source: issm/trunk-jpl/src/m/classes/modellist.m@ 13012

Last change on this file since 13012 was 13012, checked in by Mathieu Morlighem, 13 years ago

CHG: moving stuff around
File size: 11.0 KB
Line 
1%MODELLIST class definition
2%
3% Usage:
4% modellist=modellist({md1 md2 md3});
5
6classdef modellist
7 properties (SetAccess=public)
8 models = cell(0,1);
9 cluster = generic();
10 end
11 methods
12 function md_list=modelsextract(md,flags,minel,varargin) % {{{
13 %modelsextract - extract several self contained models according to a list of element flags.
14 %
15 % The difference between this routine and the modelextract.m routine (without an 's') is that
16 % as many models are extracted as there are closed contours defined in area.
17 % This routine is needed for example when doing data assimilation of ice shelves in Antarctica.
18 % Many independent ice shelves are present, and we don't want data assimilation on one ice shelf
19 % to be hindered by another totally independent ice shelf.
20 %
21 % Usage:
22 % md_list=modelsextract(md,elementfalgs,minel);
23 %
24 % Examples:
25 % md_list=modelsextract(md,md.mask.elementonfloatingice,1000);
26 %
27 % See also: EXTRUDE, COLLAPSE, MODELEXTRACT
28
29 disp('selecting pools of elements');
30 %go through flags and build as many independent element flags as there are groups of connected 1s
31 %in flags.
32
33 %2D or 3D?
34 if md.mesh.dimension==3,
35 numberofelements=md.mesh.numberofelements2d; %this will be forgotten when we get out.
36 flags=project2d(md,flags,1);
37 else
38 numberofelements=md.mesh.numberofelements;
39 end
40
41 %recover extra arguments:
42 distance=0;
43 if nargin==4,
44 distance=varargin{1};
45 end
46
47 flag_list=cell(0,1);
48
49 for i=1:size(flags,1),
50
51 if (flags(i)),
52
53 %ok, we are sure element i is part of a new pool.
54 pool=zeros(numberofelements,1);
55 pool=PropagateFlagsFromConnectivity(md.mesh.elementconnectivity,pool,i,flags);
56 flag_list{end+1,1}=pool;
57
58 %speed up rest of computation by taking pool out of flags:
59 pos=find(pool);flags(pos)=0;
60
61 end
62 end
63
64 %go through flag_list and discard any pool of less than minel elements:
65 ex_pos=[];
66 for i=1:length(flag_list),
67 if length(find(flag_list{i}))<minel,
68 ex_pos=[ex_pos; i];
69 end
70 end
71 flag_list(ex_pos)=[];
72
73 %now, if distance was specified, expand the flag_list by distance km:
74 if distance,
75 for i=1:length(flag_list),
76 flag_list{i}=PropagateFlagsUntilDistance(md,flag_list{i},distance);
77 end
78 end
79
80 %now, go use the pools of flags to extract models:
81 disp(['extracting ' num2str(size(flag_list,1)) ' models']);
82 models=cell(0,1);
83
84 for i=1:size(flag_list,1),
85 disp([' ' num2str(i) '/' num2str(size(flag_list,1))]);
86 if md.mesh.dimension==3,
87 flags2d=flag_list{i};
88 realflags=project3d(md,flags2d,'element');
89 else
90 realflags=flag_list{i};
91 end
92 models{end+1,1}=modelextract(md,realflags);
93 end
94
95 %return model list
96 md_list=modellist(models);
97
98 end %end of this function }}}
99 function md_list=modelsextractfromdomains(md,directory) % {{{
100 %modelsextractfromdomains- extract several self contained models according to a list of domains
101 %
102 % Usage:
103 % md_list=modelsextractfromdomains(md,'Basins/');
104 %
105 % Examples:
106 % md_list=modelsextract(md,'Basins/');
107 %
108 % See also: MODELSEXTRACTS, MODELEXTRACT
109
110 %go into directory and get list of files.
111 cd(directory);
112 basins=listfiles;
113 cd ..
