NAMD 2.9: Segmentation fault?

From: María Antonieta Sánchez Farrán (mfarran_at_engr.psu.edu)
Date: Tue Jul 31 2012 - 12:44:09 CDT

Dear NAMD Users,

I hope you can give me some insight on how to solve this issue. I have
tried running a simulation of a solvated protein (~35,000 atoms) using
NAMD_2.9_Linux-x86_64-ibverbs in a Red Hat Enterprise Linux Server
release 5.8. It seems that it has problems reading the PDB file although
the file exists and the path is correct. I have generated the pdb and
psf files with psfgen and no errors appear. Other mutant of this protein
runs perfectly, and there is no difference in the original input file or
method to generate the pdb and psf files. I tried to run this in the
NAMD 2.8 Multicore 64 bit version and it also failed. I traced the error
in the NAMD source files and have found that it relates to the PDB.c
code, the instance when opening a PDB file. Please find below an extract
of the log file from the simulation. I also include the log message for
different NAMD versions below. I have checked NAMD Wiki Troubleshooting,
and the archives in the mailing list but I haven't been able to find how
to sort this out. Any help would be much appreciated.

Thanks,
Maria Antonieta

In NAMD 2.9, this error appears:
Info: SUMMARY OF PARAMETERS:
Info: 180 BONDS
Info: 447 ANGLES
Info: 566 DIHEDRAL
Info: 46 IMPROPER
Info: 6 CROSSTERM
Info: 119 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.129473
Info: TIME FOR READING PDB FILE: 0.0585861
Info:
Command = zcat .Z
Filename.Z = .Z
Command = gzip -d -c .gz
Filename.gz = .gz
FATAL ERROR: Cannot open file '' for input in PDB::PDB.: No such file or
directory

In NAMD 2.7 run on the same cluster, this error appears:
ob started on lionxh38.hpc.rcc.psu.edu at Mon Jul 30 20:03:43 EDT 2012
[lionxh38:11380] *** Process received signal ***
[lionxh38:11380] Signal: Segmentation fault (11)
[lionxh38:11380] Signal code: Address not mapped (1)
[lionxh38:11380] Failing at address: 0x14e8
[lionxh38:11380] [ 0] /lib64/libpthread.so.0 [0x32f0c0eb70]
[lionxh38:11380] [ 1]
namd2(_ZN9NamdState14configListInitEP10ConfigList+0x779) [0x7e16b9]
[lionxh38:11380] [ 2] namd2(_ZN9ScriptTcl9initcheckEv+0x62) [0x82b842]
[lionxh38:11380] [ 3]
namd2(_ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x28) [0x82de88]
[lionxh38:11380] [ 4] namd2(TclInvokeStringCommand+0x91) [0x939c88]
[lionxh38:11380] [ 5] namd2 [0x96fad8]
[lionxh38:11380] [ 6] namd2(Tcl_EvalEx+0x176) [0x97011b]
[lionxh38:11380] [ 7] namd2(Tcl_EvalFile+0x134) [0x967b24]
[lionxh38:11380] [ 8] namd2(_ZN9ScriptTcl3runEPc+0x14) [0x82e244]
[lionxh38:11380] [ 9] namd2(_Z18after_backend_initiPPc+0x223) [0x4daf93]
[lionxh38:11380] [10] namd2(main+0x24) [0x4db074]
[lionxh38:11380] [11] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x32f001d994]
[lionxh38:11380] [12]
namd2(_ZNSt19basic_ostringstreamIcSt11char_traitsIcESaIcEED1Ev+0x89)
[0x4d7919]
[lionxh38:11380] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 11380 on node
lionxh38.hpc.rcc.psu.edu exited on signal 11 (Segmentation fault).

I also tried running this in NAMD 2.8 multicore version (running Ubuntu
11.04) and I receive a memory overflow message. I include the output below.

*** buffer overflow detected ***:
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2 terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7f0923291db7]
/lib/x86_64-linux-gnu/libc.so.6(+0xfdcd0)[0x7f0923290cd0]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_ZN8Molecule23build_constraint_paramsEP10StringListS1_S1_P3PDBPc+0x332)[0x90b442]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_ZN9NamdState14configListInitEP10ConfigList+0x184a)[0x92302a]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x84)[0x98a2a4]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(TclInvokeStringCommand+0x88)[0xaa93e8]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2[0xaac007]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2[0xaad422]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(Tcl_EvalEx+0x16)[0xaadc46]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(Tcl_FSEvalFileEx+0x151)[0xb0fdf1]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(Tcl_EvalFile+0x2e)[0xb0ffae]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_ZN9ScriptTcl4loadEPc+0x1a)[0x98ac7a]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_Z18after_backend_initiPPc+0x23a)[0x5019ea]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(main+0x22)[0x501d32]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)[0x7f09231b1eff]
/home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2[0x4fc8a9]

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:52 CST