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Changeset 26330 for issm/trunk-jpl/src/m/classes/clusters/lonestar.m
- Timestamp:
- 06/23/21 13:51:11 (4 years ago)
- File:
-
- 1 edited
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issm/trunk-jpl/src/m/classes/clusters/lonestar.m (modified) (2 diffs)
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issm/trunk-jpl/src/m/classes/clusters/lonestar.m
r26291 r26330 1 %LONESTAR cl ass definition1 %LONESTAR cluster class definition 2 2 % 3 3 % Usage: … … 7 7 8 8 classdef lonestar 9 properties (SetAccess=public) 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 function numprocs=np(cluster) % {{{55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{182 183 184 185 186 187 188 189 190 191 192 function Download(cluster,dirname,filelist)% {{{193 194 195 196 197 198 9 properties (SetAccess=public) 10 % {{{ 11 name = 'ls5.tacc.utexas.edu' 12 login = ''; 13 modules = {'intel/18.0.2' 'gsl'}; 14 numnodes = 1; 15 cpuspernode = 24; 16 port = 1099; 17 queue = 'normal'; 18 codepath = ''; 19 executionpath = ''; 20 interactive = 0; 21 time = 48*60*60; 22 email = ''; 23 end 24 %}}} 25 methods 26 function cluster=lonestar(varargin) % {{{ 27 28 %initialize cluster using default settings if provided 29 if (exist('lonestar_settings')==2), lonestar_settings; end 30 31 %use provided options to change fields 32 cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); 33 34 end 35 %}}} 36 function disp(cluster) % {{{ 37 % display the object 38 disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); 39 disp(sprintf(' name: %s',cluster.name)); 40 disp(sprintf(' login: %s',cluster.login)); 41 disp(sprintf(' modules: %s',strjoin(cluster.modules,', '))); 42 disp(sprintf(' port: %i',cluster.port)); 43 disp(sprintf(' numnodes: %i',cluster.numnodes)); 44 disp(sprintf(' cpuspernode: %i',cluster.cpuspernode)); 45 disp(sprintf(' np: %i',cluster.np)); 46 disp(sprintf(' queue: %s',cluster.queue)); 47 disp(sprintf(' codepath: %s',cluster.codepath)); 48 disp(sprintf(' executionpath: %s',cluster.executionpath)); 49 disp(sprintf(' interactive: %i',cluster.interactive)); 50 disp(sprintf(' time: %i',cluster.time)); 51 disp(sprintf(' email: %s',cluster.email)); 52 end 53 %}}} 54 function numprocs=nprocs(cluster) % {{{ 55 %compute number of processors 56 numprocs=cluster.numnodes*cluster.cpuspernode; 57 end 58 %}}} 59 function md = checkconsistency(cluster,md,solution,analyses) % {{{ 60 61 available_queues={'normal','development'}; 62 queue_requirements_time=[48*60*60 2*60*60]; 63 queue_requirements_np=[4104 264]; 64 65 QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,cluster.time) 66 67 %Miscelaneous 68 if isempty(cluster.login), md = checkmessage(md,'login empty'); end 69 if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end 70 if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end 71 end 72 %}}} 73 function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{ 74 75 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end 76 if(isgprof), disp('gprof not supported by cluster, ignoring...'); end 77 78 %write queuing script 79 fid=fopen([modelname '.queue'],'w'); 80 fprintf(fid,'#!/bin/bash\n'); 81 fprintf(fid,'#$ -N %s\n',modelname); 82 fprintf(fid,'#$ -q %s \n',cluster.queue); 83 fprintf(fid,'#$ -pe one-node-mpi 2-64\n'); 84 fprintf(fid,'#$ -R y\n'); 85 fprintf(fid,'#$ -m beas\n'); 86 fprintf(fid,'#$ -o %s.outlog \n',modelname); 87 fprintf(fid,'#$ -e %s.errlog \n\n',modelname); 88 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME 89 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME 90 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,modelname); 91 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname); 92 if ~io_gather, %concatenate the output files: 93 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); 94 end 95 fclose(fid); 96 end 97 %}}} 98 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ 99 100 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end 101 if(isgprof), disp('gprof not supported by cluster, ignoring...'); end 102 103 executable='issm.exe'; 104 if isdakota, 105 version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3)); 106 if (version>=6), 107 executable='issm_dakota.exe'; 108 end 109 end 110 if isoceancoupling, 111 executable='issm_ocean.exe'; 112 end 113 114 %write queuing script 115 fid=fopen([modelname '.queue'],'w'); 116 117 fprintf(fid,'#!