Index: /issm/trunk/src/m/classes/public/queue/BuildQueueingScript.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScript.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/BuildQueueingScript.m (revision 2880) @@ -0,0 +1,23 @@ +function BuildQueueingScript(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPT - +% +% Usage: +% BuildQueueingScript(md,executionpath,codepath) + +disp('building queueing script'); + +%First try and figure out if there is a special script for thie particular cluster +function_name=['BuildQueueingScript' md.cluster]; + +%some specific treatment of identical cluster, gemini, castor and pollux +if strcmpi(md.cluster,'castor') || strcmpi(md.cluster,'pollux'), + function_name='BuildQueueingScriptgemini'; +end + +if exist(function_name,'file'), + %Call this function: + eval([function_name '(md,executionpath,codepath);']); +else + %Call the generic BuildQueueingScript: + BuildQueueingScriptGeneric(md,executionpath,codepath); +end Index: /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptGeneric.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptGeneric.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptGeneric.m (revision 2880) @@ -0,0 +1,26 @@ +function BuildQueueingScriptGeneric(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPTGENERIC - ... +% +% Usage: +% BuildQueueingScriptGeneric(md,executionpath,codepath) + +global ISSM_DIR + +%Open queuing script file +scriptname=[md.name '.queue']; + +fid=fopen(scriptname,'w'); +if fid==-1, + error(['BuildQueueingScriptGenericerror message: could not open ' scriptname ' file for ascii writing']); +end + +fprintf(fid,'#!/bin/sh\n'); +fprintf(fid,'rm -rf %s/%s.lock\n',executionpath,md.name); + +if md.mem_debug==0, +fprintf(fid,'mpirun -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',md.np,codepath,AnalysisTypeFromEnum(md.analysis_type),executionpath,md.name,md.name,md.name,md.name,md.name); +else +fprintf(fid,'LD_PRELOAD=%s mpirun -np %i %s --leak-check=full %s/%s.exe %s %s.bin %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',[ISSM_DIR '/externalpackages/valgrind/install/lib/libmpidebug.so'],md.np,[ISSM_DIR '/externalpackages/valgrind/install/bin/valgrind'],codepath,AnalysisTypeFromEnum(md.analysis_type),executionpath,md.name,md.name,md.name,md.name,md.name); +end + +fclose(fid); Index: /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptcosmos.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptcosmos.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptcosmos.m (revision 2880) @@ -0,0 +1,65 @@ +function BuildQueueingScriptcosmos(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPTGEMINI - ... +% +% Usage: +% BuildQueueingScriptcosmos(md,executionpath,codepath) + +scriptname=[md.name '.queue']; + +fid=fopen(scriptname,'w'); +if fid==-1, + error(['BuildQueueingScriptcosmos error message: could not open ' scriptname ' file for ascii writing']); +end + +%check queue names: +available_queues={'debug','shortq','longq','specialq'}; +if ~ismemberi(md.queue,available_queues), + error('BuildQueueingScriptcosmos error message: availables queues are debug, shortq, longq and specialq'); +end + +%test parameters for each queue: +if strcmpi(md.queue,'debug'), + if md.np>32, + error('BuildQueueingScriptcosmos error message: debug queue only allows 32 cpus'); + end + if md.time>60, + error('BuildQueueingScriptcosmos error message: debug queue only allows 60 minutes'); + end +end + +if strcmpi(md.queue,'shortq'), + if md.np>128, + error('BuildQueueingScriptcosmos error message: shortq queue only allows 128 cpus'); + end + if md.time>180, + error('BuildQueueingScriptcosmos error message: shortq queue only allows 180 minutes'); + end +end + +if strcmpi(md.queue,'longq'), + if md.np>128, + error('BuildQueueingScriptcosmos error message: longq queue only allows 128 cpus'); + end + if md.time>720, + error('BuildQueueingScriptcosmos error message: longq queue only allows 720 minutes'); + end +end + + + +fprintf(fid,'#!