Feature/40 build wrf container

.gitignore

@@ -1,3 +1,4 @@
+libs
 *~
 .vs
 /.DS_Store

docker/iwrf/Dockerfile

@@ -0,0 +1,107 @@
+# Cornell uses ubuntu 22.04
+FROM ubuntu:22.04 as wrfbuild
+
+# Update the OS
+RUN apt -y update
+RUN apt -y upgrade
+
+# Install compilers
+RUN apt -y install cmake pkg-config build-essential wget libcurl4-openssl-dev m4
+RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor > /usr/share/keyrings/oneapi-archive-keyring.gpg
+RUN echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" > /etc/apt/sources.list.d/oneAPI.list
+RUN apt -y update
+RUN apt -y install intel-oneapi-compiler-fortran-2023.1.0 intel-oneapi-dpcpp-cpp-2023.1.0 intel-oneapi-mpi-2021.9.0 intel-oneapi-mpi-devel-2021.9.0
+RUN apt -y --fix-broken install
+RUN apt -y update
+
+# Install other required packages
+RUN apt -y install libexpat1 libexpat1-dev expat git csh file
+
+# Install packages used for debugging
+RUN apt -y install vim
+
+# Add system user
+RUN useradd -u 5000 wrfuser
+
+# Configure bash
+RUN echo 'source /etc/bash.bashrc' >> /etc/bashrc
+RUN echo 'export MPI="/opt/intel/oneapi/mpi/latest"' >> /etc/bashrc
+RUN echo 'export OPENMPI="${MPI}"' >> /etc/bashrc
+RUN echo 'export INTEL="/opt/intel/oneapi/compiler/latest/linux"' >> /etc/bashrc
+RUN echo 'export PATH="${INTEL}/bin/intel64:${MPI}/bin:${PATH}"' >> /etc/bashrc
+RUN echo 'export SCC="icx"' >> /etc/bashrc
+RUN echo 'export SFC="ifx"' >> /etc/bashrc
+RUN echo 'export I_MPI_CC="icx"' >> /etc/bashrc
+RUN echo 'export I_MPI_CXX="icpx"' >> /etc/bashrc
+RUN echo 'export I_MPI_FC="ifx"' >> /etc/bashrc
+RUN echo 'export I_MPI_F90="ifx"' >> /etc/bashrc
+RUN echo 'export FC="mpifc"' >> /etc/bashrc
+RUN echo 'export F90="mpifc"' >> /etc/bashrc
+RUN echo 'export F77="mpifc"' >> /etc/bashrc
+RUN echo 'export CC="mpicc"' >> /etc/bashrc
+RUN echo 'export CXX="mpicxx"' >> /etc/bashrc
+RUN echo 'export CPP="${CC} -E"' >> /etc/bashrc
+RUN echo 'export CC_FOR_BUILD="${CC}"' >> /etc/bashrc
+RUN echo 'export CPP_FOR_BUILD="${CPP}"' >> /etc/bashrc
+RUN echo 'export CXXCPP="${CXX} -E"' >> /etc/bashrc
+RUN echo 'export ABI="64"' >> /etc/bashrc
+RUN echo 'export FCFLAGS="-I${MPI}/include"' >> /etc/bashrc
+RUN echo 'export CFLAGS="-I${MPI}/include"' >> /etc/bashrc
+RUN echo 'export LDFLAGS="-L${MPI}/lib -L${MPI}/lib/release"' >> /etc/bashrc
+RUN echo 'export LD_LIBRARY_PATH="${MPI}/lib/release:${MPI}/lib"' >> /etc/bashrc
+RUN echo 'source /opt/intel/oneapi/setvars.sh --force > /dev/null' >> /etc/bashrc
+RUN echo 'export PATH="/opt/intel/oneapi/mpi/latest/bin:${PATH}"' >> /etc/bashrc
