| [8586] | 1 | %GENERIC cluster class definition
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| [8578] | 2 | %
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| 3 | % Usage:
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| [8586] | 4 | % cluster=generic('name','astrid','np',3);
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| 5 | % cluster=generic('name',oshostname(),'np',3,'login','username');
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| [8578] | 6 |
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| 7 | classdef generic
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| [13395] | 8 | properties (SetAccess=public)
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| 9 | % {{{
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| 10 | name='';
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| 11 | login='';
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| 12 | np=1;
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| 13 | port=0;
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| 14 | interactive=1;
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| 15 | codepath=[issmdir() '/bin'];
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| [13975] | 16 | etcpath=[issmdir() '/etc'];
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| [13395] | 17 | executionpath=[issmdir() '/execution'];
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| 18 | valgrind=[issmdir() '/externalpackages/valgrind/install/bin/valgrind'];
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| 19 | valgrindlib=[issmdir() '/externalpackages/valgrind/install/lib/libmpidebug.so'];
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| 20 | valgrindsup=[issmdir() '/externalpackages/valgrind/issm.supp'];
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| 21 | %}}}
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| 22 | end
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| 23 | methods
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| 24 | function cluster=generic(varargin) % {{{
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| [8586] | 25 |
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| [13395] | 26 | %use provided options to change fields
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| 27 | options=pairoptions(varargin{:});
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| [8586] | 28 |
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| [13395] | 29 | %get name
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| 30 | cluster.name=getfieldvalue(options,'name',oshostname());
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| [8586] | 31 |
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| [13395] | 32 | %initialize cluster using user settings if provided
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| 33 | if (exist([cluster.name '_settings'])==2), eval([cluster.name '_settings']); end
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| [8578] | 34 |
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| [13395] | 35 | %OK get other fields
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| 36 | cluster=AssignObjectFields(pairoptions(varargin{:}),cluster);
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| 37 | end
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| 38 | %}}}
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| 39 | function disp(cluster) % {{{
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| 40 | % display the object
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| 41 | disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1)));
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| 42 | disp(sprintf(' name: %s',cluster.name));
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| 43 | disp(sprintf(' login: %s',cluster.login));
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| 44 | disp(sprintf(' np: %i',cluster.np));
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| 45 | disp(sprintf(' port: %i',cluster.port));
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| 46 | disp(sprintf(' codepath: %s',cluster.codepath));
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| 47 | disp(sprintf(' executionpath: %s',cluster.executionpath));
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| [13975] | 48 | disp(sprintf(' etcpath: %s',cluster.executionpath));
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| [13395] | 49 | disp(sprintf(' valgrind: %s',cluster.valgrind));
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| 50 | disp(sprintf(' valgrindlib: %s',cluster.valgrindlib));
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| 51 | disp(sprintf(' valgrindsup: %s',cluster.valgrindsup));
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| 52 | end
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| 53 | %}}}
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| 54 | function md = checkconsistency(cluster,md,solution,analyses) % {{{
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| 55 | if cluster.np<1
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| 56 | md = checkmessage(md,['number of processors should be at least 1']);
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| 57 | end
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| 58 | if isnan(cluster.np),
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| 59 | md = checkmessage(md,'number of processors should not be NaN!');
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| 60 | end
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| 61 | end
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| 62 | %}}}
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| 63 | function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
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| [8578] | 64 |
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| [13395] | 65 | %write queuing script
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| 66 | if ~ispc(),
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| [12706] | 67 |
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| [13395] | 68 | fid=fopen([modelname '.queue'],'w');
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| 69 | fprintf(fid,'#!/bin/sh\n');
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| 70 | if ~isvalgrind,
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| 71 | if cluster.interactive
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| [16137] | 72 | if IssmConfig('_HAVE_MPI_'),
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| [13395] | 73 | fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s ',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
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| 74 | else
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| 75 | fprintf(fid,'%s/issm.exe %s %s %s ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
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| 76 | end
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| 77 | else
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| [16137] | 78 | if IssmConfig('_HAVE_MPI_'),
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| [13395] | 79 | 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);
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| 80 | else
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| 81 | fprintf(fid,'%s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
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| 82 | end
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| 83 | end
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| 84 | elseif isgprof,
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| 85 | fprintf(fid,'\n gprof %s/issm.exe gmon.out > %s.performance',cluster.codepath,modelname);
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| 86 | else
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| 87 | %Add --gen-suppressions=all to get suppression lines
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| 88 | fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
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| 89 | if ismac,
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| [16137] | 90 | if IssmConfig('_HAVE_MPI_'),
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| [13395] | 91 | fprintf(fid,'mpiexec -np %i %s --leak-check=full --dsymutil=yes --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
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| 92 | cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname], modelname,modelname,modelname);
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| 93 | else
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| 94 | fprintf(fid,'%s --leak-check=full --dsymutil=yes --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
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| 95 | cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname], modelname,modelname,modelname);
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| 96 | end
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| 97 | else
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| [16137] | 98 | if IssmConfig('_HAVE_MPI_'),
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| [13395] | 99 | fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
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| 100 | cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
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| 101 | else
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| 102 | fprintf(fid,'%s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
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| 103 | cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
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| 104 | end
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| 105 | end
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| 106 | end
