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comparison ctsm-fates.xml.SLEEP @ 0:8c7414c07367 draft

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald commit f282701cadbb0c90c2c77a52579f18b44a357e24"
author climate
date Wed, 21 Oct 2020 20:30:35 +0000
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1 <tool id="ctsm-fates" name="CTSM/FATES-EMERALD" version="2.0.1">
2 <description>Functionally Assembled Terrestrial Ecosystem Simulator</description>
3 <requirements>
4 <requirement type="package" version="2.0.1">fates-emerald</requirement>
5 <requirement type="package" version="1.32">tar</requirement>
6 <requirement type="package" version="2.35">binutils</requirement>
7 <requirement type="package" version="3">python</requirement>
8 <requirement type="package" version="2.0132">perl-xml-libxml</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 ( export HOME=`pwd` &&
12 export USER='jovyan' &&
13 mkdir -p .cime &&
14 cp '$__tool_directory__/config' .cime/config &&
15 cp '$__tool_directory__/config_compilers.xml' '.cime/config_compilers.xml' &&
16 cp '$__tool_directory__/config_machines.xml' '.cime/config_machines.xml' &&
17 mkdir inputdata &&
18 tar -xf '$inputdata' -C 'inputdata/' &&
19 mkdir output_dir &&
20 mkdir usermods_dirs &&
21 #if str($adv.condi_user_mods).strip() == 'yes'
22 # should create a new type user_mods.tar
23 cd usermods_dirs &&
24 tar xf '$user_mods' &&
25 cd .. &&
26 #end if
27 create_newcase --case '$casename' --compset 2000_DATM%1PTGSWP3_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --machine espresso --run-unsupported
28 #if str($adv.condi_user_mods).strip() == 'yes'
29 --user-mods-dir usermods_dirs
30 #end if
31 --res '$resolution' &&
32 cd '$casename' &&
33 ./case.setup > $case_info 2>&1 &&
34 #if (str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'branch')
35 ./xmlchange RUN_TYPE=$adv_period.condi_type_run.run_type &&
36 ./xmlchange RUN_REFDATE=$adv_period.condi_type_run.run_refdate &&
37 ./xmlchange RUN_REFCASE=$adv_period.condi_type_run.run_refcase &&
38 #end if
39 #if ((str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'startup') and ($adv_period.condi_type_run.run_startdate != ''))
40 ./xmlchange RUN_STARTDATE=$adv_period.condi_type_run.run_startdate &&
41 #end if
42 ./xmlchange STOP_N=$adv_period.stopn &&
43 ./xmlchange STOP_OPTION=$adv_period.stop_option &&
44 ./xmlchange CCSM_CO2_PPMV=$adv.co2 &&
45 ./xmlchange DOUT_S=FALSE &&
46 cp '$user_nl_clm_customization' user_nl_clm &&
47 ./case.build >> $case_info 2>&1 &&
48 #if (str($adv_period.condi_type_run.run_type) == 'hybrid' or str($adv_period.condi_type_run.run_type) == 'branch')
49 tar -xf '$adv_period.condi_type_run.restart' -C '../work/$casename/run/' &&
50
51 #end if
52 ./case.submit >> $case_info 2>&1 &&
53 mkdir -p restart &&
54 (cat '../work/$casename/run/rpointer'.* > $rinfo || printf "No restarts\n") &&
55 (cp '../work/$casename/run/$casename'.*.r*.*.nc restart/ || printf "No netCDF restarts\n") &&
56 (cp '../work/$casename/run/$casename'.*.r*.*.bin restart/ || printf "No bin restarts\n") &&
57 (cp '../work/$casename/run/rpointer'.* restart/ || printf "no rpointer\n") &&
58 cd restart &&
59 tar cvf $restart . &&
60 cd .. &&
61 (cp '../work/$casename/run/$casename'.*.h*.*.nc ../output_dir/ || printf "no netCDF outputs\n") &&
62 (gunzip '../work/$casename/run/'*.log.* || printf "no compressed logs") &&
63 cat '../work/$casename/run/'atm.log.* >> $atm_log &&
64 cat '../work/$casename/run/'cesm.log.* >> $cesm_log &&
65 cat '../work/$casename/run/'cpl.log.* >> $cpl_log &&
66 cat '../work/$casename/run/'lnd.log.* >> $lnd_log &&
67 cat '../work/$casename/run/'rof.log.* >> $rof_log &&
68 sleep 1000 ) ||
69 (printf "Case failed" && tar cf $work \${HOME}/work)
70 ]]></command>
71 <configfiles>
72 <configfile name="user_nl_clm_customization"><![CDATA[
73 &clm_inparm
74 hist_mfilt = 120,
75 use_fates = .true.,
