source: issm/trunk-jpl/jenkins/examples_tests.sh@ 25946

Last change on this file since 25946 was 25946, checked in by jdquinn, 4 years ago

BUG: Modifications to use gnu-sed on Pine Island under zsh
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1#!/bin/bash
2################################################################################
3# This script runs the examples tests (i.e. contents of examples directory,
4# which are implementations of the tutorials found at
5# https://issm.jpl.nasa.gov/documentation/tutorials/). It is intended to be
6# called from jenkins/jenkins.sh.
7#
8# runme files are modifed as needed to fill in statements that would otherwise
9# be added by user.
10#
11# NOTE:
12# - Indentation of replacement string literals (e.g. 'STEP_EIGHT') is set to
13# nest cleanly in this file, but will result in unclean nesting runme file
14# (which should not be an issue)
15# - Single-line string replacements in runme.m can effectively be performed
16# using sed. When performing multi-line replacements, perl is a better
17# option.
18#
19# TODO:
20# - Figure out how to remove \ and \n\ from multiline string variables while
21# preserving formatting when value is printed to file.
22################################################################################
23
24## Constants
25#
26RUNME_FILE='runme.m'
27RUN_EXAMPLE=0
28STATUS_HANDLING="\
29 disp('SUCCESS');\n\
30 catch me\n\
31 message=getReport(me);\n\
32 fprintf('%s',message);\n\
33 disp('FAILURE');\n\
34 end\n\
35 exit\n\
36"
37
38cd $ISSM_DIR/examples
39
40for dir in ./* ; do
41 if [ -d "${dir}" ]; then
42 # Some of the examples are incomplete (on purpose). As such, we will
43 # have to populate the missing steps in order to make sure that
44 # everything is working.
45
46 cd ${dir}
47
48 if [ "${dir}" == "./AMR" ]; then
49 sed -i.bak '1 s|^.*$|try\n\n&|' $RUNME_FILE
50 RUN_EXAMPLE=1
51 elif [ "${dir}" == "./Data" ]; then
52 echo 'Directory contains datasets only; no example to run.'
53 RUN_EXAMPLE=0
54 elif [ "${dir}" == "./EsaGRACE" ]; then
55 sed -i.bak 's|steps=\[1\];|steps=\[1:5\];\n\ntry\n|' $RUNME_FILE
56 RUN_EXAMPLE=1
57 elif [ "${dir}" == "./EsaWahr" ]; then
58 sed -i.bak 's|steps=\[1\];|steps=\[1:7\];\n\ntry\n|' $RUNME_FILE
59 RUN_EXAMPLE=1
60 elif [ "${dir}" == "./Functions" ]; then
61 echo "Directory contains functions only; no example to run."
62 RUN_EXAMPLE=0
63 elif [ "${dir}" == "./Greenland" ]; then
64 # STEP_SEVEN #{{{
65 STEP_SEVEN="\
66 if any(steps==7) %{{{\n\
67 disp(' Step 7: Historical Relaxation run');\n\
68 md = loadmodel('./Models/Greenland.Control_drag');\n\
69 \n\
70 load smbbox\n\
71 \n\
72 %convert mesh x,y into the Box projection\n\
73 [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71);\n\
74 [xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70);\n\
75 \n\
76 %Interpolate and set surface mass balance\n\
77 index = BamgTriangulate(x1(:),y1(:));\n\
78 smb_mo = InterpFromMeshToMesh2d(index,x1(:),y1(:),smbmean(:),xi,yi);\n\
79 smb = smb_mo*12/1000*md.materials.rho_freshwater/md.materials.rho_ice;\n\
80 md.smb.mass_balance = [smb;1 ];\n\
81 \n\
82 %Set transient options, run for 20 years, saving every 5 timesteps\n\
83 md.timestepping.time_step=0.2;\n\
84 md.timestepping.final_time=200;\n\
85 md.settings.output_frequency=5;\n\