114
115 models=cell(0,1);
116 for i=1:length(basins),
117 models{end+1,1}=modelextract(md,[directory '/' basins{i}]);
118 end
119
120 %return model list:
121 md_list=modellist(models);
122
123 end % }}}
124 function obj = modellist(varargin) % {{{
125
126 %initialize list
127 if nargin==0,
128 %Do nothing,
129 elseif nargin==1,
130 if ~isa(varargin{1},'cell'),
131 error('not supported yet');
132 end
133
134 celllist=varargin{1};
135
136 %check on size of cell list:
137 if (size(celllist,2)~=1),
138 error('modellist constructor error message: list of models should be a cell list of column size 1');
139 end
140
141 %check that only models are in the celllist:
142 for i=1:size(celllist,1),
143 if ~isa(celllist{i},'model')
144 error(['modellist constructor error message: element ' num2str(i) ' of cell list is not a model!']);
145 end
146 end
147
148 obj.models = celllist;
149 obj.cluster = obj.models{1}.cluster;
150 end
151 end % }}}
152 function val = get(obj, propName)% {{{
153 %GET - gets model propertie from a specified object ans returns the value
154 %
155 % Usage:
156 % val = get(a, propName)
157
158 switch propName
159 case 'numberofelements'
160 val = obj.numberofelements;
161 case 'numberofnodes'
162 val = obj.numberofnodes;
163 case 'elements'
164 val = obj.elements;
165 case 'x'
166 val = obj.x;
167 case 'y'
168 val = obj.y;
169 case 'z'
170 val = obj.z;
171 otherwise
172 error(['get error message: ' propName,' is not a valid model property'])
173 end
174 end % }}}
175 function obj = loadmultipleresultsfromcluster(obj) % {{{
176 %LOADMULTIPLERESULTSFROMCLUSTER - load multiple results of solution sequences from cluster
177 %
178 % Usage:
179 % obj=loadresultsfromcluster(obj);
180
181 nummodels=length(obj.models);
182
183 %Get cluster settings
184 cluster=obj.cluster;
185 name=obj.name;
186 cluster_rc_location=which('cluster.rc');
187 [codepath,executionpath]=ClusterParameters(cluster,cluster_rc_location);
188
189 %Remote tar:
190 disp('tarring results');
191 issmssh(cluster,['"cd ' executionpath '/' name ' && rm -rf file_list.txt ModelResults.tar.gz && find -iname ''*-*vs*.outbin'' > file_list.txt && tar zcvf ModelResults.tar.gz --files-from file_list.txt && rm -rf file_list.txt "']);
192
193 %copy results from cluster to present directory
194 scpin(cluster, [executionpath '/' name], {'ModelResults.tar.gz'});
195
196 %untar:
197 !tar -zxvf ModelResults.tar.gz
198
199 %ok, go through list and load results from disk:
200 for i=1:nummodels,
201 %load results for this model
202 obj.models{i}=loadresultsfromdisk(obj.models{i},[name '-' num2str(i) 'vs' num2str(nummodels) '.outbin']);
203
204 delete([name '-' num2str(i) 'vs' num2str(nummodels) '.outbin']);
205 end
206
207 %erase files
208 delete('ModelResults.tar.gz');
209 end % }}}
210 function obj = solve(obj,varargin)% {{{
211 %SOLVE - apply solution sequence for a list of models. Used in batch mode.
212 %
213 % Usage:
214 % obj=solve(obj,varargin)
215 % where varargin is a lit of paired arguments.
216 % arguments can be: 'analysis_type': 'diagnostic','thermal','prognostic','transient'
217 %
218 % Examples:
219 % obj=solve(obj,'analysis_type','diagnostic');
220
221 %recover options
222 options=pairoptions(varargin{:});
223
224 %add default options
225 options=process_solve_options(options);
226
227 %length of list
228 nummodels=length(obj.models);
229
230 %name of queue: to make it unique, add a time stamp
231 name=[obj.name '-' datestr(now,1) '-' datestr(now,'HH-MM-SS') ];
232
233 %name of cluster will be first name of list
234 cluster=obj.cluster;
235
236 %Figure out parameters for this particular cluster
237 cluster_rc_location=which('cluster.rc');
238 [codepath,executionpath]=ClusterParameters(cluster,cluster_rc_location);
239
240 %solve in batch mode:
241 for i=1:nummodels,
242
243 %model
244 mdex=obj.models{i};
245
246 %recover some fields
247 mdex.analysis_type=options.analysis_type;
248
249 mdex.name=[name '-' num2str(i) 'vs' num2str(nummodels)];
250 mdex.time=obj.time;
251 mdex.queue=obj.queue;
252 mdex.cluster=obj.cluster;
253 if ~isnan(obj.np),
254 mdex.np=obj.np;
255 end
256
257 %call solve in batch mode:
258 if strcmpi(cluster,oshostname),
259 mdex=solve(mdex,varargin{:});
260 else
261 mdex=solve(mdex,varargin{:},'batch','yes','directory',name);
262 end
263
264 %feed back
265 obj.models{i}=mdex;
266 end
267
268 %locally, we are done.
