Merge pull request NOAA-GFDL#37 from thomas-robinson/main

Fixes for building singularity container with intel

container/Singularity.intel_am4

@@ -4,6 +4,8 @@ Stage: build
 ## Singularity def file used to create AM4
 
 %post
+LD_LIBRARY_PATH=/opt/netcdf-c/lib:/opt/netcdf-fortran/lib:/opt/hdf5/lib:/opt/intel/oneapi/lib:/opt/intel/oneapi/lib/intel64/:/opt/intel/oneapi/lib/intel64/lib:/opt/intel/oneapi/lib/intel64/libfabric:${LD_LIBRARY_PATH}
+export PATH=${PATH}:/opt/netcdf-c/bin:/opt/netcdf-fortran/bin
  cd /opt
 ## Build the AM4 from github
  git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b main 

container/Singularity.intel_netcdf

@@ -1,14 +1,20 @@
 Bootstrap: docker
-From: intel/oneapi-hpckit:devel-ubuntu18.04 
+From: intel/oneapi-hpckit:2021.2-devel-ubuntu18.04 
 Stage: build
 
 %post
 ## Set up oneAPI
   apt-get -yqq update  
   apt-get -yqq upgrade
-  apt-get -yqq install git make
+  apt-get -yqq install git
+  apt-get -yqq install make
   apt-get -yqq install wget
   apt-get -yqq install m4
+  apt-get -yqq install autoconf
+  apt-get -yqq install automake
+  apt-get -yqq install libtool
+  apt-get -yqq install autogen
+  apt-get -yqq install intltool
 # use wget to fetch the Intel repository public key
 # cd /tmp
 # wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB

container/singularity_build.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-singularity build -f intel_netcdf_ubuntu.sif Singularity.intel_netcdf
-singularity build -f am4_2021.02_ubuntu_intel.sif Singularity.intel_am4
+singularity build -f intel_netcdf_ubuntu.sif Singularity.intel2021.2_netcdfc4.7.4
+singularity build -f am4_2021.03_ubuntu_intel.sif Singularity.intel_am4

exec/fms/Makefile

@@ -14,7 +14,7 @@ libFMS.a: folder configure build
 folder:
 	mkdir -p build && cd build && autoreconf -i ${SRCROOT}/FMS 
 configure: folder
-	cd build && ${SRCROOT}/FMS/configure FC="$(FC)" CC="$(CC)" FCFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS) $(CPPDEFS)" FPPFLAGS="$(FPPFLAGS)" 
+	cd build && ${SRCROOT}/FMS/configure FC="$(FC)" CC="$(CC)" FCFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS) $(CPPDEFS) $(FPPFLAGS)" FPPFLAGS="$(FPPFLAGS)" LIBS="$(LIBS)" 
 build: configure
 	cd build && make -j 20
 clean:

exec/templates/intel.mk

@@ -91,6 +91,7 @@ FPPFLAGS = -fpp -Wp,-w $(INCLUDES)
 # Fortran Compiler flags for the NetCDF library
 ifndef NETCDF_FLAGS
 FPPFLAGS += $(shell nf-config --fflags) 
+FFLAGS += $(shell nf-config --fflags)
 else
 FPPFLAGS += $(NETCDF_FLAGS)
 endif