ABF/colvar error in NAMD2.9

From: Harish Vashisth (harish.vashisth_at_gmail.com)
Date: Tue Jul 22 2014 - 11:23:13 CDT

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.


This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:38 CST