Hello –


Do you have the same problem with the new APBS 1.4?




Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997



From: M.V.Vulovic@lumc.nl [mailto:M.V.Vulovic@lumc.nl]
Sent: Friday, August 03, 2012 5:54 AM
To: apbs-users@lists.sourceforge.net
Cc: apbs-users@googlegroups.com
Subject: [apbs-users] maximum memory limit inputgen


Dear all,

I was trying to upped the maximum allowable memory used by APBS. I would like to calculate the potential distribution for a larger Hemoglobin molecule. Machine on which I am running the program has 256GB RAM memory. 

Unfortunately, I always get the same message:


Unable to allocate memory!

(This often means you don't have enough memory available for this calculation.) FATAL ERROR: Unable to allocate enough memory for problem size.

FATAL ERROR: You requested 2203582984 bytes of RAM.

FATAL ERROR: Check that your system has that much memory.

VASSERT: ASSERTION FAILURE!  filename vmem.c, line 252, (ram != ((void *)0))



This corresponds to 'only' ~2GB RAM. Could you help me to overcome this limitation?


I first call inputgen.py that should allow me to define the maximum memory :~ python ~/soft/apbs-1.3-amd64/share/tools/manip/inputgen.py --gmemceil=100000 Hb.pqr


And then as a second step I run apbs program on a newly generated  file Hb.in ~/soft/apbs-1.3-amd64/bin/apbs Hb.in

And this still gives me the same error message above.

Do you know what could be the problem? Am I doing something wrong?

thanks a lot


Leiden University Medical Center
Department of Molecular Cell Biology
Section Electron Microscopy
Postal Zone S1-P
P.O.Box 9600
2300 RC Leiden
The Netherlands
Visiting address: Einthovenweg 20
2333 ZC Leiden
E-mail: vulovic@lumc.nl
Tel:  (+31) 71 526 9265
Fax: (+31) 71 526 8270