Changeset 1111

Timestamp:

06/25/09 17:51:18 (15 years ago)

Author:

Eric.Larour

Message:

Some gemini cluster management + new geography2 for envelopped diagnostic runs

Location:

issm/trunk/src/m/classes/public

Files:

• BuildQueueingScript.m (modified) (1 diff)
• BuildQueueingScriptGeneric.m (modified) (1 diff)
• BuildQueueingScriptgemini.m (modified) (2 diffs)
• LaunchQueueJob.m (modified) (1 diff)
• LaunchQueueJobgemini.m (modified) (1 diff)
• ThicknessCorrection.m (modified) (1 diff)
• displayqmu.m (modified) (1 diff)
• geography2.m (added)
• ismodelselfconsistent.m (modified) (1 diff)
• loadresultsfromcluster.m (modified) (1 diff)
• marshall.m (modified) (1 diff)
• mesh.m (modified) (1 diff)
• setelementstype.m (modified) (1 diff)

issm/trunk/src/m/classes/public/BuildQueueingScript.m

@@ -9 +9 @@
 %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);']);

issm/trunk/src/m/classes/public/BuildQueueingScriptGeneric.m

@@ -15 +15 @@
 fprintf(fid,'#!/bin/sh\n');
 fprintf(fid,'rm -rf %s/%s.lock\n',executionpath,md.name);
-fprintf(fid,'mpirun -np %i ',md.np);
-
-if strcmpi(md.analysis_type,'diagnostic'),
-        fprintf(fid,'%s/diagnostic.exe',codepath);
-elseif strcmpi(md.analysis_type,'control'),
-        fprintf(fid,'%s/control.exe',codepath);
-elseif strcmpi(md.analysis_type,'thermal'),
-        fprintf(fid,'%s/thermal.exe',codepath);
-elseif strcmpi(md.analysis_type,'prognostic'),
-        fprintf(fid,'%s/prognostic.exe',codepath);
-elseif strcmpi(md.analysis_type,'transient'),
-        fprintf(fid,'%s/transient.exe',codepath);
-else
-        error('BuildQueueingScriptGeneric error message: unsupported solution type!');
-end
-
-fprintf(fid,' %s %s.bin %s.outbin %s.lock  2> %s.errlog >%s.outlog & ',executionpath,md.name,md.name,md.name,md.name,md.name);
+fprintf(fid,'mpirun -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock  2> %s.errlog >%s.outlog & ',md.np,codepath,md.analysis_type,executionpath,md.name,md.name,md.name,md.name,md.name);
 fclose(fid);

issm/trunk/src/m/classes/public/BuildQueueingScriptgemini.m

@@ -1 @@
-function BuildQueueingScriptgemini(md,solutiontype,executionpath,codepath)
+function BuildQueueingScriptgemini(md,executionpath,codepath)
 %BUILDQUEUEINGSCRIPTGEMINI - ...
 %
@@ -12 +12 @@
 end
 
-fprintf(fid,'#!/bin/sh\n');
-fprintf(fid,'#BSUB -n %i -W %i\n',md.np,md.time);
-fprintf(fid,'#BSUB -J %s\n',md.name);
+fprintf(fid,'#!/bin/csh\n');
+fprintf(fid,'#PBS -l walltime=%i\n',md.time);
+fprintf(fid,'#PBS -l ncpus=%i\n',md.np);
 if ~isempty(md.queue),
-        fprintf(fid,'#BSUB -q %s\n',md.queue);
+        fprintf(fid,'#PBS -q %s\n',md.queue);
 end
-fprintf(fid,'#BSUB -o %s.outlog -e %s.errlog\n',md.name,md.name);
-fprintf(fid,'cd %s\n',executionpath);
-fprintf(fid,'rm -rf %s.outlog %s.errlog %s.lock\n',md.name,md.name,md.name);
+fprintf(fid,'#PBS -o %s.outlog \n',md.name);
+fprintf(fid,'#PBS -e %s.errlog \n',md.name);
 
-if strcmpi(solutiontype,'diagnostic') ,
-        fprintf(fid,'mpirun -np %i %s/diagnostic.exe %s %s.bin %s.outbin %s.lock',md.np,codepath,executionpath,md.name,md.name,md.name);
-elseif strcmpi(solutiontype,'control') ,
-        fprintf(fid,'mpirun -np %i %s/control.exe %s %s.bin %s.outbin %s.lock',md.np,codepath,executionpath,md.name,md.name,md.name);
-elseif strcmpi(solutiontype,'thermal') ,
-        fprintf(fid,'mpirun -np %i %s/thermal.exe %s %s.bin %s.outbin %s.lock',md.np,codepath,executionpath,md.name,md.name,md.name);
-else
-        error('BuildQueueingScriptgemini error message: unsupported solution type!');
-end
+fprintf(fid,'setenv PBS_O_WORKDIR %s\n',executionpath);
+fprintf(fid,'cd $PBS_O_WORKDIR\n');
+fprintf(fid,'setenv OMP_NUM_THREADS 1\n');
+fprintf(fid,'mpirun -np %i %s/%s.exe %s %s.bin %s.outbin %s.lock',md.np,codepath,md.analysis_type,executionpath,md.name,md.name,md.name);
+
 fclose(fid);

issm/trunk/src/m/classes/public/LaunchQueueJob.m

@@ -7 +7 @@
 %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:

