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
<[email protected]> 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 <[email protected]> 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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users mailing list [email protected]
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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
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list [email protected]
https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list [email protected]
https://lists.quantum-espresso.org/mailman/listinfo/users
