Hello,
In our HPC centre one of our users encountered SIGSEGV using cpptraj
program (which was called from MMPBSA.py). We traced it, isolated
cpptraj call and collected debug information. Could you take a look at
this - is it a bug in the code or problem with the input data?
*Details*
backtrace:
> # function args file line
> -- ----------------------------
> ------------------------------------------------
> -------------------------------- ----
> #0 __memmove_avx_unaligned_erms () /lib64/libc.so.6
> #1 Frame::SetCoordinates (this=0x2696cb0,frameIn=...,maskIn=...)
> src/cpptraj/src/Frame.cpp 558
> #2 Action_Rmsd::DoAction (this=0x2696490,frameNum=221452,frm=...)
> src/cpptraj/src/Action_Rmsd.cpp 368
> #3 ActionList::DoActions
> (this=0x7fff0417cc98,frameNumIn=221452,frm=...)
> src/cpptraj/src/ActionList.cpp 94
> #4 CpptrajState::RunNormal (this=0x7fff0417cb60)
> src/cpptraj/src/CpptrajState.cpp 1354
> #5 CpptrajState::Run (this=0x7fff0417cb60)
> src/cpptraj/src/CpptrajState.cpp 500
> #6 Cpptraj::RunCpptraj
> (this=0x7fff0417cb60,argc=2,argv=0x7fff0417d048)
> src/cpptraj/src/Cpptraj.cpp 166
> #7 CpptrajProgram (argc=2,argv=0x7fff0417d048)
> src/cpptraj/src/main.cpp 18
> #8 main (argc=2,argv=0x7fff0417d048) src/cpptraj/src/main.cpp 30
amber version:
- backtrace collected with Amber 22.1 and AmberTools 22.3 (compiled with
-DOPTIMIZE=OFF and -O0 -g)
(we have tested also previous versions of Amber and they all fail on
user input)
direct command:
cat input-cpptraj.txt | cpptraj E81A.top
commands in the input-cpptraj.txt:
> trajin ../input/E81A.nc 1 224999 1
> noprogress
> rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first
> outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb
> outtraj _MMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart
> outtraj _MMPBSA_complex.mdcrd.0 onlyframes 1-224999 nobox
> strip :288
> outtraj _MMPBSA_receptor.pdb onlyframes 1 nobox pdb
> outtraj _MMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart
> outtraj _MMPBSA_receptor.mdcrd.0 onlyframes 1-224999 nobox
> unstrip
> rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first
> strip :1-287,289-576
> outtraj _MMPBSA_ligand.pdb onlyframes 1 nobox pdb
> outtraj _MMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart
> outtraj _MMPBSA_ligand.mdcrd.0 onlyframes 1-224999 nobox
> unstrip
> rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first
The call that causes SIGSEGV is the memcpy call.
> void Frame::SetCoordinates(Frame const& frameIn, AtomMask const& maskIn) {
>
> (...)
>
> for (AtomMask::const_iterator atom = maskIn.begin(); atom !=
> maskIn.end(); ++atom)
> {
> memcpy( newXptr, frameIn.X_ + ((*atom) * 3), COORDSIZE_);
> // <= SIGSEGV here!
> newXptr += 3;
> }
> }
I checked with GDB that the problem is caused by a negative value of the
source address in the memcpy call (second arg). Such a value is a
consequence of an invalid index in the "Selected_" vector of the
"maskIn" (to which the "atom" iterator points).
First values of "maskIn.Selected_":
{775042866, 3158064, 2, 3, 4, 5, 6, 7, 8, 9, ...}
So the real question is what could have caused to get such a monster
here....
---
Finally, I would like to point out a minor issue in the MMPBSA.py code.
When cpptraj fails, then MMPBSA.py also fails, but with the following
backtrace:
> Loading and checking parameter files for compatibility...
> cpptraj found! Using
> /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3/bin/cpptraj
> sander found! Using
> /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3/bin/sander
> Preparing trajectories for simulation...
> free(): invalid next size (normal)
> File
> "/net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3/bin/MMPBSA.py.MPI",
> line 99, in <module>
> app.file_setup()
> File
> "/net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3/lib/python3.9/site-packages/MMPBSA_mods/main.py",
> line 155, in file_setup
> self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES,
> File
> "/net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py",
> line 134, in make_trajectories
> traj.Run(pre + 'normal_traj_cpptraj.out')
> File
> "/net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py",
> line 687, in Run
> raise TrajError('Error running %s' % self.program)
> AttributeError: 'Trajectory' object has no attribute 'program'
> Error occurred on rank 0.
So actually, there is a bug in make_trajs.py code, because the
Trajectory object does not have a field named "program".
---
Looking forward to you help,
Andrzej Dorobisz
HPC Software Department
ACC Cyfronet AGH, Poland
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Received on Tue Dec 06 2022 - 03:00:03 PST
