There is no reason to recompile the parallel version. I am kind of
surprised that you weren't asked to install Amber in serial first...
Good luck!
Jason
On Sat, Dec 18, 2010 at 9:22 AM, George Tzotzos <gtzotzos.me.com> wrote:
> 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
>
>
> _______________________________________________
> 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
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Received on Sat Dec 18 2010 - 12:00:02 PST
