On Apr 30, 2013, at 1:54 PM, Vladimir Yamshchikov <yaximik@gmail.com> wrote:

This is the question I am trying to answer - how many threads I can use with blastx on a grid? If I could request resources by_node, use -pernode option to have one process per node, and then specify the correct number of threads for each node. But I cannot, resurces (slots) are requested per-core (per_process),

I don't believe that is true - resources are requested for the entire job, not for each process

so I was instructed to request total number of slots. However, as allocated cores are spread across the nodes, looks like it messes scheduling up causing overload.

I suggest you look at the SGE documentation - I don't think you are using it correctly




On Tue, Apr 30, 2013 at 3:46 PM, Ralph Castain <rhc@open-mpi.org> wrote:

On Apr 30, 2013, at 1:34 PM, Vladimir Yamshchikov <yaximik@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 <reuti@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 yaximik@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
> users@open-mpi.org
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