Changeset 13278

Timestamp:

09/06/12 14:56:24 (13 years ago)

Author:

schlegel

Message:

CHG: Clusters pass directory argument in issm execution to be full path to bin file.

Location:

issm/trunk-jpl/src/m/classes/clusters

Files:

• acenet.m (modified) (1 diff)
• castor.m (modified) (1 diff)
• cosmos.m (modified) (1 diff)
• discover.m (modified) (2 diffs)
• gemini.m (modified) (1 diff)
• generic.m (modified) (6 diffs)
• greenplanet.m (modified) (2 diffs)
• pfe.m (modified) (4 diffs)
• pollux.m (modified) (1 diff)

issm/trunk-jpl/src/m/classes/clusters/acenet.m

@@ -74 +74 @@
           fprintf(fid,'\n');
           fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
-                   cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+                   cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                          fclose(fid);
 

issm/trunk-jpl/src/m/classes/clusters/castor.m

@@ -62 +62 @@
                          fprintf(fid,'#PBS -o %s.outlog \n',modelname);
                          fprintf(fid,'#PBS -e %s.errlog \n',modelname);
-                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',cluster.executionpath);
+                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',[cluster.executionpath '/' dirname]);
                          fprintf(fid,'cd $PBS_O_WORKDIR\n');
                          fprintf(fid,'export OMP_NUM_THREADS=1\n');
-                         fprintf(fid,'dplace -s1 -c0-%i mpiexec -np %i %s/issm.exe %s %s %s',cluster.np-1,cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                         fprintf(fid,'dplace -s1 -c0-%i mpiexec -np %i %s/issm.exe %s %s %s',cluster.np-1,cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                          fclose(fid);
 

issm/trunk-jpl/src/m/classes/clusters/cosmos.m

@@ -60 +60 @@
                          fprintf(fid,'#PBS -o %s.outlog \n',modelname);
                          fprintf(fid,'#PBS -e %s.errlog \n',modelname);
-                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',cluster.executionpath);
+                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',[cluster.executionpath '/' dirname]);
                          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/mpiexec -np %i %s/issm.exe %s %s %s',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                         fprintf(fid,'/opt/mpich/gm/intel10.1/bin/mpiexec -np %i %s/issm.exe %s %s %s',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                          fclose(fid);
 

issm/trunk-jpl/src/m/classes/clusters/discover.m

@@ -111 +111 @@
                          fprintf(fid,'export PATH="$PATH:."\n\n');
                          fprintf(fid,'export MPI_GROUP_MAX=64\n\n');
-                         fprintf(fid,'cd $PBS_O_WORKDIR\n\n');
-                         fprintf(fid,'mpirun -np %i %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),modelname);
+                         fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname);
+                         fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                          if ~io_gather, %concatenate the output files:
                                  fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
@@ -122 +122 @@
                                  fid=fopen([modelname '.run'],'w');
                                  if ~isvalgrind,
-                                         fprintf(fid,'mpirun -np %i %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),modelname);
+                                         fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                                  else
-                                         fprintf(fid,'mpirun -np %i valgrind --leak-check=full %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),modelname);
+                                         fprintf(fid,'mpirun -np %i valgrind --leak-check=full %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                                  end
                                  if ~io_gather, %concatenate the output files:

issm/trunk-jpl/src/m/classes/clusters/gemini.m

@@ -63 +63 @@
                          fprintf(fid,'#PBS -e %s.errlog \n',modelname);
 
-                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',cluster.executionpath);
+                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',[cluster.executionpath '/' dirname]);
                          fprintf(fid,'cd $PBS_O_WORKDIR\n');
                          fprintf(fid,'export OMP_NUM_THREADS=1\n');
-                         fprintf(fid,'dplace -s1 -c0-%i mpiexec -np %i %s/issm.exe %s %s %s',cluster.np-1,cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                         fprintf(fid,'dplace -s1 -c0-%i mpiexec -np %i %s/issm.exe %s %s %s',cluster.np-1,cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                          fclose(fid);
 

