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. 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)
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
