Merge branch 'improve_env' into 'master'

Improved environment setup

See merge request !81

.gitlab-ci.yml

@@ -239,7 +239,7 @@ jug_xl:nightly:
       when: never
     - when: on_success
   artifacts:
-      expire_in: 90 days
+      expire_in: 2 days
       paths:
         - build/${BUILD_IMAGE}.sif
   script:

containers/jug/Dockerfile.dev

@@ -131,6 +131,7 @@ RUN cd /opt/spack-environment                                           \
  && echo "Grabbing environment info"                                    \
  && spack env activate --sh -d .                                        \
         | sed "s?LD_LIBRARY_PATH=?&/lib/x86_64-linux-gnu:?"             \
+        | sed '/MANPATH/ s/;$/:;/'                                      \
     > /etc/profile.d/z10_spack_environment.sh                           \
  && cd /opt/spack-environment                                           \
  && echo -n ""                                                          \
@@ -140,17 +141,7 @@ RUN cd /opt/spack-environment                                           \
         | grep software                                                 \
         | awk '{print $2}'`                                             \
  && echo "export PODIO=${PODIO};"                                       \
-        >> /etc/profile.d/z11_jug_env.sh                                \
- && echo "export BINARY_TAG=x86_64-linux-gcc9-opt"                      \
-        >> /etc/profile.d/z11_jug_env.sh                                \
- && echo "if [ ! -z \${ATHENA_PREFIX} ]; then"                          \
-        >> /etc/profile.d/z11_jug_env.sh                                \
- && echo "export LD_LIBRARY_PATH=\$ATHENA_PREFIX/lib:\$LD_LIBRARY_PATH" \
-        >> /etc/profile.d/z11_jug_env.sh                                \
- && echo "export PATH=\$ATHENA_PREFIX/bin:\$PATH"                       \
-        >> /etc/profile.d/z11_jug_env.sh                                \
- && echo "fi"                                                           \
-        >> /etc/profile.d/z11_jug_env.sh                                \
+        >> /etc/profile.d/z10_spack_environment.sh                      \
  && cd /opt/spack-environment && spack env activate .                   \
  && echo -n ""                                                          \
  && echo "Installing additional python packages"                        \
@@ -163,6 +154,7 @@ RUN cd /opt/spack-environment                                           \
  && echo "Executing cmake patch for dd4hep 16.1"                        \                
  && sed -i "s/FIND_PACKAGE(Python/#&/" /usr/local/cmake/DD4hepBuild.cmake
 
+
 ## make sure we have the entrypoints setup correctly
 ENTRYPOINT []
 CMD ["bash", "--rcfile", "/etc/profile", "-l"]
@@ -193,16 +185,18 @@ RUN find -L /usr/local/*                                                \
 ## and links therin for more info
 RUN strip --remove-section=.note.ABI-tag /usr/local/lib/libQt5Core.so
 
-COPY eic-shell /usr/local/bin/eic-shell
-COPY entrypoint.sh /usr/local/sbin/entrypoint.sh
-
 RUN spack debug report                                                  \
       | sed "s/^/ - /" | sed "s/\* \*\*//" | sed "s/\*\*//"             \
     >> /etc/jug_info                                                    \
- && spack find --no-groups --long --variants | sed "s/^/ - /" >> /etc/jug_info            \
- && echo "#!/bin/bash" > /usr/local/bin/eic-info                        \
- && echo "cat /etc/jug_info" >> /usr/local/bin/eic-info                 \
- && chmod +x /usr/local/bin/eic-info
+ && spack find --no-groups --long --variants | sed "s/^/ - /" >> /etc/jug_info
+
+COPY eic-shell /usr/local/bin/eic-shell
+COPY eic-info /usr/local/bin/eic-info
+COPY entrypoint.sh /usr/local/sbin/entrypoint.sh
+COPY eic-env.sh /etc/eic-env.sh
+COPY profile.d/a00_cleanup.sh /etc/profile.d
+COPY profile.d/z11_jug_env.sh /etc/profile.d
+COPY singularity.d /.singularity.d
 
 ## ========================================================================================
 ## STAGE 3
@@ -219,13 +213,10 @@ RUN --mount=from=staging,target=/staging                                \
     rm -rf /usr/local                                                   \
  && cp -r /staging/opt/software /opt/software                           \
  && cp -r /staging/usr/local /usr/local                                 \
- && cp /staging/etc/profile.d/z11_jug_env.sh                            \
-       /etc/profile.d/z11_jug_env.sh                                    \
- && cat /staging/etc/profile.d/z10_spack_environment.sh                 \
-       | sed '/MANPATH/ s/;$/:;/'                                       \
-       > /etc/profile.d/z10_spack_env.sh                                \
- && cat /etc/profile.d/z1*.sh > /etc/eic-env.sh                         \
- && cp /staging/etc/jug_info /etc/jug_info
+ && cp /staging/etc/profile.d/*.sh /etc/profile.d/                      \
+ && cp /staging/etc/eic-env.sh /etc/eic-env.sh                          \
+ && cp /staging/etc/jug_info /etc/jug_info                              \
+ && cp -r /staging/.singularity.d /.singularity.d                        
 