86 \n\
87 %Additional options\n\
88 md.inversion.iscontrol=0;\n\
89 md.transient.requested_outputs={'IceVolume','TotalSmb', ...\n\
90 'SmbMassBalance'};\n\
91 md.verbose=verbose('solution',true,'module',true);\n\
92 \n\
93 %Go solve\n\
94 md.cluster=generic('name',oshostname,'np',2);\n\
95 md=solve(md,'Transient');\n\
96 \n\
97 save ./Models/Greenland.HistoricTransient_200yr md;\n\
98 end %}}}\n\
99 "
100 #}}}
101 # STEP_EIGHT #{{{
102 STEP_EIGHT="\
103 if any(steps==8) %{{{\n\
104 %Load historic transient model\n\
105 md=loadmodel('./Models/Greenland.HistoricTransient_200yr');\n\
106 \n\
107 %Create Line Plots of relaxation run. Create a figure.\n\
108 figure;\n\
109 \n\
110 %Save surface mass balance, by looping through 200 years (1000 steps)\n\
111 %Note, the first output will always contain output from time step 1\n\
112 surfmb=[];\n\
113 for i=2:201;\n\
114 surfmb=[surfmb md.results.TransientSolution(i).SmbMassBalance];\n\
115 end\n\
116 \n\
117 %Plot surface mass balance time series in first subplot\n\
118 subplot(3,1,1);\n\
119 plot([1:200],mean(surfmb));\n\
120 \n\
121 %Title this plot Mean surface mass balance\n\
122 title('Mean Surface mass balance');\n\
123 \n\
124 %Save velocity by looping through 200 years\n\
125 vel=[];\n\
126 for i=2:201;\n\
127 vel=[vel md.results.TransientSolution(i).Vel];\n\
128 end\n\
129 \n\
130 %Plot velocity time series in second subplot\n\
131 subplot(3,1,2);\n\
132 plot([1:200],mean(vel));\n\
133 \n\
134 %Title this plot Mean Velocity\n\
135 title('Mean Velocity');\n\
136 \n\
137 %Save Ice Volume by looping through 200 years\n\
138 volume=[];\n\
139 for i=2:201;\n\
140 volume=[volume md.results.TransientSolution(i).IceVolume];\n\
141 end\n\
142 \n\
143 %Plot volume time series in third subplot\n\
144 subplot(3,1,3);\n\
145 plot([1:200],volume);\n\
146 \n\
147 %Title this plot Mean Velocity and add an x label of years\n\
148 title('Ice Volume');\n\
149 xlabel('years');\n\
150 end %}}}\n\
151 "
152 #}}}
153 sed -i.bak 's|steps=\[1\];|steps=\[1:8\];\n\ntry\n|' $RUNME_FILE
154 perl -0755 -p -i -e "s|if any\(steps==7\).*% step 7 end|${STEP_SEVEN}|s" $RUNME_FILE
155 perl -0755 -p -i -e "s|if any\(steps==8\).*% step 8 end|${STEP_EIGHT}|s" $RUNME_FILE
156 RUN_EXAMPLE=1
157 elif [ "${dir}" == "./IceBridge" ]; then
158 sed -i.bak 's|steps=\[1\];|steps=\[1:5\];\n\ntry\n|' $RUNME_FILE
159 perl -0755 -p -i -e "s|\n\t%Mesh greenland without.*return;\n||s" $RUNME_FILE
160 RUN_EXAMPLE=1
161 elif [ "${dir}" == "./IceflowModels" ]; then
162 sed -i.bak '1 s|^.*$|try\n\n&|' $RUNME_FILE
163 RUN_EXAMPLE=1
164 elif [ "${dir}" == "./Inversion" ]; then
165 sed -i.bak 's|steps=\[1\];|steps=\[1:4\];\n\ntry\n|' $RUNME_FILE
166 RUN_EXAMPLE=1
167 elif [ "${dir}" == "./ISMIP" ]; then
168 # TODO:
169 # - Run test again with ISMIPF configuration (will likely need to
170 # add conditional after 'RUN_EXAMPLE -eq 1' block)
171 #
172 # RUNME #{{{
173 RUNME="\
174 try\n\
175 %which steps to perform; steps are from 1 to 8\n\
176 %step 7 is specific to ISMIPA\n\
177 %step 8 is specific to ISMIPF\n\
178 \n\
179 steps=[1:7]; %ISMIPA\n\
180 %steps=[1:6,8]; %ISMIPF\n\
181 \n\
182 % parameter file to be used, choose between IsmipA.par or IsmipF.par\n\
183 ParamFile='IsmipA.par';\n\
184 %ParamFile='IsmipF.par';\n\
