buffer overflow with long file paths in psfgen in NAMD 2.11b2?

From: Brian Radak (bradak_at_anl.gov)
Date: Tue Dec 08 2015 - 15:54:28 CST

I'm hitting a weird error when running some old psfgen scripts with the
updated psfgen shipped with NAMD 2.11b2.

psfgen) reading structure from psf file aced.psf
*** buffer overflow detected ***: psfgen terminated
======= Backtrace: =========
<plus typical pointer garbage>

It was hard to make a minimal working example but it appears to happen
in readpsf when the PSF file was made with a topology file with a long
path and this same file path (or I guess one of similar length?) is
loaded again.

I've attached something like a test case, although the file path for the
"long" topology file might need to be fiddled with to make this work.
Alternatively, maybe this has to do with the fact that I keep my
topology files on a separate disk that is symlinked into my home
directory? In any event, I've never seen this problem before today.


P.S. To run the test case, first make some kind of long path for
"top_all36_prot.rtf" and modify build.pgn and alchpatch.pgn to match.
Then run the scripts through psfgen in that order:

psfgen < build.pgn && psfgen < alchpatch.pgn

Brian Radak
Theta Early Science Program Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue
Building 240, 1.D.16
Lemont, IL 60439-4871
Tel: 630/252-8643
email: bradak_at_anl.gov

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