large overhaul to move hdf4, hdf5, and netcdf4 into /opt and allow for .so libs as well

Dockerfile

@@ -7,9 +7,11 @@ ENV ZLIB_VERSION 1.2.8
 ENV JPEG_VERSION 6b
 ENV SZIP_VERSION 2.1
 ENV HDF4_VERSION 4.2.12
+# for pre-libdl dependency:
+#ENV HDF5_VERSION 1.8.10-patch1
 ENV HDF5_VERSION 1.8.17
 ENV NC4F_VERSION 4.4.4
-ENV NC4C_VERSION 4.4.1 
+ENV NC4C_VERSION 4.4.1
 
 # grab some packages we need
 RUN apt-get update && apt-get install -y byacc bison diffutils flex make
@@ -18,7 +20,7 @@ RUN apt-get update && apt-get install -y byacc bison diffutils flex make
 RUN apt-get install -y vim
 
 # get ready to build things
-RUN mkdir -p /build /usr/man/man1 /config
+RUN mkdir -p /build /usr/man/man1 /opt
 
 # perform downloads first so they get cached during development; does it make any difference afterwards?
 RUN cd /build && curl -O http://zlib.net/zlib-${ZLIB_VERSION}.tar.gz
@@ -30,16 +32,18 @@ RUN cd /build && curl -O ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-${NC4C_VER
 RUN cd /build && curl -O ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-${NC4F_VERSION}.tar.gz
 
 # add zlib
+#RUN apt-get install -y zlib-devel
 RUN cd /build && tar xzf zlib-${ZLIB_VERSION}.tar.gz && \
     cd zlib-${ZLIB_VERSION} && \
-    ./configure --prefix="/usr" && make -j4 && make install && \
-    cp configure.log /config/config.log-zlib-${ZLIB_VERSION}
+    ./configure && make -j4 && make install && \
+    cp configure.log /opt/config.log-zlib-${ZLIB_VERSION}
 
 # add libjpeg
+#RUN apt-get install -y jpeg-devel
 RUN cd /build && tar xzf jpegsrc.v${JPEG_VERSION}.tar.gz && \
     cd jpeg-${JPEG_VERSION} && \
-    ./configure --prefix="/usr" && make -j4 && make install && \
-    cp config.log /config/config.log-jpeg-${JPEG_VERSION}
+    ./configure && make -j4 && make install && \
+    cp config.log /opt/config.log-jpeg-${JPEG_VERSION}
 
 ## add szip
 #RUN cd /build && tar zxf szip-${SZIP_VERSION}.tar.gz && \
@@ -52,45 +56,52 @@ RUN cd /build && tar xzf jpegsrc.v${JPEG_VERSION}.tar.gz && \
 # enable-shared => disable-shared everywhere for now since we're most likely building static binaries anyways
 
 # add hdf4
-RUN cd /build && tar xzf hdf-${HDF4_VERSION}.tar.gz && \
+RUN cd /build && mkdir -p /opt/hdf4 && tar xzf hdf-${HDF4_VERSION}.tar.gz && \
     cd hdf-${HDF4_VERSION} && \
-    ./configure --prefix="/usr" --disable-netcdf --enable-fortran --disable-shared --with-zlib="/usr" --with-jpeg="/usr" && make -j4 && make install && \
-    cp config.log /config/config.log-hdf4-${HDF4_VERSION}
+    CFLAGS="-fPIC -DHAVE_NETCDF -fno-strict-aliasing" \
+    CXXFLAGS="-fPIC -DHAVE_NETCDF -fno-strict-aliasing" \
+    ./configure --prefix="/opt/hdf4" --disable-netcdf --enable-fortran && make -j4 && make install && \
+    cp config.log /opt/hdf4/config.log-hdf4-${HDF4_VERSION}
 
 # add hdf5
 # note - hdf5 post-1.8.11 now includes -ldl as a dependency
 # http://hdf-forum.184993.n3.nabble.com/Errors-compiling-against-Static-build-HDF5-1-8-11-Need-for-ldl-added-to-linker-arguments-td4026300.html
-RUN cd /build && tar xzf hdf5-${HDF5_VERSION}.tar.gz && \
+RUN cd /build && mkdir -p /opt/hdf5 && tar xzf hdf5-${HDF5_VERSION}.tar.gz && \
     cd hdf5-${HDF5_VERSION} && \
-    ./configure --prefix="/usr" --disable-shared --with-pic --with-zlib="/usr" --enable-cxx --enable-fortran --enable-fortran2003 --with-pthread && make -j4 && make install && \
-    cp config.log /config/config.log-hdf5-${HDF5_VERSION}
+    ./configure --prefix="/opt/hdf5" --with-pic --with-zlib="/opt/zlib" --enable-cxx --enable-fortran --enable-fortran2003 --with-pthread && make -j4 && make install && \
+    cp config.log /opt/hdf5/config.log-hdf5-${HDF5_VERSION}
 
