Index: sm/trunk/src/m/classes/public/queue/BuildMultipleQueueingScript.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildMultipleQueueingScript.m (revision 3148) +++ (revision ) @@ -1,23 +1,0 @@ -function BuildMultipleQueueingScript(cluster,name,executionpath,codepath) -%BUILDMULTIPLEQUEUEINGSCRIPT - -% -% Usage: -% BuildMultipleQueueingScript(executionpath,codepath) - -disp('building queueing script'); - -%First try and figure out if there is a special script for this particular cluster -function_name=['BuildMultipleQueueingScript' cluster]; - -%some specific treatment of identical cluster, gemini, castor and pollux -if strcmpi(cluster,'castor') || strcmpi(cluster,'pollux'), - function_name='BuildMultipleQueueingScriptgemini'; -end - -if exist(function_name,'file'), - %Call this function: - eval([function_name '(name,executionpath,codepath);']); -else - %Call the generic BuildQueueingScript: - BuildMultipleQueueingScriptGeneric(name,executionpath,codepath); -end Index: sm/trunk/src/m/classes/public/queue/BuildMultipleQueueingScriptGeneric.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildMultipleQueueingScriptGeneric.m (revision 3148) +++ (revision ) @@ -1,12 +1,0 @@ -function BuildMultipleQueueingScriptGeneric(name,executionpath,codepath) -%BUILDMULTIPLEQUEUEINGSCRIPTGENERIC - ... -% -% Usage: -% BuildMultipleQueueingScriptGeneric(executionpath,codepath) - -global ISSM_DIR - - -%not done yet -error('BuildMultipleQueueingScriptGenericerror message: not supported yet!'); - Index: sm/trunk/src/m/classes/public/queue/BuildMultipleQueueingScriptgemini.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildMultipleQueueingScriptgemini.m (revision 3148) +++ (revision ) @@ -1,23 +1,0 @@ -function BuildQueueingScriptgemini(name,executionpath,codepath) -%BUILDQUEUEINGSCRIPTGEMINI - ... -% -% Usage: -% BuildQueueingScriptgemini(md,executionpath,codepath) - -scriptname=[name '.queue']; - -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,'cd %s\n',executionpath); -fprintf(fid,'mkdir %s\n',name); -fprintf(fid,'cd %s\n',name); -fprintf(fid,'mv ../ModelList.tar.gz ./\n'); -fprintf(fid,'tar -zxvf ModelList.tar.gz\n'); -fprintf(fid,'foreach i (%s-*vs*.queue)\n',name); -fprintf(fid,'qsub $i\n'); -fprintf(fid,'end\n'); -fclose(fid); Index: /issm/trunk/src/m/classes/public/queue/BuildQueueingScript.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScript.m (revision 3148) +++ /issm/trunk/src/m/classes/public/queue/BuildQueueingScript.m (revision 3149) @@ -5,19 +5,19 @@ % BuildQueueingScript(md,executionpath,codepath) -disp('building queueing script'); +disp('check queue requirements'); +QueueRequirements(md.cluster,md.queue,md.np,md.time); -%First try and figure out if there is a special script for thie particular cluster -function_name=['BuildQueueingScript' md.cluster]; +disp('write queueing script'); -%some specific treatment of identical cluster, gemini, castor and pollux -if strcmpi(md.cluster,'castor') || strcmpi(md.cluster,'pollux'), - function_name='BuildQueueingScriptgemini'; +%open file +fid=fopen([md.name '.queue'],'w'); +if fid==-1, + error(['BuildQueueingScripterror message: could not open ' [md.name '.queue'] ' file for ascii writing']); 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 +%hand down to cluster specific script +ClusterScript(fid,md.cluster,md.name,md.queue,executionpath,codepath,md.analysis_type,md.np,md.time,md.mem_debug); + +%close file +fclose(fid); + Index: sm/trunk/src/m/classes/public/queue/BuildQueueingScriptGeneric.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptGeneric.m (revision 3148) +++ (revision ) @@ -1,27 +1,0 @@ -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: sm/trunk/src/m/classes/public/queue/BuildQueueingScriptcosmos.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptcosmos.m (revision 3148) +++ (revision ) @@ -1,65 +1,0 @@ -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: sm/trunk/src/m/classes/public/queue/BuildQueueingScriptgemini.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptgemini.m (revision 3148) +++ (revision ) @@ -1,81 +1,0 @@ -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: sm/trunk/src/m/classes/public/queue/BuildQueueingScriptgreenplanet.