Indeed it helps. Many thanks. Tests on 2 processors run fine.
Have a good day
George
On Dec 21, 2010, at 5:42 PM, Bill Miller III wrote:
> Yep, then you should run all the tests again with mpirun -np 2 (if you
> haven't already). If that continues to give no errors, then it looks like
> everything is okay. The way MMPBSA.py.MPI divides up the work on processors
> is to divide up the frames evenly for each processor, so you can't use more
> processors than frames. And since the tests only have 2 frames, mpirun -np 4
> shouldn't work.
>
> I hope that helps.
>
> Good luck!
>
> -Bill
>
> On Tue, Dec 21, 2010 at 11:20 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Hi Bill
>>
>> Thanks. I had set mpirun to 4.
>>
>> The error message is as follows:
>>
>> 2 frames were read in and processed by ptraj for use in calculation.
>> Error: You cannot have more MPI threads than frames!
>>
>> Running on 2 processors gives no error messages
>>
>> George
>>
>>
>> On Dec 21, 2010, at 4:43 PM, Bill Miller III wrote:
>>
>>> Try going into one of the test directories (like 01_Generalized_Born) and
>>> running the test by hand (i.e. ./Run.GB). You should comment out the end
>> of
>>> the execution script where the output files are removed. This way you can
>>> tell exactly where the error is occurring before the output files are
>>> removed by the script. The output files that are produced should give you
>>> some kind of indication of what the error might be.
>>>
>>> Good luck!
>>>
>>> -Bill
>>>
>>> On Tue, Dec 21, 2010 at 10:39 AM, George Tzotzos <gtzotzos.me.com>
>> wrote:
>>>
>>>>
>>>> Hi,
>>>>
>>>> I've installed on a new machine MMPBSA.py.MPI as per tutorial 3A
>>>> instructions.
>>>>
>>>> The serial tests run smoothly without error messages. The parallel
>>>> implementation of the program gives the following errors
>>>>
>>>> Any ideas?
>>>>
>>>> Many thanks
>>>>
>>>> George
>>>>
>>>> g:mmpbsa_py george1$ make test
>>>> cd 01_Generalized_Born && ./Run.GB
>>>> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>>>> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
>>>> PASSED
>>>> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> ==============================================================
>>>> cd 02_Poisson_Boltzmann && ./Run.PB
>>>> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>>>> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
>>>> PASSED
>>>> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> ==============================================================
>>>> cd 03_Alanine_Scanning && ./Run.ALA
>>>> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>>>> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
>>>> PASSED
>>>> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> ==============================================================
>>>> Mutant mdcrd can only be checked in serial
>>>> cd 04_Per_Residue_Decomp && ./Run.PerRes
>>>> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> diffing ../01_Generalized_Born/FINAL_RESULTS_MMPBSA.dat.save with
>>>> FINAL_RESULTS_MMPBSA.dat
>>>> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
>>>> PASSED
>>>> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> ==============================================================
>>>> diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat
>>>> PASSED
>>>> ==============================================================
>>>> cd 05_Pairwise_Decomp && ./Run.Pairwise
>>>> cat: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> diffing ../01_Generalized_Born/FINAL_RESULTS_MMPBSA.dat.save with
>>>> FINAL_RESULTS_MMPBSA.dat
>>>> file ddtmp.FINAL_RESULTS_MMPBSA.dat is short
>>>> PASSED
>>>> rm: FINAL_RESULTS_MMPBSA.dat: No such file or directory
>>>> ==============================================================
>>>> diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat
>>>> PASSED
>>>> ==============================================================
>>>> cd 06_NAB_Nmode && ./Run.nmode
>>>> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>>>> possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
>>>> ==============================================================
>>>> cd 07_Comprehensive && ./Run.comprehensive
>>>> diffing FINAL_RESULTS_MMPBSA_1.dat.save with FINAL_RESULTS_MMPBSA_1.dat
>>>> possible FAILURE: check FINAL_RESULTS_MMPBSA_1.dat.dif
>>>> ==============================================================
>>>> diffing FINAL_RESULTS_MMPBSA_2.dat.save with FINAL_RESULTS_MMPBSA_2.dat
>>>> possible FAILURE: check FINAL_RESULTS_MMPBSA_2.dat.dif
>>>> ==============================================================
>>>> diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat
>>>> PASSED
>>>> ==============================================================
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
>>>
>>> --
>>> Bill Miller III
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Graduate Student
>>> 352-392-6715
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Dec 21 2010 - 09:00:04 PST
