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.
Cheers,
-Michael
On Wed, Jul 21, 2010 at 2:56 PM, Michael Lerner <
mglerner+sourceforge@... <mglerner%2Bsourceforge@...>> 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.
>
> -Michael
>
>
> On Tue, Jul 20, 2010 at 7:15 PM, RaDaniel Christian 성준 <
> rendereason@...> 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.
>>
>>
>> http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F
>>
>> If someone knows what is going on, please drop a line!
>> Many thanks in advance,
>> Daniel Ra
>>
>> ---------- Forwarded message ----------
>> From: RaDaniel Christian 성준 <rendereason@...>
>> Date: Mon, Jun 7, 2010 at 7:07 PM
>> Subject: Help setting apbs tools2 on Mac
>> To: support@...
>>
>>
>> Can I get help with setting configuration files on pymol (cvs fink
>> version1.2r3pre)?
>> [ 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)

Hi All,
I bought a new MacPro and now get this message when I open PyMOL:
Note: Radeon HD cards tend not to run PyMOL well.
Use nVidia or Intel instead, if OpenGL glitches occur.
Attempting to compensate for known issues...
So the new Macs only come with Radeon video cards... there are no other choices with a Mac. This means the MacPros no are no longer a good platform for running PyMOL? I just tossed $3K down the drain?
I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I tried to render just the top half and it still crashes.
What are the OpenGL glitches that occur, are they documented somewhere?
What does PyMOL do to compensate?
I checked the PyMOL web site and under the supported operating systems and hardware there is no mention of the lack of Radeon support/poor Radeon performance. Maybe that should be added because I wouldn't have bought this new Mac if I would have known this. Is there anything I can do to make this new machine work?
I see a 64-bit version is on the horizon, will this address Radeon performance or should I go back to my old MacPro with it's nVidia 7300 video cards?
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/729-5944

Dear Jason,
I strongly support Adam's suggestion that the PyMOL website and the Wiki
display a clear warning to people planning on using PyMOL with ATI/AMD
graphics card. I have had numerous issues with ATI graphics cards + PyMOL
over the years and nVidia is unquestionably the better choice when it comes
to running professional OpenGL intensive software (like PyMOL and Blender)
on Linux or Mac OS.
Best regards,
Shiven
On Wed, Sep 29, 2010 at 11:07 AM, H. Adam Steinberg <adam@...>wrote:
> Hi All,
>
> I bought a new MacPro and now get this message when I open PyMOL:
>
> Note: Radeon HD cards tend not to run PyMOL well.
> Use nVidia or Intel instead, if OpenGL glitches occur.
> Attempting to compensate for known issues...
>
> So the new Macs only come with Radeon video cards... there are no other
> choices with a Mac. This means the MacPros no are no longer a good platform
> for running PyMOL? I just tossed $3K down the drain?
>
> I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I
> tried to render just the top half and it still crashes.
>
> What are the OpenGL glitches that occur, are they documented somewhere?
> What does PyMOL do to compensate?
>
> I checked the PyMOL web site and under the supported operating systems and
> hardware there is no mention of the lack of Radeon support/poor Radeon
> performance. Maybe that should be added because I wouldn't have bought this
> new Mac if I would have known this. Is there anything I can do to make this
> new machine work?
>
> I see a 64-bit version is on the horizon, will this address Radeon
> performance or should I go back to my old MacPro with it's nVidia 7300 video
> cards?
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/729-5944
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
>

Hi Adam,
Thanks for expressing your concerns.
This message,
> Note: Radeon HD cards tend not to run PyMOL well.
> Use nVidia or Intel instead, if OpenGL glitches occur.
> Attempting to compensate for known issues...
has been in PyMOL for a long time. It's just a fact that NVidia cards
have been less buggy and have better Linux drivers than ATI and Intel.
The heterogeneity in (buggy) hardware makes development difficult and
expensive. And, we're not the only ones running into this either: the
CCP4 list recently discussed this, and I've also been talking to John
Stone, the main VMD developer, who also faces such issues.
> So the new Macs only come with Radeon video cards... there are no other
> choices with a Mac. This means the MacPros no are no longer a good platform
> for running PyMOL? I just tossed $3K down the drain?
The new MacPros should be more than capable of running PyMOL. In
fact, the above warning is more for low-end cards which are buggier,
not the high-end ones found in MacPros. Your $3k wasn't thrown away,
you're just ahead of the curve. I'm sure more people will buy
MacPros, forcing me to follow suit. Also, if Apple hasn't already, I
hope they'll release a list of NVidia cards which will run on their
new MacPros, just like they have a list of Radeon cards for the
NVidia-based MacPros.
> I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I
> tried to render just the top half and it still crashes.
PyMOL is known to crash when trying to render large structures. This
is a legacy issue with the internal memory management, not your Radeon
card. 3L5Q is a very large PDB (79,452 atoms w/o hydrogens). I agree
wholeheartedly that PyMOL should be able to render this without
crashing. Even my machine (early 2010 Dual Quad-core MacPro w/16GB
RAM) cannot even "set surface_quality, 1" on that structure without
crashing.
> What are the OpenGL glitches that occur, are they documented somewhere?
The glitches we talk about are those like:
* blank windows or windows not opening/closing properly (Intel GM945)
* sticks not coloring properly (Intel945, some ATI cards, some VMs);
they're all blue when they should be mutlicolored
* partial geometry being rendered;
> What does PyMOL do to compensate?
We detect the video cards and add extra openGL calls (usually glFlush
or glFinish) or reorder openGL calls to workaround known problems.
> I checked the PyMOL web site and under the supported operating systems and
> hardware there is no mention of the lack of Radeon support/poor Radeon
> performance. Maybe that should be added because I wouldn't have bought this
> new Mac if I would have known this. Is there anything I can do to make this
> new machine work?
We cannot list all possible systems on which PyMOL won't run. We do
try to provide a list of machines on which it will run. Aside from
not being able to ray trace a protein that's almost big enough to see
with the naked eye, do you see any other performance issues or
glitches or artifacts? Could it be that PyMOL is in fact running okay
on your machine but the memory-bug combined with the Radeon warning
caught you off guard? If PyMOL produces other bugs on your system due
to the Radeon card or not, please email me a bug report or better yet
visit http://pymol.org/contact (choose "Bug Reporting") and file it
there so it's automatically tracked internally.
> I see a 64-bit version is on the horizon, will this address Radeon
> performance or should I go back to my old MacPro with it's nVidia 7300 video
> cards?
We wanted to release a 64-bit version for a while, but the Tcl/Tk
toolkit was not ready. I think it's still in alpha/beta. 64-bit
MacPyMOL will be released when we're sure that works.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jason.Vertrees@...
(o) +1 (603) 374-7120

