From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jul 22 2014 - 11:29:47 CDT
Suppose you have d coordinates, and n bins along each coordinate. The size
of the force array, in bytes, is 8 * n^d. Compare with your system's
available main memory.
On 22 July 2014 18:23, Harish Vashisth <harish.vashisth_at_gmail.com> 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
> 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.
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