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 Sun Jan 19 2025 - 19:00:02 PST