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptgreenplanet.m (revision 3148) +++ (revision ) @@ -1,43 +1,0 @@ -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: sm/trunk/src/m/classes/public/queue/BuildQueueingScriptpfe.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/BuildQueueingScriptpfe.m (revision 3148) +++ (revision ) @@ -1,59 +1,0 @@ -function BuildQueueingScriptpfe(md,executionpath,codepath) -%BUILDQUEUEINGSCRIPTPFE - ... -% -% Usage: -% BuildQueueingScriptpfe(md,executionpath,codepath) - -scriptname=[md.name '.queue']; - - -%check queue names: -if strcmpi(md.cluster,'pfe'), - available_queues={'long'}; - if ~ismemberi(md.queue,available_queues), - error('BuildQueueingScriptcosmos error message: availables queues are long'); - end -end - -%test parameters valid for all queues -if strcmpi(md.queue(1:4),'long'), - if md.np>2024, - error('BuildQueueingScriptcosmos error message: long queue only allows 2024 cpus'); - end - if md.time>720, - error('BuildQueueingScriptcosmos error message: long queue only allows 720 minutes'); - end - if mod(md.np,8), - error('BuildQueueingScriptcosmos error message: np should be a multiple of 8'); - end - -end - -fid=fopen(scriptname,'w'); -if fid==-1, - error(['BuildQueueingScriptpfeerror message: could not open ' scriptname ' file for ascii writing']); -end - - -fprintf(fid,'#PBS -S /bin/bash\n'); -fprintf(fid,'#PBS -N %s\n',md.name); -fprintf(fid,'#PBS -l select=%i:ncpus=8:mpiprocs=8\n',md.np/8); -fprintf(fid,'#PBS -l walltime=%i\n',md.time*60); %walltime is in seconds. -fprintf(fid,'#PBS -W group_list=s1010\n'); -fprintf(fid,'#PBS -m e\n'); -fprintf(fid,'#PBS -o %s.outlog \n',md.name); -fprintf(fid,'#PBS -e %s.errlog \n\n',md.name); - -fprintf(fid,'. /usr/share/modules/init/bash\n\n'); - -fprintf(fid,'module load comp-intel/11.1.046\n'); -fprintf(fid,'module load mpi/mpt.1.23.nas\n'); -fprintf(fid,'module load math/intel_mkl_64_10.0.011\n\n'); - -fprintf(fid,'export PATH="$PATH:."\n\n'); - -fprintf(fid,'cd $PBS_O_WORKDIR\n\n'); - -fprintf(fid,'mpiexec -verbose -np %i %s/%s.exe $PBS_O_WORKDIR %s.bin %s.outbin %s.lock',md.np,codepath,AnalysisTypeFromEnum(md.analysis_type),md.name,md.name,md.name); - -fclose(fid); Index: /issm/trunk/src/m/classes/public/queue/ClusterScript.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/ClusterScript.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/ClusterScript.m (revision 3149) @@ -0,0 +1,99 @@ +function ClusterScript(fid,cluster,name,queue,executionpath,codepath,analysis_type,np,time,mem_debug); +%CLUSTERSCRIPT cluster specific queuing script +% +% Usage: ClusterScript(fid,name,queue,executionpath,codepath,analysis_type,np,time); +% +% + + +if strcmpi(cluster,'cosmos'), + + + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%cosmos%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + fprintf(fid,'#!/bin/bash\n'); + fprintf(fid,'#PBS -l select=%i:ncpus=1\n',np); + 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',name); + fprintf(fid,'#PBS -e %s.errlog \n',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',np,codepath,AnalysisTypeFromEnum(analysis_type),executionpath,name,name,name); + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + + + +elseif (strcmpi(cluster,'astrid') | strcmpi(cluster,'larsen') | strcmpi(cluster,'wilkes')), + + + + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%astrid%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + fprintf(fid,'#!/bin/sh\n'); + fprintf(fid,'rm -rf %s/%s.lock\n',executionpath,name); + if mem_debug==0, + fprintf(fid,'mpirun -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock 2> %s.errlog >%s.outlog & ',np,codepath,AnalysisTypeFromEnum(analysis_type),executionpath,name,name,name,name,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'],np,[ISSM_DIR '/externalpackages/valgrind/install/bin/valgrind'],codepath,AnalysisTypeFromEnum(analysis_type),executionpath,name,name,name,name,name); + end + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + + + + +elseif (strcmpi(cluster,'gemini') | strcmpi(cluster,'pollux') | strcmpi(cluster,'castor')), + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%gemini%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +fprintf(fid,'#!