Hi,
Can you attach or paste the following files _MMPBSA_ptraj1.out,
_MMPBSA_ptraj2.out, _MMPBSA_ptraj3.out. Are you using a single trajectory or
triple trajectory approach?
On Fri, Jul 15, 2011 at 12:33 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
> Hi,
>
> I am still trying to debug the issue with MMPBSA.MPI. I could run the same
> input files through MMPBSA successfully but always failed with parallel
> version MMPBSA.MPI.
>
> Now, I have ruled out the previous suspicion that IOError was causing the
> crash of calculation. The real reason is that a segmentation fault exception
> was thrown during "calculating ligand contribution..." for GB calculation.
> To be more specific: "mmpbsa_py_energy -O -i _MMPBSA_gb.mdin -o
> _MMPBSA_ligand_gb.mdout.0 -p g1dimer_4hexa_nosolv.top -c
> _MMPBSA_dummyligand.inpcrd.1 -y _MMPBSA_ligand.mdcrd.0 -r
> _MMPBSA_.restrt_ligand.0 -pdb _MMPBSA_ligand.pdb" gives segmentation fault.
> There is only 1 frame in _MMPBSA_ligand_gb.mdout.0. The same thing happens
> to the other 3 processes.
>
> Another odd thing I've noticed was that "50 frames were read in and
> processed by ptraj for use in calculation" was always showing up at
> beginning of calculation for both parallel and serial run.
>
> For parallel run:
> I checked
> _MMPBSA_complex_gb.mdout.0 & _MMPBSA_receptor_gb.mdout.0 13
> frames processed
> _MMPBSA_complex_gb.mdout.1 & _MMPBSA_receptor_gb.mdout.1 13
> frames processed
> _MMPBSA_complex_gb.mdout.2 & _MMPBSA_receptor_gb.mdout.2 12
> frames processed
> _MMPBSA_complex_gb.mdout.3 & _MMPBSA_receptor_gb.mdout.3 12
> frames processed
> 13+13+12+12=50 and it's fine
>
> _MMPBSA_ligand_gb.mdout.0 1 frame processed then crashed
> _MMPBSA_ligand_gb.mdout.1 1 frame processed then crashed
> _MMPBSA_ligand_gb.mdout.2 0 frame processed then crashed
> _MMPBSA_ligand_gb.mdout.3 1 frame processed then crashed
>
> For serial run:
> I checked
> _MMPBSA_complex_gb.mdout 50 frames processed
> _MMPBSA_receptor_gb.mdout 62 frames processed
> _MMPBSA_ligand_gb.mdout 100 frames processed
>
> Could anyone give me some explanation?
>
> Thanks
> Ye
>
>
> On Jul 6, 2011, at 9:51 AM, Ye Fan wrote:
>
> > Hi Bill,
> >
> > Yes, I've downloaded the bugfix.all at "
> http://ambermd.org/bugfixesat.html" for version 1.5 and patched the source
> codes before compiling them. If you could tell me which bug particularly you
> are looking for, I can manually check it again.
> >
> > Thanks
> > Ye
> >
> > On Jul 5, 2011, at 5:14 PM, Bill Miller III wrote:
> >
> >> Have you applied all the AmberTools 1.5 bugfixes? This was a bug that I
> >> found in the code a while back, and I thought it had been added to the
> known
> >> patches.
> >>
> >> -Bill
> >>
> >> On Tue, Jul 5, 2011 at 3:53 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
> >>
> >>> Hi Bill,
> >>>
> >>> This is the last part of _MMPBSA_receptor_pb.mdout file:
> >>>
> >>>
> >>>
> --------------------------------------------------------------------------------
> >>> 4. RESULTS
> >>>
> >>>
> --------------------------------------------------------------------------------
> >>>
> >>> POST-PROCESSING OF TRAJECTORY ENERGIES
> >>> trajectory generated by ptraj
> >>> minimizing coord set # 1
> >>> Total surface charge 1.9723
> >>> Reaction field energy -3570.1196
> >>> Cavity solvation energy 54.6777
> >>>
> >>>
> >>> Maximum number of minimization cycles reached.
> >>>
> >>>
> >>> FINAL RESULTS
> >>>
> >>>
> >>>
> >>> NSTEP ENERGY RMS GMAX NAME NUMBER
> >>> 1 -3.1384E+03 1.7292E+01 1.0289E+02 N 680
> >>>
> >>> BOND = 329.2644 ANGLE = 939.0290 DIHED =
> >>> 1182.0229
> >>> VDWAALS = -670.5602 EEL = -7995.5664 EPB =
> >>> -3570.1813
> >>> 1-4 VDW = 394.1857 1-4 EEL = 6198.7732 RESTRAINT =
> >>> 0.0000
> >>> ECAVITY = 54.6777 EDISPER = 0.0000
> >>> minimization completed, ENE= -.31383551E+04 RMS= 0.172922E+02
> >>> minimizing coord set # 2
> >>> 67.611999999999995 5.7789999999999999 0.63300000000000001
> >>> pb_fdfrc(): Atom out of focusing box 251 59
> 44
> >>>
> >>>
> ------------------------------------------------------------------------------------------------------------------------
> >>>
> >>> I hope it helps.
