Same timestep for my simulation run is coming more than once and in random order in the log file

From: Chandni Tiwari (chandni.tiwari_at_monash.edu)
Date: Sun Aug 04 2019 - 09:25:36 CDT

Hi,

I am running first time on cluster, and I am supposed to run my simulation
with Charm FF, I am not sure if any of these have in-built charm ff in them?
*1. namd/2.12-ibverbs-smp-cuda *
*2. namd/2.12-multicore *
*3. namd/2.13-multicore-CUDA*

because these are the only versions present in the cluster I am using and
the log file for equilibration says "Charm++: standalone mode (*not using
charmrun*)" in the very begining itself.

Also, the second question is that the timesteps are repeating and coming in
random order in the log.
*The repeating order Ex.: (almost 45 times I see 1 timestep, which is
making my log files extremely big, more than 2 GB and it has not even
finished 100 ps)*

MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM 8.17296e+08 TO 817296
PRESSURE: 5 26288.6 57.9138 869.996 133.866 23880.6 -190.926 812.731
134.708 25296.5
GPRESSURE: 5 -6778.38 -429.12 792.803 -519.152 -9685.29 -117.788 823.406
234.272 -8617.49
ENERGY: 5 848.2463 3025.0597 2663.2808 229.0093
       -488991.0370 94130.7443 0.0000 0.0000
0.0000 -388094.6967 0.0000 -388094.6967 -388094.6967
    0.0000 25155.2325 -8360.3879 1660638.7597 25155.2325
    -8360.3879

MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM 8.17296e+08 TO 817296
PRESSURE: 5 26288.6 57.9136 869.996 133.866 23880.6 -190.926 812.731
134.708 25296.5
GPRESSURE: 5 -6778.38 -429.12 792.803 -519.152 -9685.29 -117.787 823.406
234.272 -8617.49
ENERGY: 5 848.2463 3025.0597 2663.2808 229.0093
       -488991.0373 94130.7443 0.0000 0.0000
0.0000 -388094.6970 0.0000 -388094.6970 -388094.6970
    0.0000 25155.2325 -8360.3879 1660638.7597 25155.2325
    -8360.3879

MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM 8.17296e+08 TO 817296
PRESSURE: 5 26288.6 57.9138 869.996 133.866 23880.6 -190.926 812.731
134.708 25296.5
GPRESSURE: 5 -6778.38 -429.12 792.803 -519.152 -9685.29 -117.788 823.406
234.272 -8617.49
ENERGY: 5 848.2463 3025.0597 2663.2808 229.0093
       -488991.0370 94130.7443 0.0000 0.0000
0.0000 -388094.6967 0.0000 -388094.6967 -388094.6967
    0.0000 25155.2325 -8360.3879 1660638.7597 25155.2325
    -8360.3879

MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM 8.17296e+08 TO 817296
PRESSURE: 5 26288.6 57.9136 869.996 133.866 23880.6 -190.926 812.731
134.708 25296.5
GPRESSURE: 5 -6778.38 -429.12 792.803 -519.152 -9685.29 -117.787 823.406
234.272 -8617.49
ENERGY: 5 848.2463 3025.0597 2663.2808 229.0093
       -488991.0373 94130.7443 0.0000 0.0000
0.0000 -388094.6970 0.0000 -388094.6970 -388094.6970
    0.0000 25155.2325 -8360.3879 1660638.7597 25155.2325
    -8360.3879

*My slurm script: *

#!/bin/bash
#SBATCH --job-name=peptide
#SBATCH --account=abcd
#SBATCH --time=96:00:00
#SBATCH --ntasks=48
#SBATCH --ntasks-per-node=12
#SBATCH --cpus-per-task=1
#SBATCH --partition=m3i
#SBATCH --mem-per-cpu=4000
#SBATCH --output=wt3.6_output-%j.out
#SBATCH --error=wt3.6_error-%j.err
module load namd/2.12-multicore
echo "program started"
srun namd2 relaxation.conf > relaxation1.log

*KIndly help.*
*Thankyou.*

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