Index: /issm/branches/trunk-larour-SLPS2022/src/m/classes/clusters/pfe.m =================================================================== --- /issm/branches/trunk-larour-SLPS2022/src/m/classes/clusters/pfe.m (revision 27316) +++ /issm/branches/trunk-larour-SLPS2022/src/m/classes/clusters/pfe.m (revision 27317) @@ -51,5 +51,5 @@ disp(sprintf(' queue: %s',cluster.queue)); disp(sprintf(' time: %i',cluster.time)); - disp(sprintf(' processor: %sn',cluster.processor)); + disp(sprintf(' processor: %s',cluster.processor)); disp(sprintf(' srcpath: %s',cluster.srcpath)); disp(sprintf(' extpkgpath: %s',cluster.extpkgpath)); Index: /issm/branches/trunk-larour-SLPS2022/src/m/classes/dslmme.m =================================================================== --- /issm/branches/trunk-larour-SLPS2022/src/m/classes/dslmme.m (revision 27316) +++ /issm/branches/trunk-larour-SLPS2022/src/m/classes/dslmme.m (revision 27317) @@ -38,4 +38,5 @@ return; end + nt=length(self.global_average_thermosteric_sea_level); for i=1:length(self.global_average_thermosteric_sea_level), md = checkfield(md,'field',self.global_average_thermosteric_sea_level{i},'NaN',1,'Inf',1); @@ -50,32 +51,34 @@ %check time stamps: they should all be in seconds - %global_average_thermosteric_sea_level {{{ - for i=1:nt, - h=self.global_average_thermosteric_sea_level{i}; - times=h(end,:); - avgtime=mean(times); - if(avgtime<10000) - error('dslmme checkconsistency error messages: time tags for global_average_thermosteric_sea_level should be in seconds!'); - end - end %}}} - %sea_surface_height_above_geoid {{{ - for i=1:nt, - h=self.sea_surface_height_above_geoid{i}; - times=h(end,:); - avgtime=mean(times) - if(avgtime<10000) - error('dslmme checkconsistency error messages: time tags for sea_surface_height_above_geoid should be in seconds!'); - end - end %}}} - %sea_water_pressure_at_sea_floor {{{ - for i=1:nt, - h=self.sea_water_pressure_at_sea_floor{i}; - times=h(end,:); - avgtime=mean(times) - if(avgtime<10000) - error('dslmme checkconsistency error messages: time tags for sea_water_pressure_at_sea_floor should be in seconds!'); - end - end %}}} - + checkseconds=0; + if checkseconds, + %global_average_thermosteric_sea_level {{{ + for i=1:nt, + h=self.global_average_thermosteric_sea_level{i}; + times=h(end,:); + avgtime=mean(times); + if(avgtime<10000) + error('dslmme checkconsistency error messages: time tags for global_average_thermosteric_sea_level should be in seconds!'); + end + end %}}} + %sea_surface_height_above_geoid {{{ + for i=1:nt, + h=self.sea_surface_height_above_geoid{i}; + times=h(end,:); + avgtime=mean(times) + if(avgtime<10000) + error('dslmme checkconsistency error messages: time tags for sea_surface_height_above_geoid should be in seconds!'); + end + end %}}} + %sea_water_pressure_at_sea_floor {{{ + for i=1:nt, + h=self.sea_water_pressure_at_sea_floor{i}; + times=h(end,:); + avgtime=mean(times) + if(avgtime<10000) + error('dslmme checkconsistency error messages: time tags for sea_water_pressure_at_sea_floor should be in seconds!'); + end + end %}}} + end end % }}} function disp(self) % {{{ Index: /issm/branches/trunk-larour-SLPS2022/src/m/classes/mmeofflinesolidearthsolution.m =================================================================== --- /issm/branches/trunk-larour-SLPS2022/src/m/classes/mmeofflinesolidearthsolution.m (revision 27316) +++ /issm/branches/trunk-larour-SLPS2022/src/m/classes/mmeofflinesolidearthsolution.m (revision 27317) @@ -51,4 +51,6 @@ %check time stamps: they should all be in seconds + checkseconds=0; + if checkseconds, %displacementup {{{ for i=1:sup, @@ -57,5 +59,5 @@ avgtime=mean(times); if(avgtime<10000) - error('dslmme checkconsistency error messages: time tags for displacementup should be in seconds!'); + error('mmeofflinesolidearthsolution checkconsistency error messages: time tags for displacementup should be in seconds!'); end end %}}} @@ -87,5 +89,5 @@ end end %}}} - + end end % }}} function disp(self) % {{{ @@ -99,5 +101,5 @@ function marshall(self,prefix,md,fid) % {{{ WriteData(fid,prefix,'data',4,'name','md.solidearth.external.nature','format','Integer'); %code 4 for mmeofflinesolidearthsolution class - WriteData(fid,prefix,'data',self.modelid,'name','md.solidearth.external.modelid','format','Integer'); + WriteData(fid,prefix,'data',self.modelid,'name','md.solidearth.external.modelid','format','Double'); nummodels=length(self.displacementeast); WriteData(fid,prefix,'name','md.solidearth.external.nummodels','data',nummodels,'format','Integer'); Index: /issm/branches/trunk-larour-SLPS2022/src/m/classes/modellist.m =================================================================== --- /issm/branches/trunk-larour-SLPS2022/src/m/classes/modellist.m (revision 27316) +++ /issm/branches/trunk-larour-SLPS2022/src/m/classes/modellist.m (revision 27317) @@ -8,4 +8,8 @@ models = cell(0,1); cluster = generic(); + name = ''; + end + properties (SetAccess=public) + runtimename = ''; end methods @@ -122,14 +126,13 @@ end % }}} - function self = modellist(varargin) % {{{ + function self = modellist(name,cluster,varargin) % {{{ %initialize list if nargin==0, %Do nothing, - elseif nargin==1, - if ~isa(varargin{1},'cell'), - error('not supported yet'); - end - + else + + self.name=name; + self.cluster=cluster; celllist=varargin{1}; @@ -145,7 +148,5 @@ end end - self.models = celllist; - self.cluster = self.models{1}.cluster; end end % }}} @@ -208,34 +209,35 @@ delete('ModelResults.tar.gz'); end % }}} - function self = solve(self,varargin)% {{{ + function self = solve(self,solutiontype,varargin)% {{{ %SOLVE - apply solution sequence for a list of models. Used in batch mode. % % Usage: - % self=solve(self,varargin) + % self=solve(self,solutiontype,varargin) % where varargin is a lit of paired arguments. - % arguments can be: 'analysis_type': 'stressbalance','thermal','masstransport','transient' % % Examples: - % self=solve(self,'analysis_type','stressbalance'); - + % self=solve(self,'tr','batch','yes'); + + disp('Starting multiple solve'); + + + %come up with a run time name: + c=clock; + self.runtimename=sprintf('%s-%02i-%02i-%04i-%02i-%02i-%02i-%i',self.name,c(2),c(3),c(1),c(4),c(5),floor(c(6)),feature('GetPid')); + + %recover options - options=pairoptions(varargin{:}); - - %add default options - options=process_solve_options(options); + options=pairoptions(varargin{:},'solutionstring',solutiontype); %length of list nummodels=length(self.models); - %name of queue: to make it unique, add a time stamp - name=[self.name '-' datestr(now,1) '-' datestr(now,'HH-MM-SS') ]; - - %name of cluster will be first name of list - cluster=self.cluster; - - %Figure out parameters for this particular cluster - cluster_rc_location=which('cluster.rc'); - [codepath,executionpath]=ClusterParameters(cluster,cluster_rc_location); - + %come up with unique names for all our models: + for i=1:nummodels, + self.models{i}.miscellaneous.name=sprintf('%s%i',self.models{i}.miscellaneous.name,i); + end + + names={}; + %solve in batch mode: for i=1:nummodels, @@ -244,142 +246,196 @@ mdex=self.models{i}; - %recover some fields - mdex.analysis_type=options.analysis_type; - - mdex.name=[name '-' num2str(i) 