AMBER Archive (2006)

Subject: Re: AMBER: Parallel version of Amber: error message

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Mon Feb 06 2006 - 13:21:31 CST

it looks like a library issue- do you have the libraries installed
on every machine? If not, you should compile with static linking.
have you followed the information on Linux compiling on
the Amber web page?

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University E-mail: carlos.simmerling_at_stonybrook.edu
Stony Brook, NY 11794-5115

Academic year 2005 address:
Brookhaven National Laboratory
Computational Science Center
Upton, NY 11973
===================================================================

snoze pa wrote:

> Dear AMBER Users,
>
> Anybody has good luck in compileing parallel version of amber. I
> spend two days but still sander is giving me following error using mpich.
>
> cd cytosine; ./Run.cytosine
> /home/amber8/test/cytosine/../../exe/sander: error while loading
> shared libraries: libvml.so: cannot open shared object file: No such
> file or directory
> p0_1395: p4_error: Child process exited while making connection to
> remote process on xxx.xxx.xxx: 0
> forrtl: error (69): process interrupted (SIGINT)
> p0_1395: (2.205486) net_send: could not write to fd=4, errno = 32
> ./Run.cytosine: Program error
>
> but when I use
>
> export LD_LIBRARY_PATH='/usr/intel/mkl/8.0.1/lib/32:'
> then it is giving me following error message
> cd cytosine; ./Run.cytosine
> /home/amber8/test/cytosine/../../exe/sander: error while loading
> shared libraries: libimf.so: cannot open shared object file: No such
> file or directory
> ./Run.cytosine: Program error
> make: *** [test.sander.no_lmod] Error 1
>
>
> How to compile amber in parrallel using mpich, any help will be highly
> appreciated. LAM is not working in my case so I am using mpich.
> thanks in advance
> snoze

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