Index: ../trunk-jpl/src/m/classes/clusters/sherlock.m
===================================================================
--- ../trunk-jpl/src/m/classes/clusters/sherlock.m	(nonexistent)
+++ ../trunk-jpl/src/m/classes/clusters/sherlock.m	(revision 24160)
@@ -0,0 +1,160 @@
+%PFE class definition
+%
+%   Usage:
+%      cluster=sherlock();
+%      cluster=sherlock('np',3);
+%      cluster=sherlock('np',3,'login','username');
+
+classdef sherlock
+    properties (SetAccess=public)  
+		 % {{{
+		 name          = 'sherlock'
+		 login         = '';
+		 numnodes      = 1;
+		 cpuspernode   = 24;
+		 port          = 0;
+		 codepath      = '';
+		 executionpath = '';
+		 interactive   = 0;
+		 time          = 30;
+		 memory        = 2;
+	 end
+	 %}}}
+	 methods
+		 function cluster=sherlock(varargin) % {{{
+
+			 %initialize cluster using default settings if provided
+			 if (exist('sherlock_settings')==2), sherlock_settings; end
+
+			 %use provided options to change fields
+			 cluster=AssignObjectFields(pairoptions(varargin{:}),cluster);
+		 end
+		 %}}}
+		 function disp(cluster) % {{{
+			 %  display the object
+			 disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1)));
+			 disp(sprintf('    name: %s',cluster.name));
+			 disp(sprintf('    login: %s',cluster.login));
+			 disp(sprintf('    port: %i',cluster.port));
+			 disp(sprintf('    numnodes: %i',cluster.numnodes));
+			 disp(sprintf('    cpuspernode: %i',cluster.cpuspernode));
+			 disp(sprintf('    np: %i',cluster.cpuspernode*cluster.numnodes));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+			 disp(sprintf('    interactive: %i',cluster.interactive));
+			 disp(sprintf('    time: %i',cluster.time));
+			 disp(sprintf('    memory: %i',cluster.memory));
+		 end
+		 %}}}
+		 function numprocs=np(cluster) % {{{
+			 %compute number of processors
+			 numprocs=cluster.numnodes*cluster.cpuspernode;
+		 end
+		 %}}}
+		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
+
+			 %Miscelaneous
+			 if isempty(cluster.login), md = checkmessage(md,'login empty'); end
+			 if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end
+			 if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end
+
+		 end
+		 %}}}
+		 function BuildKrigingQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
+
+			 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+			 if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+
+			 %write queuing script 
+			 fid=fopen([modelname '.queue'],'w');
+			 fprintf(fid,'#!/bin/bash\n');
+			 fprintf(fid,'#SBATCH --job-name=%s\n',mdelname);
+			 fprintf(fid,'#SBATCH -p %s \n',cluster.queue);
+			 fprintf(fid,'#SBATCH -N %i -n %i\n',cluster.numnodes,cluster.cpuspernode);
+			 fprintf(fid,'#SBATCH --time=%i\n',cluster.time*60); %walltime is in seconds.
+			 fprintf(fid,'#SBATCH --mem-per-cpu=%igb\n',cluster.memory);
+			 fprintf(fid,'#SBATCH -o %s.outlog \n',modelname);
+			 fprintf(fid,'#SBATCH -e %s.errlog \n\n',modelname);
+			 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+			 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+			 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
+			 if ~io_gather, %concatenate the output files:
+				 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			 end
+			 fclose(fid);
+		 end
+		 %}}}
+		 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
+
+			 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+			 if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+
+			 %write queuing script 
+			 fid=fopen([modelname '.queue'],'w');
+			 fprintf(fid,'#!/bin/bash\n');
+			 fprintf(fid,'#SBATCH --job-name=%s\n',modelname);
+			 fprintf(fid,'#SBATCH -N %i -n %i\n',cluster.numnodes,cluster.cpuspernode);
+			 fprintf(fid,'#SBATCH --time=%i\n',cluster.time*60); %walltime is in seconds.
+			 fprintf(fid,'#SBATCH --mem-per-cpu=%igb\n',cluster.memory);
+			 fprintf(fid,'#SBATCH -o %s.outlog \n',modelname);
+			 fprintf(fid,'#SBATCH -e %s.errlog \n\n',modelname);
+			 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+			 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+			 fprintf(fid,'mpiexec -n %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+			 if ~io_gather, %concatenate the output files:
+				 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			 end
+			 fclose(fid);
+
+			 %in interactive mode, create a run file, and errlog and outlog file
+			 if cluster.interactive,
+				 fid=fopen([modelname '.run'],'w');
+				 fprintf(fid,'mpiexec -n %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+				 if ~io_gather, %concatenate the output files:
+					 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+				 end
+				 fclose(fid);
+				 fid=fopen([modelname '.errlog'],'w');
+				 fclose(fid);
+				 fid=fopen([modelname '.outlog'],'w');
+				 fclose(fid);
+			 end
+		 end %}}}
+		 function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{
+
+			 %compress the files into one zip.
+			 compressstring=['tar -zcf ' dirname '.tar.gz '];
+			 for i=1:numel(filelist),
+				 compressstring = [compressstring ' ' filelist{i}];
+			 end
+			 if cluster.interactive,
+				 compressstring = [compressstring ' ' modelname '.errlog ' modelname '.outlog '];
+			 end
+			 system(compressstring);
+
+			 disp('uploading input file and queueing script');
+			 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
+
+		 end %}}}
+		 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
+
+			 disp('launching solution sequence on remote cluster');
+			 if ~isempty(restart)
+				 launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && hostname && sbatch ' modelname '.queue '];
+			 else
+				 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+					 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && sbatch ' modelname '.queue '];
+			 end
+			 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
+		 end %}}}
+		 function Download(cluster,dirname,filelist)% {{{
+
+			 %copy files from cluster to current directory
+			 directory=[cluster.executionpath '/' dirname '/'];
+			 issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist);
+
+		 end %}}}
+	end
+end