/bin/bash\n'); +fprintf(fid,'#PBS -l select=%i:ncpus=1\n',md.np); +fprintf(fid,'#PBS -l walltime=%i\n',md.time*60); %walltime is in seconds. +if ~isempty(md.queue), + fprintf(fid,'#PBS -q %s\n',md.queue); +end +fprintf(fid,'#PBS -o %s.outlog \n',md.name); +fprintf(fid,'#PBS -e %s.errlog \n',md.name); + +fprintf(fid,'export PBS_O_WORKDIR=%s\n',executionpath); +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/mpirun -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock',md.np,codepath,AnalysisTypeFromEnum(md.analysis_type),executionpath,md.name,md.name,md.name); +fclose(fid); Index: /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptgemini.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptgemini.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptgemini.m (revision 2880) @@ -0,0 +1,81 @@ +function BuildQueueingScriptgemini(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPTGEMINI - ... +% +% Usage: +% BuildQueueingScriptgemini(md,executionpath,codepath) + +scriptname=[md.name '.queue']; + + + +%check queue names: +if strcmpi(md.cluster,'gemini'), + available_queues={'debug','shortg','longg'}; + if ~ismemberi(md.queue,available_queues), + error('BuildQueueingScriptcosmos error message: availables queues are debug, shortg and longg'); + end + + if strcmpi(md.queue,'debug'), + if md.np>50, + error('BuildQueueingScriptgeminierror error message: debug queue only allows for 50 cpus max'); + end + + if md.time>60, + error('BuildQueueingScriptgeminierror error message: debug queue only allows for 60 minute runs'); + end + end +end + +if strcmpi(md.cluster,'castor'), + available_queues={'shortc','longc'}; + if ~ismemberi(md.queue,available_queues), + error('BuildQueueingScriptcosmos error message: availables queues are shortc and longc'); + end +end + +if strcmpi(md.cluster,'pollux'), + available_queues={'shortp','longp'}; + if ~ismemberi(md.queue,available_queues), + error('BuildQueueingScriptcosmos error message: availables queues are shortp and longp'); + end +end + +%test parameters valid for all queues +if strcmpi(md.queue(1:5),'short'), + if md.np>128, + error('BuildQueueingScriptcosmos error message: short queue only allows 128 cpus'); + end + if md.time>180, + error('BuildQueueingScriptcosmos error message: short queue only allows 180 minutes'); + end +end + +if strcmpi(md.queue(1:4),'long'), + if md.np>128, + error('BuildQueueingScriptcosmos error message: long queue only allows 128 cpus'); + end + if md.time>720, + error('BuildQueueingScriptcosmos error message: long queue only allows 720 minutes'); + end +end + +fid=fopen(scriptname,'w'); +if fid==-1, + error(['BuildQueueingScriptgeminierror message: could not open ' scriptname ' file for ascii writing']); +end + +fprintf(fid,'#!/bin/sh\n'); +fprintf(fid,'#PBS -l walltime=%i\n',md.time*60); %walltime is in seconds. +fprintf(fid,'#PBS -l ncpus=%i\n',md.np); +if ~isempty(md.queue), + fprintf(fid,'#PBS -q %s\n',md.queue); +end +fprintf(fid,'#PBS -o %s.outlog \n',md.name); +fprintf(fid,'#PBS -e %s.errlog \n',md.name); + +fprintf(fid,'export PBS_O_WORKDIR=%s\n',executionpath); +fprintf(fid,'cd $PBS_O_WORKDIR\n'); +fprintf(fid,'export OMP_NUM_THREADS=1\n'); +fprintf(fid,'dplace -s1 -c0-%i mpirun -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock',md.np-1,md.np,codepath,AnalysisTypeFromEnum(md.analysis_type),executionpath,md.name,md.name,md.name); + +fclose(fid); Index: /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptgreenplanet.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptgreenplanet.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptgreenplanet.m (revision 2880) @@ -0,0 +1,43 @@ +function BuildQueueingScriptgreenplanet(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPTGEMINI - ... +% +% Usage: +% BuildQueueingScriptgreenplanet(md,executionpath,codepath) + +scriptname=[md.name '.queue']; + +%check queue names: +if strcmpi(md.cluster,'greenplanet'), + available_queues={'rignot','default'}; + if ~ismemberi(md.queue,available_queues), + error('BuildQueueingScriptgreenplanet error message: availables queues are rignot and default'); + end + + if strcmpi(md.queue,'rignot'), + if md.np>80, + error('BuildQueueingScriptgreenplaneterror error message: debug queue only allows for 80 cpus max'); + end + + if md.time>60, + error('BuildQueueingScriptgreenplaneterror error message: debug queue only allows for 60 minute runs'); + end + end +end + +fid=fopen(scriptname,'w'); +if fid==-1, + error(['BuildQueueingScriptgreenplaneterror message: could not open ' scriptname ' file for ascii writing']); +end + +fprintf(fid,'#!/bin/csh\n'); +fprintf(fid,'#PBS -N %s\n',md.name); +fprintf(fid,'#PBS -l nodes=%i:ppn=%i\n',md.np/8,8); +fprintf(fid,'#PBS -q %s\n',md.queue); +fprintf(fid,'#PBS -m bea\n'); +fprintf(fid,'#PBS -M eric.larour@jpl.nasa.gov\n'); +fprintf(fid,'#PBS -l walltime=%i\n',md.time*60); %walltime is in seconds. + +fprintf(fid,'cd $PBS_O_WORKDIR\n'); +fprintf(fid,'mpirun -machinefile $PBS_NODEFILE -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock > %s.outlog',md.np,codepath,AnalysisTypeFromEnum(md.analysis_type),executionpath,md.name,md.name,md.name,md.name); + +fclose(fid); Index: /issm/trunk/src/m/classes/public/queue/LaunchQueueJob.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/LaunchQueueJob.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/LaunchQueueJob.m (revision 2880) @@ -0,0 +1,21 @@ +function md=LaunchQueueJob(md,executionpath,options) +%LAUNCHQUEUEJOB - ... +% +% Usage: +% LaunchQueueJob(md,executionpath) + +%First try and figure out if there is a special script for thie particular cluster +function_name=['LaunchQueueJob' md.cluster]; + +%some specific treatment of identical cluster, gemini, castor and pollux +if strcmpi(md.cluster,'castor') || strcmpi(md.cluster,'pollux'), + function_name='LaunchQueueJobgemini'; +end + +if exist(function_name,'file'), + %Call this function: + eval(['md=' function_name '(md,executionpath,options);']); +else + %Call the generic LaunchQueueJob: + md=LaunchQueueJobGeneric(md,executionpath,options); +end Index: /issm/trunk/src/m/classes/public/queue/LaunchQueueJobGeneric.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/LaunchQueueJobGeneric.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/LaunchQueueJobGeneric.m (revision 2880) @@ -0,0 +1,34 @@ +function md=LaunchQueueJobGeneric(md,executionpath,options) +%LAUNCHQUEUEJOBGENERIC - Generic routine to launch queueing job +% +% Usage: +% LaunchQueueJobGeneric(md,executionpath) + +%first, check we have the binary file and the queueing script +if ~exist([ md.name '.bin'],'file'), + error('LaunchQueueJobGeneric error message: Binary input file missing, cannot go forward'); +end + +if ~exist([ md.name '.queue'],'file'), + error('LaunchQueueJobGeneric error message: queueing script issing, cannot go forward'); +end + +if ~strcmpi(options.batch,'yes'), + + %what files are we sending? + packages={[md.name '.bin'],[md.name '.queue']}; + if md.qmu_analysis, + packages{end+1}=[md.name '.qmu.in']; + end + + disp('uploading input file and queueing script'); + scpout(md.cluster,executionpath,packages); + + disp('launching solution sequence on remote cluster'); + issmssh(md.cluster,['cd ' executionpath ' && source ' md.name '.queue ']); + +else + disp('batch mode requested: not launching job interactively'); + disp(['launch solution sequence by copying files ' md.name '.bin' ',' md.name '.queue and ' md.name '.qmu.in, onto remote cluster ' md.cluster]); + disp([' then log int ' md.cluster ' and source queue file ' md.name '.queue']); +end Index: /issm/trunk/src/m/classes/public/queue/LaunchQueueJobcosmos.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/LaunchQueueJobcosmos.