From: Richard Owczarzy (rowczarzy_at_idtdna.com)
Date: Mon Feb 01 2010 - 10:27:44 CST
Try to rename all copies of the file
FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt, so that the file does not
exist and NAMD cannot find it. You can keep renamed file in case you
need it.
The NAMD should create the correct file on startup if the file is not
present.
You should see the following output,
Info: Attempting to read FFTW data from
FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt
Richard
________________________________
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
Behalf Of Bala subramanian
Sent: Monday, February 01, 2010 3:12 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Info: Attempting to read FFTW data from
FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt
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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:55:23 CST