Thanks Bill,
This really helps. I did not compile amber11 in serial. Just parallel.
If I compile amber 11 in serial, should I recompile the parallel version too?
Thanks again
George
On Dec 18, 2010, at 3:15 PM, Bill Miller III wrote:
> Did you compile Amber in serial? MMPBSA.py.MPI uses sander, not sander.MPI.
> So to run MMPBSA.py.MPI (or MMPBSA.py) you will need to compile Amber in
> serial to get the proper sander executable.
>
> -Bill
>
>
> On Sat, Dec 18, 2010 at 9:11 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>>
>> which sander returns nothing
>>
>> which sander.MPI returns /Users/tzotzos/Programs/amber11/bin/sander.MPI
>>
>> which sander.LES.MPI /Users/tzotzos/Programs/amber11/bin/sander.LES.MPI
>>
>> Anything missing in the installation of amber11?
>>
>>
>>
>> On Dec 18, 2010, at 2:49 PM, Bill Miller III wrote:
>>
>>> That seems fine to me. Does `which sander` respond with the correct
>> location
>>> of your sander executable? Because if sander is found in a directory in
>> your
>>> path (like $AMBERHOME/bin), then MMPBSA.py and MMPBSA.py.MPI should be
>> able
>>> to find it.
>>>
>>> -Bill
>>>
>>>
>>> On Sat, Dec 18, 2010 at 8:40 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>>
>>>> Thanks Bill,
>>>>
>>>> I'm setting AMBERHOME as follows:
>>>>
>>>> export PATH=/Users/tzotzos/Programs/amber11/bin
>>>> export AMBERHOME=/Users/tzotzos/Programs/amber11
>>>>
>>>> Is there any inconsistency there?
>>>>
>>>> George
>>>>
>>>>
>>>> On Dec 18, 2010, at 2:24 PM, Bill Miller III wrote:
>>>>
>>>>> I'm not sure about your exact Amber organization and setup, but you say
>>>> that
>>>>> AMERHOME=/Users/george/Programs/amber11/
>>>>>
>>>>> Yet, ptraj is being found here:
>>>> /Users/tzotzos/Programs/amber11/bin/ptraj.
>>>>> This appears to be finding a different Amber 11 installation than the
>> one
>>>>> that you say is AMBERHOME. Is sander found
>>>>> in /Users/tzotzos/Programs/amber11/bin/ ? Do you have two different
>>>>> AMBERHOME's defined somewhere?
>>>>>
>>>>> There appears to be some sort of inconsistency in your environment.
>>>>>
>>>>> I hope that helps.
>>>>>
>>>>> -Bill
>>>>>
>>>>>
>>>>> On Sat, Dec 18, 2010 at 8:10 AM, George Tzotzos <gtzotzos.me.com>
>> wrote:
>>>>>
>>>>>> Apologies. Please find attached the mmpbsa.out file from the
>>>>>> Generalized_Born test
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> George
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Dec 18, 2010, at 2:06 PM, George Tzotzos wrote:
>>>>>>
>>>>>>> Jason,
>>>>>>>
>>>>>>> Many thanks. Indeed I had untarred the mmpbsa_py.test.tar into a new
>>>>>> directory in AMBERHOME.
>>>>>>>
>>>>>>> I did as per your suggestion and run the tests in both serial and
>>>>>> parallel modes
>>>>>>>
>>>>>>> In both cases I have outputs indicating "file
>>>>>> ddtmp.FINAL_RESULTS_MMPBSA.dat is short" (see end of this message)
>>>>>>>
>>>>>>> I moved into AMBERHOME/test/mmpbsa_py/01_Generalized_Born and
>> executed
>>>>>> the Run.GB script
>>>>>>>
>>>>>>> I'm attaching the output which indicates that sander is somehow
>> missing
>>>>>> despite the fact that AMBERHOME is set properly.
>>>>>>>
>>>>>>> george-Mac-Pro:01_Generalized_Born george$ echo $AMBERHOME
>>>>>>> /Users/george/Programs/amber11/
>>>>>>>
>>>>>>> Any ideas on this?
