Minimization failing on one machine only

From: Chris Goedde (
Date: Fri Oct 14 2016 - 15:34:10 CDT

Hi all,

Why might a system that minimizes successfully on one machine fail on a different machine?

The two machines are an iMac and and linux box. The linux box has an Nvidia GPU in it. The versions of namd are (from the log file):

NAMD 2.11 for MacOSX-x86_64-multicore
NAMD 2.11 for Linux-x86_64-multicore-CUDA

All input files (conf, pdb, psf, etc) are *identical* for the two machines. (Checked with diff.)

On the mac, namd is called as:

namd2 +p4 +isomalloc_sync run.conf > run.log &

On the linux box, it’s

namd2 +p16 +isomalloc_sync run.conf > run.log &

On the mac the system minimizes correctly, relaxing from the initial configuration to the expected minimum energy state. On the linux box, the system never minimizes (configuration doesn’t appreciably change), and in the log file I see:


interspersed throughout the minimization process. Of course I don’t see this at all in the log files from the mac.

The system is fairly simple, just water and carbon nanotubes; I don’t think the trouble is that the initial state is badly configured. But, if I wanted to troubleshoot the minimization process, I’m not sure what exactly to look for.

I don’t see what I’m doing wrong (or what’s happening differently on the two machines, other than the different versions of namd). Any suggestions appreciated; I’m really stuck here as to what’s happening.


Chris Goedde

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