Merge branch 'include_libs_check'

envs/reddwarf.yaml

@@ -6,7 +6,7 @@
 
 Description:
   Name: Reddwarf
-  Max Cores: 10
+  Max Cores: 4
   Modules: True
   LMOD_CMD: /usr/local/lmod/lmod/libexec/lmod
   HPC: False
@@ -54,12 +54,36 @@ Modsets:
       - USE_PIO2:
         Name: USE_PIO2
         Value: "true"
-      - MPAS_EXTERNAL_LIBS:
-        Name: MPAS_EXTERNAL_LIBS
-        Value: "-L${PIO}/lib -L${LIBBASE}/lib/lib -lpio -lpnetcdf -lnetcdf -lhdf5_hl -lhdf5 -ldl -lz"
+      - PNETCDF_INCLUDES:
+        Name: PNETCDF_INCLUDES
+        Value: "-I$PNETCDF/include"
+      - PNETCDF_LIBS:
+        Name: PNETCDF_LIBS
+        Value: "-L$PNETCDF/lib -lpnetcdf"
+      - NETCDF_INCLUDES:
+        Name: NETCDF_INCLUDES
+        Value: "-I$NETCDF/include"
+      - NETCDF_LIBS:
+        Name: NETCDF_LIBS
+        Value: "-L$NETCDF/lib -lnetcdf -lpnetcdf
+                -lhdf5_hl -lhdf5 -ldl -lz -lm"
+      - PIO_INCLUDES:
+        Name: PIO_INCLUDES
+        Value: "-I$PNETCDF/include -I$PIO/include"
+      - PIO_LIBS:
+        Name: PIO_LIBS
+        Value: "-L$NETCDF/lib
+                -L$PIO/lib -lpiof -lpio
+                -lnetcdf -lpnetcdf -lhdf5_hl -lz -lm"
       - MPAS_EXTERNAL_INCLUDES:
         Name: MPAS_EXTERNAL_INCLUDES
-        Value: "-I${LIBBASE}/lib/include -I${PIO}/lib/include"
+        Value: "-I/users/mcurry/build-gnu-9.1.0/lib/include
+                -I/users/mcurry/build-gnu-9.1.0/pio/2.4.3/include"
+      - MPAS_EXTERNAL_LIBS:
+        Name: MPAS_EXTERNAL_LIBS
+        Value: "-L/users/mcurry/build-gnu-9.1.0/lib/lib
+                -L/users/mcurry/build-gnu-9.1.0/pio/2.4.3/include -lpiof -lpio
+                -lpnetcdf -lnetcdf -lhdf5_hl -lhdf5 -ldl -lz -lm"
 
   ############
   # GNU-8.3.0

smarts/env.py

@@ -398,7 +398,7 @@ def _load_library(self, library, *args, **kwargs):
                 env_name = library['Name']
                 value = library['Value']
 
-                os.environ[env_name] = value
+                os.environ[env_name] = os.path.expandvars(value)
             else:
                 print("ERROR: For the library", library['Name'], "does not have a maching value name")
                 return False

tests/mpas_atm_gnu_compile/mpas_atm_gnu_compile.py

@@ -43,7 +43,7 @@ def run(self, env, result, src_dir, test_dir, hpc=None, *args, **kwargs):
             result.msg = "Could not clean MPAS atmosphere core"
             return
 
-        print("MPAS_INTEL_COMPILE: Compiling MPAS Atmosphere CORE ....")
+        print("MPAS_GNU_COMPILE: Compiling MPAS Atmosphere CORE ....")
         ierr = os.system('make -j4 gfortran CORE=atmosphere &> ../atmosphere-compile.log')
         if ierr != 0:
             result.result = "FAILED"

tests/mpas_gnu_libs_check/mpas_gnu_libs_check.py

@@ -65,8 +65,13 @@ def run(self, env, result, srcDir, testDir, hpc=None, *args, **kwargs):
 
