source: issm/trunk/src/m/classes/clusters/generic.m@ 8586

Last change on this file since 8586 was 8586, checked in by Mathieu Morlighem, 14 years ago

use generic cluster instead of larsen, astrid, wilkes, ogive and other local machines
File size: 6.4 KB
Line 
1%GENERIC cluster class definition
2%
3% Usage:
4% cluster=generic('name','astrid',);
5% cluster=generic('name','astrid','np',3);
6% cluster=generic('name',oshostname(),'np',3,'login','username');
7
8classdef generic
9 properties (SetAccess=public)
10 % {{{1
11 name='';
12 login='';
13 np=1;
14 port=0;
15 interactive=1;
16 codepath=[issmtier() '/bin'];
17 executionpath=[issmdir() '/execution'];
18 valgrind=[issmtier() '/externalpackages/valgrind/install/bin/valgrind'];
19 valgrindlib=[issmtier() '/externalpackages/valgrind/install/lib/libmpidebug.so'];
20 valgrindsup=[issmtier() '/externalpackages/valgrind/issm.supp'];
21 %}}}
22 end
23 methods
24 function cluster=generic(varargin) % {{{1
25
26 %use provided options to change fields
27 options=pairoptions(varargin{:});
28
29 %get name
30 if ~exist(options,'name'), error('option ''name'' has not been provided'); end
31 cluster.name=getfieldvalue(options,'name');
32
33 %initialize cluster using user settings if provided
34 if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end
35
36 %OK get other fields
37 for i=1:size(options.list,1),
38 fieldname=options.list{i,1};
39 fieldvalue=options.list{i,2};
40 if ismember(fieldname,properties(generic)),
41 cluster.(fieldname)=fieldvalue;
42 else
43 disp(['''' fieldname ''' is not a property of cluster generic']);
44 end
45 end
46 end
47 %}}}
48 function disp(cluster) % {{{1
49 % display the object
50 disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1)));
51 disp(sprintf(' name: %s',cluster.name));
52 disp(sprintf(' login: %s',cluster.login));
53 disp(sprintf(' np: %i',cluster.np));
54 disp(sprintf(' port: %i',cluster.port));
55 disp(sprintf(' codepath: %s',cluster.codepath));
56 disp(sprintf(' executionpath: %s',cluster.executionpath));
57 disp(sprintf(' valgrind: %s',cluster.valgrind));
58 disp(sprintf(' valgrindlib: %s',cluster.valgrindlib));
59 disp(sprintf(' valgrindsup: %s',cluster.valgrindsup));
60 end
61 %}}}
62 function IsConsistent(cluster) % {{{1
63 if cluster.np<1
64 error(['number of processors should be at least 1']);
65 end
66 if isnan(cluster.np),
67 error('number of processors should not be NaN!');
68 end
69 end
70 %}}}
71 function BuildQueueScript(cluster,md) % {{{1
72
73 %retrieve parameters
74 modelname=md.name;
75 solution_type=md.solution_type;
76 mem_debug=md.mem_debug;
77
78 %open file for writing:
79 fid=fopen([modelname '.queue'],'w');
80
81 %write instructions for launching a job on the cluster
82 fprintf(fid,'#!/bin/sh\n');
83 if mem_debug==0,
84 if cluster.interactive
85 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock ',...
86 cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname);
87 else
88 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',...
89 cluster.np,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname);
90 end
91 else
92 %fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --gen-suppressions=all --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname);
93 fprintf(fid,'LD_PRELOAD=%s mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s.bin %s.petsc %s.outbin %s.lock 2> %s.errlog >%s.outlog ',...
94 cluster.valgrindlib,cluster.np,cluster.valgrind,cluster.valgrindsup, cluster.codepath,EnumToString(solution_type),cluster.executionpath,modelname,modelname,modelname,modelname,modelname,modelname);
95 end
96
97 if md.gprof,
98 fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname);
99 end
100
101 if ~md.io_gather,
102 %concatenate the output files:
103 fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
104 end
105
106 %in interactive mode, create a run file, and errlog and outlog file
107 if cluster.interactive,
108 fid=fopen([modelname '.errlog'],'w'); fclose(fid);
109 fid=fopen([modelname '.outlog'],'w'); fclose(fid);
110 end
111
112 end
113 %}}}
114 function LaunchQueueJob(cluster,md,options)% {{{1
115
116 %lauch command, to be executed via ssh
117 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ...
118 ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue '];
119
120 if ~strcmpi(options.batch,'yes'),
121
122 %compress the files into one zip.
123 compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc '];
124 if md.qmu_analysis,
125 compressstring=[compressstring md.name '.qmu.in'];
126 end
127 if cluster.interactive,
128 compressstring=[compressstring ' ' md.name '.errlog ' md.name '.outlog '];
129 end
130 system(compressstring);
131
132 disp('uploading input file and queueing script');
133 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[md.runtimename '.tar.gz']});
134
135 disp('launching solution sequence on remote cluster');
136 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
137 else
138 disp('batch mode requested: not launching job interactively');
139 disp('launch solution sequence on remote cluster by hand');
140 end
141
142 end %}}}
143 function Download(cluster,md)% {{{1
144
145 %some check
146 if isempty(md.runtimename),
147 error('supply runtime name for results to be loaded!');
148 end
149
150 %Figure out the directory where all the files are in:
151 directory=[cluster.executionpath '/' md.runtimename '/'];
152
153 %What packages are we picking up from remote cluster
154 packages={[md.name '.outlog'],[md.name '.errlog']};
155 if md.qmu_analysis,
156 packages{end+1}=[md.name '.qmu.err'];
157 packages{end+1}=[md.name '.qmu.out'];
158 if isfield(md.qmu_params,'tabular_graphics_data'),
159 if md.qmu_params.tabular_graphics_data==true,
160 packages{end+1}='dakota_tabular.dat';
161 end
162 end
163 else
164 packages{end+1}=[md.name '.outbin'];
165 end
166
167 %copy files from cluster to present directory
168 issmscpin(cluster.name, cluster.login, cluster.port, directory, packages);
169 end %}}}
170 end
171end
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