Changeset 27531

Timestamp:

01/19/23 06:55:38 (2 years ago)

Author:

vverjans

Message:

NEW added tutorial for StISSM

Location:

issm/trunk-jpl

Files:

• examples/StISSM (added)
• examples/StISSM/DomainOutline.exp (added)
• examples/StISSM/Models (added)
• examples/StISSM/PigStISSM.par (added)
• examples/StISSM/runme.m (added)
• src/m/classes/SMBarma.py (modified) (2 diffs)
• src/m/classes/clusters/pace.m (modified) (4 diffs)
• src/m/classes/hydrologyarmapw.m (modified) (2 diffs)
• src/m/classes/stochasticforcing.py (modified) (2 diffs)
• src/m/contrib/morlighem/modeldata/interpBedmachineGreenland.m (modified) (2 diffs)
• src/m/contrib/morlighem/modeldata/interpSeaRISE.m (modified) (2 diffs)

issm/trunk-jpl/src/m/classes/SMBarma.py

@@ -20 +20 @@
         self.polynomialparams = np.nan
         self.ar_order = 0
+        self.ma_order = 0
         self.arlag_coefs = np.nan
         self.ma_order = 0
@@ -29 +30 @@
         self.elevationbins = np.nan
         self.refelevation = np.nan
+        self.datebreaks = np.nan
         self.steps_per_step = 1
         self.averaging = 0

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

@@ -9 +9 @@
         properties (SetAccess=public)
         % {{{
-                name            = 'login-phoenix-4.pace.gatech.edu' %Phoenix cluster name
+                name            = 'login-phoenix-slurm.pace.gatech.edu' %Phoenix cluster name
                 login           = ''; %personal login
                 numnodes        = 1; %number of nodes requested
@@ -17 +17 @@
                 queue           = 'inferno'; %queue
                 time            = 60; %time requested per run [minutes]
-                accountname     = 'GT-arobel3-atlas'; %group account name
+                accountname     = 'gts-arobel3-atlas'; %group account name
                 codepath        = ''; %path to issm binaries
                 executionpath   = ''; %path for execution folder
@@ -62 +62 @@
                         fid=fopen([modelname '.queue'],'w');
                         fprintf(fid,'#!/bin/sh\n');
-                        fprintf(fid,'#PBS -l walltime=%i\n',cluster.time*60); %conversion of walltime from minutes to seconds.
-                        fprintf(fid,'#PBS -N %s\n',modelname);
-                        fprintf(fid,'#PBS -l nodes=1:ppn=%i\n',cluster.np);
-                        fprintf(fid,'#PBS -l pmem=%igb\n',cluster.mem);
-                        fprintf(fid,'#PBS -q %s\n',cluster.queue);
-                        fprintf(fid,'#PBS -A %s\n',cluster.accountname);
-                
-                        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,'export PBS_O_WORKDIR=%s\n',[cluster.executionpath '/' dirname]);
-                        fprintf(fid,'cd $PBS_O_WORKDIR\n');
-                        fprintf(fid,'mpiexec -np %i %s/%s %s %s %s \n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);  
+                        fprintf(fid,'#SBATCH -t%i\n',cluster.time);
+         fprintf(fid,'#SBATCH -J%s\n',modelname);
+         fprintf(fid,'#SBATCH -N 1 --ntasks-per-node=%i\n',cluster.np);
+         %fprintf(fid,'#SBATCH -N %i\n',cluster.numnodes);
+         %fprintf(fid,'#SBATCH --ntasks=1\n');
+         %fprintf(fid,'#SBATCH --cpus-per-task=%i\n',cluster.np);
+         fprintf(fid,'#SBATCH --mem-per-cpu=%iG\n',cluster.mem);
+         fprintf(fid,'#SBATCH -p%s\n',cluster.queue);
+         fprintf(fid,'#SBATCH -A %s\n',cluster.accountname);
+         fprintf(fid,'#SBATCH -o%s/%s/%s.outlog \n',cluster.executionpath,dirname,modelname);
+         fprintf(fid,'#SBATCH -e%s/%s/%s.errlog \n\n',cluster.executionpath,dirname,modelname);
+         fprintf(fid,'export SLURM_SUBMIT_DIR=%s\n',[cluster.executionpath '/' dirname]);
+         fprintf(fid,'cd $SLURM_SUBMIT_DIR\n');
+         fprintf(fid,'export LD_LIBRARY_PATH=/opt/slurm/current/lib:/opt/pmix/current/lib:$LD_LIBRARY_PATH \n');
+         fprintf(fid,'srun --mpi=pmi2 -n %i %s/%s %s %s %s \n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
 