185 \n\
186 %Run Steps\n\
187 \n\
188 %Mesh Generation #1\n\
189 if any(steps==1) %{{{\n\
190 %initialize md as a new model #help model\n\
191 %->\n\
192 md=model();\n\
193 % generate a squaremesh #help squaremesh\n\
194 % Side is 80 km long with 20 points\n\
195 %->\n\
196 if(ParamFile=='IsmipA.par'),\n\
197 md=squaremesh(md,80000,80000,20,20);\n\
198 elseif(ParamFile=='IsmipF.par'),\n\
199 md=squaremesh(md,100000,100000,30,30);\n\
200 end\n\
201 % plot the given mesh #plotdoc\n\
202 %->\n\
203 plotmodel(md,'data','mesh')\n\
204 % save the given model\n\
205 %->\n\
206 save ./Models/ISMIP.Mesh_generation md;\n\
207 end %}}}\n\
208 \n\
209 %Masks #2\n\
210 if any(steps==2) %{{{\n\
211 % load the preceding step #help loadmodel\n\
212 % path is given by the organizer with the name of the given step\n\
213 %->\n\
214 md = loadmodel('./Models/ISMIP.Mesh_generation');\n\
215 % set the mask #help setmask\n\
216 % all MISMIP nodes are grounded\n\
217 %->\n\
218 md=setmask(md,'','');\n\
219 % plot the given mask #md.mask to locate the field\n\
220 %->\n\
221 plotmodel(md,'data',md.mask.ocean_levelset);\n\
222 % save the given model\n\
223 %->\n\
224 save ./Models/ISMIP.SetMask md;\n\
225 end %}}}\n\
226 \n\
227 %Parameterization #3\n\
228 if any(steps==3) %{{{\n\
229 % load the preceding step #help loadmodel\n\
230 % path is given by the organizer with the name of the given step\n\
231 %->\n\
232 md = loadmodel('./Models/ISMIP.SetMask');\n\
233 % parametrize the model # help parameterize\n\
234 % you will need to fil-up the parameter file defined by the\n\
235 % ParamFile variable\n\
236 %->\n\
237 md=parameterize(md,ParamFile);\n\
238 % save the given model\n\
239 %->\n\
240 save ./Models/ISMIP.Parameterization md;\n\
241 end %}}}\n\
242 \n\
243 %Extrusion #4\n\
244 if any(steps==4) %{{{\n\
245 \n\
246 % load the preceding step #help loadmodel\n\
247 % path is given by the organizer with the name of the given step\n\
248 %->\n\
249 md = loadmodel('./Models/ISMIP.Parameterization');\n\
250 % vertically extrude the preceding mesh #help extrude\n\
251 % only 5 layers exponent 1\n\
252 %->\n\
253 md=extrude(md,9,1);\n\
254 % plot the 3D geometry #plotdoc\n\
255 %->\n\
256 plotmodel(md,'data',md.geometry.base)\n\
257 % save the given model\n\
258 %->\n\
259 save ./Models/ISMIP.Extrusion md;\n\
260 end %}}}\n\
261 \n\
262 %Set the flow computing method #5\n\
263 if any(steps==5) %{{{\n\
264 \n\
265 % load the preceding step #help loadmodel\n\
266 % path is given by the organizer with the name of the given step\n\
267 %->\n\
268 md = loadmodel('./Models/ISMIP.Extrusion');\n\
269 % set the approximation for the flow computation #help setflowequation\n\
270 % We will be using the Higher Order Model (HO)\n\
271 %->\n\
272 md=setflowequation(md,'HO','all');\n\
273 % save the given model\n\
274 %->\n\
275 save ./Models/ISMIP.SetFlow md;\n\
276 end %}}}\n\
277 \n\
278 %Set Boundary Conditions #6\n\
279 if any(steps==6) %{{{\n\
280 \n\
281 % load the preceding step #help loadmodel\n\
282 % path is given by the organizer with the name of the given step\n\
283 %->\n\
284 md = loadmodel('./Models/ISMIP.SetFlow');\n\
285 % dirichlet boundary condition are known as SPCs\n\
286 % ice frozen to the base, no velocity #md.stressbalance\n\
287 % SPCs are initialized at NaN one value per vertex\n\
288 %->\n\
289 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);\n\
290 %->\n\
291 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);\n\
292 %->\n\
293 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);\n\
294 % extract the nodenumbers at the base #md.mesh.vertexonbase\n\
295 %->\n\
296 basalnodes=find(md.mesh.vertexonbase);\n\
297 % set the sliding to zero on the bed\n\
298 %->\n\
299 md.stressbalance.spcvx(basalnodes)=0.0;\n\
300 %->\n\
301 md.stressbalance.spcvy(basalnodes)=0.0;\n\
302 % periodic boundaries have to be fixed on the sides\n\
303 % create tabs with the side of the domain\n\
304 % for x\n\
305 % create maxX #help find\n\
306 %->\n\
307 maxX=find(md.mesh.x==max(md.mesh.x));\n\
308 % create minX\n\
309 %->\n\
310 minX=find(md.mesh.x==min(md.mesh.x));\n\
311 % for y, max X and minX should be excluded\n\
312 % create maxY\n\
313 %->\n\
314 maxY=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=max(md.mesh.x) & md.mesh.x~=min(md.mesh.x));\n\
315 % create minY\n\
316 %->\n\
317 minY=find(md.mesh.y==min(md.mesh.y) & md.mesh.x~=max(md.mesh.x) & md.mesh.x~=min(md.mesh.x));\n\
318 % set the node that should be paired together\n\
319 % #md.stressbalance.vertex_pairing\n\
320 %->\n\
321 md.stressbalance.vertex_pairing=[minX,maxX;minY,maxY];\n\
322 if (ParamFile=='IsmipF.par')\n\
323 % if we are dealing with IsmipF the solution is in\n\
324 % masstransport\n\
325 md.masstransport.vertex_pairing=md.stressbalance.vertex_pairing;\n\
326 end\n\
327 % save the given model\n\
328 %->\n\
329 save ./Models/ISMIP.BoundaryCondition md;\n\
330 end %}}}\n\
331 \n\
332 %Solving #7\n\
333 if any(steps==7) %{{{\n\
334 % load the preceding step #help loadmodel\n\
335 % path is given by the organizer with the name of the given step\n\
336 %->\n\
337 md = loadmodel('./Models/ISMIP.BoundaryCondition');\n\
338 % Set cluster #md.cluster\n\
339 % generic parameters #help generic\n\
340 % set only the name and number of process\n\
341 %->\n\
342 md.cluster=generic('name',oshostname(),'np',2);\n\
343 % Set which control message you want to see #help verbose\n\
344 %->\n\
345 md.verbose=verbose('convergence',true);\n\
346 % Solve #help solve\n\
347 % we are solving a StressBalanc\n\
348 %->\n\
349 md=solve(md,'Stressbalance');\n\
350 % save the given model\n\
351 %->\n\
352 save ./Models/ISMIP.StressBalance md;\n\
353 % plot the surface velocities #plotdoc\n\
354 %->\n\
355 plotmodel(md,'data',md.results.StressbalanceSolution.Vel)\n\
356 end %}}}\n\
357 \n\
358 %Solving #8\n\
359 if any(steps==8) %{{{\n\
360 % load the preceding step #help loadmodel\n\
361 % path is given by the organizer with the name of the given step\n\
362 %->\n\
363 md = loadmodel('./Models/ISMIP.BoundaryCondition');\n\
364 % Set cluster #md.cluster\n\
365 % generic parameters #help generic\n\
366 % set only the name and number of process\n\
367 %->\n\
368 md.cluster=generic('name',oshostname(),'np',2);\n\
369 % Set which control message you want to see #help verbose\n\
370 %->\n\
371 md.verbose=verbose('convergence',true);\n\
372 % set the transient model to ignore the thermal model\n\
373 % #md.transient \n\
374 %->\n\
375 md.transient.isthermal=0;\n\
376 % define the timestepping scheme\n\
