Change back to installing conda into /usr to work around change in NE…

…RSC docker runtime environment.

external/.dockerignore

@@ -3,3 +3,4 @@ conf
 README*
 tools
 Docker*
+install*

external/tools/Dockerfile-intel.in

@@ -17,8 +17,8 @@ RUN apt-get update \
 # Set up locales, to workaround a pip bug
 
 RUN locale-gen en_US.UTF-8
-ENV LANG en_US.UTF-8 
-ENV LANGUAGE en_US:en 
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
 ENV LC_ALL en_US.UTF-8
 
 # We install everything directly into /usr so that we do
@@ -47,6 +47,13 @@ ENV PYTHONUSERBASE "/tmp"
 
 @pip_pkgs@
 
+# The conda TCL packages overwrite the system-installed regex.h. So
+# now we force reinstall of the package that provides that
+
+RUN apt-get update \
+ && apt-get install -y --reinstall libc6-dev \
+ && rm -fr /var/lib/apt/lists/*
+
 # Install Intel tools to /opt/intel. We assume that the build context already
 # contains a copy of the Intel tools, and we just copy it into the image.
 
@@ -66,8 +73,8 @@ RUN cp -a /opt/intel/mkl/lib/intel64/* /usr/lib/
 RUN mkdir ./rules
 ADD rules/patch_* ./rules/
 
-RUN mkdir -p /usr/lib/python3.6/site-packages
-ENV PYTHONPATH /usr/lib/python3.6/site-packages
+#RUN mkdir -p /usr/lib/python3.6/site-packages
+#ENV PYTHONPATH /usr/lib/python3.6/site-packages
 
 # Install MPICH 3.2 which is compatible with the external
 # Cray MPICH which is prepended to LD_LIBRARY_PATH as part
@@ -183,4 +190,3 @@ ENV HOME /home/toast
 
 ENTRYPOINT ["/bin/bash", "-c"]
 CMD ["/bin/bash"]
-

external/tools/Dockerfile.in

@@ -17,8 +17,8 @@ RUN apt-get update \
 # Set up locales, to workaround a pip bug
 
 RUN locale-gen en_US.UTF-8
-ENV LANG en_US.UTF-8 
-ENV LANGUAGE en_US:en 
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
 ENV LC_ALL en_US.UTF-8
 
 # We install everything directly into /usr so that we do
@@ -47,13 +47,20 @@ ENV PYTHONUSERBASE "/tmp"
 
 @pip_pkgs@
 
+# The conda TCL packages overwrite the system-installed regex.h. So
+# now we force reinstall of the package that provides that
+
+RUN apt-get update \
+ && apt-get install -y --reinstall libc6-dev \
+ && rm -fr /var/lib/apt/lists/*
+
 # Copy all patch files to current working directory
 
 RUN mkdir ./rules
 ADD rules/patch_* ./rules/
 
-RUN mkdir -p /usr/lib/python3.6/site-packages
-ENV PYTHONPATH /usr/lib/python3.6/site-packages
+#RUN mkdir -p /usr/lib/python3.6/site-packages
+#ENV PYTHONPATH /usr/lib/python3.6/site-packages
 
 # Install MPICH 3.2 which is compatible with the external
 # Cray MPICH which is prepended to LD_LIBRARY_PATH as part
@@ -149,4 +156,3 @@ RUN python -c "import matplotlib.font_manager as fm; f = fm.FontManager"
 
 ENTRYPOINT ["/bin/bash", "-c"]
 CMD ["/bin/bash"]
-

external/tools/apply_conf.sh

@@ -14,7 +14,7 @@ module_dir="${moddir}/toast-deps"
 
 if [ "x${docker}" = "xyes" ]; then
  compiled_prefix="/usr"
- conda_prefix="/usr/local"
+ conda_prefix="/usr"
 fi
 
 # Create list of substitutions
@@ -27,7 +27,7 @@ while IFS='' read -r line || [[ -n "${line}" ]]; do
  if [ "${comment}" != "#" ]; then
 
  check=$(echo "${line}" | sed -e "s#.*=.*#=#")
- 
+
  if [ "x${check}" = "x=" ]; then
  # get the variable and its value
  var=$(echo ${line} | sed -e "s#\([^=]*\)=.*#\1#" | awk '{print $1}')
@@ -52,6 +52,3 @@ rm -f "${outfile}"
 while IFS='' read -r line || [[ -n "${line}" ]]; do
  echo "${line}" | eval sed ${confsub} >> "${outfile}"
 done < "${infile}"
-
-
-