AMBER Archive (2004)

Subject: AMBER: ptraj hbond memory allocation on opteron

From: Fabian Boes (fabian.boes_at_itb.uni-stuttgart.de)
Date: Mon Dec 13 2004 - 06:07:11 CST

Dear Amber users,

i have a strange problem with memory allocation in ptraj (amber7) on an
opteron with 16 GB of RAM running fedora core 3.

I am able to do a hbond analysis of 3075 frames but not 3100 frames or
more although there should be enough free memory.

With 3075 sets:

INPUT COORDINATE FILES
   File (/home/fbo/md2500.crd.gz) is an AMBER trajectory (with box info)
with 2000 sets
   File (/home/fbo/md3000.crd.gz) is an AMBER trajectory (with box info)
with 1075 sets

ACTIONS
       HBOND saved to series hbonds, output to file /home/fbo/hbonds.data,
       data will be sorted, intra-residue interactions will NOT be included,
       Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
       Hydrogen bond information will be dumped for occupancies > 0.00
       Estimated memory usage for this hbond call: 6109.21 MB
       donors: 376 acceptors: 448
       solvent donors: 7942 acceptors 15884

Processing AMBER trajectory file /home/fbo/md2500.crd.gz

Set 1 ..

But with some more frames (3100):

INPUT COORDINATE FILES
   File (/home/fbo/md2500.crd.gz) is an AMBER trajectory (with box info)
with 2000 sets
   File (/home/fbo/md3000.crd.gz) is an AMBER trajectory (with box info)
with 1100 sets

ACTIONS
       HBOND saved to series hbonds, output to file /home/fbo/hbonds.data,
       data will be sorted, intra-residue interactions will NOT be included,
       Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
       Hydrogen bond information will be dumped for occupancies > 0.00
       Estimated memory usage for this hbond call: 6158.83 MB
       donors: 376 acceptors: 448
       solvent donors: 7942 acceptors 15884

Processing AMBER trajectory file /home/fbo/md2500.crd.gz

ERROR in safe_malloc: Error in alloc of -2144460096 bytes

As said before, there are 16 GB available and other programs, like a big
gnuplot job, are able to use 12 GB without a problem.

If you need more information i can provide input files, compiler
versions etc.

Bye,

Fabian 

-- 

Fabian Bös

Institute of Technical Biochemistry
University of Stuttgart / Germany

Phone:   +49-711-6857481
Fax:     +49-711-6853196
Email:   fabian.boes_at_itb.uni-stuttgart.de

http://www.itb.uni-stuttgart.de

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu