source: issm/trunk/src/m/classes/clusters/generic.m@ 25836

Last change on this file since 25836 was 25836, checked in by Mathieu Morlighem, 4 years ago

merged trunk-jpl and trunk for revision 25834
File size: 14.1 KB
Line 
1%GENERIC cluster class definition
2%
3% Usage:
4% cluster=generic('name','astrid','np',3);
5% cluster=generic('name',oshostname(),'np',3,'login','username');
6
7classdef generic
8 properties (SetAccess=public)
9 % {{{
10 name = '';
11 login = '';
12 np = 1;
13 npocean = 1;
14 port = 0;
15 interactive = 1;
16 codepath = [IssmConfig('ISSM_PREFIX') '/bin'];
17 etcpath = [issmdir() '/etc'];
18 executionpath = [issmdir() '/execution'];
19 valgrind = [issmdir() '/externalpackages/valgrind/install/bin/valgrind'];
20 valgrindlib = [issmdir() '/externalpackages/valgrind/install/lib/libmpidebug.so'];
21 valgrindsup = [issmdir() '/externalpackages/valgrind/issm.supp'];
22 verbose = 1;
23 shell = '/bin/sh';
24 %}}}
25 end
26 methods
27 function cluster=generic(varargin) % {{{
28
29 %Change the defaults if ispc
30 if ispc,
31 cluster.codepath = [issmdir() '\bin'];
32 cluster.etcpath = [issmdir() '\etc'];
33 cluster.executionpath = [issmdir() '\execution'];
34 end
35
36 %use provided options to change fields
37 options=pairoptions(varargin{:});
38
39 %get name
40 cluster.name=getfieldvalue(options,'name',oshostname());
41
42 %initialize cluster using user settings if provided
43 if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end
44
45 %OK get other fields
46 cluster=AssignObjectFields(pairoptions(varargin{:}),cluster);
47 end
48 %}}}
49 function disp(cluster) % {{{
50 % display the object
51 disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1)));
52 disp(sprintf(' name: %s',cluster.name));
53 disp(sprintf(' login: %s',cluster.login));
54 disp(sprintf(' np: %i',cluster.np));
55 disp(sprintf(' npocean: %i',cluster.npocean));
56 disp(sprintf(' port: %i',cluster.port));
57 disp(sprintf(' codepath: %s',cluster.codepath));
58 disp(sprintf(' executionpath: %s',cluster.executionpath));
59 disp(sprintf(' etcpath: %s',cluster.etcpath));
60 disp(sprintf(' valgrind: %s',cluster.valgrind));
61 disp(sprintf(' valgrindlib: %s',cluster.valgrindlib));
62 disp(sprintf(' valgrindsup: %s',cluster.valgrindsup));
63 disp(sprintf(' verbose: %s',cluster.verbose));
64 disp(sprintf(' shell: %s',cluster.shell));
65 end
66 %}}}
67 function md = checkconsistency(cluster,md,solution,analyses) % {{{
68 if cluster.np<1
69 md = checkmessage(md,['number of processors should be at least 1']);
70 end
71 if isnan(cluster.np),
72 md = checkmessage(md,'number of processors should not be NaN!');
73 end
74 end
75 %}}}
76 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
77 % Which executable are we calling?
78 executable='issm.exe'; % default
79
80 if isdakota,
81 version=IssmConfig('_DAKOTA_VERSION_');
82 version=str2num(version(1:3));
83 if (version>=6),
84 executable='issm_dakota.exe';
85 end
86 end
87 if isoceancoupling,
88 executable='issm_ocean.exe';
89 end
90
91 if ~ispc(),
92 fid=fopen([modelname '.queue'],'w');
93 fprintf(fid,'#!%s\n',cluster.shell);
94 if ~isvalgrind,
95 if cluster.interactive
96 if IssmConfig('_HAVE_MPI_'),
97 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
98 else
99 fprintf(fid,'%s/%s %s %s %s',cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
100 end
101 else
102 if IssmConfig('_HAVE_MPI_'),
103 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s 2> %s.errlog > %s.outlog &',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
104 else
105 fprintf(fid,'%s/%s %s %s %s 2> %s.errlog > %s.outlog &',cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
106 end
107 end
108 elseif isgprof,
109 fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname);
110 else
111 %Add --gen-suppressions=all to get suppression lines
112 %fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib); it could be deleted
113 if ismac,
114 if IssmConfig('_HAVE_MPI_'),
115 fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --dsymutil=yes --suppressions=%s %s/%s %s %s %s 2> %s.errlog > %s.outlog ',...