76 fates_spitfire_mode = $adv_clm.fates_spitfire_mode,
77 use_fates_planthydro = $adv_clm.use_fates_planthydro,
78 use_fates_cohort_age_tracking = $adv_clm.use_fates_cohort_age_tracking,
79 use_fates_ed_st3 = $adv_clm.use_fates_ed_st3,
80 use_fates_ed_prescribed_phys = $adv_clm.use_fates_ed_prescribed_phys,
81 use_fates_logging = $adv_clm.use_fates_logging,
82 use_fates_fixed_biogeog = $adv_clm.use_fates_fixed_biogeog,
83 #if (str($adv_clm.fates_parteh_mode).strip() != '')
84 fates_parteh_mode = $adv_clm.fates_parteh_mode
85 #end if
86 /
87 ]]>
88 </configfile>
89 </configfiles>
90 <inputs>
91 <param name="inputdata" type="data" format='tar' label="inputdata for running FATES EMERALD"></param>
92 <param name="casename" type="text" value="usecase" label="Name of your case">
93 <validator type="regex" message="start with a letter and no blanks">^[A-Za-z][A-Za-z0-9]*</validator>
94 </param>
95 <param name="resolution" type="select" label="Model resolution">
96 <option value="1x1_ALP1">ALP1</option>
97 <option value="1x1_ALP2">ALP2</option>
98 <option value="1x1_ALP3">ALP3</option>
99 <option value="1x1_ALP4">ALP4</option>
100 <option value="1x1_SUB1">SUB1</option>
101 <option value="1x1_SUB2">SUB2</option>
102 <option value="1x1_SUB3">SUB3</option>
103 <option value="1x1_SUB4">SUB4</option>
104 <option value="1x1_BOR1">BOR1</option>
105 <option value="1x1_BOR2">BOR2</option>
106 <option value="1x1_BOR3">BOR3</option>
107 <option value="1x1_BOR4">BOR4</option>
108 <option value="1x1_LYG">LYG</option>
109 <option value="1x1_BUO">BUO</option>
110 <option value="1x1_HAV">HAV</option>
111 <option value="1x1_SKO">SKO</option>
112 <option value="1x1_VIKE">VIKE</option>
113 <option value="1x1_LIAH">LIAH</option>
114 <option value="1x1_FINN">FINN</option>
115 </param>
116 <section name="adv_period" title="Customize the model run period" expanded="false">
117
118 <conditional name="condi_type_run">
119 <param name="run_type" type="select" label="Determines the model run initialization type.">
120 <option value="startup" selected="true">startup</option>
121 <option value="hybrid">hybrid</option>
122 <option value="branch">branch</option>
123 </param>
124 <when value="startup">
125 <param name="run_startdate" type="text" value="" label="Run start date (yyyy-mm-dd). Only used for startup or hybrid runs.">
126 <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator>
127 </param>
128 </when>
129 <when value="branch">
130 <param name="run_refcase" type="text" value="" label="Reference case for hybrid or branch runs"></param>
131 <param name="run_refdate" type="text" value="" label="Reference date for hybrid or branch runs (yyyy-mm-dd)">
132 <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator>
133 </param>
134 <param name="restart" type="data" format='tar' label="restart for running FATES EMERALD"></param>
135 </when>
136 <when value="hybrid">
137 <param name="run_refcase" type="text" value="" label="Reference case for hybrid or branch runs"></param>
138 <param name="run_refdate" type="text" value="" label="Reference date for hybrid or branch runs (yyyy-mm-dd)">
139 <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator>
140 </param>
141 <param name="run_startdate" type="text" value="" label="Run start date (yyyy-mm-dd). Only used for startup or hybrid runs.">
142 <validator type="regex" message="YYYY-MM-DD">(^$|(\d{4}-(0[1-9]|1[0-2])-(0[1-9]|[12]\d|3[01])))</validator>
143 </param>
144 <param name="restart" type="data" format='tar' label="restart for running FATES EMERALD"></param>
145 </when>
146 </conditional>
147 <param name="stopn" type="integer" value="5" label="Provides a numerical count for STOP_OPTION."></param>
148 <param name="stop_option" type="select" label=" Sets the run length along with STOP_N and STOP_DATE">
149 <option value="ndays" selected="true">ndays</option>
150 <option value="none">none</option>
