From: Albert (mailmd2011_at_gmail.com)
Date: Sat Mar 17 2012 - 14:33:19 CDT
Dear:
I am submitting NAMD jobs in IBM blue gene cluster by command:
qqsubmit namd.ll
here is the scripts:
# @ job_name = namd_test
# @ class = kdm
# @ error = namd.err
# @ output = namd.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 00:20:00
# @ notification = error
# @ notify_user = $(user)@icm.edu.pl
# @ job_type = bluegene
# @ bg_size = 64
# @ bg_connection = MESH
# @ queue
mpirun -exe /opt/namd/namd2 -mode VN -args "equilibration.inp" -np 256
and here is my input file:
structure ../step5_assembly.xplor.psf
coordinates ../step5_assembly.pdb
set temp 310;
set outputname step6.1_equilibration;
# read system values written by CHARMM (need to convert uppercases to
lowercases)
exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/
= //g" > step5_assembly.namd.str
source step5_assembly.namd.str
temperature $temp;
outputName step6.1_equilibration; # base name for output from
this run
# NAMD writes two files at the
end, final coord and vel
# in the format of
first-dyn.coor and first-dyn.vel
firsttimestep 0; # last step of previous run
restartfreq 500; # 500 steps = every 1ps
dcdfreq 1000;
dcdUnitCell yes; # the file will contain unit cell
info in the style of
# charmm dcd files. if yes, the
dcd files will contain
# unit cell information in the
style of charmm DCD files.
xstFreq 1000; # XSTFreq: control how often the
extended systen configuration
# will be appended to the XST file
outputEnergies 125; # 125 steps = every 0.25ps
# The number of timesteps
between each energy output of NAMD
outputTiming 1000; # The number of timesteps between
each timing output shows
# time per step and time to
completion
# Force-Field Parameters
paraTypeCharmm on; # We're using charmm type
parameter file(s)
# multiple definitions may be
used but only one file per definition
exec mkdir -p toppar
exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
./toppar/par_all22_prot.prm > toppar/par_all22_prot.prm
exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ../toppar/par_all27_na.prm
> toppar/par_all27_na.prm
exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
./toppar/par_all36_carb.prm > toppar/par_all36_carb.prm
exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
./toppar/par_all36_lipid.prm > toppar/par_all36_lipid.prm
exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g"
./toppar/par_all36_cgenff.prm > toppar/par_all36_cgenff.prm
exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \
-e "278,296d" -e "s/^BOM/!&/g" -e "s/^WRN/!&/g"
./toppar/toppar_water_ions.str > toppar/toppar_water_ions.str
exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \
-e "278,296d" -e "s/^BOM/!&/g" -e "s/^WRN/!&/g"
./toppar/toppar_all36_lipid_cholesterol.str >
toppar/toppar_all36_lipid_cholesterol.str
parameters toppar/par_all22_prot.prm;
parameters toppar/par_all27_na.prm;
parameters toppar/par_all36_carb.prm;
parameters toppar/par_all36_lipid.prm;
parameters toppar/par_all36_cgenff.prm;
parameters toppar/toppar_water_ions.str;
parameters toppar/toppar_all36_lipid_cholesterol.str;
# These are specified by CHARMM
exclude scaled1-4 # non-bonded exclusion policy to
use "none,1-2,1-3,1-4,or scaled1-4"
# 1-2: all atoms pairs that are
bonded are going to be ignored
# 1-3: 3 consecutively bonded
are excluded
# scaled1-4: include all the
1-3, and modified 1-4 interactions
# electrostatic scaled by
1-4scaling factor 1.0
# vdW special 1-4 parameters in
charmm parameter file.
1-4scaling 1.0
switching on
vdwForceSwitching yes; # New option for force-based
switching of vdW
# if both switching and
vdwForceSwitching are on CHARMM force
# switching is used for vdW forces.
seed 1332005110 # Specifies a specific seed
# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10.,
with PME
switchdist 10.0; # cutoff - 2.
# switchdist - where you start
to switch
# cutoff - where you stop
accounting for nonbond interactions.
# correspondence in charmm:
# (cutnb,ctofnb,ctonnb =
pairlistdist,cutoff,switchdist)
pairlistdist 16.0; # stores the all the pairs with
in the distance it should be larger
# than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
# cycle represents the number of
steps between atom reassignments
# this means every 20/2=10 steps
the pairlist will be updated
# Integrator Parameters
timestep 1.0; # fs/step
rigidBonds all; # Bound constraint all bonds
involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step
# Constant Temperature Control ONLY DURING EQUILB
reassignFreq 500; # reassignFreq: use this to
reassign velocity every 500 steps
reassignTemp $temp;
# Periodic Boundary conditions. Need this since for a start...
cellBasisVector1 $a 0.0 0.0; # vector to the next image
cellBasisVector2 0.0 $b 0.0;
cellBasisVector3 0.0 0.0 $c;
cellOrigin 0.0 0.0 $zcen; # the *center* of the cell
wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest off; # use for non-rectangular cells
(wrap to the nearest image)
# PME (for full-system periodic electrostatics)
exec python ../checkfft.py $a $b $c > checkfft.str
source checkfft.str
PME yes;
PMEInterpOrder 6; # interpolation order (spline
order 6 in charmm)
PMEGridSizeX $fftx; # should be close to the cell size
PMEGridSizeY $ffty; # corresponds to the charmm input
fftx/y/z
PMEGridSizeZ $fftz;
# Pressure and volume control
useGroupPressure yes; # use a hydrogen-group based
pseudo-molecular viral to calcualte pressure and
# has less fluctuation, is
needed for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell yes; # yes for anisotropic system like
membrane
useConstantRatio yes; # keeps the ratio of the unit
cell in the x-y plane constant A=B
langevin on
langevinDamping 10
langevinTemp $temp
langevinHydrogen no
# planar restraint
colvars on
exec sed -e "s/Constant \$fc/Constant 5/g" -e "s/\$bb/10.0/g" -e
"s/\$sc/5.0/g" membrane_lipid_restraint.namd.col >
restraints/$outputname.col
colvarsConfig restraints/$outputname.col
# dihedral restraint
extraBonds yes
exec sed -e "s/\$FC/500/g" restraints/dihe.txt > restraints/$outputname.dihe
extraBondsFile restraints/$outputname.dihe
minimize 10000
numsteps 90000000
run 25000
after I submitted the job, I've got the following error messages:
albert_at_notos:~/charmm-gui/namd> more namd.err
------------- Processor 0 Exiting: Called CmiAbort ------------
{snd:3262,rcv:0} Reason: FATAL ERROR: couldn't create pipe: function not
implemented
while executing
"exec tr "\[:upper:\]" "\[:lower:\]" <
/home/users/albert/charmm-gui/step5_assembly.str
| sed -e "s/ = //g" > step5_assembly.namd.str"
(file "step6.1_equilibration.inp" line 8)
namd2: machine.c:1022: CmiAbort: Assertion `0' failed.
<Mar 17 20:23:46.877519> BE_MPI (ERROR): The error message in the job
record is as follo
ws:
<Mar 17 20:23:46.877575> BE_MPI (ERROR): "killed with signal 6"
thank you very much
best wishes
ALBERT
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