source: trunk/LMDZ.COMMON/libf/evolution/deftank/lib_launchPEM.sh @ 3516

Last change on this file since 3516 was 3516, checked in by jbclement, 7 days ago

PEM:
Small corrections related to r3498 (time step from integer to real) for the launching script + making a proper initilization of 'year_bp_ini' in case of there is no orbital evolution.
JBC

  • Property svn:executable set to *
File size: 13.8 KB
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1#!/bin/bash
2########################################################################
3######## Library of bash functions for the PEM launching script ########
4########################################################################
5
6# To end the launching script
7endlaunch() {
8    # Restore the previous value of LC_NUMERIC
9    LC_NUMERIC=$OLD_LC_NUMERIC
10
11    date
12    echo "Successful end of the launching script for the PEM simulation."
13    exit 0
14}
15
16# To end the launching script with error
17errlaunch() {
18    # Restore the previous value of LC_NUMERIC
19    LC_NUMERIC=$OLD_LC_NUMERIC
20
21    date
22    echo "End with error of the launching script for the PEM."
23    exit 1
24}
25
26# To check what is the job scheduler
27function job_scheduler() {
28    if command -v squeue &> /dev/null; then
29        echo "SLURM is installed on $machine."
30        name_job="#SBATCH --job-name="
31        kill_job="scancel"
32        submit_job="sbatch --parsable"
33        submit_dependjob="sbatch --parsable --dependency"
34    elif command -v qstat &> /dev/null; then
35        echo "PBS/TORQUE is installed on $machine."
36        name_job="#PBS -N "
37        kill_job="qdel"
38        submit_job="qsub"
39        submit_dependjob="qsub -W depend"
40    else
41        echo "Error: neither SLURM nor TORQUE/PBS is installed on $machine!"
42        echo "You need to adapt the script to your job scheduler."
43        errlaunch
44    fi
45}
46
47# To check if everything necessary for the launching script is ok
48checklaunch() {
49    # Save the current value of LC_NUMERIC and set it to a locale that uses a dot as the decimal separator
50    OLD_LC_NUMERIC=$LC_NUMERIC
51    LC_NUMERIC=en_US.UTF-8
52
53    if [ -v n_mars_years ] && [ ! -z "$n_mars_years" ]; then
54        if [ $(echo "$n_mars_years < 0." | bc -l) ]; then
55            echo "Error: the value of 'n_mars_years' must be >0!"
56            errlaunch
57        fi
58    elif [ -v n_earth_years ] && [ ! -z "$n_earth_years" ]; then
59        if [ $(echo "$n_earth_years < 0." | bc -l) ]; then
60            echo "Error: the value of 'n_earth_years' must be >0!"
61            errlaunch
62        fi
63    else
64        echo "Error: no number of years to be simulated has been set!"
65        errlaunch
66    fi
67    if [ $nPCM_ini -lt 2 ] || [ -z "$nPCM_ini" ]; then
68        echo "Error: the value of 'nPCM_ini' must be >1!"
69        errlaunch
70    fi
71    if [ $nPCM -lt 2 ] || [ -z "$nPCM" ]; then
72        echo "Error: the value of 'nPCM' must be >1!"
73        errlaunch
74    fi
75    if [ ! -f "PCMrun.job" ]; then
76        echo "Error: file \"PCMrun.job\" does not exist in $dir!"
77        errlaunch
78    fi
79    if [ ! -f "PEMrun.job" ]; then
80        echo "Error: file \"PEMrun.job\" does not exist in $dir!"
81        errlaunch
82    fi
83    if [ ! -f "run_PCM.def" ]; then
84        echo "Error: file \"run_PCM.def\" does not exist in $dir!"
85        errlaunch
86    fi
87    if [ ! -f "run_PEM.def" ]; then
88        echo "Error: file \"run_PEM.def\" does not exist in $dir!"
89        errlaunch
90    fi
91    if [ ! -f "context_lmdz_physics.xml" ]; then
92        echo "Error: file \"context_lmdz_physics.xml\" does not exist in $dir!"
93        errlaunch
94    fi
95    if [ ! -f "field_def_physics_mars.xml" ]; then
96        echo "Error: file \"field_def_physics_mars.xml\" does not exist in $dir!"
97        errlaunch
98    fi
99    if [ ! -f "file_def_physics_mars.xml" ]; then
100        echo "Error: file \"file_def_physics_mars.xml\" does not exist in $dir!"
