Add conda environment, fix Makefile and Macros, implement -nomodules (

#296)

* machines: add conda environment for macOS and Linux

Closes #294

* Makefile: remove uneeded (and faulty) logic around CFLAGS_HOST

The CFLAG_HOST variable was added in #257, and
some Makefile logic was added to define the variable to be blank if
the included Macros file does not define it.

However, the Make syntax is wrong, as 'ifndef' takes a variable name and
not
a reference to a variable [1], so

    ifndef $(CFLAGS_HOST)

should have been written

    ifndef CFLAGS_HOST

The effect of this error is to invert the logic of the check (!) since
if CFLAGS_HOST is defined, Make will check if a variable with name equal
to whatever CFLAGS_HOST is defined to be exists, which will most probably
be false, and the conditional will then evaluate to true and CFLAG_HOSTS
will be redefined to be blank, defeating the whole purpose of the flag.

Since there's no harm in Make referencing and empty variable, fix this
by just removing the conditional check.

[1] https://www.gnu.org/software/make/manual/html_node/Conditional-Syntax.html

* doc: add documentation for conda environment

* machines: fix Macros file for cheyenne and testmachine

These two files used outdated environment variables for
threading ("compile_threaded") and PIO ("IO_TYPE").

Replace these with the correct variables, ICE_THREADED and
ICE_IOTYPE.

Mirrors CICE-Consortium/CICE#396

* scripts: implement '-nomodules' logic for env files

Some env files wrap the calls for loading the build and run environment
in a conditional based on the argument `-nomodules`, so that
scripts that source the env file just to get the variables defined in it
do not run slower because they have to load the environment.

This logic was copied from CICE but was not implemented in the Icepack
scripts icepack.setup and setup_run_dirs.csh.

Add the argument '-nomodules' so that the logic becomes effective.

* doc: conda: add note about csh/tcsh

On Ubuntu and its derivatives, the csh shell at
/bin/csh, which is used in the shebangs of the Icepack scripts,
is not compatible with conda.

Mention that in the documentation and explain how to install tcsh as an
alternative, and configure the system such that /bin/csh points to
/bin/tcsh.

configuration/scripts/Makefile

@@ -110,10 +110,6 @@ db_flags:
 # the needed macros
 #-------------------------------------------------------------------------------
 
-ifndef $(CFLAGS_HOST)
-  CFLAGS_HOST :=
-endif
-
 $(DEPGEN): $(ICE_CASEDIR)/makdep.c
 	$(SCC) -o $@ $(CFLAGS_HOST) $<
 

configuration/scripts/icepack.batch.csh

@@ -143,6 +143,11 @@ cat >> ${jobfile} << EOFB
 # nothing to do
 EOFB
 
+else if (${ICE_MACHINE} =~ conda*) then
+cat >> ${jobfile} << EOFB
+# nothing to do
+EOFB
+
 else
   echo "${0} ERROR: ${ICE_MACHINE} unknown"
   exit -1

configuration/scripts/machines/Macros.cheyenne_intel

@@ -39,14 +39,14 @@ LIB_MPI := $(IMPILIBDIR)
 #SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff -L$(LIB_PNETCDF) -lpnetcdf -lgptl
 SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -qopenmp 
    CFLAGS += -qopenmp 
    FFLAGS += -qopenmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
    INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
    SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof

configuration/scripts/machines/Macros.conda_linux

@@ -0,0 +1,35 @@
+#==============================================================================
+# Makefile macros for conda environment, GNU/Linux systems
+#==============================================================================
+
+# Preprocessor macros
+CPPDEFS    := -DFORTRANUNDERSCORE ${ICE_CPPDEFS}
+
+# Flags for the C compiler
+CFLAGS     := -c -O2
+
+# Flags for the Fortran compiler
+FREEFLAGS  := -ffree-form
+FFLAGS     := -fconvert=big-endian -fbacktrace -ffree-line-length-none
+
+# Additional flags for the Fortran compiler when compiling in debug mode
+ifeq ($(ICE_BLDDEBUG), true)
+  FFLAGS   += -O0 -g -fcheck=bounds -finit-real=nan -fimplicit-none -ffpe-trap=invalid,zero,overflow
+else
+  FFLAGS   += -O2
+endif
+
+# C and Fortran compilers
+SCC   := gcc
+SFC   := gfortran
+CC := $(SCC)
+FC := $(SFC)
+LD := $(FC)
+
+# Necessary flag to compile with OpenMP support
+ifeq ($(ICE_THREADED), true)
+   LDFLAGS += -fopenmp
+   CFLAGS  += -fopenmp
+   FFLAGS  += -fopenmp
+endif
+

configuration/scripts/machines/Macros.conda_macos

@@ -0,0 +1,38 @@
+#==============================================================================
+# Makefile macros for conda environment, macOS systems
+#==============================================================================
+
+# Preprocessor macros
+CPPDEFS    := -DFORTRANUNDERSCORE ${ICE_CPPDEFS}
+
+# Flags for the C compiler
+CFLAGS     := -c -O2
+
+# Flags for the Fortran compiler
+FREEFLAGS  := -ffree-form
+FFLAGS     := -fconvert=big-endian -fbacktrace -ffree-line-length-none
+
+# Additional flags for the Fortran compiler when compiling in debug mode
+ifeq ($(ICE_BLDDEBUG), true)
+  FFLAGS   += -O0 -g -fcheck=bounds -finit-real=nan -fimplicit-none -ffpe-trap=invalid,zero,overflow
+else
+  FFLAGS   += -O2
+endif
+
+# C and Fortran compilers
+SCC   := clang
+SFC   := gfortran
+CC := $(SCC)
+FC := $(SFC)
+LD := $(FC)
+
+# Location of the system C header files (required on recent macOS to compile makdep)
+CFLAGS_HOST = -isysroot$(shell xcrun --show-sdk-path)
+
+# Necessary flag to compile with OpenMP support
+ifeq ($(ICE_THREADED), true)
+   LDFLAGS += -fopenmp
+   CFLAGS  += -fopenmp
+   FFLAGS  += -fopenmp
+endif
+

configuration/scripts/machines/Macros.testmachine_intel

@@ -38,14 +38,14 @@ LIB_MPI := $(IMPILIBDIR)
 
