Index: /issm/trunk-jpl/src/m/classes/clusters/discover.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/discover.m	(revision 12501)
+++ /issm/trunk-jpl/src/m/classes/clusters/discover.m	(revision 12501)
@@ -0,0 +1,189 @@
+%PFE class definition
+%
+%   Usage:
+%      cluster=discover();
+%      cluster=discover('np',3);
+%      cluster=discover('np',3,'login','username');
+
+classdef discover 
+    properties (SetAccess=public)  
+		 % {{{
+		 name=oshostname();
+		 login='';
+		 numnodes=20;
+		 cpuspernode=8; 
+		 port=1025;
+		 queue='long';
+		 time=12*60;
+		 processor='west';
+		 codepath='';
+		 executionpath='';
+		 interactive=0;
+		 bbftp=0;
+		 numstreams=8;
+		 hyperthreading=0;
+	 end
+	 properties (SetAccess=private) 
+		 np=20*8;
+		 % }}}
+	 end
+	 methods
+		 function cluster=discover(varargin) % {{{
+
+			 %initialize cluster using default settings if provided
+			 if (exist('discover_settings')==2), discover_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('    time: %i',cluster.time));
+			 disp(sprintf('    processor: %s',cluster.processor));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+			 disp(sprintf('    interactive: %i',cluster.interactive));
+			 disp(sprintf('    hyperthreading: %i',cluster.hyperthreading));
+		 end
+		 %}}}
+		 function checkconsistency(cluster,md,solution,analyses) % {{{
+
+			 available_queues={'general_long','general','general_small','debug'};
+			 queue_requirements_time=[24*60 12*60 12*60 60];
+			 queue_requirements_np=[516 1024 16 32];
+
+			 QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,cluster.time)
+
+			 %now, check cluster.cpuspernode according to processor type
+			 if ( strcmpi(cluster.processor,'neha')),
+				 if ((cluster.cpuspernode>8 ) | (cluster.cpuspernode<1)),
+					 checkmessage('cpuspernode should be between 1 and 8 for ''neha'' processors');
+				 end
+			 elseif strcmpi(cluster.processor,'west'),
+				 if ((cluster.cpuspernode>12 ) | (cluster.cpuspernode<1)),
+					 checkmessage('cpuspernode should be between 1 and 12 for ''west'' processors');
+				 end
+			 else
+				 checkmessage('unknown processor type, should be ''neha'' or ''west'' ');
+			 end
+
+			 %Miscelaneous
+			 if isempty(cluster.login), checkmessage('login empty'); end
+			 if isempty(cluster.codepath), checkmessage('codepath empty'); end
+			 if isempty(cluster.executionpath), checkmessage('executionpath empty'); end
+
+		 end
+		 %}}}
+		 function BuildQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{
+
+			 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,'#PBS -S /bin/bash\n');
+%			 fprintf(fid,'#PBS -N %s\n',modelname);
+			 fprintf(fid,'#PBS -l select=%i:ncpus=%i:proc=%s\n',cluster.numnodes,cluster.cpuspernode,cluster.processor);
+			 fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds.
+			 fprintf(fid,'#PBS -q %s \n',cluster.queue);
+			 fprintf(fid,'#PBS -W group_list=s1010\n');
+			 fprintf(fid,'#PBS -m e\n');
+			 fprintf(fid,'#PBS -o %s.outlog \n',modelname);
+			 fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
+			 fprintf(fid,'. /usr/share/modules/init/bash\n\n');
+			 fprintf(fid,'module load comp/intel-10.1.023\n');
+			 fprintf(fid,'module load mpi/impi-3.2.2.006\n');
+			 fprintf(fid,'module load lib/mkl-10.1.2.024\n\n');
+			 fprintf(fid,'export PATH="$PATH:."\n\n');
+			 fprintf(fid,'export MPI_GROUP_MAX=64\n\n');
+			 fprintf(fid,'cd $PBS_O_WORKDIR\n\n');
+			 fprintf(fid,'mpirun -np %i %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),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');
+				 if ~isvalgrind,
+					 fprintf(fid,'mpirun -np %i %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),modelname);
+				 else
+					 fprintf(fid,'mpirun -np %i valgrind --leak-check=full %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),modelname);
+				 end
+				 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 '.run '  modelname '.errlog ' modelname '.outlog '];
+			 end
+			 system(compressstring);
+
+			 disp('uploading input file and queueing script');
+			 if cluster.interactive,
+				 directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive)];
+			 else 
+				 directory=cluster.executionpath;
+			 end
+
+			 if ~cluster.bbftp,
+				 issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']});
+			 else
+				 issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']});
+			 end
+
+			 %lauch command, to be executed via ssh
+			 if ~cluster.interactive, 
+				 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+					 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && qsub ' modelname '.queue '];
+			 else
+				 launchcommand=['cd ' cluster.executionpath '/Interactive' num2str(cluster.interactive) ' && tar -zxf ' dirname '.tar.gz'];
+			 end
+
+			 disp('launching solution sequence on remote cluster');
+			 issmssh(cluster.name,cluster.login,cluster.port,launchcommand);
+		 end
+		 %}}}
+		 function Download(cluster,dirname,filelist)% {{{
+
+			 %copy files from cluster to current directory
+			 if ~cluster.interactive,
+				 directory=[cluster.executionpath '/' dirname '/'];
+			 else
+				 directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive) '/'];
+			 end
+
+			 if ~cluster.bbftp,
+				 issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist);
+			 else
+				 issmbbftpin(cluster.name, cluster.login, cluster.port, cluster.numstreams, directory, filelist);
+			 end
+
+		 end %}}}
+	end
+end