source: issm/trunk/src/m/classes/clusters/localpfe.m@ 28013

Last change on this file since 28013 was 28013, checked in by Mathieu Morlighem, 16 months ago

merged trunk-jpl and trunk for revision 28011
File size: 10.6 KB
Line 
1%LOCALPFE cluster class definition
2%
3% Usage:
4% cluster=localpfe('name','astrid','np',3);
5% cluster=localpfe('name',oshostname(),'np',3,'login','username');
6
7classdef localpfe
8 properties (SetAccess=public)
9 % {{{
10 name = '';
11 login = '';
12 np = 1;
13 npocean = 0;
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=localpfe(varargin) % {{{
28
29 %Change the defaults if ispc and not ismingw
30 if ispc & ~ismingw,
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(' interactive: %i',cluster.interactive));
58 disp(sprintf(' codepath: %s',cluster.codepath));
59 disp(sprintf(' etcpath: %s',cluster.etcpath));
60 disp(sprintf(' executionpath: %s',cluster.executionpath));
61 disp(sprintf(' valgrind: %s',cluster.valgrind));
62 disp(sprintf(' valgrindlib: %s',cluster.valgrindlib));
63 disp(sprintf(' valgrindsup: %s',cluster.valgrindsup));
64 disp(sprintf(' verbose: %s',cluster.verbose));
65 disp(sprintf(' shell: %s',cluster.shell));
66 end
67 %}}}
68 function md = checkconsistency(cluster,md,solution,analyses) % {{{
69 if cluster.np<1
70 md = checkmessage(md,['number of processors should be at least 1']);
71 end
72 if isnan(cluster.np),
73 md = checkmessage(md,'number of processors should not be NaN!');
74 end
75 end
76 %}}}
77 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
78
79 %write queuing script
80 %what is the executable being called?
81 executable='issm.exe';
82 if isdakota,
83 version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3));
84 if (version>=6),
85 executable='issm_dakota.exe';
86 end
87 end
88
89 fid=fopen([modelname '.queue'],'w');
90 fprintf(fid,'#!%s\n',cluster.shell);
91 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s \n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,modelname);
92 fclose(fid);
93
94 %in interactive mode, create a run file, and errlog and outlog file
95 if cluster.interactive,
96 fid=fopen([modelname '.run'],'w');
97 if cluster.interactive==10,
98 fprintf(fid,'module unload mpi-mvapich2/1.4.1/gcc\n');
99 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[pwd() '/run'],modelname);
100 else
101 if ~isvalgrind,
102 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,modelname);
103 %fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.nprocs(),cluster.codepath,executable,solution,[cluster.executionpath '/Interactive' num2str(cluster.interactive)],modelname);
104 else
105 fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/Interactive' num2str(cluster.interactive)],modelname);
106 end
107 end
108 if ~io_gather, %concatenate the output files:
109 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
110 end
111 fclose(fid);
112
113 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
114 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
115 end
116 end
117 %}}}
118 function BuildQueueScriptMultipleModels(cluster,dirname,modelname,solution,dirnames,modelnames,nps) % {{{
119
120 %some checks:
121 if isempty(modelname), error('BuildQueueScriptMultipleModels error message: need a non empty model name!');end
122
123 %what is the executable being called?
124 executable='issm_slc.exe';
125
126 if ispc & ~ismingw, error('BuildQueueScriptMultipleModels not support yet on windows machines');end;
127
128 %write queuing script
129 fid=fopen([modelname '.queue'],'w');
130
131 fprintf(fid,'#!%s\n',cluster.shell);
132
133 %number of cpus:
134 mpistring=sprintf('mpiexec -np %i ',cluster.np);
135
136 %executable:
137 mpistring=[mpistring sprintf('%s/%s ',cluster.codepath,executable)];
138
139 %solution name:
140 mpistring=[mpistring sprintf('%s ',solution)];
141
142 %execution directory and model name:
143 mpistring=[mpistring sprintf('%s/%s %s',cluster.executionpath,dirname,modelname)];
144
145 %inform main executable of how many icecaps, glaciers and earth models are being run:
146 mpistring=[mpistring sprintf(' %i ',length(dirnames))];
147
148 %icecaps, glaciers and earth location, names and number of processors associated:
149 for i=1:length(dirnames),
150 mpistring=[mpistring sprintf(' %s/%s %s %i ',cluster.executionpath,dirnames{i},modelnames{i},nps{i})];
151 end
152
153 %log files:
154 if ~cluster.interactive,
155 mpistring=[mpistring sprintf('2> %s.errlog> %s.outlog',modelname,modelname)];
156 end
157
158 %write this long string to disk:
159 fprintf(fid,mpistring);
160 fclose(fid);
161
162 %in interactive mode, create a run file, and errlog and outlog file
163 if cluster.interactive,
164 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
165 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
166 end
167 end
168 %}}}
169 function BuildQueueScriptIceOcean(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{
170
171 %write queuing script
172 %what is the executable being called?