 # add netcdf-c
-RUN cd /build && tar xzf netcdf-${NC4C_VERSION}.tar.gz && \
+RUN cd /build && mkdir -p /opt/netcdf4 && tar xzf netcdf-${NC4C_VERSION}.tar.gz && \
     cd netcdf-${NC4C_VERSION} && \
-    CPPFLAGS="-I/usr/include -I/usr/lib/x86_64-linux-gnu" \
-    LDFLAGS="-L/usr/lib -L/usr/lib/x86_64-linux-gnu" \
-    LD_LIBRARY_PATH=/usr/lib:/usr/lib/x86_64-linux-gnu \
-    LIBS="-ldf -lhdf5_hl -lhdf5 -ljpeg -ldl -lm -lz" \
-    ./configure --prefix="/usr" --enable-hdf4 --disable-dap --disable-shared --with-pic  && make -j4 && make install && \
-    cp config.log /config/config.log-netcdf-${NC4C_VERSION}
+    CPPFLAGS="-I/opt/hdf4/include -I/opt/hdf5/include" \
+    LDFLAGS="-L/opt/hdf4/lib -L/opt/hdf5/lib" \
+    LD_LIBRARY_PATH="/opt/zlib/lib:/opt/jpeg/lib:/opt/hdf4/lib:/opt/hdf5/lib" \
+    LIBS="-ldf -lhdf5_hl -lhdf5 -ljpeg -lm -lz" \
+    ./configure --prefix="/opt/netcdf4" --enable-hdf4 --disable-dap --with-pic  && make -j4 && make install && \
+    cp config.log /opt/netcdf4/config.log-netcdf-${NC4C_VERSION}
 
 # add netcdf-fortran
 # compiling against this requires -lnetcdff (note the extra f)
-RUN cd /build && tar xzf netcdf-fortran-${NC4F_VERSION}.tar.gz && \
+RUN cd /build && mkdir -p /opt/netcdf4 && tar xzf netcdf-fortran-${NC4F_VERSION}.tar.gz && \
     cd netcdf-fortran-${NC4F_VERSION} && \
-    CPPFLAGS="-I/usr/include -I/usr/lib/x86_64-linux-gnu" \
-    LDFLAGS="-L/usr/lib -L/usr/lib/x86_64-linux-gnu" \
-    LD_LIBRARY_PATH=/usr/lib:/usr/lib/x86_64-linux-gnu \
-    LIBS="-lnetcdf -ldf -lhdf5_hl -lhdf5 -ljpeg -ldl -lm -lz" \
-    ./configure --prefix="/usr" --disable-dap --disable-shared --with-pic && make -j4 && make install && \
-    cp config.log /config/config.log-netcdff-${NC4F_VERSION}
-
-# remove all the build cruft
-RUN rm -rf /build
-RUN rm -rf /usr/man
+    CPPFLAGS="-I/opt/hdf4/include -I/opt/hdf5/include -I/opt/netcdf4/include" \
+    LDFLAGS="-L/opt/hdf4/lib -L/opt/hdf5/lib -L/opt/netcdf4/lib" \
+    LD_LIBRARY_PATH="/opt/hdf4/lib:/opt/hdf5/lib:/opt/netcdf4/lib" \
+    LIBS="-lnetcdf -ldf -lhdf5_hl -lhdf5 -ljpeg -lm -lz" \
+    ./configure --prefix="/opt/netcdf4" --disable-dap --with-pic && make -j4 && make install && \
+    cp config.log /opt/netcdf4/config.log-netcdff-${NC4F_VERSION}
 
 # throw in some minor shell niceties
 RUN echo 'alias ls="ls --color=auto"' >> ~/.bashrc && \
     echo 'alias ll="ls -lGh $@"' >> ~/.bashrc
 
+RUN echo "export HDF4=/opt/hdf4" >> ~/.bashrc && \
+    echo "export HDF5=/opt/hdf5" >> ~/.bashrc && \
+    echo "export NETCDF=/opt/netcdf4" >> ~/.bashrc && \
+    echo "export LD_LIBRARY_PATH=${HDF4}/lib:${HDF5}/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc && \
+    echo "" >> ~/.bashrc
+
+# remove all the build cruft
+RUN rm -rf /build
+RUN rm -rf /usr/man