Mercurial > repos > siwaa > stics4carsolel

annotate stics4carsolel.bash @ 2:5e581bfc5341 draft

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"planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit c44e3ffa39b80279cb3226522f2b4f95f737e061"
author siwaa
date Fri, 28 Jan 2022 13:09:49 +0000
parents bf2d7f74d5ba
children 6a77442a3598
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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};
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6 meteo_archive=${4};
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f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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7 sim_number=$(($(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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9 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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11 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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13 echo "expected simulations: ${sim_number}"
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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14 echo "cvle block size : ${b_size}"
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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5e581bfc5341 "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit c44e3ffa39b80279cb3226522f2b4f95f737e061"
siwaa
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16 if [ "$OMPI_COMM_WORLD_RANK" == "0" ]; then
5e581bfc5341 "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit c44e3ffa39b80279cb3226522f2b4f95f737e061"
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5e581bfc5341 "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit c44e3ffa39b80279cb3226522f2b4f95f737e061"
siwaa
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18 cp -r /data/vle-2001/pkgs/CarSolEl_data/data .
5e581bfc5341 "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit c44e3ffa39b80279cb3226522f2b4f95f737e061"
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19 rm -rf data/meteo
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20 cd data
5e581bfc5341 "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit c44e3ffa39b80279cb3226522f2b4f95f737e061"
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21 unzip ${meteo_archive}
5e581bfc5341 "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit c44e3ffa39b80279cb3226522f2b4f95f737e061"
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22 cd ..
5e581bfc5341 "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit c44e3ffa39b80279cb3226522f2b4f95f737e061"
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23 fi
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25 cvle -b $b_size -i ${2} -w work -P Stics4AgFlow -P CarSolEl_sim CarSolEl.vpz
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27 if [ "$OMPI_COMM_WORLD_RANK" == "0" ]; then
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
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29 ls work_*/*_byUsm.txt | \
bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
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30 xargs -t -i tail -n +2 {} | \
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31 sort -n -k 1 -t ';' > resWithoutHeader.csv
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33 head -1 work_0/1_byUsm.txt > header.cvs
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
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35 cat header.cvs resWithoutHeader.csv > res.csv
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37 mv res.csv ${3}
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bf2d7f74d5ba "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 8e31109ca8b9104e8f66b9bf56c08cd0bfc1136f"
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39 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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41 echo "Stics4AgGlob Job ending:"
f1070dc2446c "planemo upload for repository https://forgemia.inra.fr/record/carsolel/-/tree/master/tools commit 79ec610c8fada89b587b48d008738ec75770d40a"
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42 date;