116 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname], modelname,modelname,modelname);
117 else
118 fprintf(fid,'%s --leak-check=full --dsymutil=yes --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog > %s.outlog',...
119 cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname], modelname,modelname,modelname);
120 end
121 else
122 if IssmConfig('_HAVE_MPI_'),
123 fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog > %s.outlog',...
124 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
125 else
126 fprintf(fid,'%s --leak-check=full --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog > %s.outlog',...
127 cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
128 end
129 end
130 end
131 if ~io_gather, %concatenate the output files:
132 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
133 end
134 fclose(fid);
135
136 else % Windows
137
138 fid=fopen([modelname '.bat'],'w');
139 fprintf(fid,'@echo off\n');
140
141 if IssmConfig('_HAVE_PETSC_MPI_'),
142 warning('parallel runs not allowed yet in Windows. Defaulting to 1 cpus');
143 cluster.np=1;
144 end
145
146 if cluster.np>1,
147 fprintf(fid,'"C:\\Program Files\\MPICH2\\bin\\mpiexec.exe" -n %i "%s/%s" %s ./ %s ',cluster.np,cluster.codepath,executable,solution,modelname);
148 else
149 fprintf(fid,'"%s/%s" %s ./ %s ',cluster.codepath,executable,solution,modelname);
150 end
151 fclose(fid);
152 end
153
154 %in interactive mode, create a run file, and errlog and outlog file
155 if cluster.interactive,
156 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
157 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
158 end
159 end
160 %}}}
161 function BuildQueueScriptMultipleModels(cluster,dirname,modelname,solution,dirnames,modelnames,nps) % {{{
162
163 %some checks:
164 if isempty(modelname), error('BuildQueueScriptMultipleModels error message: need a non empty model name!');end
165
166 %what is the executable being called?
167 executable='issm_slr.exe';
168
169 if ispc(), error('BuildQueueScriptMultipleModels not support yet on windows machines');end;
170
171 %write queuing script
172 fid=fopen([modelname '.queue'],'w');
173
174 fprintf(fid,'#!%s\n',cluster.shell);
175
176 %number of cpus:
177 mpistring=sprintf('mpiexec -np %i ',cluster.np);
178
179 %executable:
180 mpistring=[mpistring sprintf('%s/%s ',cluster.codepath,executable)];
181
182 %solution name:
183 mpistring=[mpistring sprintf('%s ',solution)];
184
185 %execution directory and model name:
186 mpistring=[mpistring sprintf('%s/%s %s',cluster.executionpath,dirname,modelname)];
187
188 %inform main executable of how many icecaps, glaciers and earth models are being run:
189 mpistring=[mpistring sprintf(' %i ',length(dirnames))];
190
191 %icecaps, glaciers and earth location, names and number of processors associated:
192 for i=1:length(dirnames),
193 mpistring=[mpistring sprintf(' %s/%s %s %i ',cluster.executionpath,dirnames{i},modelnames{i},nps{i})];
194 end
195
196 %log files:
197 if ~cluster.interactive,
198 mpistring=[mpistring sprintf('2> %s.errlog> %s.outlog',modelname,modelname)];
199 end
200
201 %write this long string to disk:
202 fprintf(fid,mpistring);
203 fclose(fid);
204
205 %in interactive mode, create a run file, and errlog and outlog file
206 if cluster.interactive,
207 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
208 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
209 end
210 end
211 %}}}
212 function BuildQueueScriptIceOcean(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{
213
214 %write queuing script
215 %what is the executable being called?
216 executable='issm_ocean.exe';
217
218 fid=fopen([modelname '.queue'],'w');
219 fprintf(fid,'#!%s\n',cluster.shell);
220 if ~isvalgrind,
221 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s : -np %i ./mitgcmuv\n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,modelname,cluster.npocean);
222
223 else
224 fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --dsymutil=yes --suppressions=%s %s/%s %s %s %s : -np %i ./mitgcmuv\n',...
