Hi Daniel,

The version on the wiki (http://pymolwiki.org/index.php/User:Mglerner) should handle the fink (apbs-mpi-openmpi and apbs-mpi-lammpi) and macports (apbs-mpi) versions of MPI-enabled APBS. 

Please note that the PyMOL-APBS plugin doesn't go out of its way to take advantage of parallel features; it just calls the MPI-enabled versions of APBS.

Because I test the non-parallel versions more frequently, it checks for the normal APBS first. If you want it to find the MPI by default, you can 1) uninstall the non-MPI version, 2) set the APBS_BINARY variable in the plugin directly, or 3) set the APBS_BINARY_DIR environment variable. 

It's worth noting that the environment variables weren't working in some previous versions of the plugin.



On Wed, Jul 21, 2010 at 2:56 PM, Michael Lerner <mglerner+sourceforge@gmail.com> wrote:
Hi Daniel,

Sorry for the delay! I wasn't actually aware of that talk page; you'll get a faster response if you email the PyMOL list.

The version that you can download from pymolwiki.org will fix the problems you had with the temp path. I've never used the openmpi version of APBS on the mac before, so I want to do a few more tests before I put up a version of the plugin that finds it by default. In the meantime, you can type the binary location into the APBS Location box and it should work. You don't need to worry about APBS's psize.py for the vast majority of systems.

I'll let you know when I've updated the plugin fully deal with this.

Note that the plugin will still run things using the same input files it would with a single-processor APBS.


On Tue, Jul 20, 2010 at 7:15 PM, RaDaniel Christian <rendereason@gmail.com> wrote:
I want to bring to your attention the wiki entry I posted in pymolwiki
regarding the default loading paths for apbs:
After installing with fink, none of the default paths work.


If someone knows what is going on, please drop a line!
Many thanks in advance,
Daniel Ra

---------- Forwarded message ----------
From: RaDaniel Christian <rendereason@gmail.com>
Date: Mon, Jun 7, 2010 at 7:07 PM
Subject: Help setting apbs tools2 on Mac
To: support@delsci.com

Can I get help with setting configuration files on pymol (cvs fink
[ snip ]

Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)