+RUN echo 'export WRFUSER="wrfuser"' >> /etc/bashrc
+# TODO: This is not taking effect for the stack, we had to manually run: 'ulimit -s unlimited'
+RUN echo '*    hard    stack    unlimited' >> /etc/security/limits.conf
+RUN echo '*    soft    stack    unlimited' >> /etc/security/limits.conf
+
+# Download source
+RUN mkdir -p /opt/src
+WORKDIR /opt/src
+RUN wget https://www.wrfcloud.com/libs/cmake-3.25.0-rc3.tar.gz
+RUN wget https://www.wrfcloud.com/libs/eccodes-2.27.0.tar.gz
+RUN wget https://www.wrfcloud.com/libs/g2clib-1.6.0-patch.tar.gz
+RUN wget https://www.wrfcloud.com/libs/jasper-1.900.1.tar.gz
+RUN wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.10/src/hdf5-1.10.10.tar.gz
+RUN wget https://www.wrfcloud.com/libs/libaec-v1.0.6.tar.gz
+RUN wget https://www.wrfcloud.com/libs/libpng-1.2.50.tar.gz
+RUN wget https://www.wrfcloud.com/libs/ncview-2.1.7.tar.gz
+RUN wget https://www.wrfcloud.com/libs/netcdf-4.7.3.tar.gz
+RUN wget https://www.wrfcloud.com/libs/netcdf-cxx-4.3.1.tar.gz
+RUN wget https://www.wrfcloud.com/libs/netcdf-fortran-4.5.2.tar.gz
+RUN wget https://www.wrfcloud.com/libs/szip-2.1.1.tar.gz
+RUN wget https://www.wrfcloud.com/libs/zlib-1.2.11.tar.gz
+RUN wget https://downloads.unidata.ucar.edu/udunits/2.2.28/udunits-2.2.28.tar.gz
+
+#COPY WPS.patch /tmp/WPS.patch
+COPY build_wrf.sh /tmp/build_wrf.sh
+RUN bash /tmp/build_wrf.sh
+
+
+FROM ubuntu:22.04
+
+# Update the OS
+RUN apt -y update
+RUN apt -y upgrade
+
+COPY --from=wrfbuild /home/wrfuser /home/wrfuser
+COPY --from=wrfbuild /opt/hdf5 /opt/hdf5
+COPY --from=wrfbuild /opt/jasper /opt/jasper
+COPY --from=wrfbuild /opt/libpng /opt/libpng
+COPY --from=wrfbuild /opt/netcdf /opt/netcdf
+COPY --from=wrfbuild /opt/szip /opt/szip
+COPY --from=wrfbuild /opt/udunits /opt/udunits
+COPY --from=wrfbuild /opt/zlib /opt/zlib
+COPY --from=wrfbuild /etc/bashrc /etc/bashrc
+
+# Install required runtime packages
+# Note: To get a list of Intel OneAPI runtime packages, run the following:
+#     apt-cache pkgnames intel | grep intel-oneapi-runtime
+RUN apt -y install cmake pkg-config build-essential wget libcurl4-openssl-dev m4 csh
+RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor > /usr/share/keyrings/oneapi-archive-keyring.gpg
+RUN echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" > /etc/apt/sources.list.d/oneAPI.list
+RUN apt -y update
+RUN apt -y install intel-oneapi-runtime-mpi-2021 intel-oneapi-common-vars intel-oneapi-compiler-shared-runtime-2023.1.0 intel-oneapi-compiler-fortran-runtime-2023.1.0
+
+WORKDIR /home/wrfuser

