Am 13.11.2012 um 08:58 schrieb Guillermo Marco Puche: > Hello, > > I'm trying to change the mpi config file
Why? The definitions inside the PE must match the requirements of the MPI implementations. If you want to have the settings you used for orted for a PE with name MPI just coy the lines from: $ qconf -sp orted into the PE named mpi. But then it might not work any longer with the MPI library you use usually with it. http://www.open-mpi.org/faq/?category=running#run-n1ge-or-sge Also have a look at `man sge_pe`, where the settings are explained. -- Reuti > $ qconf -mp mpi > > pe_name mpi > slots 9999 > user_lists NONE > xuser_lists NONE > start_proc_args /bin/false > stop_proc_args /bin/false > allocation_rule $fill_up > control_slaves FALSE > job_is_first_task TRUE > urgency_slots min > accounting_summary TRUE > > I've set /bin/false as start and proc args but now job holds forever on qw > state. So I'm not sure what start and proc args should be. SGE doesn't let > you to left them empty. > > Best regards, > Guillermo. > El 12/11/2012 21:07, Reuti escribió: >> Am 12.11.2012 um 20:54 schrieb Guillermo Marco Puche: >> >>> Hello, >>> >>> It seems that the program i need to use needs mpi as PE. I've tested with >>> orte and it just does the same process 16 times. >>> >>> I'm trying the same submit job script but chaning "-pe orte 16" to "-pe mpi >>> 16". >>> >>> And getting the following error: >>> >>> /opt/gridengine/default/spool/compute-0-1/active_jobs/102.1/pe_hostfile >>> compute-0-1 >>> compute-0-1 >>> compute-0-1 >>> compute-0-1 >>> compute-0-1 >>> compute-0-1 >>> compute-0-1 >>> compute-0-1 >>> compute-0-0 >>> compute-0-0 >>> compute-0-0 >>> compute-0-0 >>> compute-0-0 >>> compute-0-0 >>> compute-0-0 >>> compute-0-0 >>> rm: cannot remove `/tmp/102.1.all.q/rsh': No such file or directory >> Either ignore it or remove the start-/stop_proc_args from the PE. It tries >> to remove a file which is only created if start_proc_args is called with >> -catch_rsh. >> >> -- Reuti >> >> >>> >>> El 12/11/2012 12:18, Guillermo Marco Puche escribió: >>>> Hello, >>>> >>>> I'm currently trying with the following job script and then submiting with >>>> qsub. >>>> I don't know why it just uses cpus of one of my two compute nodes. It's >>>> not using both compute nodes. (compute-0-2 it's currently powered off >>>> node). >>>> >>>> #!/bin/bash >>>> #$ -S /bin/bash >>>> #$ -V >>>> ### name >>>> #$ -N aln_left >>>> ### work dir >>>> #$ -cwd >>>> ### outputs >>>> #$ -j y >>>> ### PE >>>> #$ -pe orte 16 >>>> ### all.q >>>> #$ -q all.q >>>> >>>> mpirun -np 16 pBWA aln -f aln_left >>>> /data_in/references/genomes/human/hg19/bwa_ref/hg19.fa >>>> /data_in/data/rawdata/HapMap_1.fastq > >>>> /data_out_2/tmp/05_11_12/mpi/HapMap_cloud.left.sai >>>> >>>> Here's all.q config file: >>>> >>>> qname all.q >>>> hostlist @allhosts >>>> seq_no 0 >>>> load_thresholds np_load_avg=1.75 >>>> suspend_thresholds NONE >>>> nsuspend 1 >>>> suspend_interval 00:05:00 >>>> priority 0 >>>> min_cpu_interval 00:05:00 >>>> processors UNDEFINED >>>> qtype BATCH INTERACTIVE >>>> ckpt_list NONE >>>> pe_list make mpich mpi orte openmpi smp >>>> rerun FALSE >>>> slots 0,[compute-0-0.local=8],[compute-0-1.local=8], \ >>>> [compute-0-2.local.sg=8] >>>> tmpdir /tmp >>>> shell /bin/csh >>>> prolog NONE >>>> epilog NONE >>>> shell_start_mode posix_compliant >>>> starter_method NONE >>>> suspend_method