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/LaunchQueueJobcosmos.m (revision 2880) @@ -0,0 +1,32 @@ +function md=LaunchQueueJobcosmos(md,executionpath,options) +%LAUNCHQUEUEJOBCOSMOS- Launch queue script for Cosmos cluster +% +% Usage: +% LaunchQueueJobcosmos(md,executionpath) + +%first, check we have the binary file and the queueing script +if ~exist([ md.name '.bin'],'file'), + error('LaunchQueueJobcosmos error message: Binary input file missing, cannot go forward'); +end + +if ~exist([ md.name '.queue'],'file'), + error('LaunchQueueJobcosmos error message: queueing script issing, cannot go forward'); +end + +%jpload both files to cluster +if ~strcmpi(options.batch,'yes'), + disp('uploading input file, queueing script and variables script'); + if md.qmu_analysis, + system(['scp ' md.name '.bin' ' ' md.name '.queue ' md.name '.qmu.in ' md.cluster ':' executionpath]); + else + system(['scp ' md.name '.bin' ' ' md.name '.queue ' md.cluster ':' executionpath]); + end + + disp('launching solution sequence on remote cluster'); + issmssh(md.cluster,['"cd ' executionpath ' && qsub -S/bin/sh ' md.name '.queue "']); +else + disp('batch mode requested: not launching job interactively'); + + %new gemini cannot launch across cluster using ssh + disp(['launch solution sequence on remote cluster by logging into it and typing qsub -S/bin/sh ' md.name '.queue']); +end Index: /issm/trunk/src/m/classes/public/queue/LaunchQueueJobgemini.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/LaunchQueueJobgemini.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/LaunchQueueJobgemini.m (revision 2880) @@ -0,0 +1,32 @@ +function md=LaunchQueueJobgemini(md,executionpath,options) +%LAUNCHQUEUEJOBGEMINI - Launch queueing script on Gemini cluster +% +% Usage: +% LaunchQueueJobgemini(md,executionpath) + +%first, check we have the binary file and the queueing script +if ~exist([ md.name '.bin'],'file'), + error('LaunchQueueJobgemini error message: Binary input file missing, cannot go forward'); +end + +if ~exist([ md.name '.queue'],'file'), + error('LaunchQueueJobgemini error message: queueing script issing, cannot go forward'); +end + +%jpload both files to cluster +if ~strcmpi(options.batch,'yes'), + disp('uploading input file, queueing script and variables script'); + if md.qmu_analysis, + system(['scp ' md.name '.bin' ' ' md.name '.queue ' md.name '.qmu.in ' md.cluster ':' executionpath]); + else + system(['scp ' md.name '.bin' ' ' md.name '.queue ' md.cluster ':' executionpath]); + end + + disp('launching solution sequence on remote cluster'); + issmssh(md.cluster,['"cd ' executionpath ' && qsub ' md.name '.queue "']); +else + disp('batch mode requested: not launching job interactively'); + + %new gemini cannot launch across cluster using ssh + disp(['launch solution sequence on remote cluster by logging into it and typing qsub < ' md.name '.queue']); +end Index: /issm/trunk/src/m/classes/public/queue/LaunchQueueJobgreenplanet.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/LaunchQueueJobgreenplanet.m (revision 2880) +++ /issm/trunk/src/m/classes/public/queue/LaunchQueueJobgreenplanet.m (revision 2880) @@ -0,0 +1,29 @@ +function md=LaunchQueueJobgreenplanet(md,executionpath,options) +%LAUNCHQUEUEJOBGEMINI - ... +% +% Usage: +% LaunchQueueJobgreenplanet(md,executionpath) + +%first, check we have the binary file and the queueing script +if ~exist([ md.name '.bin'],'file'), + error('LaunchQueueJobgreenplanet error message: Binary input file missing, cannot go forward'); +end + +if ~exist([ md.name '.queue'],'file'), + error('LaunchQueueJobgreenplanet error message: queueing script issing, cannot go forward'); +end + +%jpload both files to cluster +if ~strcmpi(options.batch,'yes'), + disp('uploading input file, queueing script and variables script'); + if md.qmu_analysis, + system(['scp -P 1025 -o HostKeyAlias=huey.jpl.nasa.gov ' md.name '.bin' ' ' md.name '.queue ' md.name '.qmu.in elarour@localhost:' executionpath]); + else + system(['scp -P 1025 -o HostKeyAlias=huey.jpl.nasa.gov ' md.name '.bin' ' ' md.name '.queue elarour@localhost:' executionpath ]); + end +else + disp('batch mode requested: not launching job interactively'); +end + +%new greenplanet cannot launch across cluster using ssh +disp(['launch solution sequence on remote cluster by logging into it and typing qsub < ' md.name '.queue']);