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
Hello,
I'm trying to change the mpi config file:
$ qconf -mp mpi
pe_namempi
slots
user_lists NONE
xuser_listsNONE
start_proc_args/bin/false
stop_proc_args /bin/false
allocation_rule$fill_up
control_slaves FALSE
job_is_first_task TRU
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 gettin
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/acti
Hello,
I figured it out then i read your answer.
Awesome ! Finaly it's working, 16 processes over 2 computes nodes :)
Thank you so much.
Best regards,
Guillermo.
El 12/11/2012 14:09, Reuti escribió:
Am 12.11.2012 um 13:47 schrieb Guillermo Marco Puche:
Hello,
This must be the problem. I've
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
> Al
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)
$
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: executin
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
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_lef
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
Hello,
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:
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.
Yo
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
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 woul
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? Do I've to be in a
specified directory to execute that command?
Thank you !
Sorry again for my ignorance.
Regards,
Guillermo.
El 25/10/2012 19:50,
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-mp
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 w
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 25.10.20
Am 25.10.2012 um 13:43 schrieb Guillermo Marco Puche:
> After reading more. I think the only thing i need is to setup my bash job
> file.
> And run it with mpiexec -n 2 /home/test/mytestjob.sh
It could be, but in general: no.
First: check the MPI implementation the application was compiled with
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 fou
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
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
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 ht
On 22 October 2012 15:31, Guillermo Marco Puche
wrote:
> Hello,
>
> I'm using a program where I can specify the number of threads I want to
> use. 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..
Hello,
I'm using a program where I can specify the number of threads I want to
use. 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
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