151 <option value="never">never</option>
152 <option value="nsteps">nsteps</option>
153 <option value="nseconds">nseconds</option>
154 <option value="nminutes">nminutes</option>
155 <option value="nhours">nhours</option>
156 <option value="nday">ndays</option>
157 <option value="nmonths">nmonths</option>
158 <option value="nyears">nyears</option>
159 <option value="date">date</option>
160 <option value="ifdays0">ifday0</option>
161 <option value="end">end</option>
162 </param>
163 </section>
164 <section name="adv_clm" title="CLM namelist customization" expanded="false">
165 <param name="use_fates_planthydro" type="boolean" label="Toggle to turn on plant hydraulics" truevalue=".true." falsevalue=".false." checked="false"/>
166 <param name="use_fates_cohort_age_tracking" type="boolean" label="Toggle to turn on cohort age tracking" truevalue=".true." falsevalue=".false." checked="false"/>
167 <param name="use_fates_ed_st3" type="boolean" label="Toggle to turn on Static Stand Structure Mode" truevalue=".true." falsevalue=".false." checked="false"/>
168 <param name="use_fates_ed_prescribed_phys" type="boolean" label="Toggle to turn on prescribed physiology" truevalue=".true." falsevalue=".false." checked="false"/>
169 <param name="use_fates_logging" type="boolean" label="Toggle to turn on the logging module" truevalue=".true." falsevalue=".false." checked="false"/>
170 <param name="use_fates_fixed_biogeog" type="boolean" label="Toggle to turn on fixed biogeography mode" truevalue=".true." falsevalue=".false." checked="false"/>
171 <param name="fates_spitfire_mode" type="select" label="Spitfire module to simulate fire">
172 <option value="0" selected="true">None</option>
173 <option value="1">Use a global constant lightning rate found in fates_params</option>
174 <option value="2">Use an external lightning dataset</option>
175 <option value="3">Use an external confirmed ignitions dataset</option>
176 <option value="4">Use external lightning and population datasets to simulate both natural and anthropogenic ignitions</option>
177 </param>
178 <param name="fates_parteh_mode" type="select" label="Switch deciding which nutrient model to use in FATES">
179 <option value="" selected="true">None</option>
180 <option value="1">1</option>
181 <option value="2">2</option>
182 </param>
183 </section>
184 <section name="adv" title="Advanced customization" expanded="false">
185 <param name="co2" type="float" value="367.0" label="Atmospheric CO2 molar ratio (by volume) only used when co2_type==constant (umol/mol)"></param>
186 <conditional name="condi_user_mods">
187 <param name="add_changes" type="select" label="user-modified source code">
188 <option value="no" selected="true">no</option>
189 <option value="yes">yes</option>
190 </param>
191 <when value="yes">
192 <param name="usermods" type="data" format="tar" label="SourceMods"></param>
193 </when>
194 <when value="no"/>
195 </conditional>
196 </section>
197 </inputs>
198 <outputs>
199 <collection name="history_files" type="list" label="${tool.name} on ${inputdata.name} (history file)">
200 <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" format="netcdf"/>
201 </collection>
202 <data name="atm_log" format="txt" label="${tool.name} on ${inputdata.name} (atm.log)"/>
203 <data name="cesm_log" format="txt" label="${tool.name} on ${inputdata.name} (cesm.log)"/>
204 <data name="cpl_log" format="txt" label="${tool.name} on ${inputdata.name} (cpl.log)"/>
205 <data name="lnd_log" format="txt" label="${tool.name} on ${inputdata.name} (lnd.log)"/>
206 <data name="rof_log" format="txt" label="${tool.name} on ${inputdata.name} (rof.log)"/>
207 <data name="restart" format="tar" label="${tool.name} on ${inputdata.name} (restart)"></data>
208 <data name="case_info" format="txt" label="${tool.name} on ${inputdata.name} (case info)"></data>
209 <data name="rinfo" format="txt" label="${tool.name} on ${inputdata.name} (restart info)"></data>
