Beniamino Sciacca wrote:
with "-c 2" I've two processes, each one running at nearly 50%.
with "-c 4" I've four processes, each one running at nearly 25%
with "-c 1" I've only one process wich runs at nearly 99%
I tried also with mdrun_Nmpi (compiled without enabling mpi), and it
runs at nearly 99%.
Is it possible that the software sees only one core?
I think your OS only sees one processor.
if Linux try:
cat /proc/cpuinfo
Beniamino
Yang Ye ha scritto:
Use top to check, you shall have two processes running at nearly 100%
with "-c 2"
Yang Ye
Beniamino Sciacca wrote:
I've just tried "mpirun -c 2 mdrun..." (34 h/ns).
It works, but the problem is the same... the simulation time....
In fact I also tried "mpirun -c 1 mdrun" (32 h/ns) and "mpirun -c 4
mdrun" (34 h/ns), but the simulation time remain the same!
Yang Ye ha scritto:
Beniamino Sciacca wrote:
I never used mprun -np 2, and I had not problem. Before I didn't
use "mprun -np 2", now I don't use "mprun -np 2" but simulation
time now is twice. It has changed from a day to the other.
However I've just tried, like you suggested, to use " -np 2" (in
grompp and in mdrun) but I obtain an error:
-------------------------------------------
"Program mdrun_d, VERSION 3.3.1
Source code file: init.c, line: 69
Fatal error:
run input file DNA8_mdEq.tpr was made for 2 nodes,
while mdrun_d expected it to be for 1 nodes.
"
-------------------------------------------
In fact I've only one node.
Try David's mpirun -c 2 mdrun
Laptop should be running in top speed, I never modified the
configuration of energy profile.
Beniamino
2006/6/3, Yang Ye <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>:
First, make sure that you used mdrun -np 2.
Second, check your energy profile. Is your laptop running in top
speed?
or does it have sleep time?
Yang Ye
Beniamino Sciacca wrote:
> I don't understand what you talking about...
> I didn't write any hostfile.... I'm not in a cluster. I only
use my
> notebook with the two cores.
> In fact I type "lamboot" without -v.......
>
> Beniamino
>
> Mark Abraham ha scritto:
>> Did your default LAM hostfile configuration (or whatever it is)
>> change from 2 processors to one?
>>
>> Mark
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--
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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