Re: [AMBER] Problem related to the parallel installation of Amber11

From: Jason Swails <>
Date: Mon, 1 Oct 2012 07:25:52 -0400

On Mon, Oct 1, 2012 at 5:11 AM, Sindrila Dutta banik <> 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 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.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Oct 01 2012 - 04:30:02 PDT
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