rdock-list-def Mailing List for rDock

Hi all,
We have made a short tutorial in rDock webpage regarding this issue.

http://rdock.sourceforge.net/how-to-run-rdock-in-parallel/

At this moment, MPI is not implemented in rDock. As Szilveszter suggested,
it is easier to use a job-scheduler (there is an example in the tutorial).
Best,
Sergio



2014-04-30 11:23 GMT+02:00 Szilveszter Juhos <szi...@gm...>:

> Hi, it is just hundred times easier to use a job-scheduler like Condor
> / LSF / GridEngine instead of implementing the MPI stuff into rDock.
> If you have a cluster, you can have Condor for free, it is relatively
> easy to install/use.
>
> Cheers:
> Szilva
>
> On Wed, Apr 30, 2014 at 10:10 AM, Jose Manuel Gally
> <jos...@un...> wrote:
> > Hi!
> >
> > I would like to know if it's possible to compile a mpi version of rDock
> in
> > order to run it on a cluster?
> > If so could someone explain to me how to do it or redirect me to the
> > relevant documentation?
> >
> > I couldn't find any mpi flag in the make files, or any documentation
> about
> > parallel installation in the pdf guides in $RBT_ROOT/docs.
> >
> > Complementary informations :
> > - The openmpi version on the cluster is 1.6.5 (x64).
> > - I am not an expert in unix environment.
> > - I have the rDock_2013_1 version.
> > - I am running on Centos 6.5 x64.
> > - I could compile rDock without any apparent problem on my local computer
> > following the Getting_Started guide.
> >
> > Thank you for your help!
> >
> > Best regards,
> > Jose Manuel
> >
> >
> > -
> >
> >
> ------------------------------------------------------------------------------
> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> > Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> > unparalleled scalability from the best Selenium testing platform
> available.
> > Simple to use. Nothing to install. Get started now for free."
> > http://p.sf.net/sfu/SauceLabs
> > _______________________________________________
> > rDock-list-def mailing list
> > rDo...@li...
> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def
> >
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

Hi, it is just hundred times easier to use a job-scheduler like Condor
/ LSF / GridEngine instead of implementing the MPI stuff into rDock.
If you have a cluster, you can have Condor for free, it is relatively
easy to install/use.

Cheers:
Szilva

On Wed, Apr 30, 2014 at 10:10 AM, Jose Manuel Gally
<jos...@un...> wrote:
> Hi!
>
> I would like to know if it's possible to compile a mpi version of rDock in
> order to run it on a cluster?
> If so could someone explain to me how to do it or redirect me to the
> relevant documentation?
>
> I couldn't find any mpi flag in the make files, or any documentation about
> parallel installation in the pdf guides in $RBT_ROOT/docs.
>
> Complementary informations :
> - The openmpi version on the cluster is 1.6.5 (x64).
> - I am not an expert in unix environment.
> - I have the rDock_2013_1 version.
> - I am running on Centos 6.5 x64.
> - I could compile rDock without any apparent problem on my local computer
> following the Getting_Started guide.
>
> Thank you for your help!
>
> Best regards,
> Jose Manuel
>
>
> -
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

Hi!

I would like to know if it's possible to compile a mpi version of rDock 
in order to run it on a cluster?
If so could someone explain to me how to do it or redirect me to the 
relevant documentation?

I couldn't find any mpi flag in the make files, or any documentation 
about parallel installation in the pdf guides in $RBT_ROOT/docs.

Complementary informations :
- The openmpi version on the cluster is 1.6.5 (x64).
- I am not an expert in unix environment.
- I have the rDock_2013_1 version.
- I am running on Centos 6.5 x64.
- I could compile rDock without any apparent problem on my local 
computer following the Getting_Started guide.

Thank you for your help!

Best regards,
Jose Manuel


-

I forward this question sent to my private email for the record.
Elnaz was missing LD_LIBRARY_PATH declaration pointing to rDock
installation LIB subdirectory as described in last paragraph of
installation page http://rdock.sourceforge.net/installation/

Daniel

---------- Forwarded message ----------
From: <ema...@us...>
Date: 2014-04-20 9:46 GMT+02:00
Subject: rDock
To: d-a...@us...
Cc: ema...@us...

Hi, I build the rDock on ubuntu 13.10 2 days ago successfully. But I could
not run it !
mehdizadeh@mehdizadeh-All-Series:~/Documents/rDock/rDock_2013.1_src$
./bin/rbcavity
./bin/rbcavity: error while loading shared libraries:
libRbt.so.rDock_2013.1_src: cannot open shared object file: No such file or
directory

could you please help me or tell me How can I get information.

Regards
Elnaz Aghdam
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