source: issm/trunk/src/m/classes/clusters/localpfe.m@ 22758

Last change on this file since 22758 was 22758, checked in by Mathieu Morlighem, 7 years ago

merged trunk-jpl and trunk for revision 22757
File size: 9.4 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
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(' port: %i',cluster.port));
56 disp(sprintf(' codepath: %s',cluster.codepath));
57 disp(sprintf(' executionpath: %s',cluster.executionpath));
58 disp(sprintf(' etcpath: %s',cluster.etcpath));
59 disp(sprintf(' valgrind: %s',cluster.valgrind));
60 disp(sprintf(' valgrindlib: %s',cluster.valgrindlib));
61 disp(sprintf(' valgrindsup: %s',cluster.valgrindsup));
62 disp(sprintf(' verbose: %s',cluster.verbose));
63 disp(sprintf(' shell: %s',cluster.shell));
64 end
65 %}}}
66 function md = checkconsistency(cluster,md,solution,analyses) % {{{
67 if cluster.np<1
68 md = checkmessage(md,['number of processors should be at least 1']);
69 end
70 if isnan(cluster.np),
71 md = checkmessage(md,'number of processors should not be NaN!');
72 end
73 end
74 %}}}
75 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
76
77 %write queuing script
78 %what is the executable being called?
79 executable='issm.exe';
80 if isdakota,
81 version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3));
82 if (version>=6),
83 executable='issm_dakota.exe';
84 end
85 end
86
87 fid=fopen([modelname '.queue'],'w');
88 fprintf(fid,'#!%s\n',cluster.shell);
89 fprintf(fid,'mpiexec -np %i %s/%s %s %s %s \n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,modelname);
90 fclose(fid);
91
92
93 %in interactive mode, create a run file, and errlog and outlog file
94 if cluster.interactive,
95 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
96 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
97 end
98 end
99 %}}}
100 function BuildQueueScriptMultipleModels(cluster,dirname,modelname,solution,dirnames,modelnames,nps) % {{{
101
102 %some checks:
103 if isempty(modelname), error('BuildQueueScriptMultipleModels error message: need a non empty model name!');end
104
105 %what is the executable being called?
106 executable='issm_slr.exe';
107
108 if ispc(), error('BuildQueueScriptMultipleModels not support yet on windows machines');end;
109
110 %write queuing script
111 fid=fopen([modelname '.queue'],'w');
112
113 fprintf(fid,'#!%s\n',cluster.shell);
114
115 %number of cpus:
116 mpistring=sprintf('mpiexec -np %i ',cluster.np);
117
118 %executable:
119 mpistring=[mpistring sprintf('%s/%s ',cluster.codepath,executable)];
120
121 %solution name:
122 mpistring=[mpistring sprintf('%s ',solution)];
123
124 %execution directory and model name:
125 mpistring=[mpistring sprintf('%s/%s %s',cluster.executionpath,dirname,modelname)];
126
127 %inform main executable of how many icecaps, glaciers and earth models are being run:
128 mpistring=[mpistring sprintf(' %i ',length(dirnames))];
129
130 %icecaps, glaciers and earth location, names and number of processors associated:
131 for i=1:length(dirnames),
132 mpistring=[mpistring sprintf(' %s/%s %s %i ',cluster.executionpath,dirnames{i},modelnames{i},nps{i})];
133 end
134
135 %log files:
136 if ~cluster.interactive,
137 mpistring=[mpistring sprintf('2> %s.errlog> %s.outlog',modelname,modelname)];
138 end
139
140 %write this long string to disk:
141 fprintf(fid,mpistring);
142 fclose(fid);
143
144 %in interactive mode, create a run file, and errlog and outlog file
145 if cluster.interactive,
146 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
147 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
148 end
149 end
150 %}}}
151 function BuildQueueScriptIceOcean(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota) % {{{
152
153 %write queuing script
154 %what is the executable being called?
155 executable='issm_ocean.exe';
156
157 fid=fopen([modelname '.queue'],'w');
158 fprintf(fid,'#!%s\n',cluster.shell);
159 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);
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 BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
170
171 %write queuing script
172 if ~ispc(),
173
174 fid=fopen([modelname '.queue'],'w');
175 fprintf(fid,'#!/bin/sh\n');
176 if ~isvalgrind,
177 if cluster.interactive
178 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
179 else
180 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);
181 end
182 elseif isgprof,
183 fprintf(fid,'\n gprof %s/kriging.exe gmon.out > %s.performance',cluster.codepath,modelname);
184 else
185 %Add --gen-suppressions=all to get suppression lines
186 fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
187 fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',...
188 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
189 end
190 if ~io_gather, %concatenate the output files:
191 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
192 end
193 fclose(fid);
194
195 else % Windows
196
197 fid=fopen([modelname '.bat'],'w');
198 fprintf(fid,'@echo off\n');
199 if cluster.interactive
200 fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname);
201 else
202 fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
203 cluster.codepath,solution,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
204 end
205 fclose(fid);
206 end
207
208 %in interactive mode, create a run file, and errlog and outlog file
209 if cluster.interactive,
210 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
211 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
212 end
213 end
214 %}}}
215 function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{
216 if ~ispc,
217
218 %compress the files into one zip.
219 compressstring=['tar -zcf ' dirname '.tar.gz '];
220 for i=1:numel(filelist),
221 compressstring = [compressstring ' ' filelist{i}];
222 end
223 if cluster.interactive,
224 compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
225 end
226 system(compressstring);
227
228 if cluster.verbose, disp('uploading input file and queueing script'); end
229 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
230 end
231 end %}}}
232 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
233
234 %figure out what shell extension we will use:
235 if isempty(strfind(cluster.shell,'csh')),
236 shellext='sh';
237 else
238 shellext='csh';
239 end
240
241 if cluster.verbose, disp('launching solution sequence on remote cluster'); end
242
243 launchcommand=['cd ' cluster.executionpath ' && rm -rf *.lock && rm -rf ADOLC* && tar -zxf ' dirname '.tar.gz && rm -rf *.tar.gz'];
244 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
245
246 end %}}}
247 function LaunchQueueJobIceOcean(cluster,modelname,dirname,filelist,restart,batch)% {{{
248
249 %figure out what shell extension we will use:
250 if isempty(strfind(cluster.shell,'csh')),
251 shellext='sh';
252 else
253 shellext='csh';
254 end
255
256 if cluster.verbose, disp('launching solution sequence on remote cluster'); end
257
258 launchcommand=['cd ' cluster.executionpath ' && rm -rf *.lock && tar -zxf ' dirname '.tar.gz && rm -rf *.tar.gz'];
259 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
260
261 end %}}}
262 function Download(cluster,dirname,filelist)% {{{
263
264 if ispc(),
265 %do nothing
266 return;
267 end
268
269 %copy files from cluster to current directory
270 issmscpin(cluster.name,cluster.login,cluster.port,cluster.executionpath,filelist);
271 end %}}}
272 end
273end
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