AMBER Archive (2006)

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

From: David LeBard (david.lebard_at_asu.edu)
Date: Mon Feb 06 2006 - 14:10:29 CST

Hi Snoze,

What are your C/Fortran flags (CFLAGS,CXXFLAGS,FFLAGS)? If you do not
have "-static" set for each, then you will need to make sure your MPICH
library sits at the same place on each machine (and, of course, the
AMBER directory as well).

Also, if you still get the same error after static compilation, you may
want to change your C++ from mpiCC to mpicc. mpiCC is known to give
some errors, and since mpicc (from intel) compiles both C/C++ code, it
can be preferable (though I am not sure why).

Good luck,

David LeBard
Dept. of Chemistry and Biochemistry
Arizona State University

On Mon, 2006-02-06 at 12:45, 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> 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
> 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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