Some dopey whereis -> which in configure, not really a fix

.ci/Dockerfile

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+#
+FROM davegill/wrf-coop:fifthtry
+MAINTAINER Dave Gill <[email protected]>
+
+#RUN echo _HERE1_
+#RUN git clone https://github.com/davegill/WRF.git davegill/WRF \
+#  && cd davegill/WRF \
+#  && git fetch origin +refs/pull/4/merge: \
+#  && git checkout -qf FETCH_HEAD \
+#  && cd .. \
+#  && mv WRF /wrf/WRF
+#RUN echo _HERE2_
+
+RUN git clone _FORK_/_REPO_.git WRF \
+  && cd WRF \
+  && git checkout _BRANCH_ \
+  && cd ..
+
+RUN curl -SL http://www2.mmm.ucar.edu/wrf/dave/script.tar | tar -xC /wrf
+
+VOLUME /wrf
+CMD ["/bin/tcsh"]

.ci/Dockerfile-first_part

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+#
+FROM centos:latest
+MAINTAINER Dave Gill <[email protected]>
+
+ENV WRF_VERSION 4.0.3
+ENV WPS_VERSION 4.0.2
+ENV NML_VERSION 4.0.2
+
+# Set up base OS environment
+
+RUN yum -y update
+RUN yum -y install scl file gcc gcc-gfortran gcc-c++ glibc.i686 libgcc.i686 libpng-devel jasper \
+  jasper-devel hostname m4 make perl tar bash tcsh time wget which zlib zlib-devel \
+  openssh-clients openssh-server net-tools fontconfig libgfortran libXext libXrender \
+  ImageMagick sudo epel-release git
+
+# Newer version of GNU compiler, required for WRF 2003 and 2008 Fortran constructs
+
+RUN yum -y install centos-release-scl \
+ && yum -y install devtoolset-8 \
+ && yum -y install devtoolset-8-gcc devtoolset-8-gcc-gfortran devtoolset-8-gcc-c++ \
+ && scl enable devtoolset-8 bash \
+ && scl enable devtoolset-8 tcsh 
+
+RUN groupadd wrf -g 9999
+RUN useradd -u 9999 -g wrf -G wheel -M -d /wrf wrfuser
+RUN mkdir /wrf \
+ &&  chown -R wrfuser:wrf /wrf \
+ &&  chmod 6755 /wrf
+
+# Build the libraries with a parallel Make
+ENV J 4
+
+# Build OpenMPI
+RUN mkdir -p /wrf/libs/openmpi/BUILD_DIR
+RUN source /opt/rh/devtoolset-8/enable \
+ && cd /wrf/libs/openmpi/BUILD_DIR \
+ && curl -L -O https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.0.tar.gz \
+ && tar -xf openmpi-4.0.0.tar.gz \
+ && cd openmpi-4.0.0 \
+ && ./configure --prefix=/usr/local &> /wrf/libs/build_log_openmpi_config \
+ && echo dummy printout to keep travis happy openmpi config \
+ && make all install \
+ && echo "make all install | awk 'NR % 1000 == 0'" \
+ && echo "make all install &> /wrf/libs/build_log_openmpi_make" \
+ && echo dummy printout to keep travis happy openmpi make \
+ && cd / \
+ && rm -rf /wrf/libs/openmpi/BUILD_DIR
+
+# Build HDF5 libraries
+RUN mkdir -p /wrf/libs/hdf5/BUILD_DIR
+RUN source /opt/rh/devtoolset-8/enable \
+ && cd /wrf/libs/hdf5/BUILD_DIR \
+ && git clone https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git \
+ && cd hdf5 \
+ && git checkout hdf5-1_10_4 \
+ && ./configure --enable-fortran --enable-cxx --enable-shared --prefix=/usr/local/ &> /wrf/libs/build_log_hdf5_config \
+ && echo dummy printout to keep travis happy hdf5 config \
+ && make install &> /wrf/libs/build_log_hdf5_make \
+ && echo dummy printout to keep travis happy hdf5 make \
+ && rm -rf /wrf/libs/hdf5/BUILD_DIR
+ENV LD_LIBRARY_PATH /usr/local/lib
+
+# Build netCDF C libraries
+RUN yum -y install libcurl-devel zlib-devel
+ENV NETCDF /wrf/libs/netcdf
+RUN mkdir -p ${NETCDF}/BUILD_DIR
+RUN source /opt/rh/devtoolset-8/enable \
+ && cd ${NETCDF}/BUILD_DIR \
