Re: [AMBER] MMPBSA.MPI running issue

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 15 Jul 2011 17:20:41 -0500

Do the MMPBSA tests pass in parallel on ember? It could be that mpi4py doesn't install properly on that system. There are a few Teragrid systems that's true for (i.e. Kraken) since the mpi4py build script expects a standard MPI installation (a functional mpicc). If this is not the case, you'll need to build mpi4py by hand before running MMPBSA.MPI.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Jul 15, 2011, at 2:27 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
> Sure, I've pasted them here.
> 
> I have _MMPBSA_ptraj1.out with _MMPBSA_ptraj1.out.[0-3]. _MMPBSA_ptraj2.out with _MMPBSA_ptraj2.out.[0-3] and _MMPBSA_ptraj3.out with _MMPBSA_ptraj3.out.[0-3]. There are also _MMPBSA_ptraj4.out, _MMPBSA_ptraj5.out and _MMPBSA_ptraj6.out.
> 
> Well, I have no idea which trajectory approach I'm using since I'm actually helping one of our users to get his MMPBSA job run on Ember(SGI Altix UV System) at NCSA.
> 
> Thanks
> Ye
> 
> _MMPBSA_ptraj1.out:
> --------------------------------------------------------------------------------------------------------------------------------------------
> \-/  
>  -/-   PTRAJ: a utility for processing trajectory files
>  /-\  
>  \-/   Version: "AMBER 11.0 integrated" (4/2010)
>  -/-   Executable is: "/u/ncsa/yefan/apps/amber11-gnu/bin/ptraj"
>  /-\   Running on 1 processor(s)
>  \-/   Residue labels:
> 
> LYS  ILE  ALA  ALA  LEU  LYS  GLN  LYS  ILE  ALA 
> SER  LEU  LYS  GLN  GLU  ILE  ASP  ALA  LEU  GLU 
> TYR  GLU  ASN  ASP  ALA  LEU  GLU  GLN  LYS  ILE 
> ALA  ALA  LEU  LYS  GLN  LYS  ILE  ALA  SER  LEU 
> LYS  GLN  GLU  ILE  ASP  ALA  LEU  GLU  TYR  GLU 
> ASN  ASP  ALA  LEU  GLU  GLN  LYS  ILE  ALA  ALA 
> LEU  LYS  GLN  LYS  ILE  ALA  SER  LEU  LYS  GLN 
> GLU  ILE  ASP  ALA  LEU  GLU  TYR  GLU  ASN  ASP 
> ALA  LEU  GLU  GLN  LYS  ILE  ARG  ALA  LEU  LYS 
> ALA  LYS  ASN  ALA  HIE  LEU  LYS  GLN  GLU  ILE 
> ALA  ALA  LEU  GLU  GLN  GLU  ILE  ALA  ALA  LEU 
> GLU  GLN  LYS  ILE  ARG  ALA  LEU  LYS  ALA  LYS 
> ASN  ALA  HIE  LEU  LYS  GLN  GLU  ILE  ALA  ALA 
> LEU  GLU  GLN  GLU  ILE  ALA  ALA  LEU  GLU  GLN 
> LYS  ILE  ARG  ALA  LEU  LYS  ALA  LYS  ASN  ALA 
> HIE  LEU  LYS  GLN  GLU  ILE  ALA  ALA  LEU  GLU 
> GLN  GLU  ILE  ALA  ALA  LEU  GLU  GLN  Na+  Na+ 
> Na+  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT 
> WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT 
> ...
> WAT 
> 
> 
> PTRAJ: Processing input from file _MMPBSA_cenptraj.in
> 
> PTRAJ: trajin g1hexa_prod_comb 5251 5300 1
>  Checking coordinates: g1hexa_prod_comb
> Rank: 0 Atoms: 41418 FrameSize: 1006483 TitleSize: 30 NumBox: 3 Seekable 1
> 
> 
> PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
> Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 38673 atoms
> 
> PTRAJ: center :1-56:223-278 mass origin
> Mask [:1-56:223-278] represents 910 atoms
> 
> PTRAJ: image origin center 
> Mask [*] represents 2745 atoms
> 
> PTRAJ: center :1-168 mass origin
> Mask [:1-168] represents 2745 atoms
> 
> PTRAJ: image origin center 
> Mask [*] represents 2745 atoms
> 
> PTRAJ: rms first mass :1-168
> Mask [:1-168] represents 2745 atoms
> 
> PTRAJ: average _MMPBSA_avgcomplex.pdb pdb
> Mask [*] represents 2745 atoms
> 
> PTRAJ: trajout _MMPBSA_complex.mdcrd nobox 
>  g1hexa_prod_comb: 7420 frames.
