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
Received on Sat Dec 18 2010 - 05:30:03 PST
