Am 12.11.2012 um 13:47 schrieb Guillermo Marco Puche: > Hello, > > This must be the problem. I've check that each compute node can only resolve > his own IP address: > > For example in compute-0-0: > > /opt/gridengine/utilbin/lx26-amd64/gethostbyaddr 10.4.0.2 > Hostname: compute-0-0.local > Aliases: compute-0-0 > Host Address(es): 10.4.0.2 > > 10.4.0.3 (compute-0-1
Check /etc/hosts file or any NIS you setup to distribute the hostnames. -- Reuti > $ /opt/gridengine/utilbin/lx26-amd64/gethostbyaddr 10.4.0.3 > error resolving ip "10.4.0.3": can't resolve ip address (h_errno = > HOST_NOT_FOUND) > > And the inverse on compute-0-1, it can resolve 10.4.0.3 but not 10.4.0.2. > > Regards, > Guillermo. > El 12/11/2012 13:35, Guillermo Marco Puche escribió: >> Hello, >> >> Ok I've patched my nodes with the RPM fix for MPI and SGE. (i forgot to >> install it on compute nodes). >> >> Removed -np 16 argument and got this new error: >> >> error: commlib error: access denied (client IP resolved to host name "". >> This is not identical to clients host name "") >> error: executing task of job 97 failed: failed sending task to >> [email protected]: can't find connection >> -------------------------------------------------------------------------- >> A daemon (pid 3037) died unexpectedly with status 1 while attempting >> to launch so we are aborting. >> >> 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. >> -------------------------------------------------------------------------- >> >> >> El 12/11/2012 13:11, Reuti escribió: >>> Am 12.11.2012 um 12:18 schrieb Guillermo Marco Puche: >>> >>>> 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 > >>> If the compute-0-2 is powered off, it won't get slots assigned by SGE. >>> >>> The 16 slots are available on the actual machine - otherwise the job should >>> be in "qw" state? As Open MPI was compiled with tight integration, the >>> argument "-np 16" isn't necessary. It will detect the granted amount of >>> slots and their location automatically. >>> >>> -- Reuti >>> >>> >>>> /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
