Re: question about repeating output text

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jun 09 2009 - 08:09:31 CDT

On Tue, 2009-06-09 at 06:58 -0400, ershela.durresi_at_yale.edu wrote:
> Dear all,
>

dear ershela,

>
> I am trying to run a simulation on NAMD and the simulation aborts almost
> immediately after I try to run it. In the output file I notice that the
> simulation parameter data keeps repeating (below is the part that keeps

this usually happens, if you launch a non-MPI program on multiple
processors via mpirun. from the output it looks as if you are
running the "charmrun" (= tcp or udp) version of (obsoltete) NAMD
version 2.5.

> repeating), which has not happened to me before. I tried to run another
> simulation of a similar size (only 40 atoms larger), and in that case I got the
> simulation to run. I would be extremely grateful if you could please offer any

please check the output, particularly the part about the NAMD version
and on how many processors it was run and compare it to this one.

cheers,
   axel.
> advice.
>
>
> Thank you so much,
> Ershela
>
> Info: Running on 1 processors.
> Info: 1333 kB of memory in use.
> Info: Running on 1 processors.
> Info: 1333 kB of memory in use.
> Measuring processor speeds... Done.
> TCL: Suspending until startup complete.
> TCL: Suspending until startup complete.
> Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
> Measuring processor speeds... Done.
> TCL: Suspending until startup complete.
> Info: Changed directory to .
> Info: Configuration file is Actin_ADF_run.namd
> Info: Changed directory to .
> Info: Configuration file is Actin_ADF_run.namd
> Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
> Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 1
> Info: NUMBER OF STEPS 5000000
> Info: STEPS PER CYCLE 16
> Info: PERIODIC CELL BASIS 1 113 0 0
> Info: PERIODIC CELL BASIS 2 0 115 0
> Info: PERIODIC CELL BASIS 3 0 0 111
> Info: PERIODIC CELL CENTER 0 0 0
> Info: LOAD BALANCE STRATEGY Other
> Info: LDB PERIOD 3200 steps
> Info: FIRST LDB TIMESTEP 80
> 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: VELOCITY FILE equil_out_T300.vel
> Info: CENTER OF MASS MOVING? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 1
> Info: DCD FILENAME 5000ps.dcd
> Info: DCD FREQUENCY 20000
> Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
> Info: XST FILENAME 5000ps.xst
> Info: XST FREQUENCY 20000
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME 5000ps
> Info: RESTART FILENAME ./res
> Info: RESTART FREQUENCY 100000
> Info: RESTART FILES WILL NOT BE OVERWRITTEN
> Info: BINARY RESTART FILES WILL BE USED
> Info: SWITCHING ACTIVE
> Info: SWITCHING ON 8
> Info: SWITCHING OFF 10
> Info: PAIRLIST DISTANCE 12
> 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 10
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 24.5
> Info: ENERGY OUTPUT STEPS 10000
> Info: MOMENTUM OUTPUT STEPS 10000
> Info: TIMING OUTPUT STEPS 10000
> Info: PRESSURE OUTPUT STEPS 10000
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 310
> Info: LANGEVIN DAMPING COEFFICIENT IS 1 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 310 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 113 116 112
> Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 1
> Info: NUMBER OF STEPS 5000000
> Info: STEPS PER CYCLE 16
> Info: PERIODIC CELL BASIS 1 113 0 0
> Info: PERIODIC CELL BASIS 2 0 115 0
> Info: PERIODIC CELL BASIS 3 0 0 111
> Info: PERIODIC CELL CENTER 0 0 0
> Info: LOAD BALANCE STRATEGY Other
> Info: LDB PERIOD 3200 steps
> Info: FIRST LDB TIMESTEP 80
> 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: VELOCITY FILE equil_out_T300.vel
> Info: CENTER OF MASS MOVING? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 1
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 1
> Info: NUMBER OF STEPS 5000000
> Info: STEPS PER CYCLE 16
> TCL: Suspending until startup complete.
> Info: DCD FILENAME 5000ps.dcd
> Info: DCD FREQUENCY 20000
> Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
> Info: XST FILENAME 5000ps.xst
> Info: XST FREQUENCY 20000
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME 5000ps
> Info: PERIODIC CELL BASIS 1 113 0 0
> Info: PERIODIC CELL BASIS 2 0 115 0
> Info: PERIODIC CELL BASIS 3 0 0 111
> Info: PERIODIC CELL CENTER 0 0 0
> Info: LOAD BALANCE STRATEGY Other
> Info: LDB PERIOD 3200 steps
> Info: FIRST LDB TIMESTEP 80
> Info: LDB BACKGROUND SCALING 1
> Info: HOM BACKGROUND SCALING 1
> Info: PME BACKGROUND SCALING 1
> Info: RESTART FILENAME ./res
> Info: RESTART FREQUENCY 100000
> Info: RESTART FILES WILL NOT BE OVERWRITTEN
> Info: BINARY RESTART FILES WILL BE USED
> 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: VELOCITY FILE equil_out_T300.vel
> Info: CENTER OF MASS MOVING? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: SWITCHING ACTIVE
> Info: SWITCHING ON 8
> Info: SWITCHING OFF 10
> Info: PAIRLIST DISTANCE 12
> Info: PAIRLIST SHRINK RATE 0.01
> Info: PAIRLIST GROW RATE 0.01
> Info: PAIRLIST TRIGGER 0.3
> Info: PAIRLISTS PER CYCLE 2
> Info: 1-4 SCALE FACTOR 1
> Info: DCD FILENAME 5000ps.dcd
> Info: DCD FREQUENCY 20000
> Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
> Info: PAIRLISTS ENABLED
> Info: MARGIN 10