+ && curl -L -O https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz \
+ && curl -L -O https://github.com/Unidata/netcdf-fortran/archive/v4.4.5.tar.gz \
+ && curl -L -O https://github.com/Unidata/netcdf4-python/archive/v1.5.1rel.tar.gz \
+ && tar -xf v4.6.2.tar.gz \
+ && cd netcdf-c-4.6.2 \
+ && ./configure --enable-shared --prefix=${NETCDF} &> /wrf/libs/build_log_ncc_config \
+ && echo dummy printout to keep travis happy ncc config \
+ && make install &> /wrf/libs/build_log_ncc_make \
+ && echo dummy printout to keep travis happy ncc make
+
+# Build netCDF Fortran libraries
+RUN source /opt/rh/devtoolset-8/enable \
+ && env \
+ && cd ${NETCDF}/BUILD_DIR \
+ && tar -xf v4.4.5.tar.gz \
+ && cd netcdf-fortran-4.4.5/ \
+ && export LD_LIBRARY_PATH=${NETCDF}/lib:${LD_LIBRARY_PATH} \
+ && CPPFLAGS=-I${NETCDF}/include LDFLAGS=-L${NETCDF}/lib ./configure --enable-shared --prefix=${NETCDF} &> /wrf/libs/build_log_ncf_config \
+ && echo dummy printout to keep travis happy ncf config \
+ && make install &> /wrf/libs/build_log_ncf_make \
+ && echo dummy printout to keep travis happy ncf make
+
+#RUN yum -y install python-pip python-setuptools
+RUN yum -y install python-pip
+RUN yum -y install python-devel
+#RUN pip install Cython
+#RUN echo pip istalled Cython
+RUN pip install --upgrade pip \
+ && pip install numpy \
+ && echo pip istalled numpy
+#RUN pip install cython \
+# && echo pip istalled cython
+RUN pip install --upgrade setuptools \
+ && echo pip istalled setuptools
+RUN ldconfig -v
+
+# Build netCDF4-python libraries
+RUN source /opt/rh/devtoolset-8/enable \
+ && cd ${NETCDF}/BUILD_DIR \
+ && tar -xf v1.5.1rel.tar.gz \
+ && cd netcdf4-python-1.5.1rel/ \
+ && export LD_LIBRARY_PATH=${NETCDF}/lib:${LD_LIBRARY_PATH} \
+ && export NETCDF4_DIR=${NETCDF} \
+ && export HDF5_DIR=/usr/local \
+ && python setup.py build \
+ && CPPFLAGS="-I${NETCDF}/include -I/usr/local/include" LDFLAGS="-L${NETCDF}/lib -L/usr/local/lib" python setup.py install \
+ && echo dummy printout to keep travis happy ncf4-python install
+#&& python setup.py build &> /wrf/libs/build_log_ncf4-python_build
+
+RUN mkdir -p /var/run/sshd \
+    && ssh-keygen -A \
+    && sed -i 's/#PermitRootLogin yes/PermitRootLogin yes/g' /etc/ssh/sshd_config \
+    && sed -i 's/#RSAAuthentication yes/RSAAuthentication yes/g' /etc/ssh/sshd_config \
+    && sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/g' /etc/ssh/sshd_config
+
+RUN mkdir -p  /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput \
+ &&  chown -R wrfuser:wrf /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local \
+ &&  chmod 6755 /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local
+
+# Download NCL
+RUN curl -SL https://ral.ucar.edu/sites/default/files/public/projects/ncar-docker-wrf/nclncarg-6.3.0.linuxcentos7.0x8664nodapgcc482.tar.gz | tar zxC /usr/local
+ENV NCARG_ROOT /usr/local
+
+# Set environment for interactive container shells
+RUN echo export LDFLAGS="-lm" >> /etc/bashrc \
+ && echo export NETCDF=${NETCDF} >> /etc/bashrc \
+ && echo export JASPERINC=/usr/include/jasper/ >> /etc/bashrc \
+ && echo export JASPERLIB=/usr/lib64/ >> /etc/bashrc \
+ && echo export LD_LIBRARY_PATH="/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> /etc/bashrc  \
+ && echo export PATH=".:/opt/rh/devtoolset-8/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH" >> /etc/bashrc