101        errlaunch
102    fi
103    if [ ! -f "iodef.xml" ]; then
104        echo "Error: file \"iodef.xml\" does not exist in $dir!"
105        errlaunch
106    fi
107    if [ ! -d "out_PCM" ]; then
108        mkdir out_PCM
109    fi
110    if [ ! -d "out_PEM" ]; then
111        mkdir out_PEM
112    fi
113    if [ ! -d "starts" ]; then
114        mkdir starts
115    fi
116    if [ ! -d "diags" ]; then
117        mkdir diags
118    fi
119    if [ $mode -ne 0 ]; then
120        job_scheduler
121    fi
122}
123
124# To convert Earth years into Mars years
125convertyears() {
126    myear=686.9725      # Number of Earth days in Martian year
127    eyear=365.256363004 # Number of days in Earth year
128    convert_years=$(echo "$myear/$eyear" | bc -l)
129    convert_years=$(printf "%.4f" $convert_years) # Rounding to the 4th decimal to respect the precision of Martian year
130    if [ -v n_mars_years ]; then
131        n_myear=$n_mars_years
132        echo "Number of years to be simulated: $n_myear Martian years."
133    elif [ -v n_earth_years ]; then
134        n_myear=$(echo "$n_earth_years/$convert_years" | bc -l)
135        echo "Number of years to be simulated: $n_earth_years Earth years = $n_myear Martian years."
136    fi
137}
138
139# To initialize the launching script
140initlaunch() {
141    echo "This is a chained simulation for PEM and PCM runs in $dir on $machine by $user."
142    convertyears
143    i_myear=0.
144    iPEM=1
145    iPCM=1
146    cp startfi.nc starts/
147    if [ -f "start.nc" ]; then
148        cp start.nc starts/
149    elif [ -f "star1D.nc" ]; then
150        cp star1D.txt starts/
151    fi
152    if [ -f "startpem.nc" ]; then
153        cp startpem.nc starts/
154    fi
155
156    # Create a file to manage years of the chained simulation and store some info from the PEM runs
157    echo $i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini > info_PEM.txt
158}
159
160# To submit the PCM runs
161# arg1: launching mode
162# arg2: number of PCM runs to launch
163# arg3: local number of the PCM run from which to start (optional)
164submitPCM() {
165    find . -type f -name "PCMrun*.job" ! -name "PCMrun.job" -delete
166    ii=1
167    if [ ! -z $3 ]; then
168        ii=$3
169    fi
170    if [ $(echo "$i_myear < $n_myear" | bc -l) ]; then
171        echo "Run PCM $iPCM: call $ii/$2..."
172        if [ $1 -eq 0 ]; then # Mode: processing scripts
173            sed -i "s/^k=[0-9]\+$/k=$(echo "3 - $nPCM_ini" | bc)/" PCMrun.job
174            ./PCMrun.job
175            if [ $? -ne 0 ]; then
176                errlaunch
177            fi
178        else # Mode: submitting jobs
179            cp PCMrun.job PCMrun${iPCM}.job
180            sed -i -E "s/($name_job[^0-9]*[0-9]*[^0-9]*)[0-9]+$/\1${iPCM}/" PCMrun${iPCM}.job
181            sed -i "s/^k=[0-9]\+$/k=$(echo "3 - $nPCM_ini" | bc)/" PCMrun${iPCM}.job
182            jobID=$(eval "$submit_job PCMrun${iPCM}.job")
183            # Create a file to cancel the dependent jobs of the cycle
184            echo "#!/bin/bash" > kill_launchPEM.sh
185            chmod +x kill_launchPEM.sh
186            echo $kill_job $jobID >> kill_launchPEM.sh
187        fi
188        ((iPCM++))
189        i_myear = $(echo "$i_myear + 1." | bc - l)
190        ((ii++))
191    else
192        endlaunch
193    fi
194    for ((i = $ii; i <= $2; i++)); do
195        if [ $(echo "$i_myear < $n_myear" | bc -l) ]; then
196            echo "Run PCM $iPCM: call $i/$2..."
197            if [ $1 -eq 0 ]; then # Mode: processing scripts
198                sed -i "s/^k=[0-9]\+$/k=$(echo "$i + 2 - $nPCM_ini" | bc)/" PCMrun.job
199                ./PCMrun.job
200                if [ $? -ne 0 ]; then
201                    errlaunch
202                fi
203            else # Mode: submitting jobs
204                cp PCMrun.job PCMrun${iPCM}.job
205                sed -i -E "s/($name_job[^0-9]*[0-9]*[^0-9]*)[0-9]+$/\1${iPCM}/" PCMrun${iPCM}.job
206                sed -i "s/^k=[0-9]\+$/k=$(echo "$i + 2 - $nPCM_ini" | bc)/" PCMrun${iPCM}.job
207                jobID=$(eval "$submit_dependjob=afterok:${jobID} PCMrun${iPCM}.job")
208                echo $kill_job $jobID >> kill_launchPEM.sh
209            fi
210            ((iPCM++))
211            i_myear = $(echo "$i_myear + 1." | bc - l)
212        else
213            endlaunch
214        fi
215    done
216}
217
218# To submit the PEM run
219# arg1: launching mode
220submitPEM() {
221    if [ $(echo "$i_myear < $n_myear" | bc -l) ]; then
222        echo "Run PEM $iPEM"
223        if [ $1 -eq 0 ]; then # Mode: processing scripts
224            ./PEMrun.job
225            if [ $? -ne 0 ]; then
226                errlaunch
227            fi
228        else # Mode: submitting jobs
229            sed -i -E "s/($name_job[^0-9]*[0-9]*[^0-9]*)[0-9]+$/\1${iPEM}/" PEMrun.job
230            jobID=$(eval "$submit_job PEMrun.job")
231            # Create a file to cancel the dependent jobs of the cycle
232            echo "#!/bin/bash" > kill_launchPEM.sh
233            chmod +x kill_launchPEM.sh
234            echo $kill_job $jobID >> kill_launchPEM.sh
235        fi
236    else
237        endlaunch
238    fi
239}
240
241# To make one cycle of PCM and PEM runs
242# arg1: launching mode
243# arg2: number of PCM runs to launch
244# arg3: local number of the PCM run from which to start (optional)
245cyclelaunch() {
246    # PCM runs
247    submitPCM $1 $2 $3
248
249    # PEM run
250    if [ $(echo "$i_myear < $n_myear" | bc -l) ]; then
251        echo "Run PEM $iPEM"
252        if [ $1 -eq 0 ]; then # Mode: processing scripts
253            ./PEMrun.job
254            if [ $? -ne 0 ]; then
255                errlaunch
256            fi
257        else # Mode: submitting jobs
258            sed -i -E "s/($name_job[^0-9]*[0-9]*[^0-9]*)[0-9]+$/\1${iPEM}/" PEMrun.job
259            jobID=$(eval "$submit_dependjob=afterok:${jobID} PEMrun.job")
260            echo $kill_job $jobID >> kill_launchPEM.sh
261        fi
262    else
263        endlaunch
264    fi
265}
266
267# To clean files after the starting run of the relaunch
268# arg1: file name prefix to clean
269# arg2: file name extension to clean
270# arg3: file number from which to clean
271cleanfiles() {
272    prefix=$1
273    extension=$2
274    if [ -z "$extension" ]; then
275        for file in ${prefix}*; do
276            num=${file#$prefix}
277            if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then
278                rm $file
279            fi
280        done
281    else
282        for file in ${prefix}*${extension}; do
283            num=${file#$prefix}
284            num=${num%$extension}
285            if [[ $num =~ ^[0-9]+$ ]] && [ $num -gt $3 ]; then
286                rm $file
287            fi
288        done
289    fi
290}
291
292# To relaunch from PCM run
293# arg1: launching mode
294relaunchPCM() {
295    iPCM=$(($irelaunch + 1))
296    cleanfiles diags/diagfi .nc $irelaunch
297    cleanfiles diags/data2reshape .nc $irelaunch
298    cleanfiles "out_PCM/run" "" $irelaunch
299    cleanfiles starts/restart1D .txt $irelaunch
300    cleanfiles starts/restart .nc $irelaunch
301    cleanfiles starts/restartfi .nc $irelaunch
302    cp starts/restartfi${irelaunch}.nc startfi.nc
303    if [ -f "starts/restart${irelaunch}.nc" ]; then
304        cp starts/restart${irelaunch}.nc start.nc
305    elif [ -f "starts/restart1D${irelaunch}.txt" ]; then
306        cp starts/restart1D${irelaunch}.txt start1D.txt
307    fi
