Thanks for your reply
I just copy "export LD_LIBRARY_PATH=$AMBERHOME/bin\:$LD_LIBRARY_PATH" and past in .bashrc, and compile it (. ~/.bashrc). But it gives the same error. Shall I have to modify this path or anything.
Thanks for your suggestion for not to use root.
Sindrila
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 1 October 2012 11:34 PM
Subject: Re: [AMBER] Problem related to the parallel installation of Amber11
On Mon, Oct 1, 2012 at 1:39 PM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> Thanks for the kind help.
>
> Now I am able to solve this issue and another problem arise.
>
> I perform all the steps as per Amber11 manual as follows
>
> ./configure -mpi gnu
> cd ../../src
> make clean
> make parallel
>
> and after the 'make parallel' I get the following comments
>
> make[1]: Leaving directory `/usr/local/amber11/src/addles'
>
> Installation of Amber11 (parallel) is complete at Mon Oct 1 21:19:38 IST
> 2012.
>
> Then I use the following command
>
> cd $AMBERHOME/test
> export DO_PARALLEL='mpirun -np 2'
> make test.parallel
>
> And it shows the following error message
>
>
> Finished parallel test suite for Amber 11 at Mon Oct 1 21:13:35 IST 2012.
> Some tests require 4 threads to run, while some will not
> run with more than 2. Please run further parallel tests with the
> appropriate number of processors. See README for details.
>
> make[1]: Target `test.parallel2' not remade because of errors.
> make[1]: Leaving directory `/usr/local/amber11/test'
> 2 file comparisons passed
> 18 file comparisons failed
> 901 tests experienced errors
> Test log file saved as logs/test_amber_parallel/2012-10-01_21-13-30.log
> Test diffs file saved as logs/test_amber_parallel/2012-10-01_21-13-30.diff
>
>
> I change the -np from 2 to 4, but it again shows the same error message.
> Please let me know how to solve this?
>
> I also try the following mpirun -np 4 sander.MPI, it gives the following
> error
>
>
> [root.sindrila local]# mpirun -np 4 sander.MPI
> sander.MPI: error while loading shared libraries: libmpi_f90.so.0: cannot
> open shared object file: No such file or directory
> sander.MPI: error while loading shared libraries: libmpi_f90.so.0: cannot
> open shared object file: No such file or directory
> sander.MPI: error while loading shared libraries: libmpi_f90.so.0: cannot
> open shared object file: No such file or directory
> sander.MPI: error while loading shared libraries: libmpi_f90.so.0: cannot
> open shared object file: No such file or directory
> [root.sindrila local]#
>
>
> How to solve this issue?
>
Add AMBERHOME/lib to your LD_LIBRARY_PATH. That is:
export LD_LIBRARY_PATH=$AMBERHOME/bin\:$LD_LIBRARY_PATH
HTH,
Jason
P.S.: I discourage you from doing all of this as root. My suggestion
instead is to install Amber in your home directory, or give your main user
ownership of your Amber directory. If something goes wrong (either through
your mistake or a package maintainer's), it's better to have it go wrong in
your user account where the damage would be limited than in the root
account that could ruin your OS.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 01 2012 - 12:00:02 PDT
