From: Maria Antonieta Sanchez Farran (mfarran_at_engr.psu.edu)
Date: Wed Aug 01 2012 - 15:25:15 CDT
Hi,
Thanks Branko, Aron and Norman for your input. The issue was solved
although it is unclear why NAMD wasn't taking the path. The path was
correct and the input files were also okay. I have other simulations
with the same path structure and they were working. I am now avoiding
the use of paths in the config file. Thanks again Branko for helping me
to check the files and figure this out!
Maria
On 08/01/2012 02:20 AM, Norman Geist wrote:
> Hi,
>
> If you read the output file correctly, the psf and pdb are loaded
> without problems. Than afterwards it tries to load another pdb file
> with an empty path. Look to your script where else you try to use a
> pdb file. Check the path as it seems namd cannot read the path to the
> file as it tells you file '' not found.
>
> Good luck
>
> Norman Geist.
>
> *Von:*owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Maria Antonieta Sanchez Farran
> *Gesendet:* Dienstag, 31. Juli 2012 21:52
> *An:* Aron Broom
> *Cc:* Branko; namd-l
> *Betreff:* Re: namd-l: NAMD 2.9: Segmentation fault?
>
>
> Thanks Branko and Aron for your suggestions. I've tried before
> re-writing the lines and using the "good" .conf from the other
> mutants, with no success. I tried it once again and I still have the
> same memory error.
>
> I will try Branko's suggestion of using VegaZZ to make sure the PDB
> file is correct. Although the PDB file can be read by VMD.
>
> Branko - I've run this simulation in a cluster and in my local
> machine, with equivalent results.
>
> I will keep trying...
>
> Maria
>
>
> On 07/31/2012 03:14 PM, Aron Broom wrote:
>
> 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 <mailto: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
> <http://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 <http://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]
>
>
>
>
>
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>
>
>
>
> --
>
> 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 <http://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
>
>
>
> --
> Maria Antonieta Sanchez Farran
> Doctoral Candidate
> Department of Chemical Engineering
> The Pennsylvania State University
-- Maria Antonieta Sanchez Farran Doctoral Candidate Department of Chemical Engineering The Pennsylvania State University
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