269 if strcmpi(cluster,oshostname),
270 return
271 end
272
273
274 %now, tar all the files and then erase them.
275 eval(['!find -iname ''' name '-*'' > file_list.txt']);
276 !tar zcvf ModelList.tar.gz --files-from file_list.txt
277 !rm -rf *.bin *.queue file_list.txt
278
279 %still have to build a launching script.
280 BuildMultipleQueueingScript(cluster,name,executionpath,codepath);
281
282 %launch jobs on remote cluster
283 LaunchMultipleQueueJob(cluster,name,executionpath);
284
285 %erase files:
286 delete([name '.queue']);
287 delete('ModelList.tar.gz');
288
289 %save name:
290 obj.name=name;
291 end % }}}
292 end
293end
294
295function BuildMultipleQueueingScript(cluster,name,executionpath,codepath)% {{{
296%BUILDMULTIPLEQUEUEINGSCRIPT -
297%
298% Usage:
299% BuildMultipleQueueingScript(executionpath,codepath)
300
301disp('building queueing script');
302
303%First try and figure out if there is a special script for this particular cluster
304function_name=['BuildMultipleQueueingScript' cluster];
305
306%some specific treatment of identical cluster, gemini, castor and pollux
307if strcmpi(cluster,'castor') || strcmpi(cluster,'pollux'),
308 function_name='BuildMultipleQueueingScriptgemini';
309end
310
311if exist(function_name,'file'),
312 %Call this function:
313 eval([function_name '(name,executionpath,codepath);']);
314else
315 %Call the generic BuildQueueingScript:
316 BuildMultipleQueueingScriptGeneric(name,executionpath,codepath);
317end
318end % }}}
319function BuildQueueingScriptgemini(name,executionpath,codepath)% {{{
320%BUILDQUEUEINGSCRIPTGEMINI - ...
321%
322% Usage:
323% BuildQueueingScriptgemini(md,executionpath,codepath)
324
325scriptname=[name '.queue'];
326
327fid=fopen(scriptname,'w');
328if fid==-1,
329 error(['BuildQueueingScriptgeminierror message: could not open ' scriptname ' file for ascii writing']);
330end
331
332fprintf(fid,'#!/bin/sh\n');
333fprintf(fid,'cd %s\n',executionpath);
334fprintf(fid,'mkdir %s\n',name);
335fprintf(fid,'cd %s\n',name);
336fprintf(fid,'mv ../ModelList.tar.gz ./\n');
337fprintf(fid,'tar -zxvf ModelList.tar.gz\n');
338fprintf(fid,'foreach i (%s-*vs*.queue)\n',name);
339fprintf(fid,'qsub $i\n');
340fprintf(fid,'end\n');
341fclose(fid);
342end% }}}
343function LaunchMultipleQueueJob(cluster,name,executionpath)% {{{
344%LAUNCHMULTIPLEQUEUEJOB - ...
345%
346% Usage:
347% LaunchMultipleQueueJob(executionpath)
348
349%First try and figure out if there is a special script for thie particular cluster
350function_name=['LaunchMultipleQueueJob' cluster];
351
352%some specific treatment of identical cluster, gemini, castor and pollux
353if strcmpi(cluster,'castor') || strcmpi(cluster,'pollux'),
354 function_name='LaunchMultipleQueueJobgemini';
355end
356
357if exist(function_name,'file'),
358 %Call this function:
359 eval([function_name '(cluster,name,executionpath);']);
360else
361 %Call the generic LaunchMultipleQueueJob:
362 LaunchMultipleQueueJobGeneric(cluster,name,executionpath);
363end
364end% }}}
365function md=LaunchMultipleQueueJobgemini(cluster,name,executionpath)% {{{
366%LAUNCHMULTIPLEQUEUEJOBGEMINI - Launch multiple queueing script on Gemini cluster
367%
368% Usage:
369% LaunchMultipleQueueJobgemini(cluster,name,executionpath)
370
371
372%first, check we have the binary file and the queueing script
373if ~exist([ name '.queue'],'file'),
374 error('LaunchMultipleQueueJobgemini error message: queueing script issing, cannot go forward');
375end
376
377if ~exist('ModelList.tar.gz','file'),
378 error('LaunchMultipleQueueJobgemini error message: inputs models file missing, cannot go forward');
379end
380
381%upload both files to cluster
382disp('uploading input file, queueing script and variables script');
383eval(['!scp ModelList.tar.gz ' name '.queue ' cluster ':' executionpath]);
384
385disp('launching solution sequence on remote cluster');
386issmssh(cluster,login,['"cd ' executionpath ' && source ' name '.queue "']);
387end% }}}
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