Problem in Running namd2

From: Sanjay H A (sanju_smg_at_lycos.com)
Date: Tue Nov 13 2007 - 01:23:09 CST

Hi ALL
I installed NAMD with Linux-i686-MPI
I downloaded all alanin input configuration files


Whwn I go for running with this command

/usr/local/mpich-1.2.6/ch_p4/bin/mpirun -np 2 -machinefile hosts namd2 alanin.namd

it segfaults with the fallowing messages

Info: NAMD 2.6 for Linux-i686-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd@ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for mpi-linux
Info: Built Mon Nov 12 13:23:56 IST 2007 by sanjay on garl-intel1.serc.iisc.ernet.in
Info: 1 NAMD 2.6 Linux-i686-MPI 2 garl-intel1.serc.iisc.ernet.in sanjay
Info: Running on 2 processors.
Info: 7964 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is alanin.namd
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 1000
Info: STEPS PER CYCLE 20
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: NO DCD TRAJECTORY OUTPUT
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME /tmp/alanin
Info: NO RESTART FILE
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 13.5
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 100
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED 12345
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB alanin.pdb
Info: STRUCTURE FILE alanin.psf
Info: PARAMETER file: XPLOR format! (default)
Info: PARAMETERS alanin.params
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 61 BONDS
Info: 179 ANGLES
Info: 38 DIHEDRAL
Info: 42 IMPROPER
Info: 0 CROSSTERM
Info: 21 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 66 ATOMS
Info: 65 BONDS
Info: 96 ANGLES
Info: 31 DIHEDRALS
Info: 32 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 195 DEGREES OF FREEDOM
Info: 55 HYDROGEN GROUPS
Info: TOTAL MASS = 783.886 amu
Info: TOTAL CHARGE = 8.19564e-08 e
Info: *****************************
Info: Entering startup phase 0 with 7964 kB of memory in use.
Info: Entering startup phase 1 with 7964 kB of memory in use.
Info: Entering startup phase 2 with 7964 kB of memory in use.
Info: Entering startup phase 3 with 7964 kB of memory in use.
Info: PATCH GRID IS 1 BY 1 BY 1
Info: REMOVING COM VELOCITY -1.37049 1.37438 -1.02066
Info: LARGEST PATCH (0) HAS 66 ATOMS
Info: CREATING 11 COMPUTE OBJECTS
Info: Entering startup phase 4 with 7964 kB of memory in use.
Info: Entering startup phase 5 with 7964 kB of memory in use.
Info: Entering startup phase 6 with 7964 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 7964 kB of memory in use.
Info: CREATING 11 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-21 AT 12.0805
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.04308e-13 AT 11.9138
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.69407e-21 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.09878e-16 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 3.95779e-32 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 1.92318e-13 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 2.46519e-32 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 3.73953e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 2.06795e-25 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 1.02505e-13 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-26 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 9.86822e-16 AT 11.9138
Info: Entering startup phase 8 with 7964 kB of memory in use.
Info: Finished startup with 7964 kB of memory in use.
Segmentation fault


Can I know the reason

Thanx in Advance
Sanjay


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