Thanks for the prompt reply. It's the first time I'm running sander.MPI on this machine. The machine has passed all tests successfully and on numerous earlier occasions I've run pmemd.MPI on 16 and 32 processors successfully.
amber11-serial produces <mdinfo>, <min.out> and <min.rst> files.
The mdinfo is shown below:
NSTEP ENERGY RMS GMAX NAME NUMBER
614 -6.6756E+04 1.3575E+01 3.8625E+01 O 15978
BOND = 29.7887 ANGLE = 288.6140 DIHED = 1342.7352
VDWAALS = 3417.4085 EEL = -80174.8566 HBOND = 0.0000
1-4 VDW = 542.7587 1-4 EEL = 7780.4877 RESTRAINT = 16.7276
EAMBER = -66773.0640
amber11-parallel on 2 processors (same as on 16) produces an empty <mdinfo> and no <min.rst> files. The <min.out> file is as the one sent before. Its results section is as below:
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
On Aug 20, 2010, at 4:03 PM, case wrote:
> On Fri, Aug 20, 2010, George Tzotzos wrote:
>>
>> In amber11_serial there's seems to be no problem.
>>
>> Yet running the same input files on a 16 processor machine, I get the
>> error message below.
>
> ??? I don't see any error message. Does the job just "hang"?
>
> Do the parallel tests work (in particular, things like dhfr/Run.dhfr.min?)
> If so, try to see the difference between what you are doing and test case.
> You might try fewer processors (even 1) to narrow down the problem.
>
> ....dac
>
>
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Received on Fri Aug 20 2010 - 08:00:03 PDT
