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Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Sun, Jan 19, 2025 at 6:48 PM Vishwaa Kannan <vishwaakannan.icloud.com>
wrote:
> Thanks for the quick reply Dr. Luo. I was using the default fill ratio. I
> have changed the fill ratio to 16 but still got an error on rank 17. I have
> attached its MDOUT file here.
>
> vishwaa.BCC-A102281:~/amber/TS/R1$ mpirun -np 20 MMPBSA.py.MPI -O -i
> mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp R1_solvated.prmtop -cp
> R1.prmtop -rp R1_rec.prmtop -lp R1_lig.prmtop -y prod.mdcrd
> Loading and checking parameter files for compatibility...
> cpptraj found! Using /home/vishwaa/amber/amber24/bin/cpptraj
> sander found! Using /home/vishwaa/amber/amber24/bin/sander
> Preparing trajectories for simulation...
> 1400 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning PB calculations with /home/vishwaa/amber/amber24/bin/sander
> calculating complex contribution...
> File "/home/vishwaa/amber/amber24/bin/MMPBSA.py.MPI", line 101, in
> <module>
> app.run_mmpbsa() # for membrane runs by automatically setting the
> membrane thickness and location.
> ^^^^^^^^^^^^^^^^
> File
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> line 225, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py",
> line 476, in run
> raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/vishwaa/amber/amber24/bin/sander failed with prmtop
> R1.prmtop!
>
>
> Error occurred on rank 17.
>
> Fatal Error!
> All files have been retained for your error investigation:
> You should begin by examining the output files of the first failed
> calculation.
> Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
> manual for file naming conventions.
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 17 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> -------------------------------------
>
> > On Jan 18, 2025, at 5:36 PM, Ray Luo via AMBER <amber.ambermd.org>
> wrote:
> >
> > Vishwaa,
> >
> > Can you share a full mdout file for one of the failed snapshots?
> >
> > My gut feeling is that you are using the default fillratio of 4 for a
> very
> > large protein dimer and the memory usage is over the physical limit on
> your
> > compute nodes.
> >
> > All the best,
> > Ray
> > --
> > Ray Luo, Ph.D.
> > Professor of Structural Biology/Biochemistry/Biophysics,
> > Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> > Biomedical Engineering, and Materials Science and Engineering
> > Department of Molecular Biology and Biochemistry
> > University of California, Irvine, CA 92697-3900
> >
> >
> > On Sat, Jan 18, 2025 at 1:34 PM Vishwaa Kannan via AMBER <
> amber.ambermd.org>
> > wrote:
> >
> >> The MMPBSA is not working properly. After narrowing it down, I suspect
> the
> >> problem lies with the protein being counted as two separate molecules
> (prob
> >> the dimer being weird), and the ligand being recognized as another,
> which
> >> could be causing the errors. I figured this out using cpptraj and list,
> >> molecule 1: 1-313, molecule 2: 314 - 627, molecule 3 (PFOA): 628. I
> tried
> >> explicitly stating it, but that did not work. What can I do to fix this
> >> error?
> >>
> >> Input file (mmpbsa.in):
> >> &general
> >> startframe=601, endframe=2000,
> >> strip_mask=":WAT,Na+",
> >> receptor_mask=":1-627",
> >> ligand_mask=":628",
> >> keep_files=2,
> >> /
> >> &pb
> >> istrng=0.100,
> >> /
> >> &decomp
> >> idecomp=1,
> >> /
> >>
> >> Terminal:
> >> vishwaa.BCC-A102281:~/amber/TS/R1$ mpirun -np 20 MMPBSA.py.MPI -O -i
> >> mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp R1_solvated.prmtop -cp
> >> R1.prmtop -rp R1_rec.prmtop -lp R1_lig.prmtop -y prod.mdcrd
> >> Loading and checking parameter files for compatibility...
> >> cpptraj found! Using /home/vishwaa/amber/amber24/bin/cpptraj
> >> sander found! Using /home/vishwaa/amber/amber24/bin/sander
> >> Preparing trajectories for simulation...
> >> 1400 frames were processed by cpptraj for use in calculation.
> >>
> >> Running calculations on normal system...
> >>
> >> Beginning PB calculations with /home/vishwaa/amber/amber24/bin/sander
> >> calculating complex contribution...
> >> File "/home/vishwaa/amber/amber24/bin/MMPBSA.py.MPI", line 101, in
> >> <module>
> >> app.run_mmpbsa() # for membrane runs by automatically setting the
> >> membrane thickness and location.
