source: issm/trunk/src/m/classes/clusters/generic.m@ 13395

Last change on this file since 13395 was 13395, checked in by Mathieu Morlighem, 12 years ago

merged trunk-jpl and trunk for revision 13393
File size: 8.3 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 port=0;
14 interactive=1;
15 codepath=[issmdir() '/bin'];
16 executionpath=[issmdir() '/execution'];
17 valgrind=[issmdir() '/externalpackages/valgrind/install/bin/valgrind'];
18 valgrindlib=[issmdir() '/externalpackages/valgrind/install/lib/libmpidebug.so'];
19 valgrindsup=[issmdir() '/externalpackages/valgrind/issm.supp'];
20 %}}}
21 end
22 methods
23 function cluster=generic(varargin) % {{{
24
25 %use provided options to change fields
26 options=pairoptions(varargin{:});
27
28 %get name
29 cluster.name=getfieldvalue(options,'name',oshostname());
30
31 %initialize cluster using user settings if provided
32 if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end
33
34 %OK get other fields
35 cluster=AssignObjectFields(pairoptions(varargin{:}),cluster);
36 end
37 %}}}
38 function disp(cluster) % {{{
39 % display the object
40 disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1)));
41 disp(sprintf(' name: %s',cluster.name));
42 disp(sprintf(' login: %s',cluster.login));
43 disp(sprintf(' np: %i',cluster.np));
44 disp(sprintf(' port: %i',cluster.port));
45 disp(sprintf(' codepath: %s',cluster.codepath));
46 disp(sprintf(' executionpath: %s',cluster.executionpath));
47 disp(sprintf(' valgrind: %s',cluster.valgrind));
48 disp(sprintf(' valgrindlib: %s',cluster.valgrindlib));
49 disp(sprintf(' valgrindsup: %s',cluster.valgrindsup));
50 end
51 %}}}
52 function md = checkconsistency(cluster,md,solution,analyses) % {{{
53 if cluster.np<1
54 md = checkmessage(md,['number of processors should be at least 1']);
55 end
56 if isnan(cluster.np),
57 md = checkmessage(md,'number of processors should not be NaN!');
58 end
59 end
60 %}}}
61 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
62
63 %write queuing script
64 if ~ispc(),
65
66 fid=fopen([modelname '.queue'],'w');
67 fprintf(fid,'#!/bin/sh\n');
68 if ~isvalgrind,
69 if cluster.interactive
70 if ismpi,
71 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s ',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
72 else
73 fprintf(fid,'%s/issm.exe %s %s %s ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
74 end
75 else
76 if ismpi,
77 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
78 else
79 fprintf(fid,'%s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
80 end
81 end
82 elseif isgprof,
83 fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname);
84 else
85 %Add --gen-suppressions=all to get suppression lines
86 fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
87 if ismac,
88 if ismpi,
89 fprintf(fid,'mpiexec -np %i %s --leak-check=full --dsymutil=yes --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
90 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname], modelname,modelname,modelname);
91 else
92 fprintf(fid,'%s --leak-check=full --dsymutil=yes --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
93 cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname], modelname,modelname,modelname);
94 end
95 else
96 if ismpi,
97 fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
98 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
99 else
100 fprintf(fid,'%s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
101 cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
102 end
103 end
104 end
105 if ~io_gather, %concatenate the output files:
106 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
107 end
108 fclose(fid);
109
110 else % Windows
111
112 fid=fopen([modelname '.bat'],'w');
113 fprintf(fid,'@echo off\n');
114 if cluster.interactive
115 fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
116 else
117 fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
118 cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
119 end
120 fclose(fid);
121 end
122
123 %in interactive mode, create a run file, and errlog and outlog file
124 if cluster.interactive,
125 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
126 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
127 end
128 end
129 %}}}
130 function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
131
132 %write queuing script
133 if ~ispc(),
134
135 fid=fopen([modelname '.queue'],'w');
136 fprintf(fid,'#!/bin/sh\n');
137 if ~isvalgrind,
138 if cluster.interactive
139 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
140 else
141 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);
142 end
143 elseif isgprof,
144 fprintf(fid,'\n gprof %s/kriging.exe gmon.out > %s.performance',cluster.codepath,modelname);
145 else
146 %Add --gen-suppressions=all to get suppression lines
147 fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
148 fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',...
149 cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
150 end
151 if ~io_gather, %concatenate the output files:
152 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
153 end
154 fclose(fid);
155
156 else % Windows
157
158 fid=fopen([modelname '.bat'],'w');
159 fprintf(fid,'@echo off\n');
160 if cluster.interactive
161 fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' modelname],modelname);
162 else
163 fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
164 cluster.codepath,EnumToString(solution),[cluster.executionpath '/' modelname],modelname,modelname,modelname);
165 end
166 fclose(fid);
167 end
168
169 %in interactive mode, create a run file, and errlog and outlog file
170 if cluster.interactive,
171 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
172 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
173 end
174 end
175 %}}}
176 function LaunchQueueJob(cluster,modelname,dirname,filelist)% {{{
177
178 %compress the files into one zip.
179 compressstring=['tar -zcf ' dirname '.tar.gz '];
180 for i=1:numel(filelist),
181 compressstring = [compressstring ' ' filelist{i}];
182 end
183 if cluster.interactive,
184 compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
185 end
186 system(compressstring);
187
188 disp('uploading input file and queueing script');
189 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
190
191 disp('launching solution sequence on remote cluster');
192 launchcommand=['source ' issmdir '/etc/environment.sh && cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
193 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && source ' modelname '.queue '];
194 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
195 end %}}}
196 function Download(cluster,dirname,filelist)% {{{
197
198 if ispc(),
199 %do nothing
200 return;
201 end
202
203 %copy files from cluster to current directory
204 directory=[cluster.executionpath '/' dirname '/'];
205 issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist);
206 end %}}}
207 end
208end
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