dev
Last change
on this file since d9afe04 was
d9afe04,
checked in by Anne Tipka <anne.tipka@…>, 19 months ago
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corrected setting up module environment in shell script templates
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-
Property mode set to
100644
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File size:
1.6 KB
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Rev | Line | |
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[17dc83a] | 1 | #!/bin/bash |
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[373b74e] | 2 | |
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| 3 | # ON ECS or HPC: |
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| 4 | # start with ecaccess-job-submit -queueName <QUEUE_NAME> <NAME_OF_THIS_FILE> on gateway server |
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[d9afe04] | 5 | # start with sbatch <NAME_OF_THIS_FILE> directly on machine |
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[373b74e] | 6 | |
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[17dc83a] | 7 | #SBATCH --chdir=/scratch/$username |
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[373b74e] | 8 | #SBATCH --qos=el |
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| 9 | #SBATCH --job-name=flex_extract |
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| 10 | #SBATCH --output=flex_extract.%j.out |
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[17dc83a] | 11 | #SBATCH --error=flex_extract.%j.out |
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[373b74e] | 12 | #SBATCH --mail-type=FAIL |
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[d9afe04] | 13 | #SBATCH --mail-user=$username |
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[373b74e] | 14 | #SBATCH --time=24:00:00 |
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| 15 | ## job output is in .ecaccess_DO_NOT_REMOVE |
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| 16 | |
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| 17 | set -x |
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| 18 | export VERSION=$version_number |
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| 19 | case $$$${EC_CLUSTER} in |
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| 20 | *ecs*) |
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[d9afe04] | 21 | module purge |
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| 22 | module load prgenv/gnu gcc/8.4.1 |
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[373b74e] | 23 | module load python3 |
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| 24 | module load ecmwf-toolbox |
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| 25 | module load ecaccess |
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| 26 | export PATH=$$$${PATH}:$fp_root_path |
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| 27 | ;; |
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| 28 | *hpc*) |
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[d9afe04] | 29 | module purge |
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| 30 | module load prgenv/gnu gcc/8.4.1 |
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[373b74e] | 31 | module load python3 |
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| 32 | module load ecmwf-toolbox |
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| 33 | module load ecaccess |
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| 34 | export SCRATCH=$$$${TMPDIR} |
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| 35 | export PATH=$$$${PATH}:$fp_root_path |
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| 36 | ;; |
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| 37 | esac |
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| 38 | |
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| 39 | cd $$$${SCRATCH} |
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| 40 | mkdir -p extract$$$$$$$$ |
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| 41 | cd extract$$$$$$$$ |
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| 42 | |
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| 43 | export CONTROL=CONTROL |
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| 44 | |
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| 45 | cat >$$$${CONTROL}<<EOF |
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| 46 | $$control_content |
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| 47 | EOF |
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| 48 | |
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| 49 | |
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| 50 | submit.py --controlfile=$$$${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1 |
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| 51 | |
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| 52 | if [ $? -eq 0 ] ; then |
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| 53 | l=0 |
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| 54 | for muser in `grep -i MAILOPS $$$${CONTROL}`; do |
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| 55 | if [ $$$${l} -gt 0 ] ; then |
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| 56 | mail -s flex.$$$${HOST}.$$$$$$$$ $$$${muser} <prot |
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[17dc83a] | 57 | sleep 1 |
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[373b74e] | 58 | fi |
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| 59 | l=$(($$$${l}+1)) |
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| 60 | done |
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| 61 | else |
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| 62 | l=0 |
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| 63 | for muser in `grep -i MAILFAIL $$$${CONTROL}`; do |
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| 64 | if [ $$$${l} -gt 0 ] ; then |
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| 65 | mail -s "ERROR! flex.$$$${HOST}.$$$$$$$$" $$$${muser} <prot |
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[17dc83a] | 66 | sleep 1 |
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[373b74e] | 67 | fi |
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| 68 | l=$(($$$${l}+1)) |
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| 69 | done |
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| 70 | fi |
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| 71 | |
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