On 8/24/12 6:01 AM, Clare wrote:
Dear Vitaly,
Thank you so much for your suggestion!!
I've run the simultion using one core as you suggested, and I can see two
outputs on step 0 and step 100 now ( shown on the bottom), but it still took
a while to only generate these two outputs.
Maybe it is indeed the problem of scaling as mentioned by Justin?
There are: 34001 Atoms
The reason that it is slow now is that you have 34001 atoms being calculated on
one core. What that demonstrates is that your simulation is stable and likely
did not crash when run in parallel. My previous comments about scaling issues
were simply a guess based on incomplete information. Your log file from the MPI
run indicated the job never even started. That's not an issue of scaling; it's
an issue of functionality. It looks to me like either mdrun_mpi or your MPI
implementation is broken or not being invoked properly. Try the test case I
suggested before, something that doesn't involve Gromacs.
-Justin
Charge group distribution at step 0: 1953 1973 2103 2032 2044 2072 2063 1967
Grid: 3 x 7 x 18 cells
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 1.99e-05
Initial temperature: 300.057 K
Started mdrun on node 0 Fri Aug 24 10:37:20 2012
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
6.66008e+03 3.06081e+03 7.94034e+02 2.55031e+02 8.61710e+02
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.40538e+03 5.11091e+04 -3.00143e+03 -4.49637e+05 -8.11103e+04
Position Rest. Potential Kinetic En. Total Energy Conserved En.
5.53187e+01 -4.68547e+05 8.57672e+04 -3.82780e+05 -3.82780e+05
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
3.00450e+02 -9.73436e+01 -2.97627e+03 3.74608e-05
DD step 4 load imb.: force 6.0%
DD step 99 load imb.: force 6.1%
Step Time Lambda
100 0.20000 0.00000
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
1.10274e+04 2.82478e+03 1.23525e+03 2.24466e+02 1.54991e+03
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
4.67051e+03 6.34091e+04 -3.00143e+03 -4.31792e+05 -8.19081e+04
Position Rest. Potential Kinetic En. Total Energy Conserved En.
1.44619e+04 -4.17298e+05 7.13854e+04 -3.45913e+05 -3.82303e+05
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.50069e+02 -9.73436e+01 -3.79866e+02 3.45085e-06
--
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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