Re: NAMD 2.9: Segmentation fault?

From: María Antonieta Sánchez Farrán (mfarran_at_engr.psu.edu)
Date: Tue Jul 31 2012 - 13:39:33 CDT

Hi Aaron,

Thanks again, here is a copy of my config file.

Maria

#########################################################################################################################
structure /gpfs/group/j/jmaranas/mas851/simulations/WATER_CORR/create-Iowa-AB40/1AML11_Iowa_withH_solv_ion.psf
coordinates /gpfs/group/j/jmaranas/mas851/simulations/WATER_CORR/create-Iowa-AB40/1AML11_Iowa_withH_solv_ion.pdb

outputName IowaAB40-rigid-pad20A-p1
set temperature 310
firsttimestep 0

# Input
paraTypeCharmm on
parameters /gpfs/group/j/jmaranas/mas851/simulations/WATER_CORR/create-Iowa-AB40/par_all27_prot_lipid.inp

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!

temperature $temperature

# Periodic Boundary conditions

# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!

cellBasisVector1 74.09 0. 0.
cellBasisVector2 0. 71.23 0.
cellBasisVector3 0. 0. 69.12
cellOrigin 30.94 0.78 1.03

wrapAll on

# Force-Field Parameters

exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 14.

# Integrator Parameters
timestep 1.0 ;
rigidBonds water
nonbondedFreq 2 ;
fullElectFrequency 4 ;
stepspercycle 20 ;

#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 80
PMEGridSizeY 75
PMEGridSizeZ 72

margin 5.0

# Constant Temperature Control
langevin on ;
langevinDamping 5 ;
langevinTemp $temperature
langevinHydrogen off ;

# Constant Pressure Control (variable volume)
useGroupPressure yes ;
useFlexibleCell no ;
useConstantArea no ;

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature

restartfreq 500 ;# 500steps = every .5ps
dcdfreq 500
xstFreq 500
outputEnergies 500
outputPressure 500

# Fixed Atoms Constraint (set PDB beta-column to 1)
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile /gpfs/group/j/jmaranas/mas851/simulations/WATER_CORR/create-Iowa-AB40/1AML11_Iowa_withH_solv_ion_fixed.pdb
fixedAtomsCol B

# Restrained atoms for initial heating-up steps
# Constrained atoms can still move, but only around a certain position.
constraints on
consRef /gpfs/group/j/jmaranas/mas851/simulations/WATER_CORR/create-Iowa-AB40/1AML11_Iowa_withH_solv_ion_constraints.pdb
consKFile /gpfs/group/j/jmaranas/mas851/simulations/WATER_CORR/create-Iowa-AB40/1AML11_Iowa_withH_solv_ion_constraints.pdb

consKCol B
###############################################################################################################################
EXECUTION
minimize 0

# turn off pressure control until later
langevinPiston off

# minimize nonbackbone atoms
minimize 3000 ;#

# min all atoms
#
fixedAtoms off
minimize 3000 ;#

# heat with Ps restrained
set temp 0;
while { $temp <= 310 } { ;#
langevinTemp $temp
run 12000 ;#
set temp [expr $temp + 10]
}

# equilibrate volume with Ps restrained
langevinPiston on
run 500000 ;#

The execution proceeds with minimization, heating, and equilibration but it doesn't go any dar

Maria

On 07/31/2012 02:17 PM, Aron Broom wrote:
> 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 <mailto: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 <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
>
>
>
>
> --
> 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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