issm/trunk/src/m/classes/public/LaunchQueueJobgemini.m

@@ -16 +16 @@
 %jpload both files to cluster
 disp('uploading input file,  queueing script and variables script');
-eval(['!scp ' md.name '.bin' ' ' md.name '.queue '  md.cluster ':' executionpath]);
+if md.qmu_analysis, 
+        eval(['!scp ' md.name '.bin' ' ' md.name '.queue '  md.name '.qmu.in ' md.cluster ':' executionpath]);
+else
+        eval(['!scp ' md.name '.bin' ' ' md.name '.queue '  md.cluster ':' executionpath]);
+end
+
+%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']);
+return;
 
 disp('launching solution sequence on remote cluster');
+
 %now call the queuing script to launch the job.
-system(['ssh  ' md.cluster ' ''cd ' executionpath ' && bsub <  ' md.name '.queue ''']);
+system(['ssh  ' md.cluster ' ''cd ' executionpath ' && qsub <  ' md.name '.queue ''']);
+

issm/trunk/src/m/classes/public/ThicknessCorrection.m

@@ -34 +34 @@
 %modify thickness
 for i=1:length(pos_shelf)
+
+        if mod(i,100)==0,
+                fprintf('\b\b\b\b\b\b\b')
+                fprintf('%5.2f%s',i/length(pos_shelf)*100,' %');
+        end
+
         %search the grid on ice sheet the closest to i
         [d posd]=min(sqrt((md.x(pos_shelf(i))-md.x(pos_GL)).^2+(md.y(pos_shelf(i))-md.y(pos_GL)).^2));

issm/trunk/src/m/classes/public/displayqmu.m

@@ -89 +89 @@
         if isempty(md.dakotadat), disp(sprintf('         dakotadat: N/A')); else disp(sprintf('         dakotadat:    [%ix%i]    (can be accessed by typing md.dakotadat)',size(md.dakotadat)));end
         disp(sprintf('         npart   : %i (number of partitions for semi-descrete qmu)',md.npart));
+        disp(sprintf('         part    : [%i] (user provided mesh partition, defaults to metis if not specified)',length(md.part)));
+
 end

issm/trunk/src/m/classes/public/ismodelselfconsistent.m

@@ -162 +162 @@
                 disp(['concurrency should be set to 1 when running dakota in library mode']);
                 bool=0;return;
+        end
+        if ~isempty(md.part),
+                if numel(md.part)~=md.numberofgrids,
+                        disp(['user supplied partition for qmu analysis should have size md.numberofgrids x 1 ']);
+                        bool=0;return;
+                end
+                if find(md.part)>=md.numberofgrids,
+                        disp(['user supplied partition should be indexed from 0 (c-convention)']);
+                        bool=0;return;
+                end
+                if md.npart~=md.numberofgrids,
+                        disp(['user supplied partition should have same size as md.npart']);
+                        bool=0;return;
+                end
+
         end
 end

issm/trunk/src/m/classes/public/loadresultsfromcluster.m

@@ -24 +24 @@
 else
         if md.qmu_analysis,
-                system(['scp ' md.cluster ':' executionpath '/' md.name '.outlog ' executionpath '/' md.name '.errlog ' executionpath '/' md.name '.outbin ' executionpath '/' md.name '.qmu.err ' executionpath '/' md.name '.qmu.out ' executionpath '/dakota_tabular.dat ./']); %get outlog, errlog and outbin files
+                system(['scp ' md.cluster ':' executionpath '/' md.name '.outlog ' md.cluster ':' executionpath '/' md.name '.errlog ' md.cluster ':' executionpath '/' md.name '.outbin ' md.cluster ':' executionpath '/' md.name '.qmu.err ' md.cluster ':' executionpath '/' md.name '.qmu.out ' md.cluster ':' executionpath '/dakota_tabular.dat ./']); %get outlog, errlog and outbin files
         else
-                system(['scp ' md.cluster ':' executionpath '/' md.name '.outlog ' executionpath '/' md.name '.errlog ' executionpath '/' md.name '.outbin ./']); %get outlog, errlog and outbin files
+                system(['scp ' md.cluster ':' executionpath '/' md.name '.outlog ' md.cluster ':' executionpath '/' md.name '.errlog ' md.cluster ':' executionpath '/' md.name '.outbin ./']); %get outlog, errlog and outbin files
         end
 end

issm/trunk/src/m/classes/public/marshall.m

@@ -73 +73 @@
 
 WriteData(fid,md.elementoniceshelf,'Mat','elementoniceshelf');
+WriteData(fid,md.elementonwater,'Mat','elementonwater');
 WriteData(fid,md.gridonicesheet,'Mat','gridonicesheet');
 WriteData(fid,md.gridoniceshelf,'Mat','gridoniceshelf');

issm/trunk/src/m/classes/public/mesh.m

@@ -77 +77 @@
 md.elementonsurface=ones(md.numberofelements,1);
 
+%Now, build the connectivity tables for this mesh.
+md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofgrids);
+md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
+
 %outline names
 md.domainoutline=readfile(domainname);

issm/trunk/src/m/classes/public/setelementstype.m

@@ -127 +127 @@
 
 %icefront for stokes
-md.segmentonneumann_diag_stokes=md.segmentonneumann_diag(find(md.elements_type(md.segmentonneumann_diag(:,end),2)),:);
+if ~isnan(md.segmentonneumann_diag),
+        md.segmentonneumann_diag_stokes=md.segmentonneumann_diag(find(md.elements_type(md.segmentonneumann_diag(:,end),2)),:);
+end
 
 %figure out solution types