Index: ../trunk-jpl/src/m/classes/clusters/computecanada.m
===================================================================
--- ../trunk-jpl/src/m/classes/clusters/computecanada.m	(nonexistent)
+++ ../trunk-jpl/src/m/classes/clusters/computecanada.m	(revision 26851)
@@ -0,0 +1,133 @@
+%COMPUTECANADA class definition
+%
+%   Usage:
+%      cluster=computecanada();
+%      cluster=computecanada('np',3);
+%      cluster=computecanada('np',3,'login','username');
+
+classdef computecanada
+    properties (SetAccess=public)  
+		 % {{{
+		 name           = ''
+		 login          = '';
+		 numtasks       = 1;
+		 cpuspertask    = 8;
+		 port           = 0;
+		 projectaccount = '';
+		 codepath       = '';
+		 executionpath  = '';
+		 time           = 24*60;
+		 memory         = 2;
+		 email          = '';
+		 mailtype       = '';
+	 end
+	 %}}}
+	 methods
+		 function cluster=computecanada(varargin) % {{{
+
+			 %initialize cluster using default settings if provided
+			 if (exist('computecanada_settings')==2), computecanada_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('    numtasks: %i',cluster.numtasks));
+			 disp(sprintf('    cpuspertask: %i',cluster.cpuspertask));
+			 disp(sprintf('    projectaccount: %s',cluster.projectaccount));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+			 disp(sprintf('    time: %i',cluster.time));
+			 disp(sprintf('    memory: %i',cluster.memory));
+			 disp(sprintf('    email: %s', cluster.email));
+			 disp(sprintf('    mailtype: %s', cluster.mailtype));
+			 
+		 end
+		 %}}}
+		 function numprocs=np(cluster) % {{{
+			 %compute number of processors
+			 numprocs=cluster.numtasks*cluster.cpuspertask;
+		 end
+		 %}}}
+		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
+			 if isempty(cluster.name), md = checkmessage(md,'name empty'); end
+			 if isempty(cluster.login), md = checkmessage(md,'login empty'); end
+			 if ~(cluster.numtasks > 0), md = checkmessage(md,'numtasks must be > 0'); end
+			 if ~(cluster.cpuspertask > 0), md = checkmessage(md,'cpuspertask must be > 0'); end
+			 if ~(cluster.port >= 0), md = checkmessage(md,'port must be >= 0'); end
+			 if isempty(cluster.projectaccount), md = checkmessage(md,'projectaccount empty'); end
+			 if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end
+			 if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end
+			 if ~(cluster.time > 0), md = checkmessage(md,'time must be > 0'); end
+			 if ~(cluster.memory > 0), md = checkmessage(md,'memory must be > 0'); end
+		 end
+		 %}}}
+		 function BuildKrigingQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{
+			 error('not implemented yet');
+		 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 --account=%s \n',cluster.projectaccount);
+			 fprintf(fid,'#SBATCH --ntasks=%i  \n',cluster.numtasks);
+			 fprintf(fid,'#SBATCH --cpus-per-task=%i\n',cluster.cpuspertask);
+			 fprintf(fid,'#SBATCH --time=%i\n',cluster.time); %walltime is in minutes
+			 fprintf(fid,'#SBATCH --mem-per-cpu=%igb\n',cluster.memory); %memory in in gigabytes
+			 fprintf(fid,'#SBATCH --mail-user=%s\n',cluster.email); %email
+			 fprintf(fid,'#SBATCH --mail-type=%s',cluster.mailtype); 
+			 fprintf(fid,'#SBATCH --output=%s.outlog \n',modelname);
+			 fprintf(fid,'#SBATCH --error=%s.errlog \n\n',modelname);
+			 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+			 fprintf(fid,'srun %s/issm.exe %s %s %s\n',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);
+		 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
+			 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