/bin/sh\n'); + fprintf(fid,'#PBS -l walltime=%i\n',time*60); %walltime is in seconds. + fprintf(fid,'#PBS -l ncpus=%i\n',np); + if ~isempty(queue), + fprintf(fid,'#PBS -q %s\n',queue); + end + fprintf(fid,'#PBS -o %s.outlog \n',name); + fprintf(fid,'#PBS -e %s.errlog \n',name); + + fprintf(fid,'export PBS_O_WORKDIR=%s\n',executionpath); + fprintf(fid,'cd $PBS_O_WORKDIR\n'); + fprintf(fid,'export OMP_NUM_THREADS=1\n'); + fprintf(fid,'dplace -s1 -c0-%i mpirun -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock',np-1,np,codepath,AnalysisTypeFromEnum(analysis_type),executionpath,name,name,name); + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + + +elseif strcmpi(cluster,'pfe'), + + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%pfe%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + fprintf(fid,'#PBS -S /bin/bash\n'); + fprintf(fid,'#PBS -N %s\n',name); + fprintf(fid,'#PBS -l select=%i:ncpus=8:mpiprocs=8\n',np/8); + fprintf(fid,'#PBS -l walltime=%i\n',time*60); %walltime is in seconds. + fprintf(fid,'#PBS -W group_list=s1010\n'); + fprintf(fid,'#PBS -m e\n'); + fprintf(fid,'#PBS -o %s.outlog \n',name); + fprintf(fid,'#PBS -e %s.errlog \n\n',name); + + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); + + fprintf(fid,'module load comp-intel/11.1.046\n'); + fprintf(fid,'module load mpi/mpt.1.23.nas\n'); + fprintf(fid,'module load math/intel_mkl_64_10.0.011\n\n'); + + fprintf(fid,'export PATH="$PATH:."\n\n'); + + fprintf(fid,'cd $PBS_O_WORKDIR\n\n'); + + fprintf(fid,'mpiexec -verbose -np %i %s/%s.exe $PBS_O_WORKDIR %s.bin %s.outbin %s.lock',np,codepath,AnalysisTypeFromEnum(analysis_type),name,name,name); + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +else + error(['ClusterScript error message: could not find settings for cluster ' cluster]); +end Index: sm/trunk/src/m/classes/public/queue/LaunchMultipleQueueJob.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/LaunchMultipleQueueJob.m (revision 3148) +++ (revision ) @@ -1,21 +1,0 @@ -function LaunchMultipleQueueJob(cluster,name,executionpath) -%LAUNCHMULTIPLEQUEUEJOB - ... -% -% Usage: -% LaunchMultipleQueueJob(executionpath) - -%First try and figure out if there is a special script for thie particular cluster -function_name=['LaunchMultipleQueueJob' cluster]; - -%some specific treatment of identical cluster, gemini, castor and pollux -if strcmpi(cluster,'castor') || strcmpi(cluster,'pollux'), - function_name='LaunchMultipleQueueJobgemini'; -end - -if exist(function_name,'file'), - %Call this function: - eval([function_name '(cluster,name,executionpath);']); -else - %Call the generic LaunchMultipleQueueJob: - LaunchMultipleQueueJobGeneric(cluster,name,executionpath); -end Index: sm/trunk/src/m/classes/public/queue/LaunchMultipleQueueJobGeneric.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/LaunchMultipleQueueJobGeneric.m (revision 3148) +++ (revision ) @@ -1,7 +1,0 @@ -function LaunchMultipleQueueJobGeneric(cluster,name,executionpath) -%LAUNCHMULTIPLEQUEUEJOBGENERIC - Generic routine to launch multiple queueing job -% -% Usage: -% LaunchMultipleQueueJobGeneric(cluster,name,executionpath) - -error('LaunchMultipleQueueJobGeneric error message: not supported yet!'); Index: sm/trunk/src/m/classes/public/queue/LaunchMultipleQueueJobgemini.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/LaunchMultipleQueueJobgemini.m (revision 3148) +++ (revision ) @@ -1,22 +1,0 @@ -function md=LaunchMultipleQueueJobgemini(cluster,name,executionpath) -%LAUNCHMULTIPLEQUEUEJOBGEMINI - Launch multiple queueing script on Gemini cluster -% -% Usage: -% LaunchMultipleQueueJobgemini(cluster,name,executionpath) - - -%first, check we have the binary file and the queueing script -if ~exist([ name '.queue'],'file'), - error('LaunchMultipleQueueJobgemini error message: queueing script issing, cannot go forward'); -end - -if ~exist('ModelList.tar.gz','file'), - error('LaunchMultipleQueueJobgemini error message: inputs models file missing, cannot go forward'); -end - -%upload both files to cluster -disp('uploading input file, queueing script and variables script'); -eval(['!scp ModelList.tar.gz ' name '.queue ' cluster ':' executionpath]); - -disp('launching solution sequence on remote cluster'); -issmssh(cluster,login,['"cd ' executionpath ' && source ' name '.queue "']); Index: /issm/trunk/src/m/classes/public/queue/QueueRequirements.