[QE-users] PBS script and tmp stogage

[janardhan H.L.]

 Dear prof. Giannozzi
I am writing to the same thread as it may be relevant  here.
I am using qe 6.5 on  3 node linux cluster.When the calculation is performed everything runs normally. When saving wf something unusual happens.1) calculation exits without time stamps and job done stamp2) this happened due to mpi exit from  one of the node which cannot write to out dir.3) scf run only starts after copying the files to slave nodes without which it will terminate saying files cannot be read.4) after pointing  outdir to common paths (via NFS).These errors  have disappeared. 
1) My question is if recent versions of QE is collecting all the wf to head node why slave nodes eco mpi abort while they have no access to head node.2) is there any way that we can restart calculations without copying to slave nodes.
Thanks and regards Janardhan 



    On Thursday, 20 February, 2020, 11:15:53 pm IST, Paolo Giannozzi <p.giannozzi at gmail.com> wrote:  
 
 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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