Benchmark / test report

Container name: Singularity.AutoDock-Vina-1.2.3-foss-2021b.localimage.sif

test script

#!/bin/bash
#SBATCH -N 1
#SBATCH --ntasks-per-node=12

#SBATCH -J plcr-autodockvina-cpu-test

PLCR=${PLCR:-/net/pr2/projects/plgrid/plggsoftware/containers}
CONT=${1:-Singularity.AutoDock-Vina-1.2.3-foss-2021b.localimage.sif}

echo "PLCR test: $SLURM_JOB_NAME"
echo "PLCR jobid: $SLURM_JOBID"
echo "PLCR path: $PLCR"

echo "Test performed on: "`date`
echo "Testing container: $CONT"
SHA=`dd bs=1M if=$PLCR/images/$CONT 2>/dev/null | sha256sum | cut -d' ' -f1`
echo "Container checksum: $SHA"

cd $TMPDIR

wget -q https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.2.3.tar.gz
tar xf v1.2.3.tar.gz
cd AutoDock-Vina-1.2.3/example/python_scripting

time singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT python first_example.py
RC=$?
echo  "Test completed, rc=$RC"
rm -rf $TMPDIR

test results

PLCR test: plcr-autodockvina-cpu-test
PLCR jobid: 383861
PLCR path: /net/pr2/projects/plgrid/plggsoftware/containers
Test performed on: Mon May 2 13:27:33 CEST 2022
Testing container: Singularity.AutoDock-Vina-1.2.3-foss-2021b.localimage.sif
Container checksum: 6da6a2a9a23eb9a1b70545bdf1f381a7de2c59026feedc9504156f1f679caa54
Computing Vina grid ... done.
Performing local search ... done.
WARNING: At low exhaustiveness, it may be impossible to utilize all CPUs.
Performing docking (random seed: -917586000) ... 
0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
Score before minimization: -12.513 (kcal/mol)
Score after minimization : -13.249 (kcal/mol)

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1       -12.78          0          0
   2        -10.8      1.099      1.823
   3       -10.76      3.012      12.43
   4       -10.65       3.74      12.21
   5        -10.2      2.581      12.59
   6       -9.063      2.475      12.72
   7       -8.939      1.587      2.662
   8       -8.639      2.843      12.66
   9        -8.43      3.937      12.61
  10       -8.163      3.535      12.22
  11       -8.012      4.069       6.57
  12       -8.011      1.757      13.58
  13       -7.915      3.796      12.74
  14       -7.786      2.308      4.048
  15       -7.538       6.93      10.58
  16       -7.459      3.041      6.024
  17         -7.4       4.66      8.777
  18       -7.244      3.994      8.408
  19       -7.206      1.908      4.287
  20       -7.115      7.521      11.93

real    0m41.228s
user    6m43.380s
sys     0m1.045s
Test completed, rc=0