From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jul 31 2012 - 13:17:38 CDT
Hmmm, still it looks like the file isn't being found, can you paste your
namd config file?
On Tue, Jul 31, 2012 at 2:13 PM, María Antonieta Sánchez Farrán <
mfarran_at_engr.psu.edu> wrote:
> 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> 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]
>>
>>
>>
>
>
> --
> 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
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:20 CST