Index: /issm/trunk/src/m/classes/@model/setdefaultparameters.m =================================================================== --- /issm/trunk/src/m/classes/@model/setdefaultparameters.m (revision 6037) +++ /issm/trunk/src/m/classes/@model/setdefaultparameters.m (revision 6038) @@ -237,6 +237,5 @@ %set petsc options for different analysis md.petscoptions=petscoptions; -%md.petscoptions=addoptions(md.petscoptions,DiagnosticHorizAnalysisEnum,asmoptions); -%md.petscoptions=addoptions(md.petscoptions,DiagnosticVertAnalysisEnum,mumpsoptions); +md.petscoptions=addoptions(md.petscoptions,DiagnosticVertAnalysisEnum,mumpsoptions); %solution speed-up Index: /issm/trunk/src/m/classes/@runsteps/savemodel.m =================================================================== --- /issm/trunk/src/m/classes/@runsteps/savemodel.m (revision 6037) +++ /issm/trunk/src/m/classes/@runsteps/savemodel.m (revision 6038) @@ -45,4 +45,4 @@ end -save(name,'md'); +save(name,'md','-v7.3'); disp(['model saved as: ' name]); Index: sm/trunk/src/m/clusters/QueueRequirements.m =================================================================== --- /issm/trunk/src/m/clusters/QueueRequirements.m (revision 6037) +++ (revision ) @@ -1,36 +1,0 @@ -function QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,queue,np,time) -%QUEUEREQUIREMENTS queue requirements in time, number of cpus, by name of queue. -% -% -% Usage: QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,np,time) -% - -%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 -if np<=0, - error('QueueRequirements: np should be a positive number'); -end Index: /issm/trunk/src/m/clusters/astrid.m =================================================================== --- /issm/trunk/src/m/clusters/astrid.m (revision 6037) +++ /issm/trunk/src/m/clusters/astrid.m (revision 6038) @@ -77,6 +77,26 @@ end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && source ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end + end %}}} Index: /issm/trunk/src/m/clusters/castor.m =================================================================== --- /issm/trunk/src/m/clusters/castor.m (revision 6037) +++ /issm/trunk/src/m/clusters/castor.m (revision 6038) @@ -80,6 +80,26 @@ end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && qsub ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && qsub ' modelname '.queue ']; + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end + end %}}} Index: /issm/trunk/src/m/clusters/cosmos.m =================================================================== --- /issm/trunk/src/m/clusters/cosmos.m (revision 6037) +++ /issm/trunk/src/m/clusters/cosmos.m (revision 6038) @@ -79,6 +79,26 @@ end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && qsub -S/bin/sh ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && qsub -S/bin/sh ' modelname '.queue ']; + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end + end %}}} Index: /issm/trunk/src/m/clusters/ericmac.m =================================================================== --- /issm/trunk/src/m/clusters/ericmac.m (revision 6037) +++ /issm/trunk/src/m/clusters/ericmac.m (revision 6038) @@ -76,6 +76,26 @@ end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && source ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end + end %}}} Index: /issm/trunk/src/m/clusters/gemini.m =================================================================== --- /issm/trunk/src/m/clusters/gemini.m (revision 6037) +++ /issm/trunk/src/m/clusters/gemini.m (revision 6038) @@ -80,6 +80,26 @@ end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && qsub ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && qsub ' modelname '.queue ']; + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end + end %}}} Index: /issm/trunk/src/m/clusters/larsen.m =================================================================== --- /issm/trunk/src/m/clusters/larsen.m (revision 6037) +++ /issm/trunk/src/m/clusters/larsen.m (revision 6038) @@ -76,6 +76,26 @@ end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && source ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end + end %}}} Index: /issm/trunk/src/m/clusters/pfe.m =================================================================== --- /issm/trunk/src/m/clusters/pfe.m (revision 6037) +++ /issm/trunk/src/m/clusters/pfe.m (revision 6038) @@ -19,4 +19,5 @@ codepath='/staff/elarour/trunk/bin'; executionpath='/nobackupp10/elarour/Testing'; + interactive=0; end properties (SetAccess=private) @@ -110,8 +111,57 @@ 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 -verbose -np %i %s/issm.exe %s $PBS_O_WORKDIR %s.bin %s.petsc %s.outbin %s.lock',cluster.np,cluster.codepath,EnumToString(analysis_type),modelname,modelname,modelname,modelname); + fclose(fid); + fid=fopen([modelname '.errlog'],'w'); + fclose(fid); + fid=fopen([modelname '.outlog'],'w'); + fclose(fid); + end end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && qsub ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + if ~cluster.interactive, + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && qsub ' modelname '.queue ']; + else + launchcommand=['cd ' cluster.executionpath '/Interactive && tar -zxf ' md.runtimename '.tar.gz']; + end + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + if cluster.interactive, + compressstring=[compressstring md.name '.run ' md.name '.errlog ' md.name '.outlog ']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + if ~cluster.interactive, + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + issmscpout(md.cluster.name,[md.cluster.executionpath '/Interactive'],md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + end + + disp('launching solution sequence on remote cluster'); + issmssh(md.cluster.name,md.cluster.login,md.cluster.port,launchcommand); + + if cluster.interactive, + error('done uploading files to interactive directory on remote cluster'); + end + + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end end %}}} Index: /issm/trunk/src/m/clusters/pollux.m =================================================================== --- /issm/trunk/src/m/clusters/pollux.m (revision 6037) +++ /issm/trunk/src/m/clusters/pollux.m (revision 6038) @@ -80,6 +80,26 @@ end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && qsub ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && qsub ' modelname '.queue ']; + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end + end %}}} Index: /issm/trunk/src/m/clusters/wilkes.m =================================================================== --- /issm/trunk/src/m/clusters/wilkes.m (revision 6037) +++ /issm/trunk/src/m/clusters/wilkes.m (revision 6038) @@ -76,6 +76,26 @@ end %}}} - function command=LaunchCommand(cluster,modelruntimename,modelname)% {{{1 - command=['cd ' cluster.executionpath ' && rm -rf ./' modelruntimename ' && mkdir ' modelruntimename ' && cd ' modelruntimename ' && mv ../' modelruntimename '.tar.gz ./ && tar -zxf ' modelruntimename '.tar.gz && source ' modelname '.queue ']; + function LaunchQueueJob(cluster,md,options)%{{{1 + + %lauch command, to be executed via ssh + launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' md.runtimename ' && mkdir ' md.runtimename ... + ' && cd ' md.runtimename ' && mv ../' md.runtimename '.tar.gz ./ && tar -zxf ' md.runtimename '.tar.gz && source ' md.name '.queue ']; + + if ~strcmpi(options.batch,'yes'), + + %compress the files into one zip. + compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; + if md.qmu_analysis, + compressstring=[compressstring md.name '.qmu.in']; + end + system(compressstring); + + disp('uploading input file and queueing script'); + issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); + else + disp('batch mode requested: not launching job interactively'); + disp('launch solution sequence on remote cluster by hand'); + end + end %}}} Index: sm/trunk/src/m/model/LaunchQueueJob.m =================================================================== --- /issm/trunk/src/m/model/LaunchQueueJob.m (revision 6037) +++ (revision ) @@ -1,40 +1,0 @@ -function LaunchQueueJob(md,options) -%LAUNCHQUEUEJOB- Launch job on cluster -% -% Usage: -% LaunchQueueJob(model,options) - -%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 missing, cannot go forward'); -end - -if md.qmu_analysis & ~exist([ md.name '.qmu.in'],'file'), - error('LaunchQueueJobcosmos error message: missing dakota input file, cannot go forward'); -end - -if ~strcmpi(options.batch,'yes'), - - %compress the files into one zip. - compressstring=['tar -zcf ' md.runtimename '.tar.gz ' md.name '.bin ' md.name '.queue ' md.name '.petsc ']; - if md.qmu_analysis, - compressstring=[compressstring md.name '.qmu.in']; - end - system(compressstring); - - disp('uploading input file and queueing script'); - issmscpout(md.cluster.name,md.cluster.executionpath,md.cluster.login,md.cluster.port,{[md.runtimename '.tar.gz']}); - - if strcmpi(options.upload,'off'), - disp('launching solution sequence on remote cluster'); - issmssh(md.cluster.name,md.cluster.login,md.cluster.port,LaunchCommand(md.cluster,md.runtimename,md.name)); - end - -else - disp('batch mode requested: not launching job interactively'); - disp('launch solution sequence on remote cluster by hand'); -end Index: /issm/trunk/src/m/model/solveparallel.m =================================================================== --- /issm/trunk/src/m/model/solveparallel.m (revision 6037) +++ /issm/trunk/src/m/model/solveparallel.m (revision 6038) @@ -5,8 +5,10 @@ % md=solveparallel(md); +%retrieve cluster: otherwise, we can't call its methods (subsref bug) +cluster=md.cluster; + %First, build a runtime name that is unique, that we will use to create %directories, name jobs, etc ... -c=clock; -md.runtimename=sprintf('%s-%i-%i-%i-%i-%i-%i-%i',md.name,c(2),c(3),c(1),c(4),c(5),floor(c(6)),GetPId()); +c=clock; md.runtimename=sprintf('%s-%i-%i-%i-%i-%i-%i-%i',md.name,c(2),c(3),c(1),c(4),c(5),floor(c(6)),GetPId()); %Marshall model data into a binary file. @@ -19,8 +21,8 @@ %Now, we need to build the queuing script, used by the cluster to launch the job. -BuildQueueScript(md.cluster,md.name,md.analysis_type,md.mem_debug); +cluster.BuildQueueScript(md.name,md.analysis_type,md.mem_debug); %Now, launch the queueing script -LaunchQueueJob(md,options); +cluster.LaunchQueueJob(md,options); if ~strcmpi(options.upload,'on'), %did we even try to run? if so, wait on lock @@ -44,5 +46,5 @@ system(['rm -rf qmu' num2str(GetPId)]); end +else + error('solveparallel done uploading test decks'); end - - Index: /issm/trunk/src/m/utils/Cluster/QueueRequirements.m =================================================================== --- /issm/trunk/src/m/utils/Cluster/QueueRequirements.m (revision 6038) +++ /issm/trunk/src/m/utils/Cluster/QueueRequirements.m (revision 6038) @@ -0,0 +1,36 @@ +function QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,queue,np,time) +%QUEUEREQUIREMENTS queue requirements in time, number of cpus, by name of queue. +% +% +% Usage: QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,np,time) +% + +%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 +if np<=0, + error('QueueRequirements: np should be a positive number'); +end