> >> ^^^^^^^^^^^^^^^^
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> >> line 225, in run_mmpbsa
> >> self.calc_list.run(rank, self.stdout)
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py",
> >> line 82, in run
> >> calc.run(rank, stdout=stdout, stderr=stderr)
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py",
> >> line 476, in run
> >> raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> >> CalcError: /home/vishwaa/amber/amber24/bin/sander failed with prmtop
> >> R1.prmtop!
> >>
> >>
> >> Error occurred on rank 6.
> >>
> >> Fatal Error!
> >> All files have been retained for your error investigation:
> >> You should begin by examining the output files of the first failed
> >> calculation.
> >> Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
> >> manual for file naming conventions.
> >> File "/home/vishwaa/amber/amber24/bin/MMPBSA.py.MPI", line 101, in
> >> <module>
> >> app.run_mmpbsa() # for membrane runs by automatically setting the
> >> membrane thickness and location.
> >> ^^^^^^^^^^^^^^^^
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> >> line 225, in run_mmpbsa
> >> self.calc_list.run(rank, self.stdout)
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py",
> >> line 82, in run
> >> calc.run(rank, stdout=stdout, stderr=stderr)
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py",
> >> line 476, in run
> >> raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> >> CalcError: /home/vishwaa/amber/amber24/bin/sander failed with prmtop
> >> R1.prmtop!
> >>
> >>
> >> Error occurred on rank 11.
> >>
> >> Fatal Error!
> >> All files have been retained for your error investigation:
> >> You should begin by examining the output files of the first failed
> >> calculation.
> >> Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
> >> manual for file naming conventions.
> >>
> --------------------------------------------------------------------------
> >> MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD
> >> with errorcode 1.
> >>
> >> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >> You may or may not see output from other processes, depending on
> >> exactly when Open MPI kills them.
> >>
> --------------------------------------------------------------------------
> >> File "/home/vishwaa/amber/amber24/bin/MMPBSA.py.MPI", line 101, in
> >> <module>
> >> app.run_mmpbsa() # for membrane runs by automatically setting the
> >> membrane thickness and location.
> >> ^^^^^^^^^^^^^^^^
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> >> line 225, in run_mmpbsa
> >> self.calc_list.run(rank, self.stdout)
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py",
> >> line 82, in run
> >> calc.run(rank, stdout=stdout, stderr=stderr)
> >> File
> >>
> "/home/vishwaa/amber/amber24/lib/python3.12/site-packages/MMPBSA_mods/calculation.py",
> >> line 476, in run
> >> raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> >> [BCC-A102281:10455] 1 more process has sent help message
> help-mpi-api.txt
> >> / mpi-abort
> >> [BCC-A102281:10455] Set MCA parameter "orte_base_help_aggregate" to 0 to
> >> see all help / error messages
> >> vishwaa.BCC-A102281:~/amber/TS/R1$
> >>
> >> Output of rank 6 ("MMPBSA_complex_pb.mdout.6"):
> >> -------------------------------------------------------
> >> Amber 24 SANDER 2024
> >> -------------------------------------------------------
> >>
> >> | Run on 01/18/2025 at 16:10:12
> >>
> >> | Executable path: /home/vishwaa/amber/amber24/bin/sander
> >> | Working directory: /home/vishwaa/amber/TS/R1
> >> | Hostname: Unknown
> >> [-O]verwriting output
> >>
> >> File Assignments:
> >> | MDIN: _MMPBSA_pb_decomp_com.mdin
> >>
> >> | MDOUT: _MMPBSA_complex_pb.mdout.6
> >>
> >> |INPCRD: _MMPBSA_dummycomplex.inpcrd
> >>
> >> | PARM: R1.prmtop
> >>
> >> |RESTRT: _MMPBSA_restrt.6
> >>
> >> | REFC: refc
> >>
> >> | MDVEL: mdvel
> >>
> >> | MDFRC: mdfrc
> >>
> >> | MDEN: mden
> >>
> >> | MDCRD: mdcrd
> >>
> >> |MDINFO: mdinfo
> >>
> >> | MTMD: mtmd
> >>
> >> |INPDIP: inpdip
> >>
> >> |RSTDIP: rstdip
> >>
> >> |INPTRA: _MMPBSA_complex.mdcrd.6
> >>
> >>
> >>
> >> Here is the input file:
> >>
> >> File generated by MMPBSA.py
> >>
> >> &cntrl
> >>
> >> ntb=0, nsnb=99999, cut=999.0, imin=5,
> >>
> >> igb=10, idecomp=1, ipb=2,
> >>
> >> dec_verbose=0,
> >>
> >> /
> >>
> >> &pb
> >>
> >> istrng=100.0, radiopt=0, maxitn=1000,
> >>
> >> fillratio=4.0,
> >>
> >> /
> >>
> >> Residues considered as REC
> >>
> >> RRES 1 627
> >>
> >> END
> >>
> >> Residues considered as LIG
> >>
> >> LRES 628 628
> >>
> >> END
> >>
> >> Residues to print
> >>
> >> RES 1 628
> >>
> >> END
> >>
> >> END
> >>
> >>
> >>
> >>
> --------------------------------------------------------------------------------
> >> 1. RESOURCE USE:
> >>
> >>
> --------------------------------------------------------------------------------
> >>
> >> | Flags:
> >>
> >> | New format PARM file being parsed.