                         fclose(fid);
@@ -97 +100 @@
                         disp('launching solution sequence on remote cluster');
                         if ~isempty(restart)
-                                launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && qsub ' modelname '.queue '];
+                                launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && sbatch ' modelname '.queue '];
                         else
                                 launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ...
-                                        ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && qsub ' modelname '.queue '];
+                                        ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz  && sbatch ' modelname '.queue '];
                         end
                         issmssh(cluster.name,cluster.login,cluster.port,launchcommand);

issm/trunk-jpl/src/m/classes/hydrologyarmapw.m

@@ -18 +18 @@
       malag_coefs              = NaN;
                 datebreaks               = NaN;
+                requested_outputs        = {};
         end
         methods
@@ -184 +185 @@
                         WriteData(fid,prefix,'data',dbreaks,'name','md.hydrology.datebreaks','format','DoubleMat','scale',yts);
                         WriteData(fid,prefix,'data',tempmonthlyfactors,'name','md.hydrology.monthlyfactors','format','DoubleMat');
-                        WriteData(fid,prefix,'data',{'FrictionWaterPressure'},'name','md.hydrology.requested_outputs','format','StringArray');
+                        
+                        %process requested outputs
+         outputs = self.requested_outputs;
+         pos  = find(ismember(outputs,'default'));
+         if ~isempty(pos),
+            outputs(pos) = [];                         %remove 'default' from outputs
+            outputs      = [outputs defaultoutputs(self,md)]; %add defaults
+         end
+         WriteData(fid,prefix,'data',outputs,'name','md.hydrology.requested_outputs','format','StringArray');
                 end % }}}
         end

issm/trunk-jpl/src/m/classes/stochasticforcing.py

@@ -79 +79 @@
         structstoch = self.structstochforcing()
         # Check if hydrologyarmapw is used
-        if type(md.hydrology).__name__ == 'hydrologyarmapw' and md.transient.ishydrology:
+        if((type(md.hydrology).__name__ == 'hydrologyarmapw') and md.transient.ishydrology==1):
             ispwHydroarma = 1
         else:
@@ -241 +241 @@
                 md.stochasticforcing.stochastictimestep = md.timestepping.time_step #by default: stochastictimestep set to ISSM time step
             # Check if hydroarmapw is used
-            if type(md.hydrology).__name__ == 'hydrologyarmapw' and md.transient.ishydrology:
+            if((type(md.hydrology).__name__ == 'hydrologyarmapw') and md.transient.ishydrology==1):
                 ispwHydroarma = 1
             else:

issm/trunk-jpl/src/m/contrib/morlighem/modeldata/interpBedmachineGreenland.m

@@ -45 +45 @@
                 ['/Users/larour/ModelData/BedMachine/' basename '-' ncdate '.nc'],...
                 ['./' basename '-' ncdate '.nc'],...
+                '/media/vincent/TOSH4TB/GeorgiaTech/DataSearch/BedMachine/BedMachineGreenland-2021-04-20.nc',...
                 };
 
@@ -89 +90 @@
 if strcmp(string,'mask') | strcmp(string,'source'),
         %Need nearest neighbor to avoid interpolation between 0 and 2
-        output = InterpFromGrid(xdata,ydata,data,double(X),double(Y),'nearest');
+        %output = InterpFromGrid(xdata,ydata,data,double(X),double(Y),'nearest');
+        output = InterpFromGridToMesh(xdata,flipud(ydata),flipud(data),double(X),double(Y),NaN); %VV
 else
-        output = InterpFromGrid(xdata,ydata,data,double(X),double(Y));
+        %output = InterpFromGrid(xdata,ydata,data,double(X),double(Y));
+        output = InterpFromGridToMesh(xdata,flipud(ydata),flipud(data),double(X),double(Y),NaN); %VV
 end
 

issm/trunk-jpl/src/m/contrib/morlighem/modeldata/interpSeaRISE.m

@@ -58 +58 @@
                         searisenc='/totten_1/ModelData/SeaRISE/Antarctica_5km_dev1.0.nc';
                 end
+   case {'vincentxps159500'}
+                if hemisphere==1
+                        searisenc = '/media/vincent/TOSH4TB/GeorgiaTech/ISSM/fromSeroussi/GrIS04Feb2022/seariseData/Greenland_5km_dev1.2.nc';
+                end
         otherwise
                 error('hostname not supported yet');
@@ -80 +84 @@
 if verbose, disp(['   -- SeaRISE: interpolating ' string]); end
 if strcmpi(string,'LandMask');
-        dataout = InterpFromGrid(xdata,ydata,data,xproj,yproj,'nearest');
+        %dataout = InterpFromGrid(xdata,ydata,data,xproj,yproj,'nearest');
+        dataout = InterpFromGridToMesh(xdata,ydata,data,xproj,yproj,NaN); %VV
 else
-        dataout = InterpFromGrid(xdata,ydata,data,xproj,yproj);
+        %dataout = InterpFromGrid(xdata,ydata,data,xproj,yproj);
+        dataout = InterpFromGridToMesh(xdata,ydata,data,xproj,yproj,NaN); %VV
 end
 dataout = reshape(dataout,size(X,1),size(X,2));