> 
> PTRAJ: Successfully read the input file.
>       Coordinate processing will occur on 50 frames.
>       Summary of I/O and actions follows:
> 
> INPUT COORDINATE FILES
>  File (g1hexa_prod_comb) is an AMBER trajectory (with box info) with 5300 sets (processing only 50)
> 
> OUTPUT COORDINATE FILE
>  File (_MMPBSA_complex.mdcrd) is an AMBER trajectory
> ACTIONS
>  1>  STRIP: 38673 atoms will be removed from trajectory: :169-13061
>  2>  CENTER to origin via center of mass, atom selection follows :1-56
>  3>  IMAGE  by molecule to origin using the center of mass, atom selection   * (All atoms are selected)
>  4>  CENTER to origin via center of mass, atom selection follows   * (All atoms are selected)
>  5>  IMAGE  by molecule to origin using the center of mass, atom selection   * (All atoms are selected)
>  6>  RMS to first frame using mass weighting
>      Atom selection follows   * (All atoms are selected)
>  7>  AVERAGE: dumping the average of the coordinates to file _MMPBSA_avgcomplex.pdb
>      start: 1  Stop [at final frame]  Offset: 1
>      Atom selection   * (All atoms are selected)
>      Output file information:  File (_MMPBSA_avgcomplex.pdb) is a PDB file
> 
> 
> Processing AMBER trajectory file g1hexa_prod_comb
> 
> ........................ 75%  100% 
> 
> 
> PTRAJ: Successfully read in 50 sets and processed 50 sets.
> 
> Dumping accumulated results (if any)
> --------------------------------------------------------------------------------------------------------------------------------------------
> 
> _MMPBSA_ptraj2.out:
> --------------------------------------------------------------------------------------------------------------------------------------------
> \-/  
>  -/-   PTRAJ: a utility for processing trajectory files
>  /-\  
>  \-/   Version: "AMBER 11.0 integrated" (4/2010)
>  -/-   Executable is: "/u/ncsa/yefan/apps/amber11-gnu/bin/ptraj"
>  /-\   Running on 1 processor(s)
>  \-/   Residue labels:
> 
> LYS  ILE  ALA  ALA  LEU  LYS  GLN  LYS  ILE  ALA 
> SER  LEU  LYS  GLN  GLU  ILE  ASP  ALA  LEU  GLU 
> TYR  GLU  ASN  ASP  ALA  LEU  GLU  GLN  LYS  ILE 
> ALA  ALA  LEU  LYS  GLN  LYS  ILE  ALA  SER  LEU 
> LYS  GLN  GLU  ILE  ASP  ALA  LEU  GLU  TYR  GLU 
> ASN  ASP  ALA  LEU  GLU  GLN  LYS  ILE  ALA  ALA 
> LEU  LYS  GLN  LYS  ILE  ALA  SER  LEU  LYS  GLN 
> GLU  ILE  ASP  ALA  LEU  GLU  TYR  GLU  ASN  ASP 
> ALA  LEU  GLU  GLN  LYS  ILE  ARG  ALA  LEU  LYS 
> ALA  LYS  ASN  ALA  HIE  LEU  LYS  GLN  GLU  ILE 
> ALA  ALA  LEU  GLU  GLN  GLU  ILE  ALA  ALA  LEU 
> GLU  GLN  LYS  ILE  ARG  ALA  LEU  LYS  ALA  LYS 
> ASN  ALA  HIE  LEU  LYS  GLN  GLU  ILE  ALA  ALA 
> LEU  GLU  GLN  GLU  ILE  ALA  ALA  LEU  GLU  GLN 
> LYS  ILE  ARG  ALA  LEU  LYS  ALA  LYS  ASN  ALA 
> HIE  LEU  LYS  GLN  GLU  ILE  ALA  ALA  LEU  GLU 
> GLN  GLU  ILE  ALA  ALA  LEU  GLU  GLN 
> 
> 
> PTRAJ: Processing input from file _MMPBSA_ligtraj.in
> 
> PTRAJ: trajin _MMPBSA_complex.mdcrd
>  Checking coordinates: _MMPBSA_complex.mdcrd
> Rank: 0 Atoms: 2745 FrameSize: 66704 TitleSize: 30 NumBox: 0 Seekable 1
> 
> 
> PTRAJ: strip :1-56:223-278
> Mask [:1-56:223-278] represents 910 atoms
> 
> PTRAJ: trajout _MMPBSA_ligand.mdcrd nobox 
>  _MMPBSA_complex.mdcrd: 50 frames.
> 
> PTRAJ: Successfully read the input file.
>       Coordinate processing will occur on 50 frames.