> >> | Version = 1.000 Date = 01/17/25 Time = 01:12:41
> >> NATOM = 10051 NTYPES = 19 NBONH = 4986 MBONA = 5196
> >> NTHETH = 11380 MTHETA = 7050 NPHIH = 23035 MPHIA = 22015
> >> NHPARM = 0 NPARM = 0 NNB = 55658 NRES = 628
> >> NBONA = 5196 NTHETA = 7050 NPHIA = 22015 NUMBND = 74
> >> NUMANG = 174 NPTRA = 199 NATYP = 38 NPHB = 0
> >> IFBOX = 0 NMXRS = 25 IFCAP = 0 NEXTRA = 0
> >> NCOPY = 0
> >>
> >> Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
> >>
> >> | CMAP information read from topology file:
> >>
> >> | Memory Use Allocated
> >> | Real 1557822
> >> | Hollerith 30783
> >> | Integer 583328
> >> | Max Pairs 1
> >> | nblistReal 0
> >> | nblist Int 0
> >> | Total 14569 kbytes
> >>
> >> | Note: 1-4 EEL scale factors are being read from the topology file.
> >>
> >> | Note: 1-4 VDW scale factors are being read from the topology file.
> >> | Duplicated 0 dihedrals
> >> | Duplicated 0 dihedrals
> >> |CMAP: Reticulating splines.
> >>
> >>
> >>
> --------------------------------------------------------------------------------
> >> 2. CONTROL DATA FOR THE RUN
> >>
> >>
> --------------------------------------------------------------------------------
> >>
> >> default_name
> >>
> >>
> >> General flags:
> >> imin = 5, nmropt = 0
> >>
> >> Nature and format of input:
> >> ntx = 1, irest = 0, ntrx = 1
> >>
> >> Nature and format of output:
> >> ntxo = 2, ntpr = 50, ntrx = 1, ntwr =
> >> 1
> >> iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> >> 0
> >> ioutfm = 1, ntwprt = 0, idecomp = 1, rbornstat=
> >> 0
> >>
> >> Potential function:
> >> ntf = 1, ntb = 0, igb = 10, nsnb =
> >> 99999
> >> ipol = 0, gbsa = 0, iesp = 0
> >> dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
> >>
> >> Frozen or restrained atoms:
> >> ibelly = 0, ntr = 0
> >>
> >> Energy minimization:
> >> maxcyc = 1, ncyc = 10, ntmin = 1
> >> dx0 = 0.01000, drms = 0.00010
> >>
> >> LOADING THE DECOMP ATOMS AS GROUPS
> >>
> >> ----- READING GROUP 1; TITLE:
> >> Residues considered as REC
> >>
> >> Number of atoms in this group = 0
> >> ----- READING GROUP 2; TITLE:
> >> Residues considered as LIG
> >>
> >> Number of atoms in this group = 0
> >> ----- READING GROUP 3; TITLE:
> >> Residues to print
> >>
> >> GRP 3 RES 1 TO 628
> >> Number of atoms in this group = 10051
> >> ----- END OF GROUP READ -----
> >> There was more stuff here, but just a bunch of atoms and their info.
> >> --
> >> Best,
> >> Vishwaa Kannan
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >>
> >>
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> >>
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Received on Mon Jan 20 2025 - 19:00:02 PST