377 % everything here should be provided in years #md.timestepping\n\
378 % give the length of the time_step (4 years)\n\
379 %->\n\
380 md.timestepping.time_step=4;\n\
381 % give final_time (20*4 years time_steps)\n\
382 %->\n\
383 md.timestepping.final_time=4*20;\n\
384 % Solve #help solve\n\
385 % we are solving a TransientSolution\n\
386 %->\n\
387 md=solve(md,'Transient');\n\
388 % save the given model\n\
389 %->\n\
390 save ./Models/ISMIP.Transient md;\n\
391 % plot the surface velocities #plotdoc\n\
392 %->\n\
393 plotmodel(md,'data',md.results.TransientSolution(20).Vel)\n\
394 end %}}}\n\
395 "
396 #}}}
397 # PAR_A #{{{
398 PAR_A="\
399 %Parameterization for ISMIP A experiment\n\
400 \n\
401 %Set the Simulation generic name #md.miscellaneous\n\
402 %->\n\
403 \n\
404 %Geometry\n\
405 disp(' Constructing Geometry');\n\
406 \n\
407 %Define the geometry of the simulation #md.geometry\n\
408 %surface is [-x*tan(0.5*pi/180)] #md.mesh\n\
409 %->\n\
410 md.geometry.surface=-md.mesh.x*tan(0.5*pi/180.);\n\
411 %base is [surface-1000+500*sin(x*2*pi/L).*sin(y*2*pi/L)]\n\
412 %L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x)\n\
413 %->\n\
414 L=max(md.mesh.x)-min(md.mesh.x);\n\
415 md.geometry.base=md.geometry.surface-1000.0+500.0*sin(md.mesh.x*2.0*pi/L).*sin(md.mesh.y*2.0*pi/L);\n\
416 %thickness is the difference between surface and base #md.geometry\n\
417 %->\n\
418 md.geometry.thickness=md.geometry.surface-md.geometry.base;\n\
419 %plot the geometry to check it out\n\
420 %->\n\
421 plotmodel(md,'data',md.geometry.thickness);\n\
422 \n\
423 disp(' Defining friction parameters');\n\
424 \n\
425 %These parameters will not be used but need to be fixed #md.friction\n\
426 %one friciton coefficient per node (md.mesh.numberofvertices,1)\n\
427 %->\n\
428 md.friction.coefficient=200.0*ones(md.mesh.numberofvertices,1);\n\
429 %one friciton exponent (p,q) per element\n\
430 %->\n\
431 md.friction.p=ones(md.mesh.numberofelements,1);\n\
432 %->\n\
433 md.friction.q=ones(md.mesh.numberofelements,1);\n\
434 \n\
435 disp(' Construct ice rheological properties');\n\
436 \n\
437 %The rheology parameters sit in the material section #md.materials\n\
438 %B has one value per vertex\n\
439 %->\n\
440 md.materials.rheology_B=6.8067e7*ones(md.mesh.numberofvertices,1);\n\
441 %n has one value per element\n\
442 %->\n\
443 md.materials.rheology_n=3*ones(md.mesh.numberofelements,1);\n\
444 \n\
445 disp(' Set boundary conditions');\n\
446 \n\
447 %Set the default boundary conditions for an ice-sheet \n\
448 % #help SetIceSheetBC\n\
449 %->\n\
450 md=SetIceSheetBC(md);\n\
451 "
452 #}}}
453 # PAR_F #{{{
454 PAR_F="\
455 %Parameterization for ISMIP F experiment\n\
456 \n\
457 %Set the Simulation generic name #md.miscellaneous\n\
458 %->\n\
459 \n\
460 %Geometry\n\
461 disp(' Constructing Geometry');\n\
462 \n\
463 %Define the geometry of the simulation #md.geometry\n\
464 %surface is [-x*tan(3.0*pi/180)] #md.mesh\n\
465 %->\n\
466 md.geometry.surface=md.mesh.x*tan(3.0*pi/180.0);\n\
467 %base is [surface-1000+100*exp(-((x-L/2).^2+(y-L/2).^2)/(10000.^2))]\n\
468 %L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x)\n\
469 %->\n\
470 L=max(md.mesh.x)-min(md.mesh.x);\n\
471 %->\n\
472 md.geometry.base=md.geometry.surface-1000.0+100.0*exp(-((md.mesh.x-L/2.0).^2.0+(md.mesh.y-L/2.0).^2.0)/(10000.^2.0));\n\