> >>>
> >>> Thanks
> >>> Ye
> >>>
> >>> On Jul 5, 2011, at 11:57 AM, Bill Miller III wrote:
> >>>
> >>>> What is at the end of the _MMPBSA_receptor_pb.mdout file? There should
> be
> >>> an
> >>>> error message or warning in that file that should help explain the
> error
> >>>> based on where the calculation ended.
> >>>>
> >>>> -Bill
> >>>>
> >>>> On Tue, Jul 5, 2011 at 12:50 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
> >>>>
> >>>>> Hi Jason,
> >>>>>
> >>>>> I have added the "use_sander=1" in the $general section of input
> file.
> >>>>> However, the computation failed with sander error:
> >>>>>
> >>>>>
> >>>>>
> >>>
> ================================================================================
> >>>>> Reading command-line arguments and input files...
> >>>>> Loading and checking parameter files for compatibility...
> >>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
> >>>>> sander found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/sander for GB
> >>>>> calculations
> >>>>> sander found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/sander for PB
> >>>>> calculations
> >>>>> Preparing trajectories for simulation...
> >>>>> 50 frames were read in and processed by ptraj for use in calculation.
> >>>>>
> >>>>> Beginning GB calculations with sander...
> >>>>> calculating complex contribution...
> >>>>> calculating receptor contribution...
> >>>>> calculating ligand contribution...
> >>>>>
> >>>>> Beginning PB calculations with sander...
> >>>>> calculating complex contribution...
> >>>>> calculating receptor contribution...
> >>>>> Error: sander error during PB calculations!
> >>>>> NOTE: All files have been retained for debugging purposes. Type
> >>> MMPBSA.py
> >>>>> --clean to erase these files.
> >>>>>
> >>>>>
> >>>
> ================================================================================
> >>>>>
> >>>>> I have serial sander built with gnu compiler.
> >>>>>
> >>>>> So, I went into the test folder of Amber11 and did `make
> test.serial.MM
> >>> `.
> >>>>> It failed at (I wanted to test sander built):
> >>>>> ========================================
> >>>>> CALCULATING TEST: 02_MMPBSA_Stability
> >>>>> ./Run.mmpbsa.test: Program error
> >>>>> make: *** [test.mm_pbsa] Error 1
> >>>>> ========================================
> >>>>>
> >>>>> I also did test under $AMBERHOME/AmberTools/test/mmpbsa_py.
> >>>>>
> >>>>> It failed at:
> >>>>> ===========================
> >>>>> 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 08_Stability && ./Run.stability
> >>>>> ./Run.stability: Program error
> >>>>> make: *** [STABILITY] Error 1
> >>>>> ===========================
> >>>>>
> >>>>> Any idea what's going wrong?
> >>>>>
> >>>>> Thank you very much
> >>>>> Ye
> >>>>>
> >>>>>
> >>>>> On Jul 2, 2011, at 7:18 PM, Jason Swails wrote:
> >>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> If you have Amber11 available, try setting the variable
> "use_sander=1"
> >>> in
> >>>>>> your MMPBSA input file (in the &general section). I'm not sure
> what's
> >>>>>> happening here, but your filesystem seems to be choking on
> simultaneous
> >>>>> file
> >>>>>> accesses or something like that (perhaps the way NAB handles files
> is
> >>>>>> causing some grief, maybe you'll have better luck with sander,
> although
> >>>>> it
> >>>>>> will take longer).
> >>>>>>
> >>>>>> HTH,
> >>>>>> Jason
> >>>>>>
> >>>>>> On Fri, Jul 1, 2011 at 5:08 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
> >>>>>>
> >>>>>>> Hi Jason,
> >>>>>>>
> >>>>>>> The serial version is only having some minor issues.
> >>>>>>>
> >>>>>>> Following is the output:
> >>>>>>>
> >>>>>>>
> >>>>>
> >>>
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
> >>>>>>> Reading command-line arguments and input files...
> >>>>>>> Loading and checking parameter files for compatibility...
> >>>>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
> >>>>>>> mmpbsa_py_energy found! Using
> >>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for GB
> >>> calculations
> >>>>>>> mmpbsa_py_energy found! Using
> >>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for PB
> >>> calculations
> >>>>>>> Preparing trajectories for simulation...
> >>>>>>> 50 frames were read in and processed by ptraj for use in
> calculation.
> >>>>>>>
> >>>>>>> Beginning GB calculations with mmpbsa_py_energy...
> >>>>>>> calculating complex contribution...
> >>>>>>> calculating receptor contribution...
> >>>>>>> calculating ligand contribution...
> >>>>>>>
> >>>>>>> Beginning PB calculations with mmpbsa_py_energy...
