Hi Hai,
I've seen this type of behavior when the mpirun command being used to run pmemd.MPI is different from the mpi installation that was used to build the executable.
I would check that which mpif90 matches which mpirun. I'd then try rebuilding from scratch with your current environment and see if the problem persists.
All the best
Ross
> On May 24, 2018, at 5:44 PM, Hai Long <spaceshiptoo.gmail.com> wrote:
>
> Hi David,
>
> It won't work with any pmemd tests in the test suite. The following is from
> the 4096wat test output. The same thing happens. It seems to me that
> pmemd.MPI somehow messed up electrostatic interactions. The vdwaals
> (6028.9517) is identical with the sander output though.
>
>
> NSTEP = 1 TIME(PS) = 1.001 TEMP(K) = NaN PRESS =
> 0.0
>
> Etot = NaN EKtot = NaN EPtot =
> NaN
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
>
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> 6028.9517
>
> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
> 0.0000
>
> Ewald error estimate: NaN
>
>
> On Thu, May 24, 2018 at 5:38 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Wed, May 23, 2018, Hai Long wrote:
>>>
>>> We recently upgraded from Amber14 to Amber18. The compiler, MPI, and MKL
>>> that I used for Amber 18 are all intel 2017.0.5. The sander, sander.MPI,
>>> and serial pmemd are all working properly. However, pmemd.MPI produces
>>> errors. The following output is from a simulation of a 5X5X5nm
>> equilibrated
>>> water box, showing something wrong with EELEC and VIRIAL:
>>
>> Thanks for the report. We would need to see the actual inputs, plus the
>> command-line options you chose, in order to try to track down the
>> problem. It looks like there is something wrong with your input
>> coordinates.
>>
>> (I'm assuming that you have run the pmemd test suite in parallel, and
>> that things look OK there. If you haven't done this, please do so,
>> since that can remove the possibility of a bad input file.)
>>
>> ....dac
>>
>>
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Received on Thu May 24 2018 - 15:30:02 PDT
