Re: ABF/colvar error in NAMD2.9

From: Aron Broom (
Date: Tue Jul 22 2014 - 11:30:49 CDT

I've used an upwards of 9 colvars at once with no issue, and with a larger
system size than that. Can you post the *.in file or whatever file
contains all your colvars definitions? I would suspect something add with
your colvars. One thing to test might be, when you are at the largest size
that has worked (I guess 4 colvars?) try just duplicating all those colvar
blocks and see if it runs. Maybe something is wrong with the 5th colvar
definition you are entering.

On Tue, Jul 22, 2014 at 12:23 PM, Harish Vashisth <
> wrote:

> Dear All:
> We have been trying to make use of many CVs (> 20) using abf/colvar
> options in NAMD2.9. These are all backbone dihedral CVs defined
> individually in multiple blocks of phi/psi, etc. We are able to run ABF
> jobs fine up to 5 CVs, but including a sixth one or more does not work. The
> error reported in the log file right after initialization of colvars module
> is:
> FATAL ERROR: Memory allocation failed on processor 0.
> Looking through previous posts, someone seemed to suggest that it is
> likely occurring due to large system size as NAMD keeps a copy of the
> system on processor 0?
> In our case, the solvated system size is ~40,000 atoms. The error occurs
> using NAMD2.9 on local workstation, our local CRAYXE6m-200 as well as on
> Stampede (XSEDE resource.) Is there an upper limit on how many CVs colvar
> module can handle?
> Any suggestions would be helpful. Thanks.
> -Harish
> --------------

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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