Changeset 22064

Timestamp:

09/08/17 04:35:05 (8 years ago)

Author:

hakesson

Message:

CHG: minor edits to cluster file

File:

• issm/trunk-jpl/src/m/classes/clusters/vilje.m (modified) (8 diffs)

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

@@ -15 +15 @@
                 procspernodes  = 16;
                 mem            = 28;
+                numstreams              = 8; %Henning added
                 queue          = 'workq';
                 time           = 2*60;
@@ -79 +80 @@
 
                         %compute number of processors
-                        cluster.np=cluster.numnodes*cluster.cpuspernode;
+%                       cluster.np=cluster.numnodes*cluster.cpuspernode;
+                        np(cluster);%=cluster.numnodes*cluster.cpuspernode;
 
                         %write queuing script 
@@ -86 +88 @@
                         fprintf(fid,'#PBS -N %s\n',modelname);
                         fprintf(fid,'#PBS -l select=%i:ncpus=%i:mpiprocs=%i\n',cluster.numnodes,cluster.cpuspernode,16);
-                        fprintf(fid,'#PBS -l walltime=%s\n',cluster.time); %walltime is in seconds.
+                        
+                        %calculate walltime in hh:mm:ss format
+                        walltime=datestr(cluster.time/(60*24),'HH:MM:SS');
+                        fprintf(fid,'#PBS -l walltime=%s\n',walltime); %walltime should be in hh:mm:ss
                         fprintf(fid,'#PBS -A %s\n',cluster.accountname);
                         fprintf(fid,'#PBS -o %s.outlog \n',modelname);
@@ -92 +97 @@
                         fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
                         fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+                        fprintf(fid,'module load intelcomp/17.0.0\n') 
+                        fprintf(fid,'module load mpt/2.14\n')
+                        fprintf(fid,'module load petsc/3.7.4d\n')
+                        fprintf(fid,'module load parmetis/4.0.3\n') 
+                        fprintf(fid,'module load mumps/5.0.2\n')
                         fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,modelname);
                         fprintf(fid,'mpiexec_mpt -n %i %s/kriging.exe %s %s\n',cluster.np,cluster.codepath,[cluster.executionpath '/' modelname],modelname);
@@ -117 +127 @@
 
                         %compute number of processors
-                        cluster.np=cluster.numnodes*cluster.cpuspernode;                     
-                        shortname = substring(modelname,1,min(12,length(modelname)));
+%                       cluster.np=cluster.numnodes*cluster.cpuspernode;
+                        np(cluster);%=cluster.numnodes*cluster.cpuspernode;                     
+%                       shortname = substring(modelname,1,min(12,length(modelname)));
 
                         %write queuing script 
                         fid=fopen([modelname '.queue'],'w');
                         fprintf(fid,'#PBS -S /bin/bash\n');
-                        fprintf(fid,'#PBS -N %s\n',shortname);
+%                       fprintf(fid,'#PBS -N %s\n',shortname);
+                        fprintf(fid,'#PBS -N %s\n',modelname);
                         fprintf(fid,'#PBS -q %s \n',cluster.queue);
                         fprintf(fid,'#PBS -l select=%i:ncpus=%i:mpiprocs=%i\n',cluster.numnodes,cluster.cpuspernode,cluster.procspernodes);
-                        fprintf(fid,'#PBS -l walltime=%s\n',duration(0,cluster.time,0)); %walltime is in minutes.
+
+                        %calculate walltime in hh:mm:ss format
+                        walltime=datestr(cluster.time/(60*24),'HH:MM:SS');
+%                       fprintf(fid,'#PBS -l walltime=%s\n',duration(0,cluster.time,0)); %walltime is in minutes.
+%                       fprintf(fid,'#PBS -l walltime=%s\n',10); %walltime is in minutes.
+                        fprintf(fid,'#PBS -l walltime=%s\n',walltime); %walltime should be in hh:mm:ss
+%                       fprintf(fid,'#PBS -l walltime=%i\n',walltime); %walltime is in hh:mm:ss
                         fprintf(fid,'#PBS -A %s\n',cluster.accountname);
                         fprintf(fid,'#PBS -o %s.outlog \n',[cluster.executionpath '/' dirname '/' modelname]);
@@ -132 +150 @@
                         fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME
                         fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n');       %FIXME
+                        fprintf(fid,'module load intelcomp/17.0.0\n') 
+                        fprintf(fid,'module load mpt/2.14\n')
+                        fprintf(fid,'module load petsc/3.7.4d\n')
+                        fprintf(fid,'module load parmetis/4.0.3\n') 
+                        fprintf(fid,'module load mumps/5.0.2\n')
                         fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname);
-                        fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
+                        fprintf(fid,'mpiexec_mpt -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
 
                         if ~io_gather, %concatenate the output files:
@@ -143 +166 @@
                         if cluster.interactive,
                                 fid=fopen([modelname '.run'],'w');
-                                fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
+                                fprintf(fid,'mpiexec_mpt -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname);
                                 if ~io_gather, %concatenate the output files:
                                         fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname);
@@ -164 +187 @@
                         disp('uploading input file and queueing script');
                         directory=cluster.executionpath;
-                        issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']});
-
-                end
-                %}}}
-                function LaunchQueueJob(cluster,modelname,dirname,filelist)% {{{
+%                       issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']});
+                        issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']});
+
+                end
+                %}}}
+                function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{
 
                         disp('launching solution sequence on remote cluster');