From: Maria Antonieta Sanchez Farran (mfarran_at_engr.psu.edu)
Date: Tue Jul 31 2012 - 14:52:10 CDT
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]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 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
>>>
>>>
>>> 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
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