Index: /issm/trunk-jpl/src/m/classes/clusters/hpc_simba2.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/hpc_simba2.m	(revision 27290)
+++ /issm/trunk-jpl/src/m/classes/clusters/hpc_simba2.m	(revision 27290)
@@ -0,0 +1,278 @@
+%HPC class definition
+%
+%   Usage:
+%      cluster=hpc_simba();
+%      cluster=hpc_simba('np',3);
+%      cluster=hpc_simba('np',3,'login','username');
+
+classdef hpc_simba2
+    properties (SetAccess=public)  
+		 % {{{
+		 name='simba20'
+		 login='inwoo';
+		 numnodes=18;    % number of nodes at 2019-11 installation
+		 cpuspernode=36; % default number of cpus at each node
+		 node=1;         % number of nodes for calculating 
+		 np=4;           % number of cpus for calculating at each node
+		 port=0;        % not know open port
+		 queue='pub64';
+		 codepath= [];
+		 executionpath=[];
+		 interactive=0;
+		 verbose=0;     % show process of downloading
+		 isqsub=1;
+	 end
+	 %}}}
+	 methods
+		 function cluster=hpc_simba2(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);
+
+			 % where is "ISSM_DIR"?
+			 if strcmpi(cluster.name,'simba00')
+				 ISSM_DIR=getenv('ISSM_DIR');
+			 elseif strcmpi(cluster.name,'simba20')
+				 ISSM_DIR='/home/inwoo/issm/trunk-jpl/';
+			 else
+				 error(sprintf('ERROR: %s is not supported cluster name...'))
+			 end
+			 cluster.codepath=sprintf('%s/bin',ISSM_DIR);
+
+			 % define specific user
+			 [~, s] = system('whoami'); % get user name
+			 s = s(1:end-1);
+			 cluster.login=s;
+			 if strcmpi(s,'inwoo'),
+				 %cluster.executionpath=sprintf('%s/execution/',ISSM_DIR);
+				 cluster.executionpath='/data2/inwoo/execution';
+			 elseif strcmpi(s,'emilia'),
+				 cluster.executionpath='/home/DATA/emilia-model/executionlog';
+			 end
+		 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('    node: %i',cluster.node));
+			 disp(sprintf('    cpuspernode: %i',cluster.cpuspernode));
+			 disp(sprintf('    np: %i',cluster.np));
+			 disp(sprintf('    queue: %s',cluster.queue));
+			 disp(sprintf('    codepath: %s',cluster.codepath));
+			 disp(sprintf('    executionpath: %s',cluster.executionpath));
+			 disp(sprintf('    interactive: %i',cluster.interactive));
+			 disp(sprintf('    isqub: %i',cluster.isqsub));
+		 end
+		 %}}}
+		 function md = checkconsistency(cluster,md,solution,analyses) % {{{
+
+			 available_queues={'pub64','free64','free48','free*,pub64','free*'};
+			 queue_requirements_time=[Inf Inf Inf Inf Inf];
+			 queue_requirements_np=[64 64 48 48 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
+
+			 %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,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,'#PBS -q workq\n');
+			 fprintf(fid,'#PBS -S /bin/bash\n');      % set shell name
+			 fprintf(fid,'#PBS -N %s\n',modelname);   % set job name
+			 % 8 node is available at simba
+			 if (cluster.node >= cluster.numnodes),
+				 fprintf('cluster node   : simba%02\n', cluster.node);
+				 fprintf('number of node : %d\n', cluster.numnodes);
+				 error('ERROR: cluster node is higher than number of nodes');
+			 end
+			 % node             -> how many nodes do you use?
+			 % ppn (cluster.np) -> how many cpus do you use? 
+			 fprintf(fid,'#PBS -l nodes=%d:ppn=%d\n',cluster.node,cluster.np);
+			 fprintf(fid,'#PBS -o %s.outlog \n',modelname);
+			 fprintf(fid,'#PBS -e %s.errlog \n',modelname);
+			 fprintf(fid,'\n');
+			 fprintf(fid,'source ~/.bashrc\n');                          % FIXME
+			 fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
+			 fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+			 fprintf(fid,'\n');
+			 fprintf(fid,'module load intel18/compiler-18\n');
+			 fprintf(fid,'module load intel18/mvapich2-2.2\n');
+			 fprintf(fid,'\n');
+			 fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
+
+			 if true, % HACK
+				 % NOTE: old version
+				 % fprintf(fid,'mpiexec -genv MV2_ENABLE_AFFINITY 0 -np %i %s/issm.exe %s %s %s\n',cluster.np*cluster.node,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+				 % NOTE: new version 
+				 % not requires np processor and machine file. Execution of ISSM is operated under PBS. 
