[QE-users] Fwd: PBS script and tmp stogage

[alberto]

---------- Forwarded message ---------
Da: alberto <voodoo.bender at gmail.com>
Date: gio 20 feb 2020 04:54 PM
Subject: PBS script and tmp stogage
To: <users at lists.quantum-espresso.org>


Hi,
I'm using QE in some single point simulations.
In particular I'm running scf/nscf calculations

In my block input

calculation = 'nscf' ,
                restart_mode = 'from_scratch' ,
                      outdir = './tmp_qe' ,
                  pseudo_dir =
'/home/alberto/QUANTUM_ESPRESSO/BASIS/upf_files/' ,
                      prefix = 'BIS-IMID-PbI4_SR' ,
                   verbosity = 'high' ,
               etot_conv_thr = 1.0D-8 ,
               forc_conv_thr = 1.0D-7 ,
                  wf_collect = .true.

the out dir is located in /home/alberto/ and I notice that the
writing/reading time is very long

I would use /tmp dir of one node where the jobs is running.
(my cluster has got some nodes xeon to 20 CPU every nodes)

This is my PBS script

## Script for parallel Quantum Espresso job by Alberto
## Run script with 3 arguments:
## $1 = Name of input-file, without extension
## $2 = Numbers of nodes to use (ncpus=nodes*20)
## $3 = Module to run

if [ -z "$1" -o -z "$2" -o -z "$3" ]; then
echo "Usage: $0 <input_file> <np> <module> "
fi

if [ $2 -ge 8 ]; then
NODES=$(($2/20))
CPUS=20
else
NODES=1
CPUS=$2
fi

cat<<EOF>$1.job
#!/bin/bash
#PBS -l
nodes=xeon1:ppn=$CPUS:xeon20+xeon2:ppn=$CPUS:xeon20+xeon3:ppn=$CPUS:xeon20+xeon4:ppn=$CPUS:xeon20+xeon5:ppn=$CPUS:xeon20+xeon6:ppn=$CPUS:xeon20
#PBS -l walltime=9999:00:00
#PBS -N $1
#PBS -e $1.err
#PBS -o $1.sum
#PBS -j oe
job=$1      # Name of input file, no extension
project=\$PBS_O_WORKDIR
cd \$project
cat \$PBS_NODEFILE > \$PBS_O_WORKDIR/nodes.txt

export OMP_NUM_THREADS=$(($2/40))
time /opt/openmpi-1.4.5/bin/mpirun -machinefile \$PBS_NODEFILE -np $2
/opt/qe-6.4.1/bin/$3 -ntg $(($2/60)) -npool $(($2/60)) < $1.inp > $1.out
EOF

qsub $1.job

how could I use the directory /tmp and avoid that the nscf calculation
don't stop it because no files are found! really the files are present, but
they are divided on different nodes

regards

Alberto
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