Subject: AutoDock 3.0 Compilation on Linux

From: "Michael D. Bartberger" <[email-masked]>
Date: Wed, 9 Aug 2000 17:45:59 -0700 (PDT)

Hello all:

I am having a problem with AutoDock under Red Hat Linux 6.2.  (2.2.16-3smp
kernel, although I am, of course, only trying to compile AutoDock in
serial for use on 1 processor).

Using the source code from ver. 3.00, and the instructions of Pierre
Scotney for patching AutoDock 3.0 located at

http://www.medstv.unimelb.edu.au/~pierre/autodock/

I was able to compile each of the modules (autotors, autogrid,
autodock) with no problem.

Using a sample input from a project of one of our students (which
runs succesfully on an SGI) I tested out the Linux port.  Autotors runs 
perfectly and gives correct reults.  However, I am having a problem with
autodock.  The program seems to run; however, there appears to be what
looks like a serious memory leak or garbage collection problem (pardon my
ignorance; I'm not quite sure).   What happens is that memory usage for
the job, as indicated by 'top' (our boxes are equipped with 512 MB of RAM)
climbs higher and higher, past the point where all physical memory is
exceeded and the program begins encroaching on swap space.   The machine
then slows to a crawl as the swap partition thrashes.   Even the swap use
climbs higher and higher (with all physical memory being used by the
program as well) until the job is killed by hand.   Something is
definitely wrong.

Our nodes are dual Pentium-III 800 MHz machines with an out-of-the-box
installation of Red Hat Linux 6.2, which has been upgraded to the
2.2.16-3smp kernel as provided by Red Hat in RPM form.   We are simply
trying to run autodock in serial on one of the processors in this box.
All compilers, libraries, etc. are directly from the RH 6.2 CD.  There is
nothing particularly exotic about our OS/software installation.

I was curious if anyone has seen such behavior before, and if so,
whether a workaround might exist.

Alternatively, a new/different set of compilation instructions/patches 
starting with "fresh" AutoDock 3.0 source would also be appreciated. 

I notice that Scripps has an AutoDock version 3.05 now,
and perhaps that might be worth a try.

Thanks in advance for any assistance anyone can provide.

 Best regards,
-Mike Bartberger
 Chemistry/Biochemistry, UCLA

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| Michael D. Bartberger, Ph.D.                 TEL:  310.206.0553 |
| Department of Chemistry and Biochemistry     FAX:  310.206.1843 |
| University of California, Los Angeles                           |
| Los Angeles, California 90095-1569            [email-masked] |
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