VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Feb 16 2009 - 12:26:19 CST

On Mon, 16 Feb 2009, Yinglong Miao wrote:

YM> Dear VMD developers/users,
YM>
YM> I have been running a VMD script that involves loading PSF/PDB files and
YM> writing DCD files for a pretty large system (~3M atoms). The program seems
YM> to run fine with files processed properly, but error messages like "***
YM> glibc detected *** free(): invalid pointer: 0x00000000102a8f28 ***" keep
YM> coming up during the program running. I am not sure whether it comes from
YM> large system processing or something regarding memory. I looked it up in the

this most certainly points to internal memory corruption.
do you run external binaries while processing your files,
or is this all VMD?

there are a bunch of possible causes and it is generally
hard to tell where exactly the origin is without experience
and the proper tools.

before entering a wild goose chase, can you please try running
the same script with the latest alpha/beta binaries that john
has posted. if the problem persists, it needs to be tracked down,
but the details of that process are better discussed off-list.

cheers,
   axel.

YM> list archives but found no clue. Has anyone come into such cases? Your help
YM> will be appreciated!
YM>
YM> Thanks!
YM>
YM> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.