From 2c6de99c069ca8c37507bbf60575189461f47006 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:10:29 +0000
Subject: [PATCH 01/19] modified the EESSI-pilot-install-software.sh

---
 EESSI-pilot-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index 026919157f..b99836d6e4 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -188,7 +188,7 @@ fi
 pr_diff=$(ls [0-9]*.diff | head -1)
 
 # use PR patch file to determine in which easystack files stuff was added
-for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eessi.*yml$'); do
+for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing'); do
 
     echo -e "Processing easystack file ${easystack_file}...\n\n"
 

From 77d124b9fd2cee2be60dc47ab7ae8ae473ec791f Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:12:25 +0000
Subject: [PATCH 02/19] modified the .github/workflows/tests_readme.yml

---
 .github/workflows/tests_readme.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests_readme.yml b/.github/workflows/tests_readme.yml
index ac906125ab..d229879f67 100644
--- a/.github/workflows/tests_readme.yml
+++ b/.github/workflows/tests_readme.yml
@@ -19,10 +19,10 @@ jobs:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
 
-        - name: verify if README.md is consistent with EESSI_PILOT_VERSION from init/eessi_defaults
+        - name: verify if README.md is consistent with EESSI_VERSION from init/eessi_defaults
           run: |
             source init/eessi_defaults
-            grep "${EESSI_PILOT_VERSION}" README.md
+            grep "${EESSI_VERSION}" README.md
 
         - name: verify if README.md is consistent with EESSI_CVMFS_REPO from init/eessi_defaults
           run: |

From 9e400259bf588c02f33ea6da2182eb583b05f1cd Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:17:50 +0000
Subject: [PATCH 03/19] modified the README.md

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index af83bb16fd..07ec32e495 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
 # Software layer
 
-The software layer of the EESSI project uses [EasyBuild](https://easybuild.readthedocs.io), [Lmod](https://lmod.readthedocs.io) and [archspec](https://archspec.readthedocs.io).
+The software layer of the EESSI project uses [EasyBuild](https://docs.easybuild.io), [Lmod](https://lmod.readthedocs.io) and [archspec](https://archspec.readthedocs.io).
 
-See also https://eessi.github.io/docs/software_layer.
+See also https://www.eessi.io/docs/software_layer .
 