225 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,cluster.executionpath,modelname,cluster.npocean);
226 end
227 fclose(fid);
228
229 %in interactive mode, create a run file, and errlog and outlog file
230 if cluster.interactive,
231 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
232 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
233 end
234 end
235 %}}}
236 function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
237
238 %write queuing script
239 if ~ispc(),
240
241 fid=fopen([modelname '.queue'],'w');
242 fprintf(fid,'#!/bin/sh\n');
243 if ~isvalgrind,
244 if cluster.interactive
245 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
246 else
247 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
248 end
249 elseif isgprof,
250 fprintf(fid,'\n gprof %s/kriging.exe gmon.out > %s.performance',cluster.codepath,modelname);
251 else
252 %Add --gen-suppressions=all to get suppression lines
253 %fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib); it could be deleted
254 fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',...
255 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
256 end
257 if ~io_gather, %concatenate the output files:
258 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
259 end
260 fclose(fid);
261
262 else % Windows
263
264 fid=fopen([modelname '.bat'],'w');
265 fprintf(fid,'@echo off\n');
266 if cluster.interactive
267 fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname);
268 else
269 fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
270 cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
271 end
272 fclose(fid);
273 end
274
275 %in interactive mode, create a run file, and errlog and outlog file
276 if cluster.interactive,
277 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
278 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
279 end
280 end
281 %}}}
282 function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{
283
284 if ~ispc,
285
286 %compress the files into one zip.
287 compressstring=['tar -zcf ' dirname '.tar.gz '];
288 for i=1:numel(filelist),
289 if ~exist(filelist{i},'file')
290 error(['File ' filelist{i} ' not found']);
291 end
292 compressstring = [compressstring ' ' filelist{i}];
293 end
294 if cluster.interactive,
295 compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
296 end
297 system(compressstring);
298
299 if cluster.verbose, disp('uploading input file and queueing script'); end
300 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
301 end
302 end %}}}
303 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
304
305 if ~ispc,
306
307 %figure out what shell extension we will use:
308 if isempty(strfind(cluster.shell,'csh')),
309 shellext='sh';
310 else
311 shellext='csh';
312 end
313
314 if cluster.verbose, disp('launching solution sequence on remote cluster'); end
315
316 if ~isempty(restart)
317 launchcommand=['source ' cluster.etcpath '/environment.' shellext ' && cd ' cluster.executionpath ' && cd ' dirname ' && source ' modelname '.queue '];
318 else
319 if ~batch,
320 launchcommand=['source ' cluster.etcpath '/environment.' shellext ' && cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
321 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && source ' modelname '.queue '];
322 else
323 launchcommand=['source ' cluster.etcpath '/environment.' shellext ' && cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
324 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz '];
325 end
326 end
327 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
328 else
329 system([modelname '.bat']);
330 end
331
332 end %}}}
333 function LaunchQueueJobIceOcean(cluster,modelname,dirname,filelist,restart,batch)% {{{
334
335 if ~ispc,
336
337 %figure out what shell extension we will use:
338 if isempty(strfind(cluster.shell,'csh')),
339 shellext='sh';
340 else
341 shellext='csh';
342 end
343
344 if cluster.verbose, disp('launching solution sequence on remote cluster'); end
345
346 if ~isempty(restart)
347 launchcommand=['source ' cluster.etcpath '/environment.' shellext ' && cd ' cluster.executionpath ' && cd ' dirname ' && source ' modelname '.queue '];
348 else
349 if ~batch,
350 launchcommand=['source ' cluster.etcpath '/environment.' shellext ' && cd ' cluster.executionpath ' && tar -zxf ' dirname '.tar.gz && source ' modelname '.queue '];
351 else
352 launchcommand=['source ' cluster.etcpath '/environment.' shellext ' && cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
353 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz '];
354 end
355 end
356 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
357 else
358 system([modelname '.bat']);
359 end
360
361 end %}}}
362 function Download(cluster,dirname,filelist)% {{{
363
364 if ispc(),
365 %do nothing
366 return;
367 end
368
369 %copy files from cluster to current directory
370 directory=[cluster.executionpath '/' dirname '/'];
371 issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist);
372 end %}}}
373 end
374end
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