 ARG JUG_VERSION=1
 RUN echo "" >> /etc/jug_info                                            \

containers/jug/eic-env.sh

+#!/bin/bash
+
+for i in /etc/profile.d/*.sh; do
+  source $i
+done
+
+export PS1='eic-shell> \[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
+export LS_COLORS='rs=0:di=01;34:ln=01;36:mh=00:pi=40;33'
+export GREP_OPTIONS='--color=auto'
+
+## redefine ls and less as functions, as this is something we
+## can import into our plain bash --norc --noprofile session
+## (aliases cannot be transferred to a child shell)
+function ls {
+  /bin/ls --color=auto
+}
+function less {
+  /usr/bin/less -R
+}
+MYSHELL=$(ps -p $$ | awk '{print($4);}' | tail -n1)
+## only export the functions for bash, as this does not work
+## in all shells and we only care about bash here. Note that
+## the singularity startup runs in plain sh which requires the
+## if statement
+if [ "$MYSHELL" == "bash" ]; then
+  export -f ls
+  export -f less
+fi
+unset MYSHELL

containers/jug/eic-info

+#!/bin/bash
+
+cat /etc/jug_info

containers/jug/eic-shell

 #!/usr/bin/env bash
 
-## Force environment to be clean
-export LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:/usr/local/lib64:/usr/local/lib"
-export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-[ ! -z "$CC" ] && unset CC
-[ ! -z "$CXX" ] && unset CXX
-[ ! -z "$JUPYTER_CONFIG_DIR" ] && unset JUPYTER_CONFIG_DIR
-[ ! -z "$JUPYTER_PATH" ] && unset JUPYTER_PATH
-[ ! -z "$CLING_STANDARD_PCH" ] && unset CLING_STANDARD_PCH
-[ ! -z "$USER_PATH" ] && unset USER_PATH
-[ ! -z "$SHLIB_PATH ] && unset SHLIB_PATH
-[ ! -z "$LIBPATH ] && unset $LIBPATH
-[ ! -z "$CMAKE_PREFIX_PATH" ] && unset CMAKE_PREFIX_PATH
-[ ! -z "$SOFTWARE_HOME" ] && unset SOFTWARE_HOME
-[ ! -z "$ROOTSYS" ] && unset ROOTSYS
-
-## Properly setup environment
-source /etc/eic-env.sh
-
 piped_args=()
 if [ -p /dev/stdin ]; then
   # If we want to read the input line by line
@@ -26,12 +8,15 @@ if [ -p /dev/stdin ]; then
   done
 fi
 
+## Properly setup environment
+source /etc/eic-env.sh
+
+
 ### Fire off bash
 if [ "${#piped_args[@]}" != "0" ]; then
-  echo "${#piped_args[@]}"
-  printf "%s\n" "${piped_args[@]}" | bash -s -- --norc
+  printf "%s\n" "${piped_args[@]}" | bash -s -- --norc --noprofile
 elif [ $# -gt 0 ]; then
-  exec bash --norc -c "$@"
+  exec bash -c "$@"
 else
-  exec bash --norc
+  exec bash --norc --noprofile
 fi

containers/jug/entrypoint.sh

 #!/usr/bin/env bash
 
-source /etc/profile
 ## Force environment to be clean
 source /etc/eic-env.sh
 

containers/jug/profile.d/a00_cleanup.sh

+#!/bin/bash
+
+## Force environment to be clean
+export LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:/usr/local/lib64:/usr/local/lib"
+export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+[ ! -z "$CC" ] && unset CC
+[ ! -z "$CXX" ] && unset CXX
+[ ! -z "$JUPYTER_CONFIG_DIR" ] && unset JUPYTER_CONFIG_DIR
+[ ! -z "$JUPYTER_PATH" ] && unset JUPYTER_PATH
+[ ! -z "$CLING_STANDARD_PCH" ] && unset CLING_STANDARD_PCH
+[ ! -z "$USER_PATH" ] && unset USER_PATH
+[ ! -z "$SHLIB_PATH" ] && unset SHLIB_PATH
+[ ! -z "$LIBPATH" ] && unset $LIBPATH
+[ ! -z "$CMAKE_PREFIX_PATH" ] && unset CMAKE_PREFIX_PATH
+[ ! -z "$SOFTWARE_HOME" ] && unset SOFTWARE_HOME
+[ ! -z "$ROOTSYS" ] && unset ROOTSYS

containers/jug/profile.d/z11_jug_env.sh

+#!/bin/bash
+
+export BINARY_TAG=x86_64-linux-gcc9-opt
+if [ ! -z ${ATHENA_PREFIX} ]; then
+  if [  "$LD_LIBRARY_PATH" != *"${ATHENA_PREFIX}/lib"* ]; then
+    export LD_LIBRARY_PATH=$ATHENA_PREFIX/lib:$LD_LIBRARY_PATH
+    export PATH=$ATHENA_PREFIX/bin:$PATH
+  fi
+fi

containers/jug/singularity.d/env/99-zz_jug_env.sh

+#!/bin/bash
+
+source /etc/eic-env.sh

spack.yaml

@@ -18,6 +18,7 @@ spack:
           +root7 +tmva +vc +xrootd +ssl ^mesa+opengl 
           -llvm -osmesa
     - pythia8@8303 +fastjet
+    - fastjet@3.3.3
     - hepmc3@3.2.2 +python +rootio 
     - stow@2.3.1
     - cairo@1.16.0 +fc+ft+X+pdf+gobject