>>>>>>>
>>>>>>> Many thanks for your help
>>>>>>>
>>>>>>> George
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ============================================================
>>>>>>>
>>>>>>> $ export DO_PARALLEL='mpirun -np 12'
>>>>>>>
>>>>>>> $ 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
>>>>>>> ==============================================================
>>>>>>>
>>>>>>>
>>>>>>> On Dec 18, 2010, at 1:39 AM, Jason Swails wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> My comments are placed below
>>>>>>>>
>>>>>>>> On Fri, Dec 17, 2010 at 2:07 PM, George Tzotzos <gtzotzos.me.com>
>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Sorry to come back on this one.
>>>>>>>>>
>>>>>>>>> mmpbsa_py george1$ make test
>>>>>>>>>
>>>>>>>>> produces the output below.
>>>>>>>>>
>>>>>>>>> I've checked the list and saw that this problem has been
>> encountered
>>>>>>>>> previously. However, I didn't find a satisfactory solution for my
>>>> case.
>>>>>>>>>
>>>>>>>>> The weird thing is that the test produce outputs that appear to be
>>>> OK.
>>>>>> I'm
>>>>>>>>> attaching an example for the NAB_Nmode test
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I'm using Python 2.6.1
>>>>>>>>>
>>>>>>>>> I have installed AmberTools1.4 and amber11-parallel. I have no
>>>> previous
>>>>>>>>> installations of amber.
>>>>>>>>>
>>>>>>>>> Any clues how to solve this.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks again
>>>>>>>>>
>>>>>>>>> George
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> cd 01_Generalized_Born && ./Run.GB
>>>>>>>>> ./Run.GB: line 37: ../../dacdif: No such file or directory
>>>>>>>>>
>>>>>>>>
>>>>>>>> It can't find dacdif, which is in $AMBERHOME/test. What this
>> suggests
>>>>>> is
>>>>>>>> that the mmpbsa_py test directory is unpacked in the wrong place.
>>>> This
>>>>>>>> directory should be placed in $AMBERHOME/test.
>>>>>>>>
>>>>>>>> Be sure to follow all of the instructions here:
>>>>>>>>
>>>>>>
>>>>
>> http://ambermd.org/tutorials/advanced/tutorial3/py_script/compile.htmincluding
>>>>>>>> the instructions of where to place the files. This may also be
>>>>>>>> why the nab_nmode script did not work (it has to be placed in
>>>>>> $AMBERHOME/src
>>>>>>>> in order for it to find the compilers).
>>>>>>>>
>>>>>>>> Good luck!
>>>>>>>> Jason
>>>>>>>>
>>>>>>>>
>>>>>>>> cd 02_Poisson_Boltzmann && ./Run.PB
>>>>>>>>> ./Run.PB: line 37: ../../dacdif: No such file or directory
>>>>>>>>> cd 03_Alanine_Scanning && ./Run.ALA
>>>>>>>>> ./Run.ALA: line 42: ../../dacdif: No such file or directory
>>>>>>>>> Mutant mdcrd can only be checked in serial
>>>>>>>>> cd 04_Per_Residue_Decomp && ./Run.PerRes
>>>>>>>>> ./Run.PerRes: line 40: ../../dacdif: No such file or directory
>>>>>>>>> ./Run.PerRes: line 41: ../../dacdif: No such file or directory
>>>>>>>>> cd 05_Pairwise_Decomp && ./Run.Pairwise
>>>>>>>>> ./Run.Pairwise: line 40: ../../dacdif: No such file or directory
>>>>>>>>> ./Run.Pairwise: line 41: ../../dacdif: No such file or directory
>>>>>>>>> cd 06_NAB_Nmode && ./Run.nmode
>>>>>>>>> ./Run.nmode: line 34: ../../dacdif: No such file or directory
>>>>>>>>> cd 07_Comprehensive && ./Run.comprehensive
>>>>>>>>> ./Run.comprehensive: line 71: ../../dacdif: No such file or
>> directory
>>>>>>>>> ./Run.comprehensive: line 72: ../../dacdif: No such file or
>> directory
>>>>>>>>> ./Run.comprehensive: line 73: ../../dacdif: No such file or
>> directory
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> 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 Sat Dec 18 2010 - 06:30:05 PST
