Fix for Sh > 2.* issue, and new environment files and template for running on maths2 (Exeter)

src/extra/env/maths2

@@ -0,0 +1,6 @@
+echo loadmodules for maths2 machines
+
+export F90=mpiifort
+export CC=mpiicc
+
+export GFDL_MKMF_TEMPLATE=maths2

src/extra/python/isca/codebase.py

@@ -7,7 +7,7 @@
 
 from isca import GFDL_WORK, GFDL_BASE, GFDL_SOC, _module_directory, get_env_file
 from .loghandler import Logger
-from .helpers import url_to_folder, destructive, useworkdir, mkdir, cd, git, P, git_run_in_directory
+from .helpers import url_to_folder, destructive, useworkdir, mkdir, cd, git, P, git_run_in_directory, check_for_sh_stdout
 
 import pdb
 
@@ -137,7 +137,7 @@ def is_clean(self):
 
     @property
     def git_commit(self):
-        return self.git.log('-1', '--format="%H"').stdout.decode('utf8')
+        return check_for_sh_stdout(self.git.log('-1', '--format="%H"'))
 
     # @property
     # def git_diff(self):
@@ -162,11 +162,11 @@ def write_source_control_status(self, outfile):
 
             # write out the git commit id of GFDL_BASE
             file.write("\n\n*---commit hash used for code in GFDL_BASE, including this python module---*:\n")
-            file.write(gfdl_git.log('-1', '--format="%H"').stdout.decode('utf8'))
+            check_for_sh_stdout(file.write(gfdl_git.log('-1', '--format="%H"')))
 
             # if there are any uncommited changes in the working directory,
             # add those to the file too
-            source_status = self.git.status("-b", "--porcelain").stdout.decode('utf8')
+            source_status = check_for_sh_stdout(self.git.status("-b", "--porcelain"))
             # filter the source status for changes in specific files
             filetypes = ('.f90', '.inc', '.c')
             source_status = [line for line in source_status.split('\n')
@@ -178,7 +178,7 @@ def write_source_control_status(self, outfile):
                 file.write("*---git status output (only f90 and inc files)---*:\n")
                 file.write('\n'.join(source_status))
                 file.write('\n\n*---git diff output---*\n')
-                source_diff = self.git.diff('--no-color').stdout.decode('utf8')
+                source_diff = check_for_sh_stdout(self.git.diff('--no-color'))
                 file.write(source_diff)
 
     def read_path_names(self, path_names_file):

src/extra/python/isca/helpers.py

@@ -66,11 +66,19 @@ def git_run_in_directory(GFDL_BASE_DIR, dir_in):
 
     try:
         codedir_git = git.bake('-C', GFDL_BASE_DIR)        
-        git_test = codedir_git.log('-1', '--format="%H"').stdout
+        git_test = check_for_sh_stdout(codedir_git.log('-1', '--format="%H"'))
         baked_git_fn = git.bake('-C', dir_in)
     except:
         codedir_git = git.bake('--git-dir='+GFDL_BASE_DIR+'/.git', '--work-tree='+GFDL_BASE_DIR)
-        git_test = codedir_git.log('-1', '--format="%H"').stdout
+        git_test = check_for_sh_stdout(codedir_git.log('-1', '--format="%H"'))
         baked_git_fn = git.bake('--git-dir='+dir_in+'/.git', '--work-tree='+dir_in)        
 
-    return baked_git_fn        
+    return baked_git_fn       
+
+def check_for_sh_stdout(input_exp):
+    """Versions of sh>2.* have started returning str types rather than a sh.RunningCommand type. To distinguish these possibilites, this function looks at the output of a sh expression, and asks for stdout and decodes it only if the type is a sh.RunningCommand."""
+
+    if type(input_exp)==sh.RunningCommand:     
+        input_exp=input_exp.stdout.decode('utf8')
+
+    return input_exp

src/extra/python/isca/templates/mkmf.template.maths2

@@ -0,0 +1,28 @@
+# template for the Intel fortran compiler
+# typical use with mkmf
+# mkmf -t template.ifc -c"-Duse_libMPI -Duse_netCDF" path_names /usr/local/include
+CPPFLAGS = `nc-config --cflags`
+NETCDF_LIBS = `nc-config --libs`
+
+# FFLAGS:
+#  -fpp: Use the fortran preprocessor
+#  -stack_temps:  Put temporary runtime arrays on the stack, not heap.
+#  -safe_cray_ptr: Cray pointers don't alias other variables.
+#  -ftz: Denormal numbers are flushed to zero.
+#  -assume byterecl: Specifies the units for the OPEN statement as bytes.
+#  -shared-intel:  Load intel libraries dynamically
+#  -i4: 4 byte integers
+#  -r8: 8 byte reals
+#  -g: Generate symbolic debugging info in code
+#  -O2: Level 2 speed optimisations
+#  -diag-disable 6843:
+#       This suppresses the warning: `warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value.` of which
+#       there are a lot of instances in the GFDL codebase.
+FFLAGS = $(CPPFLAGS) -fpp -stack_temps -safe_cray_ptr -ftz -assume byterecl -shared-intel -i4 -r8 -g -O2 -diag-disable 6843 -mcmodel large
+#FFLAGS = $(CPPFLAGS) -fltconsistency -stack_temps -safe_cray_ptr -ftz -shared-intel -assume byterecl -g -O0 -i4 -r8 -check -warn -warn noerrors -debug variable_locations -inline_debug_info -traceback
+FC = $(F90)
+LD = $(F90) $(NETCDF_LIBS)
+#CC = mpicc
+
+LDFLAGS = -lnetcdff -lnetcdf -lmpi -shared-intel -lhdf5_hl -lhdf5 -lm -lz -lsz -lbz2 -lxml2 -lcurl
+CFLAGS = -D__IFC

src/extra/python/requirements.txt

@@ -1,7 +1,7 @@
 sh
 jinja2
-git+git://github.com/marshallward/f90nml.git#egg=f90nml
+f90nml
 numpy
 pandas
 xarray
-tqdm
+tqdm