AMBER Archive (2006)

Subject: RE: AMBER: amber9

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Fri Jul 14 2006 - 18:33:00 CDT

Hi
Thanks for the notes on that.
The problem is that I am still trying to run my compiled sande.MPI on
single machine with 2 processors so far, without even trying to go to
larger configurations.
I checked mpirun -np 1 and the problem is the same.
In the same environment I can run amber8 (-np 1 or -np 2...)

Thanks
Piotr

On Fri, 14 Jul 2006, Ross Walker wrote:

> Date: Fri, 14 Jul 2006 15:37:19 -0700
> From: Ross Walker <ross_at_rosswalker.co.uk>
> Reply-To: amber_at_scripps.edu
> To: amber_at_scripps.edu
> Subject: RE: AMBER: amber9
>
> Hi Piotr,
>
>> sander.MPI: error while loading shared libraries: libsvml.so:
>> cannot open shared object file: No such file or directory
>>
>> This fortran library is located in my case in /opt/intel_fc_80/lib
>> and my environment is properly setup for recognizing the path
>> to this directory.
>> (maybe the program tries to load it from /usr/local/bin/lib?)
>>
>> (this is excerpt from env:
>> LD_LIBRARY_PATH=/usr/local/lib:/opt/intel_fc_80/lib)
>
> Are you certain every node has the libraries installed in the same place and
> all are correctly setting up LD_LIBRARY_PATH? When running shared library
> executables in parallel all of the nodes need to have access to the library
> and all need to have the path setup correctly.
>
> I typically get around this on large clusters by copying the whole of
> intel_fc_80/lib to ~/lib and then edit my .cshrc files to add ~/lib to my
> LD_LIBRARY_PATH and my PATH (just to be sure). Then I make sure that the job
> submission system is setup so that it correctly sources my cshrc file on
> every node before doing the mpirun command.
>
> You might also want to try and see if you can compile statically (may or may
> not work depending on your mpi installation.)
>
> Note, also check to see if mpirun -np 1 works - I.e. 1 thread run on the
> node you are physically logged into.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu