Jason, Dwight
Thank you very much for the suggestions. Before I proceed with either solution. I notice in my amber11/bin directory that amongst the installed files are: alamdcrd.pyc and inputparse.pyc.
Are these what I should expect to have?
Thanks in advance
George
On Jun 14, 2010, at 7:32 PM, Jason Swails wrote:
> Hello,
>
> One more comment: I would urge you against changing the input parameters
> inside the script itself. That is what the input file is for. We changed
> the parallel implementation quite a bit, so that it parallelizes the script
> instead of using parallel executables for reasons exactly like this. Not
> all MPIs were found to play nice with our old python script (they all play
> much nicer now). I've seen this error before, and there was really no way
> of fixing it short of installing a different MPI that happened to work. The
> new script does still have mpi_cmd and nproc as elements in the INPUT array,
> but they are no longer used (one of the reasons I urge you to use the input
> file and see the manual for the available options). It was just too much of
> a pain to remove them and adjust the indexes.
>
> Also, something I just learned is that 2.6 or later is needed to run
> MMPBSA.py (I had been telling people it was 2.5, but I just learned
> yesterday that even that is too old).
>
> Good luck!
> Jason
>
> On Mon, Jun 14, 2010 at 12:42 PM, Dwight McGee <dwight.mcgee.gmail.com>wrote:
>
>> Hi George,
>>
>> Judging from your from the email below I would assume that you are using
>> one of the older MMPBSA.py scripts. We have made several updates and
>> developed a more efficient way to run the MMPBSA.py in parallel
>> (MMPBSA.py.MPI). The new program can be downloaded from:
>> http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htm
>> You will need to have a version of python which is 2.5 or later and install
>> mpi4py.
>> Instructions on how to do this can be found on our website.
>> Good Luck!
>>
>> On Mon, Jun 14, 2010 at 12:10 PM, George Tzotzos <gtzotzos.me.com> wrote:
>>
>>> Hi everybody,
>>>
>>> I've attempted to run MMPBSA.py on a parallel amber11 installation.
>>>
>>> My machine is a quad core iMac running on Intel Core i7
>>>
>>> I did edit the MMPBSA.py file as follows:
>>>
>>> 1. Changed INPUT.append('3') to INPUT.append('4')
>>>
>>> 2. Changed the next line from INPUT.append('none') to
>> INPUT.append('mpirun
>>> -np 4')
>>>
>>> The error messages that I get are as follows:
>>>
>>>
>>> g:MMPBSA george1$ MMPBSA.py -O -i mmpbsa_1b.in -o
>> FINAL_RESULTS_MMPBSA.dat
>>> -sp 2wc6_bom_solv.prmtop -cp 2wc6_bom.prmtop -rp 2wc6.prmtop -lp
>> bom.prmtop
>>> -y *.mdcrd
>>> ptraj found! Using /Users/george1/Programs/amber11_parallel/bin/ptraj
>>> sander.MPI found! Using
>>> /Users/george1/Programs/amber11_parallel/bin/sander.MPI
>>> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
>> modified
>>> Bondi radii (mbondi)
>>>
>>> Preparing trajectories with ptraj...
>>> 200 frames were read in and processed by ptraj for use in calculation.
>>>
>>> Starting sander calls
>>>
>>> Starting gb calculation...
>>>
>>> Error: specified more groups ( 2 ) than the number of
>> processors
>>> ( 1 ) !
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> Error: specified more groups ( 2 ) than the number of
>> processors
>>> ( 1 ) !
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> Error: specified more groups ( 2 ) than the number of
>> processors
>>> ( 1 ) !
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> Error: specified more groups ( 2 ) than the number of
>> processors
>>> ( 1 ) !
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> Starting pb calculation...
>>>
>>> Error: specified more groups ( 2 ) than the number of
>> processors
>>> ( 1 ) !
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> Error: specified more groups ( 2 ) than the number of
>> processors
>>> ( 1 ) !
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> Error: specified more groups ( 2 ) than the number of
>> processors
>>> ( 1 ) !
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> Error: specified more groups ( 2 ) than the number of
>> processors
>>> ( 1 ) !
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> Error: Sander error! GB mdout file was not created.
>>> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
>>> --clean to erase these files.
>>>
>>> Looking forward to your suggestions how to fix this problems,
>>>
>>> Best regards
>>>
>>> George
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> T. Dwight McGee Jr.
>> Quantum Theory Project
>> University of Florida
>> Graduate Student
>> dwight.mcgee.gmail.com
>>
>> "Problems cannot be solved at the same level of awareness that created
>> them."
>> Albert Einstein
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jun 15 2010 - 00:00:03 PDT