210 <data name="work" format="tar" label="${tool.name} on ${inputdata.name} (workdir)">
211 </data>
212 </outputs>
213 <tests>
214 <test>
215 <param name="inputdata" value="inputdata_test.tar" />
216 <param name="casename" value="test" />
217 <param name="resolution" value="1x1_ALP1" />
218 <param name="run_startdate" value="2000-01-01" />
219 <param name="stop_option" value="nsteps" />
220 <param name="stopn" value="1" />
221 <output name="atm_log" ftype="txt" file="atm.log">
222 <assert_contents>
223 <has_text text="(datm_comp_final) atm: end of main integration loop" />
224 </assert_contents>
225 </output>
226 <output name="cesm_log" ftype="txt" file="cesm.log">
227 <assert_contents>
228 <has_text text="pes participating in computation for CLM" />
229 </assert_contents>
230 </output>
231 <output name="cpl_log" ftype="txt" file="cpl.log">
232 <assert_contents>
233 <has_text text="SUCCESSFUL TERMINATION" />
234 </assert_contents>
235 </output>
236 <output name="lnd_log" ftype="txt" file="lnd.log">
237 <assert_contents>
238 <has_text text="Successfully" />
239 </assert_contents>
240 </output>
241 <output name="rof_log" ftype="txt" file="rof.log">
242 <assert_contents>
243 <has_text text="MOSART model initialization" />
244 </assert_contents>
245 </output>
246 <output name="case_info" ftype="txt" file="case_info.txt">
247 <assert_contents>
248 <has_text text="MODEL BUILD HAS FINISHED SUCCESSFULLY" />
249 <has_line_matching expression="Submitted job" />
250 </assert_contents>
251 </output>
252 <output name="work" ftype="tar" file="workdir.tar">
253 <assert_contents>
254 <has_size value="0"/>
255 </assert_contents>
256 </output>
257 <output name="restart" ftype="tar" file="restart.tar" compare="sim_size" delta="100" />
258 <output name="rinfo" ftype="txt" file="restart_info.txt">
259 <assert_contents>
260 <has_line_matching expression="*datm.r.2000-01-01-01800.nc*" />
261 <has_line_matching expression="*datm.rs1.2000-01-01-01800.bin*" />
262 <has_line_matching expression="*cpl.r.2000-01-01-01800.nc*" />
263 <has_line_matching expression="*clm2.r.2000-01-01-01800.nc*" />
264 </assert_contents>
265 </output>
266 <output_collection name="history_files" count="0">
267 </output_collection>
268 </test>
269 </tests>
270 <help><![CDATA[
271
272 **The Functionally Assembled Terrestrial Ecosystem Simulator (FATES)**
273 ==========================================================================
274
275 This tool create and run CTSM-FATES EMERALD experiments from fates-emerald release.
276
277 This version of FATES is maintained by the University of Oslo.
278
279 Currently available resolution are as following:
280
281 SeedClim Sites:
282 ~~~~~~~~~~~~~~~
283
284 - ALP1,61.0243N,8.12343E
285 - ALP2,60.8231N,7.27596E
286 - ALP3,60.8328N,7.17561E
287 - ALP4,60.9335N,6.41504E
288 - SUB1,60.8203N,8.70466E
289 - SUB2,60.8760N,7.17666E
290 - SUB3,61.0866N,6.63028E
291 - SUB4,60.5445N,6.51468E
292 - BOR1,61.0355N,9.07876E
293 - BOR2,60.8803N,7.16982E
294 - BOR3,60.6652N,6.33738E
295 - BOR4,60.6901N,5.96487E
296
297 LandPress Sites:
298 ~~~~~~~~~~~~~~~~
299
300 - LYG,60.70084N,5.092566E
301 - BUO,65.83677N,12.224506E
302 - HAV,64.779N,11.2193E
303 - SKO,65.79602N,12.219299E
304
305 Three-D Sites:
306 ~~~~~~~~~~~~~~
307
308 - VIKE,60.88019N,7.16990E
309 - JOAS,60.86183N,7.16800E
310 - LIAH,60.85994N,7.19504E
311
312
313 Finnmark Site:
314 ~~~~~~~~~~~~~~
315
316 - FINN,69.341088N,25.293524E
317
318 ]]></help>
319 <citations>
320
321 </citations>
322 <edam_topics>
323 <edam_topic>topic_3855</edam_topic>
324 <edam_topic>topic_3318</edam_topic>
325 <edam_topic>topic_3050</edam_topic>
326 <edam_topic>topic_0610</edam_topic>
327 </edam_topics>
328 <edam_operations>
329 <edam_operation>operation_3946</edam_operation>
330 <edam_operation>operation_2426</edam_operation>
331 </edam_operations>
332 </tool>