473 %thickness is the difference between surface and base #md.geometry\n\
474 %->\n\
475 md.geometry.thickness=md.geometry.surface-md.geometry.base;\n\
476 %plot the geometry to check it out\n\
477 %->\n\
478 plotmodel(md,'data',md.geometry.thickness);\n\
479 \n\
480 disp(' Defining friction parameters');\n\
481 \n\
482 %These parameters will not be used but need to be fixed #md.friction\n\
483 %one friciton coefficient per node (md.mesh.numberofvertices,1)\n\
484 %conversion form year to seconds with #md.constants.yts\n\
485 %->\n\
486 md.friction.coefficient=sqrt(md.constants.yts/(1000*2.140373*10^-7))*ones(md.mesh.numberofvertices,1);\n\
487 %one friciton exponent (p,q) per element\n\
488 %->\n\
489 md.friction.p=ones(md.mesh.numberofelements,1);\n\
490 %->\n\
491 md.friction.q=zeros(md.mesh.numberofelements,1);\n\
492 \n\
493 disp(' Construct ice rheological properties');\n\
494 \n\
495 %The rheology parameters sit in the material section #md.materials\n\
496 %B has one value per vertex\n\
497 %->\n\
498 md.materials.rheology_B=(1/(2.140373*10^-7/md.constants.yts))*ones(md.mesh.numberofvertices,1);\n\
499 %n has one value per element\n\
500 %->\n\
501 md.materials.rheology_n=1*ones(md.mesh.numberofelements,1);\n\
502 \n\
503 disp(' Set boundary conditions');\n\
504 \n\
505 %Set the default boundary conditions for an ice-sheet \n\
506 % #help SetIceSheetBC\n\
507 %->\n\
508 md=SetIceSheetBC(md);\n\
509 \n\
510 disp(' Initializing velocity and pressure');\n\
511 \n\
512 %initialize the velocity and pressurefields of #md.initialization\n\
513 %->\n\
514 md.initialization.vx=zeros(md.mesh.numberofvertices,1);\n\
515 %->\n\
516 md.initialization.vy=zeros(md.mesh.numberofvertices,1);\n\
517 %->\n\
518 md.initialization.vz=zeros(md.mesh.numberofvertices,1);\n\
519 %->\n\
520 md.initialization.pressure=zeros(md.mesh.numberofvertices,1);\n\
521 "
522 #}}}
523 perl -0755 -p -i'.bak' -e "s|^.*$|${RUNME}|s" $RUNME_FILE
524 perl -0755 -p -i'.bak' -e "s|^.*$|${PAR_A}|s" IsmipA.par
525 perl -0755 -p -i'.bak' -e "s|^.*$|${PAR_F}|s" IsmipF.par
526 RUN_EXAMPLE=1
527 elif [ "${dir}" == "./Jakobshavn" ]; then
528 sed -i.bak 's|steps=\[1\];|steps=\[1:4\];\n\ntry\n|' $RUNME_FILE
529 RUN_EXAMPLE=1
530 elif [ "${dir}" == "./LcurveAnalysis" ]; then
531 sed -i.bak 's|steps=\[1\];|steps=\[1:4\];\n\ntry\n|' $RUNME_FILE
532 RUN_EXAMPLE=1
533 elif [ "${dir}" == "./Mesh" ]; then
534 # NOTE: Cannot test exptool region selection without GUI
535 sed -i.bak 's|steps=\[1\];|steps=\[1:7\];\n\ntry\n|' $RUNME_FILE
536 RUN_EXAMPLE=1
537 elif [ "${dir}" == "./Pig" ]; then
538 # STEP_SIX #{{{
539 STEP_SIX="\
540 if any(steps==6) %{{{\n\
541 % Load Model\n\
542 md = loadmodel('./Models/PIG_Control_drag');\n\
543 % Disable inversion\n\
544 md.inversion.iscontrol=0;\n\
545 % Extrude Mesh\n\
546 disp(' Extruding mesh');\n\
547 number_of_layers=3;\n\
548 md=extrude(md,number_of_layers,1);\n\
549 % Set Flowequation\n\
550 disp(' Using HO Ice Flow Model');\n\
551 md=setflowequation(md,'HO','all');\n\
552 % Solve\n\
553 md=solve(md,'Stressbalance');\n\
554 % Save Model\n\
555 save ./Models/PIG_ModelHO md;\n\
556 end %}}}\n\
557 "
558 #}}}
559 mv ./DomainOutline.bkp ./DomainOutline.exp > /dev/null 2>&1
