:
Hi Cristobal
Does it run only on the head node alone?
(Fuego? Agua? Acatenango?)
Try to put only the head node on the hostfile and execute
with mpiexec.
--> i will try only with the head node, and post results back
This may help sort out what is going on.
Hopefully it will run on the head node.
Also, do you have Infinband connecting the nodes?
The error messages refer to the openib btl (i.e. Infiniband),
and complains of
no we are just using normal network 100MBit/s , since i am just
testing yet.
"perhaps a missing symbol, or compiled for a different
version of Open MPI?".
It sounds as a mixup of versions/builds.
--> i agree, somewhere there must be the remains of the older
version
Did you configure/build OpenMPI from source, or did you install
it with apt-get?
It may be easier/less confusing to install from source.
If you did, what configure options did you use?
-->i installed from source, ./configure
--prefix=/opt/openmpi-1.4.2 --with-sge --without-xgid
--disable--static
Also, as for the OpenMPI runtime environment,
it is not enough to set it on
the command line, because it will be effective only on the
head node.
You need to either add them to the PATH and LD_LIBRARY_PATH
on your .bashrc/.cshrc files (assuming these files and your home
directory are *also* shared with the nodes via NFS),
or use the --prefix option of mpiexec to point to the OpenMPI
main
directory.
yes, all nodes have their PATH and LD_LIBRARY_PATH set up
properly inside the login scripts ( .bashrc in my case )
Needless to say, you need to check and ensure that the OpenMPI
directory (and maybe your home directory, and your work
directory)
is (are)
really mounted on the nodes.
--> yes, doublechecked that they are
I hope this helps,
--> thanks really!
Gus Correa
Update: i just reinstalled openMPI, with the same parameters,
and it
seems that the problem has gone, i couldnt test entirely but
when i
get back to lab ill confirm.
best regards! Cristobal
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