[email protected] wrote:
Hi All
I have similar problem using gromacs 4.0.2.
The MD simulation (5 ns) on single processor is complited in 5 days, but
the same MD can`t be complited on cluster on 4 or 8 processors. The MD
simulation is stopped without any error message.
Any help would be appreciated
Which MPI implementation are you using? Some are known to be buggy. Also, to
rule out any other potentially buggy behavior, upgrade to version 4.0.5; 4.0.2
is several months old.
-Justin
Carmen
To,
David van der Spoel
Dear Sir,
I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a
problem.
I am giving job for 500000 steps step size 0.002ps (total 1ns) but my
job is stopped after 470000 steps. when i run this on 4 processors.
But the same job is completed on 2 processors.Why this happing i am not
able to understand.
Another thing is that job for 1500000 steps step size 0.002ps (total
3ns) is stopped after 375000 steps on 2 processors
and after 587000 steps on 4 processors, without any error message.
What could be the problem and how to solve it, please help me.
even i tried the 2 same jobs for 1000000 steps step size 0.002ps (total
2ns), one on single processor it is completed in 8 days
but the same job is stop after 550000 steps on 4 processors.
Is there any change is required in MPI coding or in .mdp files. Sir if
you need any other please let me know.
Please solve my problem, I will be highly obliged.
DvdS:
Please upgrade to a recent version. 3.2.1 is more than five years old.
With warm regards.
Shikhar
--
------------------------------------------------------------
Shikhar Gupta
Senior Research Fellow
Pharmacoinformatics Department
Block- A (Room No.- 208)
National Institute of Pharmaceutical Education & Research( NIPER )
Sec- 67, S.A.S Nagar
Mohali, Punjab (India)
Web-Site: www.niper.ac.in <http://www.niper.ac.in>
PIN- 160062
Email:[email protected]
<mailto:email%[email protected]>,[email protected]
<mailto:[email protected]>
--
------------------------------------------------------------
Shikhar Gupta
Senior Research Fellow
Pharmacoinformatics Department
Block- A (Room No.- 208)
National Institute of Pharmaceutical Education & Research( NIPER )
Sec- 67, S.A.S Nagar
Mohali, Punjab (India)
Web-Site: www.niper.ac.in <http://www.niper.ac.in>
PIN- 160062
Email:[email protected]
<mailto:email%[email protected]>,[email protected]
<mailto:[email protected]>
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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