 ## Pilot software stack
 
@@ -12,10 +12,10 @@ You can set up your environment by sourcing the init script:
 $ source /cvmfs/pilot.nessi.no/versions/2023.06/init/bash
 Found EESSI pilot repo @ /cvmfs/pilot.nessi.no/versions/2023.06!
 Derived subdirectory for software layer: x86_64/intel/broadwell
-Using x86_64/intel/broadwell subdirectory for software layer (HARDCODED)
+Using x86_64/intel/broadwell subdirectory for software layer
 Initializing Lmod...
 Prepending /cvmfs/pilot.nessi.no/versions/2023.06/software/x86_64/intel/broadwell/modules/all to $MODULEPATH...
-Environment set up to use EESSI pilot software stack, have fun!
+Environment set up to use EESSI (2023.06), have fun!
 [EESSI pilot 2023.06] $
 ```
 

From 1bba6721e22fbb8e5b5de417854995bf2ed285ce Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:19:23 +0000
Subject: [PATCH 04/19] modified the init/Magic_Castle/bash

---
 init/Magic_Castle/bash | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/init/Magic_Castle/bash b/init/Magic_Castle/bash
index 85e4d54241..896a6b1810 100644
--- a/init/Magic_Castle/bash
+++ b/init/Magic_Castle/bash
@@ -6,7 +6,7 @@ EESSI_SILENT=1
 source $(dirname "$BASH_SOURCE")/../eessi_environment_variables
 
 # Don't change the default prompt
-# export PS1="[EESSI pilot $EESSI_PILOT_VERSION] $ "
+# export PS1="[EESSI pilot $EESSI_VERSION] $ "
 
 # Provide a clean MODULEPATH
 export MODULEPATH_ROOT=$EESSI_MODULEPATH
@@ -36,4 +36,4 @@ else
    module reload
 fi
 
-echo "Environment set up to use EESSI pilot software stack (${EESSI_PILOT_VERSION}), have fun!"
+echo "Environment set up to use EESSI pilot software stack (${EESSI_VERSION}), have fun!"

From 586cd9c96ec5e71efd9c510c53efdaac9ec4d5b1 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:26:02 +0000
Subject: [PATCH 05/19] modified the init/bash

---
 init/Magic_Castle/{eessi_pilot_python3 => eessi_python3} | 8 ++++----
 init/bash                                                | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)
 rename init/Magic_Castle/{eessi_pilot_python3 => eessi_python3} (73%)

diff --git a/init/Magic_Castle/eessi_pilot_python3 b/init/Magic_Castle/eessi_python3
similarity index 73%
rename from init/Magic_Castle/eessi_pilot_python3
rename to init/Magic_Castle/eessi_python3
index a762ac7b84..8fd37e9c87 100755
--- a/init/Magic_Castle/eessi_pilot_python3
+++ b/init/Magic_Castle/eessi_python3
@@ -12,10 +12,10 @@ export EESSI_SILENT=1
 # for MacOS due to the use of `readlink`)
 source $(dirname "$(readlink -f "$BASH_SOURCE")")/../eessi_environment_variables
 
-eessi_pilot_python=$(ls ${EESSI_SOFTWARE_PATH}/software/Python/3*GCCcore*/bin/python | sed 1q)
-if [ -f "$eessi_pilot_python" ]; then
-  $eessi_pilot_python "$@"
+eessi_python=$(ls ${EESSI_SOFTWARE_PATH}/software/Python/3*GCCcore*/bin/python | sed 1q)
+if [ -f "$eessi_python" ]; then
+  $eessi_python "$@"
 else
-  echo "ERROR: No EESSI pilot python 3 available."
+  echo "ERROR: No EESSI python 3 available."
   false
 fi
diff --git a/init/bash b/init/bash
index ea605db0b5..ae2ff40526 100644
--- a/init/bash
+++ b/init/bash
@@ -13,7 +13,7 @@ source $(dirname "$BASH_SOURCE")/eessi_environment_variables
 # only continue if setting EESSI environment variables worked fine
 if [ $? -eq 0 ]; then
 
-    export PS1="[EESSI pilot $EESSI_PILOT_VERSION] $ "
+    export PS1="[EESSI $EESSI_PILOT_VERSION] $ "
 
     # add location of commands provided by compat layer to $PATH;
     # see https://github.com/EESSI/software-layer/issues/52
@@ -28,12 +28,12 @@ if [ $? -eq 0 ]; then
     module use $EESSI_MODULEPATH
 
     #echo >> $output
-    #echo "*** Known problems in the ${EESSI_PILOT_VERSION} pilot software stack ***" >> $output
+    #echo "*** Known problems in the ${EESSI_VERSION} pilot software stack ***" >> $output
     #echo >> $output
     #echo "1) ..." >> $output
     #echo >> $output
     #echo >> $output
 
-    echo "Environment set up to use EESSI pilot software stack, have fun!" >> $output
+    echo "Environment set up to use EESSI (${EESSI_VERSION}), have fun!"
 
 fi

From dff52749bb4cf519f770edf3fda739a3617d01a6 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:30:18 +0000
Subject: [PATCH 06/19] modified the init/eessi_defaults