 SLIBS   := -L$(LIB_NETCDF) -lnetcdf -lnetcdff -L$(LIB_PNETCDF) -lpnetcdf -lgptl
 
-ifeq ($(compile_threaded), true) 
+ifeq ($(ICE_THREADED), true) 
    LDFLAGS += -openmp 
    CFLAGS += -openmp 
    FFLAGS += -openmp 
 endif
 
 ### if using parallel I/O, load all 3 libraries.  PIO must be first!
-ifeq ($(IO_TYPE), pio)
+ifeq ($(ICE_IOTYPE), pio)
    PIO_PATH:=/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/lib
    INCLDIR += -I/glade/u/apps/ch/opt/pio/2.2/mpt/2.15f/intel/17.0.1/include
    SLIBS   := $(SLIBS) -L$(PIO_PATH) -lpiof

configuration/scripts/machines/env.conda_linux

@@ -0,0 +1,41 @@
+#!/bin/csh -f
+
+set inp = "undefined"
+if ($#argv == 1) then
+  set inp = $1
+endif
+
+if ("$inp" != "-nomodules") then
+
+# Init conda
+if ! $?CONDA_EXE then
+  echo ""
+  echo "${0}: conda executable not found, see the Icepack documentation for how to initialize your login shell to use conda"
+  echo ""
+  exit 1
+endif
+source `$CONDA_EXE info --base`/etc/profile.d/conda.csh
+# Activate "icepack" conda environment
+conda activate icepack
+if $status then
+  echo ""
+  echo "${0}: 'icepack' conda environment not found, see the Icepack documentation for how to create the conda icepack env"
+  echo ""
+  exit 1
+endif
+
+endif
+
+setenv ICE_MACHINE_ENVNAME conda
+setenv ICE_MACHINE_COMPILER linux
+setenv ICE_MACHINE_MAKE make
+setenv ICE_MACHINE_WKDIR  $HOME/icepack-dirs/runs
+setenv ICE_MACHINE_INPUTDATA $HOME/icepack-dirs/input
+setenv ICE_MACHINE_BASELINE $HOME/icepack-dirs/baseline
+setenv ICE_MACHINE_SUBMIT " "
+setenv ICE_MACHINE_TPNODE 4
+setenv ICE_MACHINE_ACCT P0000000
+setenv ICE_MACHINE_QUEUE "debug"
+setenv ICE_MACHINE_BLDTHRDS 4
+setenv ICE_MACHINE_QSTAT " "
+

configuration/scripts/machines/env.conda_macos

@@ -0,0 +1,41 @@
+#!/bin/csh -f
+
+set inp = "undefined"
+if ($#argv == 1) then
+  set inp = $1
+endif
+
+if ("$inp" != "-nomodules") then
+
+# Init conda
+if ! $?CONDA_EXE then
+  echo ""
+  echo "${0}: conda executable not found, see the Icepack documentation for how to initialize your login shell to use conda"
+  echo ""
+  exit 1
+endif
+source `$CONDA_EXE info --base`/etc/profile.d/conda.csh
+# Activate "icepack" conda environment
+conda activate cice
+if $status then
+  echo ""
+  echo "${0}: 'cice' conda environment not found, see the Icepack documentation for how to create the conda icepack env"
+  echo ""
+  exit 1
+endif
+
+endif
+
+setenv ICE_MACHINE_ENVNAME conda
+setenv ICE_MACHINE_COMPILER macos
+setenv ICE_MACHINE_MAKE make
+setenv ICE_MACHINE_WKDIR  $HOME/icepack-dirs/runs
+setenv ICE_MACHINE_INPUTDATA $HOME/icepack-dirs/input
+setenv ICE_MACHINE_BASELINE $HOME/icepack-dirs/baseline
+setenv ICE_MACHINE_SUBMIT " "
+setenv ICE_MACHINE_TPNODE 4
+setenv ICE_MACHINE_ACCT P0000000
+setenv ICE_MACHINE_QUEUE "debug"
+setenv ICE_MACHINE_BLDTHRDS 4
+setenv ICE_MACHINE_QSTAT " "
+

configuration/scripts/machines/environment.yml

@@ -0,0 +1,11 @@
+name: icepack
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+# Build dependencies
+  - compilers
+  - make
+# Python dependencies for building the HTML documentation
+  - sphinx
+  - sphinxcontrib-bibtex

configuration/scripts/setup_run_dirs.csh

@@ -1,7 +1,7 @@
 #! /bin/csh -f
 
 source ./icepack.settings
-source ${ICE_CASEDIR}/env.${ICE_MACHCOMP} || exit 2
+source ${ICE_CASEDIR}/env.${ICE_MACHCOMP} -nomodules || exit 2
 
 if !(-d ${ICE_RUNDIR}) then
   echo "mkdir ${ICE_RUNDIR}"