Dear experts,
I am trying to run MMPBSA.py.MPI and I get the following error, which does not appear with MMPBSA.py. I saw there are a few threads talking about it, but I did not find a solution, maybe I missed it.
Any help will be appreciated,
Best regards,
Fabian
>./mmpbsa.sh
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
cpptraj found! Using /home/amber20/amber20/bin/cpptraj
sander found! Using /home/amber20/amber20/bin/sander
Preparing trajectories for simulation...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
At line 174 of file /home/amber20/amber20_src/AmberTools/src/sander/getcor.F90 (unit = 9, file = '_MMPBSA_dummycomplex.inpcrd')
Fortran runtime error: End of file
Error termination. Backtrace:
#0 0x7fd37d1e532a
#1 0x7fd37d1e5ed5
#2 0x7fd37d1e669d
#3 0x7fd37d35cca3
#4 0x7fd37d35d28a
#5 0x7fd37d359e8f
#6 0x7fd37d35e79c
#7 0x7fd37d35f72c
#8 0x55c40254b823
#9 0x55c4024f0e78
#10 0x55c4024ee6b2
#11 0x55c4024ee70e
#12 0x7fd37cbe2bf6
#13 0x55c4023466b9
#14 0xffffffffffffffff
At line 116 of file /home/amber20/amber20_src/AmberTools/src/sander/trajene.F90 (unit = 24, file = '_MMPBSA_complex.mdcrd.0')
Fortran runtime error: End of file
Error termination. Backtrace:
File "/home/amber20/amber20/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 428, in run
error_list = [s.strip() for s in out.split('\n')
TypeError: a bytes-like object is required, not 'str'
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 0 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.
--------------------------------------------------------------------------
#0 0x7efdac19d32a
#1 0x7efdac19ded5
#2 0x7efdac19e69d
#3 0x7efdac314ca3
#4 0x7efdac31528a
#5 0x7efdac311e8f
#6 0x7efdac31679c
#7 0x7efdac31772c
#8 0x55bddaa632c6
#9 0x55bddaa61d3e
#10 0x55bddaa5a6b2
#11 0x55bddaa5a70e
#12 0x7efdabb9abf6
#13 0x55bdda8b26b9
#14 0xffffffffffffffff
File "/home/amber20/amber20/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 428, in run
error_list = [s.strip() for s in out.split('\n')
TypeError: a bytes-like object is required, not 'str'
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 0 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.
--------------------------------------------------------------------------
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
At line 174 of file /home/amber20/amber20_src/AmberTools/src/sander/getcor.F90 (unit = 9, file = '_MMPBSA_dummycomplex.inpcrd')
Fortran runtime error: End of file
Error termination. Backtrace:
#0 0x7f1992dc232a
#1 0x7f1992dc2ed5
#2 0x7f1992dc369d
#3 0x7f1992f39ca3
#4 0x7f1992f3a28a
#5 0x7f1992f36e8f
#6 0x7f1992f3b79c
#7 0x7f1992f3c72c
#8 0x5608c51af823
#9 0x5608c5154e78
#10 0x5608c51526b2
#11 0x5608c515270e
#12 0x7f19927bfbf6
#13 0x5608c4faa6b9
#14 0xffffffffffffffff
File "/home/amber20/amber20/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 428, in run
error_list = [s.strip() for s in out.split('\n')
TypeError: a bytes-like object is required, not 'str'
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 0 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.
--------------------------------------------------------------------------
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
File "/home/amber20/amber20/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/amber20/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py", line 428, in run
error_list = [s.strip() for s in out.split('\n')
TypeError: a bytes-like object is required, not 'str'
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 0 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.
--------------------------------------------------------------------------
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
11 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /home/amber20/amber20/bin/sander
calculating complex contribution...
^C[mpiexec.amber2] Sending Ctrl-C to processes as requested
[mpiexec.amber2] Press Ctrl-C again to force abort
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
MMPBSA.py.MPI interrupted! Program terminated. All files are kept.
Fabian Glaser
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Tel +972 (0) 4 8293701
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Received on Thu Feb 03 2022 - 01:00:02 PST
