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

From: Sindrila Dutta banik <>
Date: Mon, 1 Oct 2012 17:11:47 +0800 (SGT)

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.

With best regards

 From: David A Case <>
To: AMBER Mailing List <>
Sent: Monday, 1 October 2012 7:32 AM
Subject: Re: [AMBER] Problem related to the parallel installation og Amber11
On Mon, Oct 01, 2012, Ben Roberts wrote:
> Red Hat comes with its own package manager, not synaptic. As you say,
> it has RPM, and there may be a GUI front end that you can use if you're
> more comfortable with that.

I think(?) that you can probably use the Fedora instructions (at the Amber web
page) for RedHat as well.  Essentially, you use "yum" rather that "apt-get" as
the package manager.

> If you continue having difficulties with FFTW installation on your Red
> Hat system, you may be better off trying channels geared towards Red Hat
> users and administrators, or (failing that) towards FFTW users. Here
> on the Amber list, we aren't set up to offer support for getting
> third-party packages working on third-party operating systems.

I don't agree here: FFTW is required for many things in Amber, and we try to
help users out.  However, your problem is not really with FFTW, but with the
lack of MPI.  Look at the end of the fftw log:

checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
configure: error: couldn't find mpi library for --enable-mpi

Basically, you are trying to install parallel Amber without having an MPI
installation (or at least one that can be found by the configure program).
It just happens that fftw is the first thing to break.

As usual, *my* advice is to run the configure_mpich2 script in
$AMBERHOME/AmberTools/src.  This will set up your MPI in a state that is
consistent with the rest of Amber, and has everything in the right place, (as
long as you put $AMBERHOME/bin in your PATH.)  [I know that others on the list
often/always tell people to use a package manager to get MPI, but that seems to
have a catch-22 for people who don't know how to find the package manager on
their system.]


AMBER mailing list
AMBER mailing list
Received on Mon Oct 01 2012 - 02:30:03 PDT
Custom Search