[QE-users] PBS script and tmp stogage

[Paolo Giannozzi]

It's a long story. By default, recent versions of QE collect both the
wavefunctions and the charge density into a single array on a single
processor that writes them to file. Even if you do not have a parallel file
system, your data is no longer spread on scratch directories that are not
visible to the other processors. This means that in principle it is
possible to restart, witj several potential caveats:
- there is no guarantee that a batch queuing system will distribute
processes across processors in the same way as in the previous run;
- pseudopotential files are in principle read from data file so they may
still be a source of problems;
- if you parallelize on k-points, with Nk pools, one process per pool will
write wavefunctions, that will thus end up on Nk different processors.

Paolo

On Thu, Feb 20, 2020 at 4:54 PM alberto <voodoo.bender at gmail.com> wrote:

> 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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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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