> >>>>>>> calculating complex contribution...
> >>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
> >>>>>>> Total surface charge 2.9598
> >>>>>>> Reaction field energy -4821.5307
> >>>>>>> Cavity solvation energy 77.1504
> >>>>>>> ...
> >>>>>>> ...
> >>>>>>> Reaction field energy -4763.0697
> >>>>>>> Cavity solvation energy 78.8077
> >>>>>>> calculating receptor contribution...
> >>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
> >>>>>>> Total surface charge 1.9721
> >>>>>>> Reaction field energy -3552.3284
> >>>>>>> ...
> >>>>>>> ...
> >>>>>>> Reaction field energy -5066.6010
> >>>>>>> Cavity solvation energy 62.5406
> >>>>>>> calculating ligand contribution...
> >>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
> >>>>>>> Total surface charge 0.9867
> >>>>>>> Reaction field energy -2684.2835
> >>>>>>> ...
> >>>>>>> ...
> >>>>>>> Reaction field energy -2737.6791
> >>>>>>> Cavity solvation energy 34.1780
> >>>>>>>
> >>>>>>> Timing:
> >>>>>>> Total setup time: 0.031 min.
> >>>>>>> Creating trajectories with Ptraj: 0.084 min.
> >>>>>>> Total calculation time: 29.421 min.
> >>>>>>> Total GB calculation time (sander): 1.623 min.
> >>>>>>> Total PB calculation time (sander): 27.798 min.
> >>>>>>> Statistics calculation & output writing: 0.002 min.
> >>>>>>> Total time taken: 29.538 min.
> >>>>>>>
> >>>>>>>
> >>>>>>> MMPBSA.py Finished! Thank you for using. Please report any bugs to
> >>>>>>> amber.ambermd.org
> >>>>>>>
> >>>>>>>
> >>>>>
> >>>
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
> >>>>>>>
> >>>>>>> Thanks
> >>>>>>> Ye
> >>>>>>>
> >>>>>>> On Jul 1, 2011, at 11:39 AM, Jason Swails wrote:
> >>>>>>>
> >>>>>>>> Does it work in serial if you test it on just the first couple
> >>> frames?
> >>>>>>>>
> >>>>>>>> On Fri, Jul 1, 2011 at 10:00 AM, Ye Fan <yefan.ncsa.uiuc.edu>
> wrote:
> >>>>>>>>
> >>>>>>>>> Hi,
> >>>>>>>>>
> >>>>>>>>> I came across some errors when running MMPBSA.MPI. Following is
> the
> >>>>>>> output:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>
> >>>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
> >>>>>>>>> Running MMPBSA.MPI on 4 processors...
> >>>>>>>>> Reading command-line arguments and input files...
> >>>>>>>>> Loading and checking parameter files for compatibility...
> >>>>>>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
> >>>>>>>>> mmpbsa_py_energy found! Using
> >>>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for GB
> >>>>> calculations
> >>>>>>>>> mmpbsa_py_energy found! Using
> >>>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for PB
> >>>>> calculations
> >>>>>>>>> Preparing trajectories for simulation...
> >>>>>>>>> 2150 frames were read in and processed by ptraj for use in
> >>>>> calculation.
> >>>>>>>>>
> >>>>>>>>> Beginning GB calculations with mmpbsa_py_energy...
> >>>>>>>>> calculating complex contribution...
> >>>>>>>>> calculating receptor contribution...
> >>>>>>>>> calculating ligand contribution...
> >>>>>>>>> close failed in file object destructor:
> >>>>>>>>> IOError: [Errno 9] Bad file descriptor
> >>>>>>>>> close failed in file object destructor:
> >>>>>>>>> IOError: [Errno 9] Bad file descriptor
> >>>>>>>>> close failed in file object destructor:
> >>>>>>>>> IOError: [Errno 9] Bad file descriptor
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>
> >>>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
> >>>>>>>>>
> >>>>>>>>> I have AmberTool 1.5 with Amber 11 fully patched and compiled
> with
> >>> gnu
> >>>>>>>>> compiler. Mpi4py is built with openmpi-1.4.3.
> >>>>>>>>>
> >>>>>>>>> Any idea what's going wrong?
> >>>>>>>>>
> >>>>>>>>> Thanks
> >>>>>>>>> Ye
> >>>>>>>>> _______________________________________________
> >>>>>>>>> AMBER mailing list
> >>>>>>>>> AMBER.ambermd.org
> >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> Jason M. Swails
> >>>>>>>> Quantum Theory Project,
> >>>>>>>> University of Florida
> >>>>>>>> Ph.D. Candidate
> >>>>>>>> 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
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Jason M. Swails
> >>>>>> Quantum Theory Project,
> >>>>>> University of Florida
> >>>>>> Ph.D. Candidate
> >>>>>> 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
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> 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
> >
>
> _______________________________________________
> AMBER mailing list
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> 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
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Received on Fri Jul 15 2011 - 10:00:04 PDT