+
+RUN echo setenv LDFLAGS "-lm" >> /etc/csh.cshrc \
+ && echo setenv NETCDF "${NETCDF}" >> /etc/csh.cshrc \
+ && echo setenv JASPERINC "/usr/include/jasper/" >> /etc/csh.cshrc \
+ && echo setenv JASPERLIB "/usr/lib64/" >> /etc/csh.cshrc \
+ && echo setenv LD_LIBRARY_PATH "/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> /etc/csh.cshrc \
+ && echo setenv PATH ".:/opt/rh/devtoolset-8/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH" >> /etc/csh.cshrc
+
+RUN mkdir /wrf/.ssh ; echo "StrictHostKeyChecking no" > /wrf/.ssh/config
+COPY default-mca-params.conf /wrf/.openmpi/mca-params.conf
+RUN mkdir -p /wrf/.openmpi
+RUN chown -R wrfuser:wrf /wrf/
+
+# all root steps completed above, now below as regular userID wrfuser
+USER wrfuser
+WORKDIR /wrf
+
+# Download data
+ARG argname=tutorial
+RUN echo DAVE $argname
+RUN if [ "$argname" = "tutorial" ] ; then curl -SL http://www2.mmm.ucar.edu/wrf/src/wps_files/geog_low_res_mandatory.tar.gz | tar -xzC /wrf/WPS_GEOG ; fi
+RUN if [ "$argname" = "tutorial" ] ; then curl -SL http://www2.mmm.ucar.edu/wrf/TUTORIAL_DATA/colorado_march16.new.tar.gz | tar -xzC /wrf/wrfinput ; fi
+RUN if [ "$argname" = "tutorial" ] ; then curl -SL http://www2.mmm.ucar.edu/wrf/src/namelists_v$NML_VERSION.tar.gz  | tar -xzC /wrf/wrfinput ; fi
+RUN if [ "$argname" = "tutorial" ] ; then curl -SL http://www2.mmm.ucar.edu/wrf/TUTORIAL_DATA/WRF_NCL_scripts.tar.gz | tar -xzC /wrf ; fi
+#RUN if [ "$argname" = "regtest" ]  ; then curl -SL http://www2.mmm.ucar.edu/wrf/dave/DATA/Data_small/data_SMALL.tar.gz | tar -xzC /wrf ; fi
+COPY data_smaller.tar /wrf/data_smaller.tar
+RUN tar -xf /wrf/data_smaller.tar \
+    && rm /wrf/data_smaller.tar
+RUN if [ "$argname" = "regtest" ]  ; then curl -SL http://www2.mmm.ucar.edu/wrf/dave/nml.tar.gz | tar -xzC /wrf ; fi
+RUN if [ "$argname" = "regtest" ]  ; then curl -SL http://www2.mmm.ucar.edu/wrf/dave/script.tar | tar -xC /wrf ; fi
+
+# Download wps source
+RUN if [ "$argname" = "tutorial" ] ; then git clone https://github.com/wrf-model/WPS.git WPS ; fi
+
+ENV JASPERINC /usr/include/jasper
+ENV JASPERLIB /usr/lib64
+ENV NETCDF_classic 1
+ENV LD_LIBRARY_PATH /opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}
+ENV PATH  .:/opt/rh/devtoolset-8/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH
+
+RUN ssh-keygen -f /wrf/.ssh/id_rsa -t rsa -N '' \
+    && chmod 600 /wrf/.ssh/config \
+    && chmod 700 /wrf/.ssh \
+    && cp /wrf/.ssh/id_rsa.pub /wrf/.ssh/authorized_keys
+#

.ci/Dockerfile-second_part

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+#
+FROM davegill/wrf-coop:fifthtry
+MAINTAINER Dave Gill <[email protected]>
+
+#RUN echo _HERE1_
+#RUN git clone https://github.com/davegill/WRF.git davegill/WRF \
+#  && cd davegill/WRF \
+#  && git fetch origin +refs/pull/4/merge: \
+#  && git checkout -qf FETCH_HEAD \
+#  && cd .. \
+#  && mv WRF /wrf/WRF
+#RUN echo _HERE2_
+
+RUN git clone https://github.com/wrf-model/WRF.git WRF \
+  && cd WRF \
+  && git checkout release-v4.1.1 \
+  && git checkout master \
+  && git checkout develop \
+  && git checkout release-v4.1 \
+  && cd ..
+
+RUN curl -SL http://www2.mmm.ucar.edu/wrf/dave/script.tar | tar -xC /wrf
+
+VOLUME /wrf
+CMD ["/bin/tcsh"]

.ci/README.md

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+# CI scripts