From: María Antonieta Sánchez Farrán (mfarran_at_engr.psu.edu)
Date: Tue Jul 31 2012 - 13:47:05 CDT
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
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:52 CST