From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Mon Feb 01 2010 - 03:12:04 CST
Friends,
I am a new to NAMD. I submitted a simulation with NAMD. The output file does
not show any error but the last line of it contains the message 'Info:
Attempting to read FFTW data from
FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt'. The job stops within seconds.
I have pasted below the complete output. Kindly write me what is going
wrong. The NAMD was not compilled from source but from a binary tarball
(NAMD_2.7b1_Linux-Itanium-MPI-Altix.tar.gz)
Charm++> Running on MPI version: 1.2 multi-thread support: MPI_THREAD_SINGLE
(max supported: MPI_THREAD_SINGLE)
Charm++> MPI timer is synchronized!
Charm warning> Randomization of stack pointer is turned on in Kernel, run
'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it. Thread
migration may not work!
Charm++> cpu topology info is being gathered!
Charm++> 1 unique compute nodes detected!
Info: NAMD 2.7b1 for Linux-Itanium-MPI-Altix
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 60100 for mpi-linux-ia64-mpt-iccstatic
Info: Built Mon Mar 23 02:51:35 CDT 2009 by jphillip on co-login
Info: 1 NAMD 2.7b1 Linux-Itanium-MPI-Altix 20 nirvana bala
Info: Running on 20 processors.
Info: Charm++/Converse parallel runtime startup completed at 0.0754943 s
Info: 18.2031 MB of memory in use based on sbrk
Info: Changed directory to ..
Info: Configuration file is pr1
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE /home1/bala/AGO_NODNA/PR1.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 500000
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 99.5074 0 0
Info: PERIODIC CELL BASIS 2 -33.1694 93.8175 0
Info: PERIODIC CELL BASIS 3 33.1694 46.9087 81.2484
Info: PERIODIC CELL CENTER 51.907 51.677 52.0055
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1Info: MAX PAIR PARTITIONS 8
Info: SELF PARTITION ATOMS 154
Info: SELF2 PARTITION ATOMS 154
Info: PAIR PARTITION ATOMS 318
Info: PAIR2 PARTITION ATOMS 637
Info: MIN ATOMS PER PATCH 100
Info: VELOCITY FILE /home1/bala/AGO_NODNA/PR1.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 0.833333
Info: DCD FILENAME /home1/bala/AGO_NODNA/PR2.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME /home1/bala/AGO_NODNA/PR2
Info: RESTART FILENAME /home1/bala/AGO_NODNA/rsrt
Info: RESTART FREQUENCY 500
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 14
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 2.5
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 19
Info: ENERGY OUTPUT STEPS 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 303
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT 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 303 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 4.28085e-05 4.28085e-05 4.28085e-05
Info: CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 108 108 108
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from
FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt
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