<div dir="ltr"><div>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:<br></div><div>- there is no guarantee that a batch queuing system will distribute processes across processors in the same way as in the previous run;</div><div>- pseudopotential files are in principle read from data file so they may still be a source of problems;<br></div><div>- 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.</div><div><br></div><div>Paolo<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 20, 2020 at 4:54 PM alberto <<a href="mailto:voodoo.bender@gmail.com">voodoo.bender@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">Hi, <br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">I'm using QE in some single point simulations. <br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">In particular I'm running scf/nscf calculations <br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">In my block input <br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">calculation = 'nscf' ,<br> restart_mode = 'from_scratch' ,<br> outdir = './tmp_qe' ,<br> pseudo_dir = '/home/alberto/QUANTUM_ESPRESSO/BASIS/upf_files/' ,<br> prefix = 'BIS-IMID-PbI4_SR' ,<br> verbosity = 'high' ,<br> etot_conv_thr = 1.0D-8 ,<br> forc_conv_thr = 1.0D-7 ,<br> wf_collect = .true.</div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">the out dir is located in /home/alberto/ and I notice that the writing/reading time is very long</div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">I would use /tmp dir of one node where the jobs is running.</div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">(my cluster has got some nodes xeon to 20 CPU every nodes)</div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">This is my PBS script</div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small">## Script for parallel Quantum Espresso job by Alberto<br>## Run script with 3 arguments:<br>## $1 = Name of input-file, without extension<br>## $2 = Numbers of nodes to use (ncpus=nodes*20)<br>## $3 = Module to run<br><br>if [ -z "$1" -o -z "$2" -o -z "$3" ]; then<br> echo "Usage: $0 <input_file> <np> <module> "<br>fi<br><br>if [ $2 -ge 8 ]; then<br> NODES=$(($2/20))<br> CPUS=20<br>else<br> NODES=1<br> CPUS=$2<br>fi<br><br>cat<<EOF>$1.job<br>#!/bin/bash<br>#PBS -l nodes=xeon1:ppn=$CPUS:xeon20+xeon2:ppn=$CPUS:xeon20+xeon3:ppn=$CPUS:xeon20+xeon4:ppn=$CPUS:xeon20+xeon5:ppn=$CPUS:xeon20+xeon6:ppn=$CPUS:xeon20<br>#PBS -l walltime=9999:00:00<br>#PBS -N $1<br>#PBS -e $1.err<br>#PBS -o $1.sum<br>#PBS -j oe<br>job=$1 # Name of input file, no extension<br>project=\$PBS_O_WORKDIR<br>cd \$project<br>cat \$PBS_NODEFILE > \$PBS_O_WORKDIR/nodes.txt <br><br>export OMP_NUM_THREADS=$(($2/40))<br>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<br>EOF<br><br>qsub $1.job</div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><br></div><div class="gmail_default" style="font-family:courier new,monospace;font-size:small"><div><div><span lang="en"><span title="">how could I use the directory /tmp and avoid that the nscf calculation don't stop it because no files are found! </span><span lang="en"><span title="">really the files are present, but they are divided on different nodes</span></span><br><br><span title="">regards</span></span></div><div><br></div><div>Alberto<br></div><div><span lang="en"><span title=""></span></span><span></span></div></div></div></div>
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