Am 25.10.2012 um 19:36 schrieb Guillermo Marco Puche: > Hello, > > I've no idea who compiled the application. I just found on seqanswers forum > that pBWA was a nice speed up to the original BWA since it supports native > OPEN MPI. > > As you told me i'll look further on how to compile open-mpi with SGE. If > anyone knows a good introduction/tutorial to this would be appreciated.
The Open MPI site has huge documentation: http://www.open-mpi.org/faq/?category=building#build-rte-sge http://www.open-mpi.org/faq/?category=running#run-n1ge-or-sge Be sure that during execution you pick the correct `mpiexec` and LD_LIBRARY_PATH from you own build. You can also adjust the location of Open MPI with the usual --prefix. I put it in --prefix==$HOME/local/openmpi-1.6.2_shared_gcc refelcting the version I built. -- Reuti > Then i'll try to run it with my current version of open-mpi and update if > needed. > > Thanks. > > Best regards, > Guillermo. > > El 25/10/2012 18:53, Reuti escribió: >> Please keep the list posted, so that others can participate on the >> discussion. I'm not aware of this application, but maybe someone else is on >> the list who could be of broader help. >> >> Again: who compiled the application, as I can see only the source at the >> site you posted? >> >> -- Reuti >> >> >> Am 25.10.2012 um 13:23 schrieb Guillermo Marco Puche: >> >>> $ ompi_info | grep grid >>> >>> Returns nothing. Like i said I'm newbie to MPI. >>> I didn't know that I had to compile anything. I've Rocks installation out >>> of the box. >>> So MPI is installed but nothing more I guess. >>> >>> I've found an old thread in Rocks discuss list: >>> https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2012-April/057303.html >>> >>> >>> User asking is using this script: >>> >>> *#$ -S /bin/bash* >>> >>> *#* >>> >>> *#* >>> >>> *# Export all environment variables* >>> >>> *#$ -V* >>> >>> *# specify the PE and core #* >>> >>> *#$ -pe mpi 128* >>> >>> *# Customize job name* >>> >>> *#$ -N job_hpl_2.0* >>> >>> *# Use current working directory* >>> >>> *#$ -cwd* >>> >>> *# Join stdout and stder into one file* >>> >>> *#$ -j y* >>> >>> *# The mpirun command; note the lack of host names as SGE will provide them >>> >>> on-the-fly.* >>> >>> *mpirun -np $NSLOTS ./xhpl >> xhpl.out* >>> >>> >>> >>> But then I read this: >>> >>> >>> in rocks sge PE >>> mpi is loosely integrated >>> mpich and orte are tightly integrated >>> qsub require args are different for mpi mpich with orte >>> >>> mpi and mpich need machinefile >>> >>> by default >>> mpi, mpich are for mpich2 >>> orte is for openmpi >>> regards >>> -LT >>> >>> >>> The program I need to run is pBWA: >>> http://pbwa.sourceforge.net/ >>> >>> It uses MPI. >>> >>> At this moment i'm kinda confused on which is the next step. >>> >>> I thought i just could run with MPI and a simple SGE job pBWA with multiple >>> processes. >>> >>> Regards, >>> Guillermo. >>> >>> >>> El 25/10/2012 13:17, Reuti escribió: >>>> Am 25.10.2012 um 13:11 schrieb Guillermo Marco Puche: >>>> >>>> >>>>> Hello Reuti, >>>>> >>>>> I got stoned here. I've no idea what MPI library I've got. I'm using >>>>> Rocks Cluster Viper 5.4.3 which comes out with Centos 5.6, SGE, SPM, OPEN >>>>> MPI and MPI. >>>>> >>>>> How can i check which library i got installed? >>>>> >>>>> I found this: >>>>> >>>>> $ mpirun -V >>>>> mpirun (Open MPI) 1.4.3 >>>>> >>>>> Report bugs to >>>>> >>>>> http://www.open-mpi.org/community/help/ >>>> Good, and this one you also used to compile the application? >>>> >>>> The check whether Open MPI was build with SGE support: >>>> >>>> $ ompi_info | grep grid >>>> MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.6.2) >>>> >>>> -- Reuti >>>> >>>> >>>> >>>>> Thanks, >>>>> >>>>> Best regards, >>>>> Guillermo. >>>>> >>>>> El 25/10/2012 13:05, Reuti escribió: >>>>> >>>>>> Am 25.10.2012 um 10:37 schrieb Guillermo Marco Puche: >>>>>> >>>>>> >>>>>> >>>>>>> Hello ! >>>>>>> >>>>>>> I found a new version of my tool which supports multi-threading but >>>>>>> also MPI or OPENMPI for more additional processes. >>>>>>> >>>>>>> I'm kinda new to MPI with SGE. What would be the good command for qsub >>>>>>> or config inside a job file to ask SGE to work with 2 MPI processes? >>>>>>> >>>>>>> Will the following code work in a SGE job file? >>>>>>> >>>>>>> #$ -pe mpi 2 >>>>>>> >>>>>>> That's supposed to make job work with 2 processes instead of 1. >>>>>>> >>>>>>> >>>>>> Not out of the box: it will grant 2 slots for the job according to the >>>>>> allocation rules of the PE. But how to start your application in the >>>>>> jobscript inside the granted allocation is up to you. Fortunately the >>>>>> MPI libraries got an (almost) automatic integration into queuing systems >>>>>> nowadays without further user intervention. >>>>>> >>>>>> Which MPI library do you use when you compile your application of the >>>>>> mentioned ones above? >>>>>> >>>>>> -- Reuti >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Regards, >>>>>>> Guillermo. >>>>>>> >>>>>>> El 22/10/2012 17:19, Reuti escribió: >>>>>>> >>>>>>> >>>>>>>> Am 22.10.2012 um 16:31 schrieb Guillermo Marco Puche: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> I'm using a program where I can specify the number of threads I want >>>>>>>>> to use. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> Only threads and not additional processes? Then you are limited to one >>>>>>>> node, unless you add something like >>>>>>>> http://www.kerrighed.org/wiki/index.php/Main_Page or >>>>>>>> http://www.scalemp.com >>>>>>>> >>>>>>>> >>>>>>>> to get a cluster wide unique process and memory space. >>>>>>>> >>>>>>>> -- Reuti >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> I'm able to launch multiple instances of that tool in separate nodes. >>>>>>>>> For example: job_process_00 in compute-0-0, job_process_01 in >>>>>>>>> compute-1 etc.. each job is calling that program which splits up in 8 >>>>>>>>> threads (each of my nodes has 8 CPUs). >>>>>>>>> >>>>>>>>> When i setup 16 threads i can't split 8 threads per node. So I would >>>>>>>>> like to split them between 2 compute nodes. >>>>>>>>> >>>>>>>>> Currently I've 4 compute nodes and i would like to speed up the >>>>>>>>> process setting 16 threads of my program splitting between more than >>>>>>>>> one compute node. At this moment I'm stuck using only 1 compute node >>>>>>>>> per process with 8 threads. >>>>>>>>> >>>>>>>>> Thank you ! >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> Guillermo. >>>>>>>>> _______________________________________________ >>>>>>>>> users mailing list >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> [email protected] >>>>>>>>> https://gridengine.org/mailman/listinfo/users >>>>>>> _______________________________________________ >>>>>>> users mailing list >>>>>>> >>>>>>> >>>>>>> [email protected] >>>>>>> https://gridengine.org/mailman/listinfo/users > _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
