source: issm/branches/trunk-larour-NatGeoScience2016/src/m/classes/clusters/cosmos.m

%COSMOS class definition
%
%   Usage:
%      cluster=cosmos();
%      cluster=cosmos('np',3);
%      cluster=cosmos('np',3,'login','username');

classdef cosmos
    properties (SetAccess=public) 
                 % {{{
                 name='cosmos'
                 login='username';
                 np=128;
                 port=0;
                 queue='shortq';
                 time=3*60;
                 codepath='/work00/edw/issm-2.0/bin';
                 executionpath='/work00/edw/Execution';
                 %}}}
         end
         methods
                 function cluster=cosmos(varargin) % {{{
                         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('    np: %i',cluster.np));
                         disp(sprintf('    port: %i',cluster.port));
                         disp(sprintf('    queue: %s',cluster.queue));
                         disp(sprintf('    time: %i',cluster.time));
                         disp(sprintf('    codepath: %s',cluster.codepath));
                         disp(sprintf('    executionpath: %s',cluster.executionpath));
                 end
                 %}}}
                 function md = checkconsistency(cluster,md,solution,analyses) % {{{

                         available_queues={'debug','shortq','longq'};
                         queue_requirements_time=[60*1 60*3 60*17];
                         queue_requirements_np=[32 128 256];

                         QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,cluster.time)
                 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,'#PBS -l select=%i:ncpus=1\n',cluster.np);
                         fprintf(fid,'#PBS -N %s\n',modelname);
                         fprintf(fid,'#PBS -l walltime=%i\n',time*60); %walltime is in seconds.
                         fprintf(fid,'#PBS -q %s\n',queue);
                         fprintf(fid,'#PBS -o %s.outlog \n',modelname);
                         fprintf(fid,'#PBS -e %s.errlog \n',modelname);
                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',[cluster.executionpath '/' dirname]);
                         fprintf(fid,'cd $PBS_O_WORKDIR\n');
                         fprintf(fid,'export OMP_NUM_THREADS=1\n');
                         fprintf(fid,'ulimit -s unlimited\n');
                         fprintf(fid,'ulimit -c 0\n');
                         fprintf(fid,'/opt/mpich/gm/intel10.1/bin/mpiexec -np %i %s/issm.exe %s %s %s',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
                         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
                         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)% {{{

                         disp('launching solution sequence on remote cluster');
                         if ~isempty(restart)
                                 launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && qsub ' modelname '.queue '];
                         else
                                 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
                                         ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && qsub ' 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