AMBER Archive (2009)

Subject: Re: [AMBER] Testing parallel amber10: no

From: Francesco Pietra (
Date: Wed Apr 08 2009 - 05:03:09 CDT

On Wed, Apr 8, 2009 at 11:35 AM, Atro Tossavainen
<> wrote:
>> ./configure_amber -openmpi -nobintray ifort
> Surely you must have meant "nobintraj"?  But it's a non-issue, really,
> as far as this is concerned.
>> /usr/local/amber10/exe/sander.MPI: error while loading shared
>> libraries: cannot open shared object file: no such
>> file or directory
> The link loader cannot find the shared library that the program depends
> on.  It's not in the standard path for searching shared libraries, your
> executables have been compiled without -rpath, and your LD_LIBRARY_PATH
> does not include the directory that contains the libraries either.  You
> need to fix either of the two latter ones.

I understand this. However, everything about is sourced correctly from
my .bashrc from the intel *.sh. Now, I have purged the version 10 of
the intel compilers and mkl (i had made a deb package). I am
installing the deb package (just made) of the intels 11 (the
ambertools refused to compile with version 10 icc not finding
limits.h) and mkl. Then I recompile openmpi with these. If I do not
succeed to compile amber10 thereafter, I'll remove everything about
intels to try with gnu compilers and libraries. This will be nothing
for amber, though bad for the electronic calculations. But I was
unable to do better.
> --
> Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
> Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
> +358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
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