My two cents on this issue.
I run PyMOL 1.3 on a PackardBell EasyNote TJ62 laptop, which has an ATI
Radeon HD 4570, with no glitches at all.
BUT, I use Gentoo Linux with the free xf86-video-ati driver, v6.13.1. My
version of xorg-server is 1.7.7, MESA is at 7.8.2 and libdrm is at
2.4.21. With Gentoo Linux you compile everything form source and the
system is rock solid.
When PyMOL 1.3 launches on my laptop (using it right now) I see this
message:
===
PyMOL(TM) Molecular Graphics System, Version 1.3.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org";.
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected 2 CPU cores. Enabled multithreaded rendering.
===
No mention whatsoever to the ATI warning. However, I used to see the
warning when I was the suffering user of ATI's official drivers for Linux.
So, to everyone running Linux with an ATI card, just get rid of the
official ATI drivers and use the free xf86-video-ati driver instead. It
works much better and you don't get any OpenGL performance penalty.
Ramiro Tellez Sanz
Dept. Physical Chemistry
University of Almeria
Spain
El 29/09/10 20:14, Jason Vertrees escribió:
> Hi Adam,
>
> Thanks for expressing your concerns.
>
> This message,
>
>> Note: Radeon HD cards tend not to run PyMOL well.
>> Use nVidia or Intel instead, if OpenGL glitches occur.
>> Attempting to compensate for known issues...
> has been in PyMOL for a long time. It's just a fact that NVidia cards
> have been less buggy and have better Linux drivers than ATI and Intel.
> The heterogeneity in (buggy) hardware makes development difficult and
> expensive. And, we're not the only ones running into this either: the
> CCP4 list recently discussed this, and I've also been talking to John
> Stone, the main VMD developer, who also faces such issues.
>
>
>> So the new Macs only come with Radeon video cards... there are no other
>> choices with a Mac. This means the MacPros no are no longer a good platform
>> for running PyMOL? I just tossed $3K down the drain?
> The new MacPros should be more than capable of running PyMOL. In
> fact, the above warning is more for low-end cards which are buggier,
> not the high-end ones found in MacPros. Your $3k wasn't thrown away,
> you're just ahead of the curve. I'm sure more people will buy
> MacPros, forcing me to follow suit. Also, if Apple hasn't already, I
> hope they'll release a list of NVidia cards which will run on their
> new MacPros, just like they have a list of Radeon cards for the
> NVidia-based MacPros.
>
>
>> I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I
>> tried to render just the top half and it still crashes.
> PyMOL is known to crash when trying to render large structures. This
> is a legacy issue with the internal memory management, not your Radeon
> card. 3L5Q is a very large PDB (79,452 atoms w/o hydrogens). I agree
> wholeheartedly that PyMOL should be able to render this without
> crashing. Even my machine (early 2010 Dual Quad-core MacPro w/16GB
> RAM) cannot even "set surface_quality, 1" on that structure without
> crashing.
>
>
>> What are the OpenGL glitches that occur, are they documented somewhere?
> The glitches we talk about are those like:
> * blank windows or windows not opening/closing properly (Intel GM945)
> * sticks not coloring properly (Intel945, some ATI cards, some VMs);
> they're all blue when they should be mutlicolored
> * partial geometry being rendered;
>
>
>> What does PyMOL do to compensate?
> We detect the video cards and add extra openGL calls (usually glFlush
> or glFinish) or reorder openGL calls to workaround known problems.
>
>
>> I checked the PyMOL web site and under the supported operating systems and
>> hardware there is no mention of the lack of Radeon support/poor Radeon
>> performance. Maybe that should be added because I wouldn't have bought this
>> new Mac if I would have known this. Is there anything I can do to make this
>> new machine work?
> We cannot list all possible systems on which PyMOL won't run. We do
> try to provide a list of machines on which it will run. Aside from
> not being able to ray trace a protein that's almost big enough to see
> with the naked eye, do you see any other performance issues or
> glitches or artifacts? Could it be that PyMOL is in fact running okay
> on your machine but the memory-bug combined with the Radeon warning
> caught you off guard? If PyMOL produces other bugs on your system due
> to the Radeon card or not, please email me a bug report or better yet
> visit http://pymol.org/contact (choose "Bug Reporting") and file it
> there so it's automatically tracked internally.
>
>
>> I see a 64-bit version is on the horizon, will this address Radeon
>> performance or should I go back to my old MacPro with it's nVidia 7300 video
>> cards?
> We wanted to release a 64-bit version for a while, but the Tcl/Tk
> toolkit was not ready. I think it's still in alpha/beta. 64-bit
> MacPyMOL will be released when we're sure that works.
>
> Cheers,
>
> -- Jason
>