>       Summary of I/O and actions follows:
> 
> INPUT COORDINATE FILES
>  File (_MMPBSA_complex.mdcrd) is an AMBER trajectory with 50 sets
> 
> OUTPUT COORDINATE FILE
>  File (_MMPBSA_ligand.mdcrd) is an AMBER trajectory
> ACTIONS
>  1>  STRIP: 910 atoms will be removed from trajectory: :1-56
> 
> 
> Processing AMBER trajectory file _MMPBSA_complex.mdcrd
> 
> ........................ 75%  100% 
> 
> 
> PTRAJ: Successfully read in 50 sets and processed 50 sets.
> 
> Dumping accumulated results (if any)
> --------------------------------------------------------------------------------------------------------------------------------------------
> 
> _MMPBSA_ptraj3.out:
> --------------------------------------------------------------------------------------------------------------------------------------------
> \-/  
>  -/-   PTRAJ: a utility for processing trajectory files
>  /-\  
>  \-/   Version: "AMBER 11.0 integrated" (4/2010)
>  -/-   Executable is: "/u/ncsa/yefan/apps/amber11-gnu/bin/ptraj"
>  /-\   Running on 1 processor(s)
>  \-/   Residue labels:
> 
> LYS  ILE  ALA  ALA  LEU  LYS  GLN  LYS  ILE  ALA 
> SER  LEU  LYS  GLN  GLU  ILE  ASP  ALA  LEU  GLU 
> TYR  GLU  ASN  ASP  ALA  LEU  GLU  GLN  LYS  ILE 
> ALA  ALA  LEU  LYS  GLN  LYS  ILE  ALA  SER  LEU 
> LYS  GLN  GLU  ILE  ASP  ALA  LEU  GLU  TYR  GLU 
> ASN  ASP  ALA  LEU  GLU  GLN  LYS  ILE  ALA  ALA 
> LEU  LYS  GLN  LYS  ILE  ALA  SER  LEU  LYS  GLN 
> GLU  ILE  ASP  ALA  LEU  GLU  TYR  GLU  ASN  ASP 
> ALA  LEU  GLU  GLN  LYS  ILE  ARG  ALA  LEU  LYS 
> ALA  LYS  ASN  ALA  HIE  LEU  LYS  GLN  GLU  ILE 
> ALA  ALA  LEU  GLU  GLN  GLU  ILE  ALA  ALA  LEU 
> GLU  GLN  LYS  ILE  ARG  ALA  LEU  LYS  ALA  LYS 
> ASN  ALA  HIE  LEU  LYS  GLN  GLU  ILE  ALA  ALA 
> LEU  GLU  GLN  GLU  ILE  ALA  ALA  LEU  GLU  GLN 
> LYS  ILE  ARG  ALA  LEU  LYS  ALA  LYS  ASN  ALA 
> HIE  LEU  LYS  GLN  GLU  ILE  ALA  ALA  LEU  GLU 
> GLN  GLU  ILE  ALA  ALA  LEU  GLU  GLN 
> 
> 
> PTRAJ: Processing input from file _MMPBSA_rectraj.in
> 
> PTRAJ: trajin _MMPBSA_complex.mdcrd
>  Checking coordinates: _MMPBSA_complex.mdcrd
> Rank: 0 Atoms: 2745 FrameSize: 66704 TitleSize: 30 NumBox: 0 Seekable 1
> 
> 
> PTRAJ: strip :57-84:279-306
> Mask [:57-84:279-306] represents 455 atoms
> 
> PTRAJ: trajout _MMPBSA_receptor.mdcrd nobox 
>  _MMPBSA_complex.mdcrd: 50 frames.
> 
> PTRAJ: Successfully read the input file.
>       Coordinate processing will occur on 50 frames.
>       Summary of I/O and actions follows:
> 
> INPUT COORDINATE FILES
>  File (_MMPBSA_complex.mdcrd) is an AMBER trajectory with 50 sets
> 
> OUTPUT COORDINATE FILE
>  File (_MMPBSA_receptor.mdcrd) is an AMBER trajectory
> ACTIONS
>  1>  STRIP: 455 atoms will be removed from trajectory: :57-84
> 
> 
> Processing AMBER trajectory file _MMPBSA_complex.mdcrd
> 
> ........................ 75%  100% 
> 
> 
> PTRAJ: Successfully read in 50 sets and processed 50 sets.
> 
> Dumping accumulated results (if any)
> --------------------------------------------------------------------------------------------------------------------------------------------
> 
> On Jul 15, 2011, at 11:47 AM, Dwight McGee wrote:
> 
>> 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 wit
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Received on Fri Jul 15 2011 - 15:30:03 PDT
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