VMD-L Mailing List

From: Reuter Nathalie (reuter_at_bichat.inserm.fr)
Date: Wed Dec 12 2001 - 11:20:53 CST

Dear NAMD developpers,

I have a problem when I run NAMD on my linux cluster (AMD 1.2GHz
processors, RedHat 7.2?). I use the version 2.3b2 for linux (i686, no
Scyld). I am trying to run an MD simulation with PBC, reassigning
velocities. Here is the error message I have :

ReceiveDatagram: recv: Resource temporarily unavailable

It happens when the program is writing velocities in the restart file
(WRITING VELOCITIES TO RESTART FILE AT STEP 10). It can happen at
another stage of the calculation; if I run the same input file several
time, it will not always stop at the same step number. This problem I
also have with other type of calculations (MD without reassignement of
the velocities), whenever the namd has to write on the disk (the
coordinates in the trajectory file for example).

I guess this is a problem related to the configuration of my cluster and
the way the CPUs communicate with the main disk but I have no idea what
precisely should be checked. Other programs like Charmm run without any
problem. (NAMD on one processor works perfectly).

What on my machines should I check ? Do you by chance have an idea on
where the problem may come from ?

Thanks in advance for your help,

Nathalie Reuter 

--
Nathalie REUTER, PhD
U.410 INSERM
Faculte de medecine Xavier Bichat
16, rue Henri Huchard
BP 416
75870 PARIS Cedex 18
tel : (33) 01.44.85.61.32
fax : (33) 01.42.28.87.65