issm/trunk-jpl/src/m/classes/clusters/generic.m

@@ -68 +68 @@
                                 if ~isvalgrind,
                                         if cluster.interactive
-                                                fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s ',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                                                fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s ',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                                         else
-                                                fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+                                                fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                                         end
                                 elseif isgprof,
@@ -79 +79 @@
                                         if ismac, 
                                                 fprintf(fid,'mpiexec -np %i %s --leak-check=full --dsymutil=yes --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
-                                                cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+                                                cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname], modelname,modelname,modelname);
                                         else
                                                 fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/issm.exe %s %s %s 2> %s.errlog >%s.outlog ',...
-                                                cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+                                                cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                                         end
                                 end
@@ -95 +95 @@
                                 fprintf(fid,'@echo off\n');
                                 if cluster.interactive
-                                        fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                                        fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                                 else
                                         fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
-                                                cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+                                                cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                                 end
                                 fclose(fid);
@@ -119 +119 @@
                                 if ~isvalgrind,
                                         if cluster.interactive
-                                                fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,cluster.executionpath,modelname);
+                                                fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
                                         else
-                                                fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,cluster.executionpath,modelname,modelname,modelname);
+                                                fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
                                         end
                                 elseif isgprof,
@@ -129 +129 @@
                                         fprintf(fid,'LD_PRELOAD=%s \\\n',cluster.valgrindlib);
                                         fprintf(fid,'mpiexec -np %i %s --leak-check=full --suppressions=%s %s/kriging.exe %s %s 2> %s.errlog >%s.outlog ',...
-                                                cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,cluster.executionpath,modelname,modelname,modelname);
+                                                cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,[cluster.executionpath '/' modelname],modelname,modelname,modelname);
                                 end
                                 if ~io_gather, %concatenate the output files:
@@ -141 +141 @@
                                 fprintf(fid,'@echo off\n');
                                 if cluster.interactive
-                                        fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                                        fprintf(fid,'"%s/issm.exe" %s "%s" %s ',cluster.codepath,EnumToString(solution),[cluster.executionpath '/' modelname],modelname);
                                 else
                                         fprintf(fid,'"%s/issm.exe" %s "%s" %s 2> %s.errlog >%s.outlog',...
-                                                cluster.codepath,EnumToString(solution),cluster.executionpath,modelname,modelname,modelname);
+                                                cluster.codepath,EnumToString(solution),[cluster.executionpath '/' modelname],modelname,modelname,modelname);
                                 end
                                 fclose(fid);

issm/trunk-jpl/src/m/classes/clusters/greenplanet.m

@@ -82 +82 @@
                          fprintf(fid,'#PBS -e %s.errlog \n\n',modelname);
                          fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
-                         fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                         fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                          if ~io_gather, %concatenate the output files:
                                  fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
@@ -91 +91 @@
                          if cluster.interactive,
                                  fid=fopen([modelname '.run'],'w');
-                                 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                                 fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                                  if ~io_gather, %concatenate the output files:
                                          fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);

issm/trunk-jpl/src/m/classes/clusters/pfe.m

@@ -125 +125 @@
                          fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
                          fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
-                         fprintf(fid,'cd $PBS_O_WORKDIR\n\n');
-                         fprintf(fid,'mpiexec -np %i %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname '/' modelname]);
+                         fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname);
+                         fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                          if ~io_gather, %concatenate the output files:
                                  fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
@@ -136 +136 @@
                                  fid=fopen([modelname '.run'],'w');
                                  if ~isvalgrind,
-                                         fprintf(fid,'mpiexec -np %i %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),modelname);
-                                 else
-                                         fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/issm.exe %s $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,EnumToString(solution),modelname);
+                                         fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
+                                 else
+                                         fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                                  end
                                  if ~io_gather, %concatenate the output files:
@@ -176 +176 @@
                          fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
                          fprintf(fid,'export MPI_GROUP_MAX=64\n\n');
-                         fprintf(fid,'cd $PBS_O_WORKDIR\n');
-                         fprintf(fid,'mpiexec -np %i %s/kriging.exe $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname '/' modelname]); %FIXME
+                         fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,modelname);
+                         fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname); %FIXME
                          if ~io_gather, %concatenate the output files:
                                  fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
@@ -187 +187 @@
                                  fid=fopen([modelname '.run'],'w');
                                  if ~isvalgrind,
-                                         fprintf(fid,'mpiexec -np %i %s/kriging.exe $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname '/' modelname]);
-                                 else
-                                         fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/kriging.exe $PBS_O_WORKDIR %s\n',cluster.np,cluster.codepath,modelname);
+                                         fprintf(fid,'mpiexec -np %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
+                                 else
+                                         fprintf(fid,'mpiexec -np %i valgrind --leak-check=full %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
                                  end
                                  if ~io_gather, %concatenate the output files:

issm/trunk-jpl/src/m/classes/clusters/pollux.m

@@ -62 +62 @@
                          fprintf(fid,'#PBS -o %s.outlog \n',modelname);
                          fprintf(fid,'#PBS -e %s.errlog \n',modelname);
-                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',cluster.executionpath);
+                         fprintf(fid,'export PBS_O_WORKDIR=%s\n',[cluster.executionpath '/' dirname]);
                          fprintf(fid,'cd $PBS_O_WORKDIR\n');
                          fprintf(fid,'export OMP_NUM_THREADS=1\n');
-                         fprintf(fid,'dplace -s1 -c0-%i mpiexec -np %i %s/issm.exe %s %s %s',cluster.np-1,cluster.np,cluster.codepath,EnumToString(solution),cluster.executionpath,modelname);
+                         fprintf(fid,'dplace -s1 -c0-%i mpiexec -np %i %s/issm.exe %s %s %s',cluster.np-1,cluster.np,cluster.codepath,EnumToString(solution),[cluster.executionpath '/' dirname],modelname);
                          fclose(fid);