560 sed -i.bak "s|steps=\[1\];|steps=\[1:7\];\ntry\n|" $RUNME_FILE
561 perl -0755 -p -i -e "s|if any\(steps==6\).*% step 6 end|${STEP_SIX}|s" $RUNME_FILE
562 RUN_EXAMPLE=1
563 elif [ "${dir}" == "./Pig2" ]; then
564 STEP_NINE="\n disp('Needs work!'); exit"
565 sed -i.bak 's|steps=\[1\];|steps=\[1:9\];\n\ntry\n|' $RUNME_FILE
566 perl -0755 -p -i -e "s|if any\(steps==9\).*% step 9 end|${STEP_NINE}|s" $RUNME_FILE
567 RUN_EXAMPLE=1
568 elif [ "${dir}" == "./PigSensitivity" ]; then
569 # STEP_FOUR # {{{
570 STEP_FOUR="\
571 if any(steps==4)\n\
572 %Load model\n\
573 md = loadmodel('./Models/PIG_Transient');\n\
574 \n\
575 %Change external forcing basal melting rate and surface mass balance)\n\
576 md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1);\n\
577 md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1);\n\
578 md.smb.mass_balance=2*md.smb.mass_balance;\n\
579 \n\
580 %Define time steps and time span of the simulation\n\
581 md.timestepping.time_step=0.1;\n\
582 md.timestepping.final_time=10;\n\
583 \n\
584 %Request additional outputs\n\
585 md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'};\n\
586 \n\
587 %Solve\n\
588 md=solve(md,'Transient');\n\
589 \n\
590 %Save model\n\
591 save ./Models/PIG_SMB md;\n\
592 end\n\
593 "
594 #}}}
595 sed -i.bak 's|steps=\[1\];|steps=\[1:4\];\n\ntry\n|' $RUNME_FILE
596 sed -i '' "s|if any(steps==4)|&${STEP_FOUR}|" $RUNME_FILE
597 RUN_EXAMPLE=1
598 elif [ "${dir}" == "./shakti" ]; then
599 sed -i.bak 's|steps=\[1:3\];|steps=\[1:3\];\n\ntry\n|' $RUNME_FILE
600 RUN_EXAMPLE=1
601 elif [ "${dir}" == "./SlrFarrell" ]; then
602 # TODO: Convert from md.slr
603 sed -i.bak 's|steps=\[1\];|steps=\[1:5\];\n\ntry\n|' $RUNME_FILE
604 RUN_EXAMPLE=0
605 elif [ "${dir}" == "./SlrGRACE" ]; then
606 # TODO: Convert from md.slr
607 sed -i.bak 's|steps=\[1\];|steps=\[1:7\];\n\ntry\n|' $RUNME_FILE
608 RUN_EXAMPLE=0
609 elif [ "${dir}" == "./SlrGRACE_NIMS" ]; then
610 # TODO: Convert from md.slr
611 sed -i.bak 's|steps=\[1\];|steps=\[1:8\];\n\ntry\n|' $RUNME_FILE
612 RUN_EXAMPLE=0
613 elif [ "${dir}" == "./SquareIceShelf" ]; then
614 sed -i.bak '1 s|^.*$|try\n\n&|' $RUNME_FILE
615 RUN_EXAMPLE=1
616 elif [ "${dir}" == "./UncertaintyQuantification" ]; then
617 sed -i.bak 's|steps=\[1\];|steps=\[1:7\];\n\ntry\n|' $RUNME_FILE
618 RUN_EXAMPLE=1
619 else
620 echo "Not implemented yet!"
621 exit 1
622 fi
623
624 if [ $RUN_EXAMPLE -eq 1 ]; then
625 echo "Testing example: $(basename $dir)"
626 LOG_RUNME_FILE="matlab_log_$(basename $dir)_examples.log"
627 echo -e ${STATUS_HANDLING} >> ${RUNME_FILE}
628 $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; runme" -logfile $ISSM_DIR/nightlylog/$LOG_RUNME_FILE
629 echo "starting: $(basename $dir)" >> $ISSM_DIR/nightlylog/matlab_log_examples.log
630 cat $ISSM_DIR/nightlylog/$LOG_RUNME_FILE >> $ISSM_DIR/nightlylog/matlab_log_examples.log
631 echo "finished: $(basename $dir)" >> $ISSM_DIR/nightlylog/matlab_log_examples.log
632 mv -f ${RUNME_FILE}.bak ${RUNME_FILE}
633 fi
634
635 # Extra clean up
636 if [ "${dir}" == "./ISMIP" ]; then
637 mv -f IsmipA.par.bak IsmipA.par
638 mv -f IsmipF.par.bak IsmipF.par
639 fi
640
641 if [ "${dir}" == "./Pig" ]; then
642 mv -f DomainOutline.exp DomainOutline.bkp
643 fi
644
645 cd ..
646 fi
647done
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