Re: [AMBER-Developers] 28 Mar release candidates for Amber11/AmberTools-1.4

From: Jason Swails <>
Date: Mon, 29 Mar 2010 11:37:14 -0400

On Mon, Mar 29, 2010 at 11:24 AM, case <> wrote:
> On Mon, Mar 29, 2010, wrote:
>> not sure if this warrants putting on bugzilla, but when I tried to
>> configure the release candidate for parallel, I visited the openmpi
>> homepage and downloaded their latest version from the website provided by
>> configure, which is called openmpi-1.4.1. The configure_openmpi script has
>> the name openmpi-1.4 hardcoded and fails.
> I applied your changes...thanks.  Of course, I'm sure that openmpi will
> have version 1.4.2 out soon, so we may need to think about this some more.
> ....dave

If we are sure that the upcoming versions of openmpi are going to
work, then we can probably loop through the directory names and
compare the beginning of each string to "openmpi-1.4" and set MPIDIR
to that. For example:

for dir in `ls -1 $AMBERHOME/src`; do
if [ ${dir:0:11} = "openmpi-1.4" ]; then
if [ "$MPIDIR" = "NONE" ]; then
echo "OpenMPI not found, download, whatever error message"
exit 1

This allows you to be as non-stringent as you wish, and take only the
first 9 characters and require "openmpi-1" or just take the first 7
characters and require "openmpi". The above script is not tested, but
I use something to that effect in in $AMBERHOME/src/mmpbsa_py
to get part of the python version (namely 2 or 3). Someone with an
ubuntu machine should check to make sure that it is POSIX compliant
and will work with all "sh"'s, not just bash.

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Mon Mar 29 2010 - 09:00:03 PDT
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