Running fulldirect in parallel

From: Tom Coles (
Date: Sun Oct 07 2012 - 15:08:11 CDT

I was trying to use the fulldirect method and found that it only works in serial mode; there is an error every time I try to run it in parallel. I know that fulldirect is very slow and inefficient, but I need to do a simulation of a non-periodic system.

Anyway, I looked at the source code and noticed that the doWork method in ComputeFullDirect.C calls the sendMessage method in Communicate.C for all PEs and not just PE 0, but sendMessage gives an error for any non-zero PE.

sendMessage accepted any PE in NAMD2.5b1 and earlier, so fulldirect worked in parallel until that time. However, it was changed to only accept PE 0 for NAMD2.5 and later. I would like to try to make it work in parallel again, so I was wondering why there was a problem with non-zero PEs in Communicate.C and if there is recommended alternative way of performing the communication required by fulldirect?

Thanks for any help,
Tom Coles

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:39 CST