NONE >>>> resume_method NONE >>>> terminate_method NONE >>>> notify 00:00:60 >>>> owner_list NONE >>>> user_lists NONE >>>> xuser_lists NONE >>>> subordinate_list NONE >>>> complex_values NONE >>>> projects NONE >>>> xprojects NONE >>>> calendar NONE >>>> initial_state default >>>> s_rt INFINITY >>>> h_rt INFINITY >>>> s_cpu INFINITY >>>> h_cpu INFINITY >>>> s_fsize INFINITY >>>> h_fsize INFINITY >>>> s_data INFINITY >>>> h_data INFINITY >>>> s_stack INFINITY >>>> h_stack INFINITY >>>> s_core INFINITY >>>> h_core INFINITY >>>> s_rss INFINITY >>>> h_rss INFINITY >>>> s_vmem INFINITY >>>> h_vmem INFINITY >>>> >>>> Best regards, >>>> Guillermo. >>>> >>>> >>>> El 05/11/2012 12:01, Reuti escribió: >>>>> Hi, >>>>> >>>>> Am 05.11.2012 um 10:55 schrieb Guillermo Marco Puche: >>>>> >>>>>> I've managed to compile Open MPI for Rocks: >>>>>> ompi_info | grep grid >>>>>> MCA ras: gridengine (MCA v2.0, API v2.0, Component >>>>>> v1.4.3) >>>>>> >>>>>> Now I'm really confused on how i should run my pBWA program with Open >>>>>> MPI. >>>>>> Program website (http://pbwa.sourceforge.net/) suggests something like: >>>>>> >>>>>> sqsub -q mpi -n 240 -r 1h --mpp 4G ./pBWA bla bla bla... >>>>> Seems to be a local proprietary command on Sharcnet, or at least a >>>>> wrapper to another unknown queuing system. >>>>> >>>>> >>>>>> I don't have sqsub, but qsub provided by SGE. "-q" option isn't valid >>>>>> for SGE since it's for queue selection. >>>>> Correct, the SGE paradigm is to request resources and SGE will select an >>>>> appropriate queue for your job which fullfils the requirements. >>>>> >>>>> >>>>>> Maybe the solution is to create a simple job bash script and include >>>>>> parallel environment for SGE and the number of slots (since pBWA >>>>>> internally supports Open MPI) >>>>> How is your actal setup of your SGE? Most likely you will need to define >>>>> a PE and request it during submission like for any other Open MPI >>>>> application: >>>>> >>>>> $ qsub -pe orte 240 -l h_rt=1:00:00,h_vmem=4G ./pBWA bla bla bla... >>>>> >>>>> Assuming "-n" gives the number of cores. >>>>> Assuming "-r 1h" means wallclock time: -l h_rt=1:00:00 >>>>> Assuming "--mpp 4G" requests the memory per slot: -l h_vmem=4G >>>>> >>>>> Necessary setup: >>>>> >>>>> http://www.open-mpi.org/faq/?category=running#run-n1ge-or-sge >>>>> >>>>> -- Reuti >>>>> >>>>> >>>>>> Regards, >>>>>> Guillermo. >>>>>> >>>>>> El 26/10/2012 12:21, Reuti escribió: >>>>>>> Am 26.10.2012 um 12:02 schrieb Guillermo Marco Puche: >>>>>>> >>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> Like I said i'm using Rocks cluster 5.4.3 and it comes with mpirun >>>>>>>> (Open MPI) 1.4.3. >>>>>>>> But $ ompi_info | grep gridengine shows nothing. >>>>>>>> >>>>>>>> So I'm confused if I've to update and rebuild open-mpi into the latest >>>>>>>> version. >>>>>>>> >>>>>>> You can also remove the supplied version 1.4.3 from your system and >>>>>>> build it from source with SGE support. But I don't see the advantage of >>>>>>> using an old version. ROCKS supplies the source of their used version >>>>>>> of Open MPI? >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Or if i can keep that current version of MPI and re-build it (that >>>>>>>> would be the preferred option to keep the stability of the cluster) >>>>>>>> >>>>>>> If you compile and install only in your own $HOME (as normal user, no >>>>>>> root access necessary), then