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?
With best regards
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 4:55 PM
Subject: Re: [AMBER] Problem related to the parallel installation of Amber11
On Mon, Oct 1, 2012 at 5:11 AM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> Respected Sir,
>
> As per your advice to run the configure_mpich2 script in
> $AMBERHOME/AmberTools/src, I tried it. But it shows that the command not
> found because there is no such file. The list of files which are in folder
> are as follows:
>
> antechamber chamber etc lapack
> netcdf pbsa rism xray
> arpack cifparse fftw-2.1.5 leap
> netcdf_config.log pnetcdf semantics
> blas config.h fftw2_config.log lib
> nss pnetcdf_config.log sff
> byacc configure gleap Makefile
> ptraj sqm
> c9x-complex configure_openmpi include nab
> reduce ucpp-1.3
>
>
> As there is a file namely configure_openmpi (I think this might be related
> to the MPI), I run this script file. And it gives the following error
>
> Setting AMBERHOME to /usr/local/amber11/AmberTools
>
> You must download openmpi and extract it here
> (for example, type 'tar xvfj openmpi-1.4.1.tar.bz2')
> See http://www.open-mpi.org/software/ompi/v1.4/ for more info;
> Then, re-run this script.
>
>
> Then I download the bz2 file and extract and re run the script. Again it
> gives the same error. Noteably, As I extract it only a new folder is
> created and no other files.
>
> Please help me out, how to solve this problem.
>
You need to download openmpi-1.4.1.tar.bz2 (note the version 1.4.1, do not
download 1.4.5). Also, make sure you extract it in
$AMBERHOME/AmberTools/src so the directory
$AMBERHOME/AmberTools/src/openmpi-1.4.1 exists.
HTH,
Jason
--
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 - 11:00:03 PDT