         # PNetCDF - C and Fortran
 
+        from subprocess import Popen
+
         ## C
-        if os.system('mpicc -o c_pnetcdf pnetcdf.c -I$PNETCDF/include -L$PNETCDF/lib -lpnetcdf'):
+
+
+        os.system('echo c_pnetcdf $PNETCDF_INCLUDES pnetcdf.c $PNETCDF_LIBS > out')
+        if os.system('mpicc -o c_pnetcdf $PNETCDF_INCLUDES pnetcdf.c $PNETCDF_LIBS'):
             print("Failed to compile pnetcdf.c with mpicc")
             result.result = "FAILED"
             result.msg = "Failed to compile a C PNetCDF (pnetcdf.c) with mpicc!"
@@ -75,7 +80,7 @@ def run(self, env, result, srcDir, testDir, hpc=None, *args, **kwargs):
             print("MPAS_GNU_LIBS_CHECK: Can compile a C PNetCDF Program!")
 
         ## Fortran
-        if os.system('mpif90 -c pnetcdf.f90 -I$PNETCDF/include -L$PNETCDF/lib -lpnetcdf'):
+        if os.system('mpif90 -c pnetcdf.f90 $PNETCDF_INCLUDES $PNETCDF_LIBS'):
             print("Failed to compile mpi.f90 with mpif90")
             result.result = "FAILED"
             result.msg = "Failed to copmile a Fortran PNetCDF (pnetcdf.f90) with mpif90!"
@@ -86,7 +91,8 @@ def run(self, env, result, srcDir, testDir, hpc=None, *args, **kwargs):
         # NetCDF - C and Fortran
 
         ## C
-        if os.system('mpicc -o c_netcdf netcdf.c -I$NETCDF/include -I$PNETCDF/include -L$NETCDF/lib -L$PNETCDF/lib -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -ldl -lz'):
+        if os.system('mpicc -o c_netcdf netcdf.c $NETCDF_INCLUDES $PNETCDF_INCLUDES' 
+                                               ' $NETCDF_LIBS $PNETCDF_LIBS'):
             print("Failed to compile netcdf.c with mpicc")
             result.result = "FAILED"
             result.msg = "Failed to compile a C NetCDF program (netcdf.c) with mpicc!"
@@ -95,7 +101,8 @@ def run(self, env, result, srcDir, testDir, hpc=None, *args, **kwargs):
             print("MPAS_GNU_LIBS_CHECK: Can compile a C NetCDF Program!")
 
         ## Fortran
-        if os.system('mpif90 -c netcdf.f90 -I$NETCDF/include -I$PNETCDF/include -L$NETCDF/lib -L$PNETCDF/lib -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -ldl -lz -lm'):
+        if os.system('mpif90 -c netcdf.f90 $NETCDF_INCLUDES $PNETCDF_INCLUDES' 
+                                         ' $NETCDF_LIBS $PNETCDF_LIBS'):
             print("Failed to compile netcdf.f90 with mpif90")
             result.result = "FAILED"
             result.msg = "Failed to compile a Fortran NetCDF program (netcdf.f90) with mpif90!"
@@ -117,7 +124,8 @@ def run(self, env, result, srcDir, testDir, hpc=None, *args, **kwargs):
 
         ## Fortran
         print("PIO: ", os.environ['PIO'])
-        if os.system('mpif90 -o piof piof.f90 -I$PIO/include -I$NETCDF/include -I$PNETCDF/include -L$PIO/lib -L$NETCDF/lib -L$PNETCDF/lib -lpiof -lpioc -lgptl -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -ldl -lz -lm'):
+        if os.system('mpif90 -o piof piof.f90 $PIO_INCLUDES $NETCDF_INCLUDES $PNETCDF_INCLUDE'
+                                            ' $PIO_LIBS $NETCDF_LIBS $PNETCDF_LIBS'):
             print("Failed to compile piof.f90 with mpif90")
             result.result = "FAILED"
             result.msg = "Failed to compile a Fortran PIO program (pio.f90) with mpif90!"