FFTW problem

From: Jyh-Shyong Ho (c00jsh00_at_nchc.org.tw)
Date: Wed Sep 27 2006 - 04:02:57 CDT

Hi, NAMD users,

I have a problem in running NAMD, with the attached input file test.namd,
I got the following log file:

The NAMD job begins at: Wed Sep 27 15:22:53 CST 2006
Info: NAMD 2.6b2 for Linux-amd64-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_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-amd64-gcc
Info: Built Mon Aug 21 11:27:15 CST 2006 by chem on fea01
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Info: 1 NAMD 2.6b2 Linux-amd64-MPI 4 cpa061 u30jas00
Info: Running on 4 processors.
Info: 29492 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is test.namd
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 100000
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 45 0 0
Info: PERIODIC CELL BASIS 2 0 45 0
Info: PERIODIC CELL BASIS 3 0 0 45
Info: PERIODIC CELL CENTER 0 0 0
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME 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 0
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME test.dcd
Info: DCD FREQUENCY 2500
Info: DCD FIRST STEP 2500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME test.out
Info: RESTART FILENAME test.rst
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 11.5
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 0.1
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 14.1
Info: ENERGY OUTPUT STEPS 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 379
Info: LANGEVIN DAMPING COEFFICIENT IS 10 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 379 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.312341
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 64 64 64
Info: Attempting to read FFTW data from FFTW_NAMD_2.6b2_Linux-amd64-MPI.txt
Info: Optimizing 6 FFT steps. 1... 2...The NAMD job completes at: Wed
Sep 27 15:23:00 CST 2006

The program stoped at this point without going further, and file
FFTW_NAMD_2.6b2_Linux-amd64-MPI.txt
cannot be found. Any one know what happened to the program?

Thank you for any hint.

Jyh-Shyong Ho, Ph.D.
Research Scientist
National Center for High Performance Computing
Hsinchu, Taiwan, ROC


# test speed in quntaum,high speed,si-qu simulation at 379 K

# protocol params
numsteps 100000

# Force Field
paratypecharmm on
parameters par_all27_prot_lipid.inp
exclude scaled1-4 # 1-2 and 1-3 interactions are excluded and 1-4 interactions are modified.
1-4scaling 1.0 # scaling factor for 1-4 interactions.

# Molecular System
coordinates banaLC.pdb
structure banaLC.psf
#bincoordinates banaLC_simu11.rst.coor
#binvelocities banaLC_simu11.rst.vel
#extendedsystem banaLC_simu11.rst.xsc

# Unit Cell and PBC
cellBasisVector1 45.0 0.0 0.0
cellBasisVector2 0.0 45.0 0.0
cellBasisVector3 0.0 0.0 45.0
cellOrigin 0.0 0.0 0.0

# Particle Mesh Edward Summation
#PME on
#PMEGridSizeX 64
#PMEGridSizeY 64
#PMEGridSizeZ 64

# approximations
switching on
switchdist 8
cutoff 10
pairlistdist 11.5
stepspercycle 10 # neighbour list updating frequency
margin 0.1 # An internal tuning parameter used in determining the size of cubes of space

# protocol
temperature 0
seed 78134
rigidBonds all # all X-H bonds are constrained
timestep 2.0
fullElectFrequency 2 # number of timesteps between each full electrostatics evaluation

langevin on
langevinDamping 10

langevinTemp 379.0

#reassignFreq 50
#reassignTemp 300.0
#reassignIncr 25.0
#reassignHold 300.0

#rescaleFreq 50
#rescaleTemp 300.0

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

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 379.0

# output
DCDunitcell on
wrapall on
outputname test.out # output PDB file
restartname test.rst
DCDfile test.dcd
restartfreq 1000
outputenergies 1000
outputtiming 1000
dcdfreq 2500
binaryoutput no
#imdon yes # interactive MD
#imdfreq 1 # timestep between sending coordinates
#imdport 3111 # free port number to expect a connection

# Particle Mesh Edward Summation
PME on
PMEGridSizeX 64
PMEGridSizeY 64
PMEGridSizeZ 64

# script
run 500000

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