docker/iwrf/WPS.patch

@@ -0,0 +1,136 @@
+--- WPS/ungrib/src/cio.c	2024-03-22 21:46:05.026504170 +0000
++++ WPS-patch/ungrib/src/cio.c	2024-03-22 22:03:15.537543342 +0000
+@@ -48,8 +48,6 @@
+ #endif
+
+ /* ****************************************************************** */
+-
+-c_open(unit, nunit, name, mode, err, oflag)
+  /*
+   * unit  = Fortran unit number 
+   * nunit = UNIX file descriptor associated with 'unit'
+@@ -64,12 +62,15 @@
+           =  1 : file name and unit number printed (and errors)
+           = -1 : no print at all (not even errors)
+   */
+-    int             *unit;
+-    int             *nunit;
+-    int             *mode;
+-    int             *err;
+-    int             *oflag;
+-    char            name[FORT_FILE_LEN];
++int
++c_open(
++      int             *unit,
++      int             *nunit,
++      char            name[FORT_FILE_LEN],
++      int             *mode,
++      int             *err,
++      int             *oflag
++      )
+ {
+     int             fd, i;
+     char            fname[FORT_FILE_LEN];
+@@ -114,8 +115,6 @@
+ }
+
+ /* ****************************************************************** */
+-bn_seek(fd, bread, mode, iprint)
+-
+ /*  Move the read/write file pointer
+        fd     : Unix file descriptor.
+        bread  : Number of bytes to move the pointer.
+@@ -128,9 +127,13 @@
+    Location 0 [bn_seek(fd,0,-1,0)] puts us just before the first byte, 
+    so the next bn_read will get byte 1.
+ */
+-
+-    int            *fd, *bread, *mode, *iprint;
+-
++int
++bn_seek(
++        int *fd,
++        int *bread,
++        int *mode,
++        int *iprint
++        )
+ {
+     off_t           i, offset;
+     int             how_to_space;
+@@ -151,8 +154,6 @@
+ }
+
+ /* ****************************************************************** */
+-
+-bn_read(fd, buf, nbuf, bread, ios, idiag)
+  /*
+   * fd = UNIX file descriptor number (NOT a Fortran unit) 
+   * buf = area into which to read 
+@@ -163,8 +164,15 @@
+           2 = Error in reading
+   * idiag : if non-zero, error and EOF messages will be printed
+   */
+-
+-    int            *fd, *nbuf, buf[], *bread, *ios, *idiag;
++int
++bn_read(
++        int *fd,
++        int  buf[],
++        int *nbuf,
++        int *bread,
++        int *ios,
++        int *idiag
++        )
+ {
+     int             bytesread;
+
+@@ -197,17 +205,21 @@
+ }
+
+ /* ****************************************************************** */
+-
+-bnwrit_(fd, buf, nbuf, bwritten, err, idiag)
+-    int            *fd, *nbuf, buf[], *bwritten, *err, *idiag;
+-
+  /*
+   * fd = UNIX file descriptor number (NOT a Fortran unit) buf = area from
+   * which to write nbuf = number of bytes to write to fd bwritten = number
+   * actually written err = UNIX error number returned to FORTRAN idiag : if
+   * non-zero, error and EOF messages will be printed
+   */
+-
++int
++bnwrit_(
++        int *fd,
++        int  buf[],
++        int *nbuf,
++        int *bwritten,
++        int *err,
++        int *idiag
++        )
+ {
+     int             byteswritten;
+
+@@ -231,8 +243,6 @@
+ }
+
+ /* ****************************************************************** */
+-
+-c_close(nunit, iprint, err)
+ /*
+ Close a C (UNIX?) file descriptor:
+   nunit  : (INPUT)  : The C (UNIX?) file descriptor to close.
+@@ -241,7 +251,12 @@
+   err    : (OUTPUT) : Error flag ( err = 0 : Successful close)
+                                  ( err = 1 : Error on close)
+      */
+-    int            *nunit, *iprint, *err;
++int
++c_close(
++        int *nunit,
++        int *iprint,
++        int *err
++        )
+ {
+     extern int      errno;	/* I/O error return */
+     int             istat;

docker/iwrf/build.sh

@@ -0,0 +1,3 @@
+#! /bin/bash
+
+docker build --no-cache -f Dockerfile . 2>&1 | tee build.log