there is no impact to any system tool at >>>>>>> all. You just have to take care which version you use by setting the >>>>>>> correct $PATH and $LD_LIBRARY_PATH during compilation of your >>>>>>> application and during execution of it. Therefore I suggested to >>>>>>> include the name of the used compiler and Open MPI version in the build >>>>>>> installation's directory name. >>>>>>> >>>>>>> There was a question about the to be used version of `mpiexec` just on >>>>>>> the MPICH2 mailing list, maybe it's additional info: >>>>>>> >>>>>>> >>>>>>> http://lists.mcs.anl.gov/pipermail/mpich-discuss/2012-October/013318.html >>>>>>> >>>>>>> >>>>>>> -- Reuti >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Thanks ! >>>>>>>> >>>>>>>> Best regards, >>>>>>>> Guillermo. >>>>>>>> >>>>>>>> El 26/10/2012 11:59, Reuti escribió: >>>>>>>> >>>>>>>>> Am 26.10.2012 um 09:40 schrieb Guillermo Marco Puche: >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hello, >>>>>>>>>> >>>>>>>>>> Thank you for the links Reuti ! >>>>>>>>>> >>>>>>>>>> When they talk about: >>>>>>>>>> >>>>>>>>>> shell $ ./configure --with-sge >>>>>>>>>> >>>>>>>>>> It's in bash shell or in any other special shell? >>>>>>>>>> >>>>>>>>> There is no special shell required (please have a look at the INSTALL >>>>>>>>> file in Open MPI's tar-archive). >>>>>>>>> >>>>>>>>> >>>>>>>>>> Do I've to be in a specified directory to execute that command? >>>>>>>>>> >>>>>>>>> Depends. >>>>>>>>> >>>>>>>>> As it's set up according to the >>>>>>>>> http://en.wikipedia.org/wiki/GNU_build_system >>>>>>>>> , you can either: >>>>>>>>> >>>>>>>>> $ tar -xf openmpi-1.6.2.tar.gz >>>>>>>>> $ cd openmpi-1.6.2 >>>>>>>>> $ ./configure --prefix=$HOME/local/openmpi-1.6.2_gcc --with-sge >>>>>>>>> $ make >>>>>>>>> $ make install >>>>>>>>> >>>>>>>>> It's quite common to build inside the source tree. But if it is set >>>>>>>>> up in the right way, it also supports building in different >>>>>>>>> directories inside or outside the source tree which avoids a `make >>>>>>>>> distclean` in case you want to generate different builds: >>>>>>>>> >>>>>>>>> $ tar -xf openmpi-1.6.2.tar.gz >>>>>>>>> $ mkdir openmpi-gcc >>>>>>>>> $ cd openmpi-gcc >>>>>>>>> $ ../openmpi-1.6.2/configure --prefix=$HOME/local/openmpi-1.6.2_gcc >>>>>>>>> --with-sge >>>>>>>>> $ make >>>>>>>>> $ make install >>>>>>>>> >>>>>>>>> While at the time in another window you can execute: >>>>>>>>> >>>>>>>>> $ mkdir openmpi-intel >>>>>>>>> $ cd openmpi-intel >>>>>>>>> $ ../openmpi-1.6.2/configure --prefix=$HOME/local/openmpi-1.6.2_intel >>>>>>>>> CC=icc CXX=icpc FC=ifort F77=ifort --disable-vt --with-sge >>>>>>>>> $ make >>>>>>>>> $ make install >>>>>>>>> >>>>>>>>> (Not to confuse anyone: there is bug in combination of Intel compiler >>>>>>>>> and GNU headers with the above version of Open MPI, disabling >>>>>>>>> VampirTrace support helps.) >>>>>>>>> >>>>>>>>> -- Reuti >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Thank you ! >>>>>>>>>> Sorry again for my ignorance. >>>>>>>>>> >>>>>>>>>> Regards, >>>>>>>>>> Guillermo. >>>>>>>>>> >>>>>>>>>> El 25/10/2012 19:50, Reuti escribió: >>>>>>>>>> >>>>>>>>>>> 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 >>> _______________________________________________ >>> users mailing list >>> [email protected] >>> https://gridengine.org/mailman/listinfo/users >>> > _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