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 24.5
> TCL: Suspending until startup complete.
> Info: XST FILENAME 5000ps.xst
> Info: XST FREQUENCY 20000
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME 5000ps
> Info: ENERGY OUTPUT STEPS 10000
> Info: MOMENTUM OUTPUT STEPS 10000
> Info: TIMING OUTPUT STEPS 10000
> Info: PRESSURE OUTPUT STEPS 10000
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 310
> Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> TCL: Suspending until startup complete.
> Info: RESTART FILENAME ./res
> Info: RESTART FREQUENCY 100000
> Info: RESTART FILES WILL NOT BE OVERWRITTEN
> Info: BINARY RESTART FILES WILL BE USED
> 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 310 K
> Info: PRESSURE CONTROL IS GROUP-BASED
> Info: INITIAL STRAIN RATE IS 0 0 0
> Charm++: standalone mode (not using charmrun)
> 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 113 116 112
> Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
> Info: SWITCHING ACTIVE
> Info: SWITCHING ON 8
> Info: SWITCHING OFF 10
> Info: PAIRLIST DISTANCE 12
> Info: PAIRLIST SHRINK RATE 0.01
> Info: PAIRLIST GROW RATE 0.01
> Info: PAIRLIST TRIGGER 0.3
> Info: PAIRLISTS PER CYCLE 2
> Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
> Info: PAIRLISTS ENABLED
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 1
> Info: NUMBER OF STEPS 5000000
> Info: STEPS PER CYCLE 16
> Info: MARGIN 10
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 24.5
> Info: ENERGY OUTPUT STEPS 10000
> Info: MOMENTUM OUTPUT STEPS 10000
> Info: TIMING OUTPUT STEPS 10000
> Info: PERIODIC CELL BASIS 1 113 0 0
> Info: PERIODIC CELL BASIS 2 0 115 0
> Info: PERIODIC CELL BASIS 3 0 0 111
> Info: PERIODIC CELL CENTER 0 0 0
> Info: LOAD BALANCE STRATEGY Other
> Info: LDB PERIOD 3200 steps
> Info: FIRST LDB TIMESTEP 80
> Info: LDB BACKGROUND SCALING 1
> Info: HOM BACKGROUND SCALING 1
> Info: PME BACKGROUND SCALING 1
> Info: PRESSURE OUTPUT STEPS 10000
> 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: VELOCITY FILE equil_out_T300.vel
> Info: CENTER OF MASS MOVING? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 1
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 310
> Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> Info: DCD FILENAME 5000ps.dcd
> Info: DCD FREQUENCY 20000
> Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
> Info: XST FILENAME 5000ps.xst
> Info: XST FREQUENCY 20000
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME 5000ps
> 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 310 K
> Info: PRESSURE CONTROL IS GROUP-BASED
> Info: INITIAL STRAIN RATE IS 0 0 0
> Info: RESTART FILENAME ./res
> Info: RESTART FREQUENCY 100000
> Info: RESTART FILES WILL NOT BE OVERWRITTEN
> Info: BINARY RESTART FILES WILL BE USED
> Info: SWITCHING ACTIVE
> Info: SWITCHING ON 8
> Info: SWITCHING OFF 10
> Info: PAIRLIST DISTANCE 12
> Info: PAIRLIST SHRINK RATE 0.01
> Info: PAIRLIST GROW RATE 0.01
> Info: PAIRLIST TRIGGER 0.3
> Info: PAIRLISTS PER CYCLE 2
> 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 113 116 112
> Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
> Info: PAIRLISTS ENABLED
> Info: MARGIN 10
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 24.5
> Info: ENERGY OUTPUT STEPS 10000
> Info: MOMENTUM OUTPUT STEPS 10000
> Info: TIMING OUTPUT STEPS 10000
> Info: PRESSURE OUTPUT STEPS 10000
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 310
> Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> Info: NAMD 2.5 for Linux-i686
> 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 Kale et al., J. Comp. Phys. 151:283-312 (1999)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 050612 for net-linux-icc
> Info: Built Fri Sep 26 17:33:59 CDT 2003 by jim on lisboa.ks.uiuc.edu
> Info: Sending usage information to NAMD developers via UDP. Sent data is:
> Charm++: standalone mode (not using charmrun)
> Info: NAMD 2.5 for Linux-i686
> 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 Kale et al., J. Comp. Phys. 151:283-312 (1999)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 050612 for net-linux-icc
> Info: Built Fri Sep 26 17:33:59 CDT 2003 by jim on lisboa.ks.uiuc.edu
> Info: Sending usage information to NAMD developers via UDP. Sent data is:
> 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 310 K
> Info: PRESSURE CONTROL IS GROUP-BASED
> Info: INITIAL STRAIN RATE IS 0 0 0
> Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
> Info: 1 NAMD 2.5 Linux-i686 1 ib072.bulldogj pd234
> Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
> Charm++: standalone mode (not using charmrun)
> Info: Running on 1 processors.
> Info: 1333 kB of memory in use.
> Info: 1 NAMD 2.5 Linux-i686 1 ib074.bulldogj pd234
> 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 113 116 112
> Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
> Measuring processor speeds... Done.
> Info: Running on 1 processors.
> Info: 1333 kB of memory in use.
> Info: EXTENDED SYSTEM FILE equil_out_T300.xsc
> Info: Changed directory to .
> Measuring processor speeds... Done.
> Info: NAMD 2.5 for Linux-i686
> Info:
>
>
>
>
>
>
>
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

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