'vs' num2str(nummodels)]; - mdex.time=self.time; - mdex.queue=self.queue; - mdex.cluster=self.cluster; - if ~isnan(self.np), - mdex.np=self.np; - end - %call solve in batch mode: - if strcmpi(cluster,oshostname), + disp(sprintf(' marshalling model %i/%i',i,nummodels)); + if strcmpi(self.cluster,oshostname), mdex=solve(mdex,varargin{:}); else - mdex=solve(mdex,varargin{:},'batch','yes','directory',name); + mdex=solve(mdex,solutiontype,varargin{:},'batch','yes'); end %feed back self.models{i}=mdex; + + %record name: + names{end+1}=sprintf('%s.tar.gz',mdex.private.runtimename); end %locally, we are done. - if strcmpi(cluster,oshostname), + if strcmpi(self.cluster,oshostname), return end - - %now, tar all the files and then erase them. - eval(['!find -iname ''' name '-*'' > file_list.txt']); - !tar zcvf ModelList.tar.gz --files-from file_list.txt - !rm -rf *.bin *.queue file_list.txt + + %tar files: + tar('ModelList.tar.gz',names); %still have to build a launching script. - BuildMultipleQueueingScript(cluster,name,executionpath,codepath); + self.BuildQueueingScript(solutiontype); + + %upload data + self.UploadQueueJob(); %launch jobs on remote cluster - LaunchMultipleQueueJob(cluster,name,executionpath); + self.LaunchQueueJob(); %erase files: - delete([name '.queue']); delete('ModelList.tar.gz'); - %save name: - self.name=name; end % }}} + function self = loadresults(self) % {{{ + + nummodels=length(self.models); + cluster=self.cluster; + + %solve in batch mode: + directory=sprintf('%s/Interactive%i',cluster.executionpath,cluster.interactive); + filelist={}; + for i=1:nummodels, + filelist{end+1}= sprintf('%s/%s.outbin',self.models{i}.private.runtimename,self.models{i}.miscellaneous.name); + end + issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); + + %load results: + for i=1:nummodels, + self.models{i}=loadresultsfromdisk(self.models{i},sprintf('%s.outbin',self.models{i}.miscellaneous.name)); + end + + end %}}} + function num= nummodels(self) % {{{ + num=length(self.models); + end %}}} + function BuildQueueingScript(self,solution)% {{{ + + scriptname=[self.runtimename '.queue']; + cluster=self.cluster; + dirname=self.runtimename; + modelname=self.name; + nummodels=length(self.models); + + %recover and process solve options %{{{ + if strcmpi(solution,'sb') || strcmpi(solution,'Stressbalance') + solution = 'StressbalanceSolution'; + elseif strcmpi(solution,'mt') || strcmpi(solution,'Masstransport') + solution = 'MasstransportSolution'; + elseif strcmpi(solution,'oceant') || strcmpi(solution,'Oceantransport') + solution = 'OceantransportSolution'; + elseif strcmpi(solution,'th') || strcmpi(solution,'Thermal') + solution = 'ThermalSolution'; + elseif strcmpi(solution,'ss') || strcmpi(solution,'Steadystate') + solution = 'SteadystateSolution'; + elseif strcmpi(solution,'tr') || strcmpi(solution,'Transient') + solution = 'TransientSolution'; + elseif strcmpi(solution,'mc') || strcmpi(solution,'Balancethickness') + solution = 'BalancethicknessSolution'; + elseif strcmpi(solution,'Balancethickness2') + solution = 'Balancethickness2Solution'; + elseif strcmpi(solution,'mcsoft') || strcmpi(solution,'BalancethicknessSoft') + solution = 'BalancethicknessSoftSolution'; + elseif strcmpi(solution,'bv') || strcmpi(solution,'Balancevelocity') + solution = 'BalancevelocitySolution'; + elseif strcmpi(solution,'bsl') || strcmpi(solution,'BedSlope') + solution = 'BedSlopeSolution'; + elseif strcmpi(solution,'ssl') || strcmpi(solution,'SurfaceSlope') + solution = 'SurfaceSlopeSolution'; + elseif strcmpi(solution,'hy') || strcmpi(solution,'Hydrology') + solution = 'HydrologySolution'; + elseif strcmpi(solution,'da') || strcmpi(solution,'DamageEvolution') + solution = 'DamageEvolutionSolution'; + elseif strcmpi(solution,'gia') || strcmpi(solution,'Gia') + solution = 'GiaSolution'; + elseif strcmpi(solution,'lv') || strcmpi(solution,'Love') + solution = 'LoveSolution'; + elseif strcmpi(solution,'esa') || strcmpi(solution,'Esa') + solution = 'EsaSolution'; + elseif strcmpi(solution,'smp') || strcmpi(solution,'Sampling') + solution = 'SamplingSolution'; + else + error(['solution ' solution ' not supported!']); + end + %}}} + + executable='issm.exe'; + + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#PBS -S /bin/bash\n'); + fprintf(fid,'#PBS -l select=%i:ncpus=%i:model=%s\n',cluster.numnodes,cluster.cpuspernode,cluster.processor); + fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %walltime is in seconds. + fprintf(fid,'#PBS -q %s\n',cluster.queue); + fprintf(fid,'#PBS -W group_list=%s\n',cluster.grouplist); + fprintf(fid,'#PBS -m e\n'); + fprintf(fid,'#PBS -o %s/%s/%s.outlog \n',cluster.executionpath,dirname,modelname); + fprintf(fid,'#PBS -e %s/%s/%s.errlog \n\n',cluster.executionpath,dirname,modelname); + fprintf(fid,'. /usr/share/modules/init/bash\n\n'); + for i=1:numel(cluster.modules), fprintf(fid,['module load ' cluster.modules{i} '\n']); end + fprintf(fid,'export PATH="$PATH:."\n\n'); + fprintf(fid,'export MPI_LAUNCH_TIMEOUT=520\n'); + fprintf(fid,'export MPI_GROUP_MAX=64\n\n'); + fprintf(fid,'export ISSM_DIR="%s"\n',cluster.srcpath); %FIXME + + fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME + fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname); + + for i=1:nummodels, + fprintf(fid,'cd %s && mpiexec -np %i /u/scicon/tools/bin/mbind.x %s/%s %s %s/%s/%s && cd ..\n',self.models{i}.private.runtimename,cluster.nprocs(),cluster.codepath,executable,solution,cluster.executionpath,self.runtimename,self.models{i}.private.runtimename); + end + fclose(fid); + + %in interactive mode, create a run file, and errlog and outlog file + if cluster.interactive, + fid=fopen([modelname '.run'],'w'); + for i=1:nummodels, + fprintf(fid,'cd %s && mpiexec -np %i /u/scicon/tools/bin/mbind.x %s/%s %s %s/%s %s && cd ..\n',self.models{i}.private.runtimename,cluster.nprocs(),cluster.codepath,executable,solution,[cluster.executionpath '/Interactive' num2str(cluster.interactive)] ,self.models{i}.private.runtimename,self.models{i}.miscellaneous.name); + end + fclose(fid); + fid=fopen([modelname '.errlog'],'w'); fclose(fid); + fid=fopen([modelname '.outlog'],'w'); fclose(fid); + end + end% }}} + function UploadQueueJob(self) % {{{ + + cluster=self.cluster; + + %compress the files into one zip. + compressstring=sprintf('tar -zcf %s.tar.gz ModelList.tar.gz %s.queue ',self.name,self.name); + if cluster.interactive, + compressstring = sprintf('%s %s.run %s.errlog %s.outlog',compressstring, self.name,self.name,self.name); + end + system(compressstring); + + disp('uploading input file and queueing script'); + if cluster.interactive, + directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive)]; + else + directory=cluster.executionpath; + end + + issmscpout(cluster.name,directory,cluster.login,cluster.port,{[self.name '.tar.gz']}); + + end + %}}} + function LaunchQueueJob(self)% {{{ + %LAUNCHQUEUEJOB - LAUNCH MULTIPLE QUEUEING SCRIPT ON PFE CLUSTER + % + % Usage: + % LaunchQueueJob(self) + + cluster=self.cluster; + modelname=self.name; + nummodels=length(self.models); + + disp('uploading inputs files'); + if cluster.interactive, + launchcommand=sprintf('cd %s/Interactive%i && tar -zxf %s.tar.gz && tar -zxvf ModelList.tar.gz ',cluster.executionpath,cluster.interactive,modelname); + for i=1:nummodels, + launchcommand=sprintf('%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxvf %s.tar.gz && cd .. ',launchcommand,self.models{i}.private.runtimename, ... + self.models{i}.private.runtimename, self.models{i}.private.runtimename, self.models{i}.private.runtimename); + end + else + launchcommand=['cd ' cluster.executionpath ' && mkdir ' self.runtimename... + ' && cd ' self.runtimename ' && mv ../' self.runtimename '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && qsub ' modelname '.queue ']; + end + + disp('launching solution sequence on remote cluster'); + issmssh(cluster.name,cluster.login,cluster.port,launchcommand); + end end end - -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 -end % }}} -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); -end% }}} -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 -end% }}} -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 "']); -end% }}} Index: /issm/branches/trunk-larour-SLPS2022/src/m/contrib/larour/glacier_inventory.m =================================================================== --- /issm/branches/trunk-larour-SLPS2022/src/m/contrib/larour/glacier_inventory.m (revision 27316) +++ /issm/branches/trunk-larour-SLPS2022/src/m/contrib/larour/glacier_inventory.m (revision 27317) @@ -183,5 +183,5 @@ %Go through O2 regions: for i=subsetregions, - %for i=33, + %for i=89:150, string=self.boxes(i).RGI_CODE; disp(['progressing with region ' num2str(i) ' ' string]); @@ -210,9 +210,17 @@ case 32, radius=60; case 33, radius=10; + case 36, radius=10; case 41, radius=75; case 42, radius=45; + case 51, radius=10; case 61, radius=66; + case 63, radius=10; case 68, radius=10; + case 77, radius=10; case 82, radius=30; + case 83, radius=20; + case 89, radius=20; + case 90, radius=10; + case 93, radius=10; otherwise, end % }}} Index: /issm/branches/trunk-larour-SLPS2022/src/m/contrib/larour/groundedicearea.m =================================================================== --- /issm/branches/trunk-larour-SLPS2022/src/m/contrib/larour/groundedicearea.m (revision 27317) +++ /issm/branches/trunk-larour-SLPS2022/src/m/contrib/larour/groundedicearea.m (revision 27317) @@ -0,0 +1,68 @@ +function [totalarea,groundediceelements]=groundedicearea(md) + + times=md.timestepping.start_time:md.timestepping.time_step:md.timestepping.final_time; + nt=length(times); + + totalarea=zeros(nt,1); + areas=GetAreasSphericalTria(md.mesh.elements,md.mesh.lat,md.mesh.long,planetradius('earth')); + + rho_ice=md.materials.rho_ice; + rho_water=md.materials.rho_water; + oceanarea=3.619e+14; + + groundediceelements=zeros(md.mesh.numberofelements,nt); + for t=1:nt-1, + + time=times(t); + + tocean=md.mask.ocean_levelset(end,:); + ind=findind(time,tocean); + ocean=md.mask.ocean_levelset(1:end-1,ind); + + tice=md.mask.ice_levelset(end,:); + ind=findind(time,tice); + ice=md.mask.ice_levelset(1:end-1,ind); + + masks.isiceonly=isiceonly(ice(md.mesh.elements)); + masks.isoceanin=isoceanin(ocean(md.mesh.elements)); + masks.isfullyfloating=isfullyfloating(ocean(md.mesh.elements)); + masks.notfullygrounded=notfullygrounded(ocean(md.mesh.elements)); + + %Go through elements and sum up: + pos=find(masks.isiceonly & ~masks.isfullyfloating); + totalarea(t)=sum(areas(pos)); + + flags=zeros(md.mesh.numberofelements,1); + flags(pos)=1; + groundediceelements(:,t)=flags; + end +end +function ind=findind(t,ts) % {{{ + + nts=length(ts); + if t=ts(end), + ind=nts; + end; + for i=2:nts-1, + if (t>=ts(i) & t