Re: NAMD 2.9: Segmentation fault?

From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jul 31 2012 - 14:14:55 CDT

Maybe try retyping the coordinate part of the file. That is, delete that
line entirely, and reenter it. I think it is something like Branko
suggested, some minor little problem with how things are being read that is
keeping it from finding your actual PDB file.

You said a bunch of mutants ran fine? Do the config files look the same?
Can you just take one of those mutant files, and change the location of the
file path manually to be this one that isn't working?

Essentially the error message is telling you that NAMD think you want it to
open nothing for the PDB, that is, it thinks " is the name of the PDB file
you entered after "coordinates". So it must be some very minor specific
little problem.

~Aron

On Tue, Jul 31, 2012 at 2:47 PM, María Antonieta Sánchez Farrán <
mfarran_at_engr.psu.edu> wrote:

> Thanks Branko, my namd configuration files (and all my files are made in
> linux). I am not sure what could be happening with the PDB.c code - for
> some reason it doesn't read the file.
>
> Maria
>
>
> On 07/31/2012 02:42 PM, Branko wrote:
>
> Maria,
>
> Did you made your namd configuration file in windows? End of lines
> (different in linux and windows) from time to time can make problems. It
> is likely that some lines in your configuration file cannot be read
> properly; likely you check everything else and should be OK.
>
> Branko
>
> On 7/31/2012 8:14 PM, María Antonieta Sánchez Farrán wrote:
>
> Dear Branko,
>
> Yes, I have an ASCII pdb file. I can perfectly load the structures and I
> see that there is no problem with it.
>
> Maria
>
> On 07/31/2012 02:02 PM, Branko wrote:
>
> Maria,
>
> Do you have ASCII pdb file? If you have try to use this file without
> packing (i.e. tgz, gz, or similar). System of ~ 35,000 is snot so big, so
> it is reasonable to pack the files only for transfer from (for example)
> computer to computer or similar. Can you load your PDB file to VMD (or GUI
> taht you use), and check is everything is OK?
>
> Branko
>
> On 7/31/2012 7:44 PM, María Antonieta Sánchez Farrán wrote:
>
> 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]
>
>
>
>
> No virus found in this incoming message.
> Checked by AVG - www.avg.com
> Version: 9.0.930 / Virus Database: 2437.1.1/5167 - Release Date: 07/31/12 09:25:00
>
>
>
>
> --
> María Antonieta Sánchez Farrán
> Doctoral Candidate
> Department of Chemical Engineering
> The Pennsylvania State University
>
>
>
> No virus found in this incoming message.
> Checked by AVG - www.avg.com
> Version: 9.0.930 / Virus Database: 2437.1.1/5167 - Release Date: 07/31/12 09:25:00
>
>
>
>
> --
> María Antonieta Sánchez Farrán
> Doctoral Candidate
> Department of Chemical Engineering
> The Pennsylvania State University
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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