/bin/bash\n'); 118 fprintf(fid,'#SBATCH -J %s \n',modelname); 119 fprintf(fid,'#SBATCH -p %s \n',cluster.queue); 120 fprintf(fid,'#SBATCH -o %s.outlog \n',modelname); 121 fprintf(fid,'#SBATCH -e %s.errlog \n',modelname); 122 fprintf(fid,'#SBATCH -n %i \n',cluster.numnodes*max(cluster.np/cluster.numnodes,24)); 123 fprintf(fid,'#SBATCH -N %i \n',cluster.numnodes); 124 fprintf(fid,'#SBATCH -t %02i:%02i:00 \n\n',floor(cluster.time/3600),floor(mod(cluster.time,3600)/60)); 125 for i=1:numel(cluster.modules), 126 fprintf(fid,['module load ' cluster.modules{i} '\n']); 127 end 128 129 if isdakota, 130 fprintf(fid,'export KMP_AFFINITY="granularity=fine,compact,verbose" \n\n'); 131 end 132 133 if length(find(cluster.email=='@'))>0 134 fprintf(fid,'#SBATCH --mail-user=%s \n',cluster.email); 135 fprintf(fid,'#SBATCH --mail-type=end \n\n'); 136 137 %fprintf(fid,'ssh login1 "mail -s ''SLURM Jobid=${SLURM_JOBID} Name=${SLURM_JOB_NAME} Began on Lonestar 5.'' %s <<< ''Job Started'' " \n\n',cluster.email); 138 end 139 140 fprintf(fid,'export PATH="$PATH:."\n\n'); 141 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME 142 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME 143 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname); 144 fprintf(fid,'ibrun -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); 145 if ~io_gather, %concatenate the output files: 146 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); 147 end 148 149 fclose(fid); 150 151 %in interactive mode, create a run file, and errlog and outlog file 152 if cluster.interactive, 153 fid=fopen([modelname '.run'],'w'); 154 fprintf(fid,'ibrun -np %i %s/%s %s %s %s\n',cluster.np,executable,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); 155 if ~io_gather, %concatenate the output files: 156 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); 157 end 158 fclose(fid); 159 fid=fopen([modelname '.errlog'],'w'); 160 fclose(fid); 161 fid=fopen([modelname '.outlog'],'w'); 162 fclose(fid); 163 end 164 end %}}} 165 function UploadQueueJob(cluster,modelname,dirname,filelist) % {{{ 166 167 %compress the files into one zip. 168 compressstring=['tar -zcf ' dirname '.tar.gz ']; 169 for i=1:numel(filelist), 170 compressstring = [compressstring ' ' filelist{i}]; 171 end 172 if cluster.interactive, 173 compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog ']; 174 end 175 system(compressstring); 176 177 disp('uploading input file and queueing script'); 178 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']}); 179 180 end %}}} 181 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch) % {{{ 182 183 disp('launching solution sequence on remote cluster'); 184 if ~isempty(restart) 185 launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && hostname && sbatch ' modelname '.queue ']; 186 else 187 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... 188 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && hostname && sbatch ' modelname '.queue ']; 189 end 190 issmssh(cluster.name,cluster.login,cluster.port,launchcommand); 191 end %}}} 192 function Download(cluster,dirname,filelist) % {{{ 193 194 %copy files from cluster to current directory 195 directory=[cluster.executionpath '/' dirname '/']; 196 issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); 197 198 end %}}} 199 199 end 200 200 end
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