Changeset 25684

Timestamp:

10/13/20 12:04:18 (4 years ago)

Author:

jdquinn

Message:

CHG: MATLAB -> Python; clean up

Location:

issm/trunk-jpl/src/m

Files:

• classes/clusters/generic.m (modified) (2 diffs)
• classes/clusters/generic.py (modified) (2 diffs)
• classes/clusters/generic_static.py (modified) (2 diffs)
• classes/clusters/local.py (added)
• dev/devpath.py (modified) (1 diff)
• mesh/meshintersect3d.py (modified) (1 diff)

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

@@ -95 +95 @@
                                         if cluster.interactive
                                                 if IssmConfig('_HAVE_MPI_'),
-                                                        fprintf(fid,'mpiexec -np %i %s/%s %s %s %s \n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
+                                                        fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
                                                 else
-                                                        fprintf(fid,'%s/%s %s %s %s ',cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
+                                                        fprintf(fid,'%s/%s %s %s %s',cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname);
                                                 end
                                         else
                                                 if IssmConfig('_HAVE_MPI_'),
-                                                        fprintf(fid,'mpiexec -np %i %s/%s %s %s %s 2> %s.errlog >%s.outlog &',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
+                                                        fprintf(fid,'mpiexec -np %i %s/%s %s %s %s 2> %s.errlog > %s.outlog &',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                                                 else
-                                                        fprintf(fid,'%s/%s %s %s %s 2> %s.errlog >%s.outlog &',cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
+                                                        fprintf(fid,'%s/%s %s %s %s 2> %s.errlog > %s.outlog &',cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                                                 end
                                         end
@@ -113 +113 @@
                                         if ismac,
                                                 if IssmConfig('_HAVE_MPI_'),
-                                                        fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --dsymutil=yes --suppressions=%s %s/%s %s %s %s 2> %s.errlog >%s.outlog ',...
+                                                        fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --dsymutil=yes --suppressions=%s %s/%s %s %s %s 2> %s.errlog > %s.outlog ',...
                                                         cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname], modelname,modelname,modelname);
                                                 else
-                                                        fprintf(fid,'%s --leak-check=full --dsymutil=yes --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog >%s.outlog ',...
+                                                        fprintf(fid,'%s --leak-check=full --dsymutil=yes --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog > %s.outlog',...
                                                         cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname], modelname,modelname,modelname);
                                                 end
                                         else
                                                 if IssmConfig('_HAVE_MPI_'),
-                                                        fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog >%s.outlog ',...
+                                                        fprintf(fid,'mpiexec -np %i %s --leak-check=full --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog > %s.outlog',...
                                                         cluster.np,cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                                                 else
-                                                        fprintf(fid,'%s --leak-check=full --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog >%s.outlog ',...
+                                                        fprintf(fid,'%s --leak-check=full --error-limit=no --suppressions=%s %s/%s %s %s %s 2> %s.errlog > %s.outlog',...
                                                         cluster.valgrind,cluster.valgrindsup,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname,modelname,modelname);
                                                 end

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

@@ -104 +104 @@
                         fid.write('mpiexec -np {} {}/{} {} {}/{} {}'.format(self.np, self.codepath, executable, solution, self.executionpath, dirname, modelname))
                     else:
-                        fid.write('{}/{} {} {}/{} {} '.format(self.codepath, executable, solution, self.executionpath, dirname, modelname))
+                        fid.write('{}/{} {} {}/{} {}'.format(self.codepath, executable, solution, self.executionpath, dirname, modelname))
                 else:
                     if IssmConfig('_HAVE_MPI_')[0]:
-                        fid.write('mpiexec -np {} {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog'.
+                        fid.write('mpiexec -np {} {}/{} {} {}/{} {} 2> {}.errlog > {}.outlog'.
                                   format(self.np, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname))
                     else:
-                        fid.write('{}/{} {} {}/{} {} 2>{}.errlog>{}.outlog '.
+                        fid.write('{}/{} {} {}/{} {} 2> {}.errlog > {}.outlog '.
                                   format(self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname))
             elif isgprof:
@@ -122 +122 @@
 
                 if IssmConfig('_HAVE_MPI_')[0]:
-                    fid.write('mpiexec -np {} {} --leak-check=full {} {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog '.
+                    fid.write('mpiexec -np {} {} --leak-check=full {} {}/{} {} {}/{} {} 2> {}.errlog > {}.outlog '.
                               format(self.np, self.valgrind, supstring, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname))
                 else:
-                    fid.write('{} --leak-check=full {} {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog '.
+                    fid.write('{} --leak-check=full {} {}/{} {} {}/{} {} 2> {}.errlog > {}.outlog '.
                               format(self.valgrind, supstring, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname))
 

issm/trunk-jpl/src/m/classes/clusters/generic_static.py

@@ +1 @@
+import math
+import os
+import socket
+import subprocess
+
 import numpy as np
-import socket
-import os
-import math
-import subprocess
+
 from IssmConfig import IssmConfig
 from issmdir import issmdir
-from pairoptions import pairoptions
 from issmssh import issmssh
 from issmscpin import issmscpin
 from issmscpout import issmscpout
 import MatlabFuncs as m
+from pairoptions import pairoptions
 
 
@@ -58 +60 @@
     def checkconsistency(self, md, solution, analyses):  # {{{
         if self.np < 1:
-            md = checkmessage(md, 'number of processors should be at least 1')
-        if math.isnan(self.np):
-            md = checkmessage(md, 'number of processors should not be NaN!')
+            md.checkmessage('number of processors should be at least 1')
+        if np.isnan(self.np):
+            md.checkmessage('number of processors should not be NaN!')
 
         return md

issm/trunk-jpl/src/m/dev/devpath.py

@@ -10 +10 @@
 if ISSM_DIR is None:
     raise NameError('"ISSM_DIR" environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!')
-
-# NOTE: Now having user install netcdf4 via pip
-#
-# #Get paths to locally installed Python libraries
-# tpls = [
-#     'cftime', # Needed for netCDF4
-#     'netCDF4'
-# ]
-# for tpl in os.listdir(ISSM_DIR + '/externalpackages'):
-#     tpl_path = ISSM_DIR + '/externalpackages/' + tpl
-#     for dirpath, dirnames, filenames in os.walk(tpl_path):
-#         install_lib_path = dirpath + '/install/lib'
-#         for dirpath, dirnames, filenames in os.walk(install_lib_path):
-#             for dirname in dirnames:
-#                 if dirname in tpls:
-#                     dir = dirpath + '/' + dirname
-#                     for file in os.listdir(dir):
-#                         if file.find(".py") != -1:
-#                             if file.find(".pyc") == -1:
-#                                 if dirpath not in sys.path:
-#                                     sys.path.append(dirpath)
 
 #Go through src/m and append any directory that contains a *.py file to PATH

issm/trunk-jpl/src/m/mesh/meshintersect3d.py

@@ -63 +63 @@
         raise RuntimeError('issue with transition vector having one empty slot')
 
-    # Convert results to type 'int' to avoid modifying structures to which they are assigned
+    # Convert results to type 'int' to avoid modifying structures to which 
+    # results are assigned
     indices = indices.astype(int)