Mercurial > repos > siwaa > stics4carsolel

annotate stics4carsolel.bash @ 1:bf2d7f74d5ba draft

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"planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
author siwaa
date Mon, 22 Nov 2021 15:15:08 +0000
parents f1070dc2446c
children 5e581bfc5341
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
siwaa
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1 echo "Stics4CarSolEl Job starting:"
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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2 date;
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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4 n_slots=${1};
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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5 csv_plan=${2};
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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6 sim_number=$(($(cat ${csv_plan} | wc -l) - 1));
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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8 b_size=1
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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10 echo "number of GALAXY_SLOTS: ${1}"
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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12 echo "expected simulations: ${sim_number}"
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
siwaa
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13 echo "cvle block size : ${b_size}"
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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15 cvle -b $b_size -i ${2} -w work -P Stics4AgFlow -P CarSolEl_sim CarSolEl.vpz
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
siwaa
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17 if [ "$OMPI_COMM_WORLD_RANK" == "0" ]; then
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
siwaa
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19 ls work_*/*_byUsm.txt | \
bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
siwaa
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20 xargs -t -i tail -n +2 {} | \
bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
siwaa
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21 sort -n -k 1 -t ';' > resWithoutHeader.csv
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
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23 head -1 work_0/1_byUsm.txt > header.cvs
bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
siwaa
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25 cat header.cvs resWithoutHeader.csv > res.csv
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
siwaa
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27 mv res.csv ${3}
bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
siwaa
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29 fi
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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31 echo "Stics4AgGlob Job ending:"
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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32 date;