From: Jim Pfaendtner (jpfaendt_at_hec.utah.edu)
Date: Fri May 01 2009 - 07:56:02 CDT

Hi John,

Thanks for your prompt response. I did everything as you said and it
seems to be working (based on several test jobs). I can now call the
vmd _LINUXAMD64 executable (now statically linked) with the CNL job
submission program aprun.

I had to tweak my submission script a bit to set up all of the
environment variables properly. Also, the compiled vmd program needs
everything in the installation directory, so the entire contents have
to be transferred over to scratch if one is working on a system that
does not allow access to the home directories from compute nodes (as
in my case).

One other note is that I also had to download and compile the static
version of netcdf which was required for the vmd plugins. In the end
I built vmd using:

./configure LINUXAMD64 TCL NETCDF STATIC

and I only needed minor adjustments to the Makefile to set paths, etc.

Jim

On May 1, 2009, at 8:20 AM, John Stone wrote:

>
> Hi,
> Yes, it is possible to build VMD with static linkage, but it
> will be somewhat tricky. For your application in particular, you'll
> first have to have a statically linkable version Tcl compiled and
> ready for use. Once you've got Tcl compiled, then you'll need to
> build the VMD plugins for static-linkage only. You can probably hack
> the 64-bit linux compile target and simply disable the shared object
> plugin builds. Once you get the plugins compiled as a static library,
> building VMD itself with only static linkage will just be a matter of
> tweaking a few options with the 'configure' script, disabling all of
> the optional features that you don't need. I'd start with one of the
> "linux.text" configurations in vmd/Makefile, and then tweak from
> there.
> I don't currently have convenient access to an XT for compiling VMD,
> otherwise I'd offer to help do the build for you. Let us know if you
> have questions. If anyone else has compiled other non-trivial
> packages
> for the Cray XT, feel free to chime in...
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, May 01, 2009 at 08:03:07AM +0200, Jim Pfaendtner wrote:
>> Dear VMD-l,
>>
>> For a variety of reasons, I need to run VMD on a Cray XT machine with
>> CNL from the compute nodes. That is, I have to call VMD using the
>> aprun command within my job submission script. The main reason is
>> the
>> enormous amount of post-processing I want to do on some very large
>> systems is not suitable for the login nodes which do not have a large
>> amount of memory and a 15 minute limit for user-run executables.
>>
>> This currently does not work when I attempt it with the
>> vmd_LINUXAMD64
>> executable (this executable works fine on the front end). At a bare
>> minimum the executables for CNL have to be statically linked and the
>> VMD binaries I downloaded seem to be dynamically linked. I have no
>> idea what else might be required.
>>
>> 1) Is it possible to build a VMD binary that will run using aprun on
>> CNL?
>>
>> 2) If so, could someone point me in the right direction to get
>> started?
>>
>> Thank you,
>>
>> Jim
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078