On Apr 30, 2013, at 1:34 PM, Vladimir Yamshchikov <yaxi...@gmail.com> wrote:

> I asked grid IT and they said they had to kill it as the job was overloading 
> nodes. They saw loads up to 180 instead of close to 12 on 12-core nodes. They 
> think that blastx is not an openmpi application, so openMPI is spawning 
> between 64-96 blastx processes, each of which is then starting up 96 worker 
> threads. Or if blastx can work with openmpi, my blastx synthax mpirun syntax 
> is wrong. Any advice?
> I was advised earlier to use –pe openmpi [ARG} , where  ARG = 
> number_of_processes x number_of_threads , and then pass desired number of 
> threads as ‘ mpirun –np $NSLOTS cpus-per-proc [ number_of_threads]’. When I 
> did that, I got an error that more threads were requested than number of 
> physical cores.
> 

How many threads are you trying to launch?? If it is a 12-core node, then you 
can't have more than 12 - sounds like you are trying to startup 96!

>  
> 
> 
> 
> 
> On Tue, Apr 30, 2013 at 2:35 PM, Reuti <re...@staff.uni-marburg.de> wrote:
> Hi,
> 
> Am 30.04.2013 um 21:26 schrieb Vladimir Yamshchikov:
> 
> > My recent job started normally but after a few hours of running died with 
> > the following message:
> >
> > --------------------------------------------------------------------------
> > A daemon (pid 19390) died unexpectedly with status 137 while attempting
> > to launch so we are aborting.
> 
> I wonder why it rose the failure only after running for hours. As 137 = 128 + 
> 9 it was killed, maybe by the queuing system due to the set time limit? If 
> you check the accouting, what is the output of:
> 
> $ qacct -j <job_id>
> 
> -- Reuti
> 
> 
> > There may be more information reported by the environment (see above).
> >
> > This may be because the daemon was unable to find all the needed shared
> > libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
> > location of the shared libraries on the remote nodes and this will
> > automatically be forwarded to the remote nodes.
> > --------------------------------------------------------------------------
> > --------------------------------------------------------------------------
> > mpirun noticed that the job aborted, but has no info as to the process
> > that caused that situation.
> >
> > The scheduling script is below:
> >
> > #$ -S /bin/bash
> > #$ -cwd
> > #$ -N SC3blastx_64-96thr
> > #$ -pe openmpi* 64-96
> > #$ -l h_rt=24:00:00,vf=3G
> > #$ -j y
> > #$ -M yaxi...@gmail.com
> > #$ -m eas
> > #
> > # Load the appropriate module files
> > # Should be loaded already
> > #$ -V
> >
> > mpirun -np $NSLOTS blastx -query 
> > $UABGRID_SCRATCH/SC/AdQ30/fasta/SC1-IS4-Ind1-153ngFr1sep1run1R1AdQ30.fasta 
> > -db nr -out 
> > $UABGRID_SCRATCH/SC/blastx/SC/SC1-IS4-Ind1-153ngFr1sep1run1R1AdQ30.out 
> > -evalue 0.001 -max_intron_length 100000 -outfmt 5 -num_alignments 20 
> > -lcase_masking -num_threads $NSLOTS
> >
> > What caused this termination? It does not seem scheduling problem as the 
> > program run several hours with 96 threads. My $LD_LIBRARY_PATH does have 
> > /share/apps/openmpi/1.6.4-gcc/lib entry, so how else should I modify it?
> >
> > Vladimir
> > _______________________________________________
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
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