From: María Antonieta Sánchez Farrán (mfarran_at_engr.psu.edu)
Date: Tue Jul 31 2012 - 13:13:03 CDT
Hi Aron,
Thanks for your email. Yes, the path is correct. It will problems even
if I put it in the same folder. I forgot to mention that I can open the
pdb and psf files properly in VMD and everything looks okay.
Maria
On 07/31/2012 01:52 PM, Aron Broom wrote:
> this is a problem with the path to find the file I think. Maybe try
> explicitly stating the path in the config file (e.g. /home/file ). It
> might also be that the file format is wrong. I know I've seen this
> before when I had minor problems like those mentioned above.
>
> ~Aron
>
> On Tue, Jul 31, 2012 at 1:44 PM, María Antonieta Sánchez Farrán
> <mfarran_at_engr.psu.edu <mailto:mfarran_at_engr.psu.edu>> 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]
>
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
-- María Antonieta Sánchez Farrán Doctoral Candidate Department of Chemical Engineering The Pennsylvania State University
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