Index: ../trunk-jpl/src/m/classes/clusters/hpc.m
===================================================================
--- ../trunk-jpl/src/m/classes/clusters/hpc.m	(revision 0)
+++ ../trunk-jpl/src/m/classes/clusters/hpc.m	(revision 18695)
@@ -0,0 +1,162 @@
+%PFE class definition
+%
+%   Usage:
+%      cluster=hpc();
+%      cluster=hpc('np',3);
+%      cluster=hpc('np',3,'login','username');
+
+classdef hpc
+    properties (SetAccess=public)  
+		 % {{{
+		 name='hpc.oit.uci.edu'
+		 login='';
+		 numnodes=1;
+		 cpuspernode=4; 
+		 port=0;
+		 queue='pub64';
+		 codepath='';
+		 executionpath='';
+		 interactive=0;
+	 end
+	 properties (SetAccess=private) 
+		 np=20*8;
+		 % }}}
+	 end
+	 methods
+		 function cluster=hpc(varargin) % {{{
+
+			 %initialize cluster using default settings if provided
+			 if (exist('hpc_settings')==2), hpc_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('    queue: %s',cluster.queue));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+			 disp(sprintf('    interactive: %i',cluster.interactive));
+		 end
+		 %}}}
+		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
+
+			 available_queues={'pub64','free64','free48'};
+			 queue_requirements_time=[Inf Inf Inf Inf];
+			 queue_requirements_np=[64 64 48];
+
+			 QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1)
+
+			 %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,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
+
+			 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+			 if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+
+			 %compute number of processors
+			 cluster.np=cluster.numnodes*cluster.cpuspernode;
+
+			 %write queuing script 
+			 fid=fopen([modelname '.queue'],'w');
+			 fprintf(fid,'#!/bin/bash\n');
+			 fprintf(fid,'#$ -N %s\n',modelname);
+			 fprintf(fid,'#$ -q %s \n',cluster.queue);
+			 fprintf(fid,'#$ -pe one-node-mpi 2-64\n');
+			 fprintf(fid,'#$ -R y\n');
+			 fprintf(fid,'#$ -m beas\n');
+			 fprintf(fid,'#$ -o %s.outlog \n',modelname);
+			 fprintf(fid,'#$ -e %s.errlog \n\n',modelname);
+			 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+			 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,modelname);
+			 fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
+			 if ~io_gather, %concatenate the output files:
+				 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			 end
+			 fclose(fid);
+		 end
+		 %}}}
+		 function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
+
+			 if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end
+			 if(isgprof),    disp('gprof not supported by cluster, ignoring...'); end
+
+			 %compute number of processors
+			 cluster.np=cluster.numnodes*cluster.cpuspernode;
+
+			 %write queuing script 
+			 fid=fopen([modelname '.queue'],'w');
+			 fprintf(fid,'#!/bin/bash\n');
+			 fprintf(fid,'#$ -N %s\n',modelname);
+			 fprintf(fid,'#$ -q %s \n',cluster.queue);
+			 fprintf(fid,'#$ -pe one-node-mpi 2-64\n');
+			 fprintf(fid,'#$ -R y\n');
+			 fprintf(fid,'#$ -m beas\n');
+			 fprintf(fid,'#$ -o %s.outlog \n',modelname);
+			 fprintf(fid,'#$ -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/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(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 -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(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 LaunchQueueJob(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']});
+
+			 disp('launching solution sequence on remote cluster');
+			  launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+											 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && qsub ' modelname '.queue '];
+			 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