308    if [ $irelaunch -le $nPCM_ini ]; then
309        # PCM relaunch during the initialization cycle
310        iPEM=1
311        cleanfiles diags/diagpem .nc $iPEM
312        cleanfiles "out_PEM/run" "" $iPEM
313        cleanfiles starts/restart1D_postPEM .txt $iPEM
314        cleanfiles starts/restart_postPEM .nc $iPEM
315        cleanfiles starts/restartfi_postPEM .nc $iPEM
316        cleanfiles starts/restartpem .nc $iPEM
317        i_myear=$irelaunch
318        sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt
319        rm -f startpem.nc
320        if [ $irelaunch -eq $(($nPCM_ini - 1)) ]; then
321            cp diags/data2reshape${irelaunch}.nc data2reshape_Y1.nc
322            cyclelaunch $1 $nPCM_ini $iPCM
323        elif [ $irelaunch -eq $nPCM_ini ]; then
324            cp diags/data2reshape$(($irelaunch - 1)).nc data2reshape_Y1.nc
325            cp diags/data2reshape${irelaunch}.nc data2reshape_Y2.nc
326            submitPEM $1 # The next job is a PEM run
327        else
328            cyclelaunch $1 $nPCM_ini $iPCM
329        fi
330    else
331        # PCM relaunch during a cycle
332        iPEM=$(echo "($iPCM - $nPCM_ini)/$nPCM + 1" | bc)
333        il=$(echo "($irelaunch - $nPCM_ini + 1)%$nPCM + 1" | bc)
334        cleanfiles diags/diagpem .nc $iPEM
335        cleanfiles "out_PEM/run" "" $iPEM
336        cleanfiles starts/restart1D_postPEM .txt $iPEM
337        cleanfiles starts/restart_postPEM .nc $iPEM
338        cleanfiles starts/restartfi_postPEM .nc $iPEM
339        cleanfiles starts/restartpem .nc $iPEM
340        cp starts/restartpem${iPEM}.nc startpem.nc
341        if [ $il -eq $(($nPCM - 1)) ]; then # Second to last PCM run
342            i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $il))
343            sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt
344            cp diags/data2reshape${irelaunch}.nc data2reshape_Y1.nc
345            cyclelaunch $1 $nPCM $il
346        elif [ $il -eq $nPCM ]; then # Last PCM run so the next job is a PEM run
347            i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $nPCM))
348            sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt
349            cp diags/data2reshape$(($irelaunch - 1)).nc data2reshape_Y1.nc
350            cp diags/data2reshape${irelaunch}.nc data2reshape_Y2.nc
351            submitPEM $1
352        else
353            i_myear=$(($(awk "NR==$iPEM {print \$1}" "info_PEM.txt") + $il))
354            sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt
355            cyclelaunch $1 $nPCM $il
356        fi
357    fi
358}
359
360# To relaunch from PEM run
361# arg1: launching mode
362relaunchPEM() {
363    iPEM=$(echo "$irelaunch + 1" | bc)
364    iPCM=$(echo "$nPCM_ini + $nPCM*($irelaunch - 1) + 1" | bc)
365    i_myear=$(awk "NR==$(($iPEM + 1)) {print \$1}" "info_PEM.txt")
366    sed -i "1s/.*/$i_myear $n_myear $convert_years $iPCM $iPEM $nPCM $nPCM_ini/" info_PEM.txt
367    cleanfiles diags/diagfi .nc $(($iPCM - 1))
368    cleanfiles "out_PCM/run" "" $(($iPCM - 1))
369    cleanfiles starts/restart1D .txt $(($iPCM - 1))
370    cleanfiles starts/restart .nc $(($iPCM - 1))
371    cleanfiles starts/restartfi .nc $(($iPCM - 1))
372    cleanfiles diags/data2reshape .nc $(($iPCM - 1))
373    cleanfiles diags/diagpem .nc $irelaunch
374    cleanfiles "out_PEM/run" "" $irelaunch
375    cleanfiles starts/restart1D_postPEM .txt $irelaunch
376    cleanfiles starts/restart_postPEM .nc $irelaunch
377    cleanfiles starts/restartfi_postPEM .nc $irelaunch
378    cleanfiles starts/restartpem .nc $irelaunch
379    cp starts/restartpem${irelaunch}.nc startpem.nc
380    cp starts/restartfi_postPEM${irelaunch}.nc startfi.nc
381    if [ -f "starts/restart_postPEM${irelaunch}.nc" ]; then
382        cp starts/restart_postPEM${irelaunch}.nc start.nc
383    elif [ -f "starts/restart1D_postPEM${irelaunch}.txt" ]; then
384        cp starts/restart1D_postPEM${irelaunch}.txt start1D.txt
385    fi
386    cyclelaunch $1 $nPCM
387}
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