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| 107 | if ~io_gather, %concatenate the output files:
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| 108 | fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
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| 109 | end
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| 110 | fclose(fid);
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| [12706] | 111 |
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| [13395] | 112 | else % Windows
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| [12706] | 113 |
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| [13395] | 114 | fid=fopen([modelname '.bat'],'w');
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| 115 | fprintf(fid,'@echo off\n');
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| [15396] | 116 |
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| 117 | if cluster.np>1,
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| 118 | fprintf(fid,'"C:\\Program Files\\MPICH2\\bin\\mpiexec.exe" -n %i "%s/issm.exe" %s ./ %s ',cluster.np,cluster.codepath,EnumToString(solution),modelname);
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| [13395] | 119 | else
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| [15396] | 120 | fprintf(fid,'"%s/issm.exe" %s ./ %s ',cluster.codepath,EnumToString(solution),modelname);
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| [13395] | 121 | end
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| 122 | fclose(fid);
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| 123 | end
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| [8578] | 124 |
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| [13395] | 125 | %in interactive mode, create a run file, and errlog and outlog file
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| 126 | if cluster.interactive,
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| 127 | fid=fopen([modelname '.errlog'],'w'); fclose(fid);
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| 128 | fid=fopen([modelname '.outlog'],'w'); fclose(fid);
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| 129 | end
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| 130 | end
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| 131 | %}}}
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| 132 | function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
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| [12706] | 133 |
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| [13395] | 134 | %write queuing script
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| 135 | if ~ispc(),
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| [12706] | 136 |
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| [13395] | 137 | fid=fopen([modelname '.queue'],'w');
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| 138 | fprintf(fid,'#!/bin/sh\n');
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| 139 | if ~isvalgrind,
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| 140 | if cluster.interactive
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| 141 | fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
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| 142 | else
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| 143 | 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);
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| 144 | end
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| 145 | elseif isgprof,
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| 146 | fprintf(fid,'\n gprof %s/kriging.exe gmon.out > %s.performance',cluster.codepath,modelname);
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| 147 | else
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| 148 | %Add --gen-suppressions=all to get suppression lines
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| 149 | fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
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| 150 | fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',...
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| 151 | cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
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| 152 | end
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| 153 | if ~io_gather, %concatenate the output files:
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| 154 | fprintf(fid,'\ncat %s.outbin.* > %s.outbin',modelname,modelname);
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| 155 | end
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| 156 | fclose(fid);
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| [11527] | 157 |
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| [13395] | 158 | else % Windows
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| [8578] | 159 |
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| [13395] | 160 | fid=fopen([modelname '.bat'],'w');
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| 161 | fprintf(fid,'@echo off\n');
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| 162 | if cluster.interactive
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| 163 | fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' modelname],modelname);
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| 164 | else
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| 165 | fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
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| 166 | cluster.codepath,EnumToString(solution),[cluster.executionpath '/' modelname],modelname,modelname,modelname);
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| 167 | end
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| 168 | fclose(fid);
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| 169 | end
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| [8578] | 170 |
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| [13395] | 171 | %in interactive mode, create a run file, and errlog and outlog file
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| 172 | if cluster.interactive,
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| 173 | fid=fopen([modelname '.errlog'],'w'); fclose(fid);
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| 174 | fid=fopen([modelname '.outlog'],'w'); fclose(fid);
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| 175 | end
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| 176 | end
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| 177 | %}}}
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| 178 | function LaunchQueueJob(cluster,modelname,dirname,filelist)% {{{
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| [8578] | 179 |
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| [15396] | 180 | if ~ispc,
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| 181 | %compress the files into one zip.
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| 182 | compressstring=['tar -zcf ' dirname '.tar.gz '];
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| 183 | for i=1:numel(filelist),
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| 184 | compressstring = [compressstring ' ' filelist{i}];
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| 185 | end
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| 186 | if cluster.interactive,
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| 187 | compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
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| 188 | end
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| 189 | system(compressstring);
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| [11527] | 190 |
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| [15396] | 191 | disp('uploading input file and queueing script');
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| 192 | issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
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| [11527] | 193 |
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| [15396] | 194 | disp('launching solution sequence on remote cluster');
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| 195 | launchcommand=['source ' cluster.etcpath '/environment.sh && cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
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| 196 | ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && source ' modelname '.queue '];
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| 197 | issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
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| 198 | else
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| 199 | system([modelname '.bat']);
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| 200 | end
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| [13395] | 201 | end %}}}
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| 202 | function Download(cluster,dirname,filelist)% {{{
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| [11527] | 203 |
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| [13395] | 204 | if ispc(),
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| [12706] | 205 | %do nothing
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| 206 | return;
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| [8578] | 207 | end
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| 208 |
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| [12706] | 209 | %copy files from cluster to current directory
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| 210 | directory=[cluster.executionpath '/' dirname '/'];
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| 211 | issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist);
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| [11527] | 212 | end %}}}
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| [8578] | 213 | end
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| 214 | end
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