173 executable='issm_ocean.exe';
174
175 fid=fopen([modelname '.queue'],'w');
176 fprintf(fid,'#!%s\n',cluster.shell);
177 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);
178 fclose(fid);
179
180 %in interactive mode, create a run file, and errlog and outlog file
181 if cluster.interactive,
182 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
183 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
184 end
185 end
186 %}}}
187 function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
188
189 %write queuing script
190 if ~ispc,
191
192 fid=fopen([modelname '.queue'],'w');
193 fprintf(fid,'#!/bin/sh\n');
194 if ~isvalgrind,
195 if cluster.interactive
196 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
197 else
198 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);
199 end
200 elseif isgprof,
201 fprintf(fid,'\n gprof %s/kriging.exe gmon.out > %s.performance',cluster.codepath,modelname);
202 else
203 %Add --gen-suppressions=all to get suppression lines
204 fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
205 fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',...
206 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
207 end
208 if ~io_gather, %concatenate the output files:
209 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
210 end
211 fclose(fid);
212
213 else % Windows
214
215 fid=fopen([modelname '.bat'],'w');
216 fprintf(fid,'@echo off\n');
217 if cluster.interactive
218 fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname);
219 else
220 fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
221 cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
222 end
223 fclose(fid);
224 end
225
226 %in interactive mode, create a run file, and errlog and outlog file
227 if cluster.interactive,
228 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
229 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
230 end
231 end
232 %}}}
233 function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{
234 if ~ispc | ismingw,
235
236 %compress the files into one zip.
237 compressstring=['tar -zcf ' dirname '.tar.gz '];
238 for i=1:numel(filelist),
239 compressstring = [compressstring ' ' filelist{i}];
240 end
241 if cluster.interactive,
242 compressstring = [compressstring ' ' modelname '.run ' modelname '.errlog ' modelname '.outlog '];
243 end
244 system(compressstring);
245
246 if cluster.verbose, disp('uploading input file and queuing script'); end
247 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
248 end
249 end %}}}
250 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
251
252 %figure out what shell extension we will use:
253 if isempty(strfind(cluster.shell,'csh')),
254 shellext='sh';
255 else
256 shellext='csh';
257 end
258
259 if cluster.verbose, disp('launching solution sequence on remote cluster'); end
260
261 launchcommand=['cd ' cluster.executionpath ' && rm -rf *.lock && rm -rf ADOLC* && tar -zxf ' dirname '.tar.gz && rm -rf *.tar.gz'];
262 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
263
264 end %}}}
265 function LaunchQueueJobIceOcean(cluster,modelname,dirname,filelist,restart,batch)% {{{
266
267 %figure out what shell extension we will use:
268 if isempty(strfind(cluster.shell,'csh')),
269 shellext='sh';
270 else
271 shellext='csh';
272 end
273
274 if cluster.verbose, disp('launching solution sequence on remote cluster'); end
275
276 launchcommand=['cd ' cluster.executionpath ' && rm -rf *.lock && tar -zxf ' dirname '.tar.gz && rm -rf *.tar.gz'];
277 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
278
279 end %}}}
280 function Download(cluster,dirname,filelist)% {{{
281
282 if ispc && ~ismingw,
283 %do nothing
284 return;
285 end
286
287 %copy files from cluster to current directory
288 issmscpin(cluster.name,cluster.login,cluster.port,cluster.executionpath,filelist);
289 end %}}}
290 end
291end
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