Hii David,
I have successfully calculated 3D-RISM in serial mode using the command:
"../rism3d.snglpnt --pdb 1.pdb --prmtop par22.prmtop -y 1.nc --xvv
1drism_tp3.xvv --buffer 15.0 --grdspc 1.0,1.0,1.0 --centering -1"
and the end part of the output file is as follows:
###########################################################################
Frame: 5 of 5
solutePotentialEnergy 7.76634868E+003
-1.22943885E+003 0.00000000E+000 5.25759067E+002 1.41726362E+003
9.81498493E+002 0.00000000E+000 2.44732864E+003 0.00000000E+000
0.00000000E+000 3.62393772E+003
rism_excessChemicalPotential 3.62393772E+003
5.02355065E+003 -1.39961293E+003
rism_solventPotentialEnergy -6.10980535E+002
-5.07624215E+002 -1.03356319E+002
rism_partialMolarVolume 2.69812419E+004
rism_totalParticlesBox
1.52269900E+004 3.04539286E+004
rism_totalChargeBox -2.14411896E-002
-1.26993097E+004 1.26992882E+004
rism_excessParticlesBox
-8.99162807E+002 -1.79837703E+003
rism_excessChargeBox -2.14411896E-002
7.49901781E+002 -7.49923222E+002
rism_excessParticles
-8.99162807E+002 -1.79837703E+003
rism_excessCharge -2.14411896E-002
7.49901781E+002 -7.49923222E+002
rism_KirkwoodBuff
-2.69779741E+004 -2.69787454E+004
rism_DCFintegral
-4.80882486E+005 9.30932998E+004
3D-RISM processing complete.
|Timing summary:
| Initialize 0.109
| Molec. Dyn. 0.000
| Normal Mode 0.000
| Conj. Grad. 0.000
| Newton 0.000
|-------------------------
| Total 0.109
|1st derivative timing summary:
| constraints 0.000
| bonds 0.000
| angles 0.003
| torsions 0.004
| pairlist 0.748
| nonbond 0.450
| gen. Born 0.000
| Poisson Boltzmann 0.000
| 3D-RISM 474.030
| Other 0.000
|-------------------------
| Total 475.236
|3D-RISM memory allocation summary
|Type Maximum
|Integer 0.00185 GB
|Real 0.16370 GB
|Logical 0.00000 GB
|Character 0.00000 GB
|------------------------
|Total 0.16462 GB
|CPU Timer summary for 3D-RISM Total
| 3D-RISM initialization 0.107 ( 0.02%)
| Excess Chemical Potential 0.044 ( 21.36%)
| Other 0.162 ( 78.64%)
| Thermodynamics 0.206 ( 0.04%)
| Solvation box resize 0.667 ( 0.14%)
| Cuv propagation 0.100 ( 0.02%)
| FFT 62.468 (
32.82%)
| Overlap 14.061 (
35.35%)
Lapack 0.018 (
0.05%)
| Project 25.670 (
64.54%)
| Other 0.020 (
0.05%)
| MDIIS Advance 39.772 (
20.90%)
| Other 88.092 (
46.28%)
| R1RISM 190.332 ( 99.99%)
| Other 0.021 ( 0.01%)
| RXRISM 190.353 ( 40.22%)
| Lennard-Jones 4.858 ( 1.72%)
| Asymptotics 277.299 ( 98.28%)
| Potential 282.163 ( 59.62%)
| Solve 3D-RISM 473.284 ( 99.96%)
| 3D-RISM 473.491 ( 99.98%)
|3D-RISM Total 473.599 (100.00%)
#######################################################################################
But failed to run in parallel mode using the "rism3d.snglpnt.MPI" with
2/4/6/8 np and getting the same error.
One question comes to my mind after reading the post on amber mailing list
(the post link is mentioned below) that does amber seriously need different
MPI setup for parallel processing because I could easily run NAMD/ GROMACS.
http://archive.ambermd.org/201304/0375.html
Thanks,
Priti
On Thu, Jun 28, 2018 at 11:56 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Thu, Jun 28, 2018, PRITI ROY wrote:
> >
> > Thank you for your responce. I tried with both of the procedure which you
> > have suggested, but getting same error. Is it due to MPI setup or
> incorrect
> > input file?
>
> See if reducing the number of MPI threads (say to 2 or 4) helps, or
> changes anything. If not, see if the calculation works in serial mode.
> If using a smaller number of threads does help, try to find the largest
> number of threads that works.
>
> Even with "bad" grid sizes, you should not get MPI crashes, so I suspect
> that something else is wrong; but if not, we need to make the code more
> robust.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jun 28 2018 - 22:00:02 PDT
