Re: question about repeating output text

From: Ng Yao Zong (ngyz_at_bii.a-star.edu.sg)
Date: Wed Dec 22 2010 - 21:37:13 CST

Dear all,

I ran NAMD2.7 on a cluster using mpirun and encountered a similar
problem where I received multiple, repeating output. In this case, I was
reassigning velocities:

REASSIGNING VELOCITIES AT STEP 41 TO 0.082 KELVIN.
REASSIGNING VELOCITIES AT STEP 40 TO 0.08 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 43 TO 0.086 KELVIN.
REASSIGNING VELOCITIES AT STEP 41 TO 0.082 KELVIN.
REASSIGNING VELOCITIES AT STEP 43 TO 0.086 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 43 TO 0.086 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 43 TO 0.086 KELVIN.
REASSIGNING VELOCITIES AT STEP 43 TO 0.086 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 43 TO 0.086 KELVIN.
REASSIGNING VELOCITIES AT STEP 43 TO 0.086 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 42 TO 0.084 KELVIN.
REASSIGNING VELOCITIES AT STEP 44 TO 0.088 KELVIN.

I believe the namd compilation was originally for charmrun.

1) Do I need to recompile namd for mpirun?

2) Will the multiple output affect my results (apart from the output file)?

3) Is there a way to specify output from namd from only one
processor/node to solve this problem?

Thank you for your kind advice.

Regards,

Andy

On Tue, 2009-06-09 at 06:58 -0400, ershela.durresi_at_yale.edu
<mailto:ershela.durresi_at_yale.edu?Subject=Re:%20%20question%20about%20repeating%20output%20text>
wrote:
/> Dear all, /
/> /

dear ershela,

/> /
/> I am trying to run a simulation on NAMD and the simulation aborts
almost /
/> immediately after I try to run it. In the output file I notice that the /
/> simulation parameter data keeps repeating (below is the part that keeps /

this usually happens, if you launch a non-MPI program on multiple
processors via mpirun. from the output it looks as if you are
running the "charmrun" (= tcp or udp) version of (obsoltete) NAMD
version 2.5.

/> repeating), which has not happened to me before. I tried to run another /
/> simulation of a similar size (only 40 atoms larger), and in that case
I got the /
/> simulation to run. I would be extremely grateful if you could please
offer any /

please check the output, particularly the part about the NAMD version
and on how many processors it was run and compare it to this one.

cheers,
    axel.

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