AMBER Archive (2006)

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

From: Mingfeng Yang (mfyang_at_gmail.com)
Date: Mon Feb 06 2006 - 14:29:38 CST

As Dr. Simmerling said, did you do static linking?
Compilation won't be a problem withou static linking, but when the
system load compiled sander into memory, it needs load in its dependent
library also.

Enable "-static" when you configure the installation.

--Mingfeng

snoze pa wrote:
> I have all intel cc/ff/lib are installed. while compiling mpich it is
> not giving me any error message. Same it true with Amber.
> I am following the instructions given in page
> http://amber.scripps.edu/cluster_info/index.html
> it is only when I am running sander can be seen from my previous example
> snoze
>
> On 2/6/06, *Carlos Simmerling* <carlos.simmerling_at_stonybrook.edu
> <mailto:carlos.simmerling_at_stonybrook.edu>> wrote:
>
> 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
> <mailto: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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