VMD-L Mailing List

From: Patrick Burney (pburney_at_u.washington.edu)
Date: Wed Sep 08 2010 - 19:04:38 CDT

Hey guys,

I just upgraded my workstation's ram so that I could view larger trajectories in vmd. However, now that I have 8gbs of ram, I still find I can only load dcds smaller than about 3.0gb without running into the usual error code 12 (see below). I've been watching some plots of the system's memory allocation and noticed that I get the error (see below) right after the vmd program is being allocated 2.96gb of memory. This is strange to me because at the moment, the system has 6.9gb of memory "Free".
I've run a few different memtests and also tried this on another workstation we upgraded with the old memory from mine to no avail. It may help to know that I'm using a 27'' iMac (intel x86_64) running snow leopard. If this problem winds up being a consequence of my operating system, I applogize for wasting your time.

vmd > animate delete all
vmd > animate read dcd wtbound_smaller.dcd beg 0 end -1 waitfor all
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file wtbound_smaller.dcd
VMD(42925,0xa0703500) malloc: *** mmap(size=16777216) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
terminate called after throwing an instance of 'std::bad_alloc'
  what(): std::bad_alloc
Abort trap

Thanks for the help,
Patrick Burney
University of Washington
Department of Chemical Engineering