+				 fprintf(fid,'mpiexec -genv MV2_ENABLE_AFFINITY 0 -np %d %s/issm.exe %s %s %s\n',...
+					 cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+			 else
+				 % use machine file for obtaining cluster nodes
+				 fprintf(fid,'mpiexec -machinefile %s -np %i %s/issm.exe %s %s %s\n',[cluster.executionpath '/' dirname '/simba.host'],cluster.np*cluster.node,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+			 end 
+			 if ~io_gather, %concatenate the output files:
+				 fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
+			 end
+			 fclose(fid);
+
+			 %% generate machinefile "simba.host" file for SIMBA
+			 %fid = fopen('simba.host','w');
+			 %nodeorder = [1:cluster.numnodes, 0];
+
+			 %% generate host of simba 
+			 %for i = 1:cluster.numnodes-1,
+			 %   fprintf(fid,'simba%02d:%2d\n',nodeorder(i),cluster.cpuspernode);
+			 %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,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
+
+			 % add machine file for SIMBA operation
+			 %compressstring = [compressstring ' ' 'simba.host'];
+			 system(compressstring);
+
+			 if cluster.verbose
+				 disp('hpc_simba2: uploading input file and queueing script');
+				 if exist(sprintf('%s.tar.gz',dirname))
+					fprintf('hpc_simba2: -- we find %s.tar.gz\n',dirname);
+				 end
+				 fprintf('hpc_simba2: -- remote hostname: %s\n',cluster.name);
+			 end
+			 
+			 % use rclone for upload model.
+			 isrclone = 0;
+			 if isrclone,
+				 command = ['ssh simba20 "rclone copy simba00:' pwd '/' dirname '.tar.gz ' cluster.executionpath '"'];
+				 system(command);
+			 else
+				 if strfind(cluster.executionpath,'/data2/')
+					 launchcommand = ['cp ' pwd '/' dirname '.tar.gz ' cluster.executionpath];
+					 issmssh(oshostname,cluster.login,cluster.port,launchcommand);
+				 else % using scpout for exporting data...
+					 issmscpout(cluster.name,cluster.executionpath,cluster.login,cluster.port,{[dirname '.tar.gz']});
+				 end
+			 end
+		 end %}}}
+		 function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
+			 disp('launching solution sequence on remote cluster: simba20');
+			 if ~isempty(restart)
+				 if cluster.isqsub 
+					 launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && hostname && qsub ' modelname '.queue '];
+				 else
+					 launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && hostname && source' modelname '.queue '];
+				 end
+			 else
+				 if cluster.isqsub 
+					 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+						 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && qsub ' modelname '.queue '];
+				 else
+					 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
+						 ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && hostname && source ' modelname '.queue '];
+				 end
+			 end
+			 
+			 if cluster.verbose
+				 fprintf('check simulation at\n');
+				 fprintf('%s/%s\n',cluster.executionpath,dirname);
+			 end
+
+			 % launch simulation
+			 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 '/'];
+			
+			 isrclone = 0;
+			 if isrclone,
+				 command = ['ssh simba20 "rclone copy ' directory ' simba00:' pwd '/'];
+				 for i = 1:length(filelist)
+					 command = [command ' --include ' filelist{i}];
+				 end
+				 if cluster.verbose,
+					 command = [command ' --progress '];
+				 end
+				 command = [command '"'];
+				 %assignin('base','command',command); 
+
+				 disp('download outputs....');
+				 system(command);
+				 disp('download outputs.... done...');
+			 else
+				 % In case of "SIMBA" machine, it shares the data storage. If following directory is set we do not need to download load file with using "issmscpin". Directly read file...
+				 if 1==strfind(cluster.executionpath,'/data2/')
+					 % tricky part for assign "cluster.name" as "simba00".
+					 disp('hpc_simba2: download file from /data2/ directory!!! Not use scpin.');
+					 issmscpin('simba00',cluster.login,cluster.port,directory,filelist);
+				 else
+					 issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist);
+				 end
+			 end
+		 end %}}}
+	end
+end