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/QueueRequirements.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/QueueRequirements.m (revision 3149) @@ -0,0 +1,119 @@ +function QueueRequirements(cluster,queue,np,time) +%QUEUEREQUIREMENTS queue requirements in time, number of cpus, by name of queue. +% +% +% Usage: QueueRequirements(cluster,queue,np,time) +% + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%cluster settings%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +if strcmpi(cluster,'cosmos'), + + available_queues={'debug','shortq','longq','specialq'}; + queue_requirements_time=[60 180 720 1440]; + queue_requirements_np=[32 128 256 256]; + queue_requirements_modulo=[1 1 1 1]; + +elseif strcmpi(cluster,'gemini'), + + available_queues={'debug','shortg','longg'}; + queue_requirements_time=[60 180 720]; + queue_requirements_np=[50 50 50]; + queue_requirements_modulo=[1 1 1 ]; + +elseif strcmpi(cluster,'castor'), + + available_queues={'shortc','longc'}; + queue_requirements_time=[180 720]; + queue_requirements_np=[128 128]; + queue_requirements_modulo=[1 1 ]; + +elseif strcmpi(cluster,'pollux'), + + available_queues={'shortp','longp'}; + queue_requirements_time=[180 720]; + queue_requirements_np=[128 128]; + queue_requirements_modulo=[1 1 ]; + +elseif strcmpi(cluster,'astrid'), + + available_queues={'none'}; + queue_requirements_time=[Inf]; + queue_requirements_np=[16]; + queue_requirements_modulo=[1 ]; + +elseif strcmpi(cluster,'larsen'), + + available_queues={'none'}; + queue_requirements_time=[Inf]; + queue_requirements_np=[8]; + queue_requirements_modulo=[1 ]; + +elseif strcmpi(cluster,'wilkes'), + + available_queues={'none'}; + queue_requirements_time=[Inf]; + queue_requirements_np=[8]; + queue_requirements_modulo=[1 ]; + +elseif strcmpi(cluster,'pfe'), + + available_queues={'long'}; + queue_requirements_time=[7200]; + queue_requirements_np=[2048]; + queue_requirements_modulo=[8 ]; + +else + error(['BuildQueueingScript error message: cannot find requirements for ' cluster ]); +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%end settings%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%Ok, go through requirements for current queue: +index=ismemberi(queue,available_queues); +if ~index, + %ok, either we a generic cluster, with 'none' queue, or we could not find the queue reqruirements + if strcmpi(available_queues{1},'none'), + %reset index to 1, so we can fish the requirements + index=1; + else + string=available_queues{1}; + for i=2:length(available_queues), + string=[string ' ' available_queues{i}]; + end + error(['QueueRequirements error message: availables queues are ' string]); + end +end + +%check on time requirements +rtime=queue_requirements_time(index); + +if time<=0, + error('QueueRequirements: time should be a positive number'); +end + +if time>rtime, + error(['QueueRequirements: time should be < ' num2str(rtime) ' for queue: ' queue]); +end + +%check on np requirements +rnp=queue_requirements_np(index); +rmod=queue_requirements_modulo(index); + +if np<=0, + error('QueueRequirements: np should be a positive number'); +end + +if np>rnp, + error(['QueueRequirements: np should be < ' num2str(rnp) ' for queue: ' queue]); +end + +%check np is a multiple of the queue multiple +if mod(np,rmod), + error(['QueueRequirements: np should be a multiple of ' num2str(rmod) ' for queue: ' queue]); +end Index: /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScript.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScript.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScript.m (revision 3149) @@ -0,0 +1,23 @@ +function BuildMultipleQueueingScript(cluster,name,executionpath,codepath) +%BUILDMULTIPLEQUEUEINGSCRIPT - +% +% Usage: +% BuildMultipleQueueingScript(executionpath,codepath) + +disp('building queueing script'); + +%First try and figure out if there is a special script for this particular cluster +function_name=['BuildMultipleQueueingScript' cluster]; + +%some specific treatment of identical cluster, gemini, castor and pollux +if strcmpi(cluster,'castor') || strcmpi(cluster,'pollux'), + function_name='BuildMultipleQueueingScriptgemini'; +end + +if exist(function_name,'file'), + %Call this function: + eval([function_name '(name,executionpath,codepath);']); +else + %Call the generic BuildQueueingScript: + BuildMultipleQueueingScriptGeneric(name,executionpath,codepath); +end Index: /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScriptGeneric.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScriptGeneric.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScriptGeneric.m (revision 3149) @@ -0,0 +1,12 @@ +function BuildMultipleQueueingScriptGeneric(name,executionpath,codepath) +%BUILDMULTIPLEQUEUEINGSCRIPTGENERIC - ... +% +% Usage: +% BuildMultipleQueueingScriptGeneric(executionpath,codepath) + +global ISSM_DIR + + +%not done yet +error('BuildMultipleQueueingScriptGenericerror message: not supported yet!'); + Index: /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScriptgemini.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScriptgemini.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/multiple/BuildMultipleQueueingScriptgemini.m (revision 3149) @@ -0,0 +1,23 @@ +function BuildQueueingScriptgemini(name,executionpath,codepath) +%BUILDQUEUEINGSCRIPTGEMINI - ... +% +% Usage: +% BuildQueueingScriptgemini(md,executionpath,codepath) + +scriptname=[name '.queue']; + +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,'cd %s\n',executionpath); +fprintf(fid,'mkdir %s\n',name); +fprintf(fid,'cd %s\n',name); +fprintf(fid,'mv ../ModelList.tar.gz ./\n'); +fprintf(fid,'tar -zxvf ModelList.tar.gz\n'); +fprintf(fid,'foreach i (%s-*vs*.queue)\n',name); +fprintf(fid,'qsub $i\n'); +fprintf(fid,'end\n'); +fclose(fid); Index: /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJob.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJob.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJob.m (revision 3149) @@ -0,0 +1,21 @@ +function LaunchMultipleQueueJob(cluster,name,executionpath) +%LAUNCHMULTIPLEQUEUEJOB - ... +% +% Usage: +% LaunchMultipleQueueJob(executionpath) + +%First try and figure out if there is a special script for thie particular cluster +function_name=['LaunchMultipleQueueJob' cluster]; + +%some specific treatment of identical cluster, gemini, castor and pollux +if strcmpi(cluster,'castor') || strcmpi(cluster,'pollux'), + function_name='LaunchMultipleQueueJobgemini'; +end + +if exist(function_name,'file'), + %Call this function: + eval([function_name '(cluster,name,executionpath);']); +else + %Call the generic LaunchMultipleQueueJob: + LaunchMultipleQueueJobGeneric(cluster,name,executionpath); +end Index: /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJobGeneric.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJobGeneric.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJobGeneric.m (revision 3149) @@ -0,0 +1,7 @@ +function LaunchMultipleQueueJobGeneric(cluster,name,executionpath) +%LAUNCHMULTIPLEQUEUEJOBGENERIC - Generic routine to launch multiple queueing job +% +% Usage: +% LaunchMultipleQueueJobGeneric(cluster,name,executionpath) + +error('LaunchMultipleQueueJobGeneric error message: not supported yet!'); Index: /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJobgemini.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJobgemini.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/multiple/LaunchMultipleQueueJobgemini.m (revision 3149) @@ -0,0 +1,22 @@ +function md=LaunchMultipleQueueJobgemini(cluster,name,executionpath) +%LAUNCHMULTIPLEQUEUEJOBGEMINI - Launch multiple queueing script on Gemini cluster +% +% Usage: +% LaunchMultipleQueueJobgemini(cluster,name,executionpath) + + +%first, check we have the binary file and the queueing script +if ~exist([ name '.queue'],'file'), + error('LaunchMultipleQueueJobgemini error message: queueing script issing, cannot go forward'); +end + +if ~exist('ModelList.tar.gz','file'), + error('LaunchMultipleQueueJobgemini error message: inputs models file missing, cannot go forward'); +end + +%upload both files to cluster +disp('uploading input file, queueing script and variables script'); +eval(['!scp ModelList.tar.gz ' name '.queue ' cluster ':' executionpath]); + +disp('launching solution sequence on remote cluster'); +issmssh(cluster,login,['"cd ' executionpath ' && source ' name '.queue "']); Index: /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptGeneric.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptGeneric.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptGeneric.m (revision 3149) @@ -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/old/BuildQueueingScriptcosmos.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptcosmos.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptcosmos.m (revision 3149) @@ -0,0 +1,22 @@ +function BuildQueueingScriptcosmos(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPTGEMINI - ... +% +% Usage: +% BuildQueueingScriptcosmos(md,executionpath,codepath) + + +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. +fprintf(fid,'#PBS -q %s\n',md.queue); +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/old/BuildQueueingScriptgemini.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptgemini.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptgemini.m (revision 3149) @@ -0,0 +1,22 @@ +function BuildQueueingScriptgemini(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPTGEMINI - ... +% +% Usage: +% BuildQueueingScriptgemini(md,executionpath,codepath) + +scriptname=[md.name '.queue']; +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/old/BuildQueueingScriptgreenplanet.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptgreenplanet.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptgreenplanet.m (revision 3149) @@ -0,0 +1,21 @@ +function BuildQueueingScriptgreenplanet(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPTGEMINI - ... +% +% Usage: +% BuildQueueingScriptgreenplanet(md,executionpath,codepath) + +scriptname=[md.name '.queue']; + + +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 $PBS_NODEFILE -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock > %s.outlog',md.np,codepath,AnalysisTypeFromEnum(md.analysis_type),executionpath,md.name,md.name,md.name,md.name); + +fclose(fid); Index: /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptpfe.m =================================================================== --- /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptpfe.m (revision 3149) +++ /issm/trunk/src/m/classes/public/queue/old/BuildQueueingScriptpfe.m (revision 3149) @@ -0,0 +1,49 @@ +function BuildQueueingScriptpfe(md,executionpath,codepath) +%BUILDQUEUEINGSCRIPTPFE - ... +% +% Usage: +% BuildQueueingScriptpfe(md,executionpath,codepath) + +scriptname=[md.name '.queue']; + + + available_queues={'long'}; + if ~ismemberi(md.queue,available_queues), + end + if md.time>720, + error('BuildQueueingScriptcosmos error message: long queue only allows 720 minutes'); + end + if mod(md.np,8), + error('BuildQueueingScriptcosmos error message: np should be a multiple of 8'); + end + +end + +fid=fopen(scriptname,'w'); +if fid==-1, + error(['BuildQueueingScriptpfeerror message: could not open ' scriptname ' file for ascii writing']); +end + + +fprintf(fid,'#PBS -S /bin/bash\n'); +fprintf(fid,'#PBS -N %s\n',md.name); +fprintf(fid,'#PBS -l select=%i:ncpus=8:mpiprocs=8\n',md.np/8); +fprintf(fid,'#PBS -l walltime=%i\n',md.time*60); %walltime is in seconds. +fprintf(fid,'#PBS -W group_list=s1010\n'); +fprintf(fid,'#PBS -m e\n'); +fprintf(fid,'#PBS -o %s.outlog \n',md.name); +fprintf(fid,'#PBS -e %s.errlog \n\n',md.name); + +fprintf(fid,'. /usr/share/modules/init/bash\n\n'); + +fprintf(fid,'module load comp-intel/11.1.046\n'); +fprintf(fid,'module load mpi/mpt.1.23.nas\n'); +fprintf(fid,'module load math/intel_mkl_64_10.0.011\n\n'); + +fprintf(fid,'export PATH="$PATH:."\n\n'); + +fprintf(fid,'cd $PBS_O_WORKDIR\n\n'); + +fprintf(fid,'mpiexec -verbose -np %i %s/%s.exe $PBS_O_WORKDIR %s.bin %s.outbin %s.lock',md.np,codepath,AnalysisTypeFromEnum(md.analysis_type),md.name,md.name,md.name); + +fclose(fid);