---
 init/eessi_defaults | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/init/eessi_defaults b/init/eessi_defaults
index a4ccaf054e..3fdfa53976 100644
--- a/init/eessi_defaults
+++ b/init/eessi_defaults
@@ -9,4 +9,7 @@
 #
 
 export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/pilot.nessi.no}"
-export EESSI_PILOT_VERSION="${EESSI_PILOT_VERSION_OVERRIDE:=2023.06}"
+export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=2023.06}"
+# use archdetect by default, unless otherwise specified
+export EESSI_USE_ARCHDETECT="${EESSI_USE_ARCHDETECT:=1}"
+export EESSI_USE_ARCHSPEC="${EESSI_USE_ARCHSPEC:=0}"

From baf0cc783ae12d48079187e140d1eb50cca58c04 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:35:53 +0000
Subject: [PATCH 07/19] modified the init/eessi_environment_variables

---
 init/eessi_environment_variables | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 10ac1926f4..42f4b6b76a 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -15,11 +15,11 @@ function error() {
     false
 }
 
-# set up minimal environment: $EESSI_PREFIX, $EESSI_PILOT_VERSION, $EESSI_OS_TYPE, $EESSI_CPU_FAMILY, $EPREFIX
+# set up minimal environment: $EESSI_PREFIX, $EESSI_VERSION, $EESSI_OS_TYPE, $EESSI_CPU_FAMILY, $EPREFIX
 source $EESSI_INIT_DIR_PATH/minimal_eessi_env
 
 if [ -d $EESSI_PREFIX ]; then
-  echo "Found EESSI pilot repo @ $EESSI_PREFIX!" >> $output
+  echo "Found EESSI repo @ $EESSI_PREFIX!" >> $output
 
   export EESSI_EPREFIX=$EPREFIX
   if [ -d $EESSI_EPREFIX ]; then
@@ -29,11 +29,13 @@ if [ -d $EESSI_PREFIX ]; then
       # if archdetect is enabled, use internal code
       export EESSI_SOFTWARE_SUBDIR=$(${EESSI_INIT_DIR_PATH}/eessi_archdetect.sh cpupath)
       echo "archdetect says ${EESSI_SOFTWARE_SUBDIR}" >> $output
-    else
+    elif [ "$EESSI_USE_ARCHSPEC" == "1" ]; then
       # note: eessi_software_subdir_for_host.py will pick up value from $EESSI_SOFTWARE_SUBDIR_OVERRIDE if it's defined!
       export EESSI_EPREFIX_PYTHON=$EESSI_EPREFIX/usr/bin/python3
       export EESSI_SOFTWARE_SUBDIR=$($EESSI_EPREFIX_PYTHON ${EESSI_INIT_DIR_PATH}/eessi_software_subdir_for_host.py $EESSI_PREFIX)
       echo "archspec says ${EESSI_SOFTWARE_SUBDIR}" >> $output
+    else
+      error "Don't know how to detect host CPU, giving up!"
     fi
     if [ ! -z $EESSI_SOFTWARE_SUBDIR ]; then
 
@@ -82,5 +84,5 @@ if [ -d $EESSI_PREFIX ]; then
     error "Compatibility layer directory $EESSI_EPREFIX not found!"
   fi
 else
-  error "EESSI pilot repository at $EESSI_PREFIX not found!"
+  error "EESSI repository at $EESSI_PREFIX not found!"
 fi

From 76c927975566568b35dd294a5ce6a174133f4cc0 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:36:52 +0000
Subject: [PATCH 08/19] modified the init/minimal_eessi_env

---
 init/minimal_eessi_env | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/init/minimal_eessi_env b/init/minimal_eessi_env
index b7cb7c5e9e..5b3562068d 100644
--- a/init/minimal_eessi_env
+++ b/init/minimal_eessi_env
@@ -4,11 +4,11 @@
 # $BASH_SOURCE points to correct path, see also http://mywiki.wooledge.org/BashFAQ/028
 EESSI_INIT_DIR_PATH=$(dirname $(realpath $BASH_SOURCE))
 
-# set up defaults: EESSI_CVMFS_REPO, EESSI_PILOT_VERSION
+# set up defaults: EESSI_CVMFS_REPO, EESSI_VERSION
 #   script takes *_OVERRIDEs into account
 source ${EESSI_INIT_DIR_PATH}/eessi_defaults
 
-export EESSI_PREFIX=$EESSI_CVMFS_REPO/versions/$EESSI_PILOT_VERSION
+export EESSI_PREFIX=$EESSI_CVMFS_REPO/versions/$EESSI_VERSION
 
 if [[ $(uname -s) == 'Linux' ]]; then
     export EESSI_OS_TYPE='linux'

From d58436b5a491ad3ad1d3a2ecff4d97951a30f0b7 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 12:56:28 +0000
Subject: [PATCH 09/19] modified the load_easybuild_module.sh in PR376

---
 load_easybuild_module.sh | 27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/load_easybuild_module.sh b/load_easybuild_module.sh
index 4ff2a3c37c..c23caff532 100755
--- a/load_easybuild_module.sh
+++ b/load_easybuild_module.sh
@@ -71,21 +71,28 @@ else
     check_exit_code $? "${ok_msg}" "${fail_msg}"
 
     # maybe the module obtained with --install-latest-eb-release is exactly the EasyBuild version we wanted?
+    IGNORE_CACHE=''
     module avail 2>&1 | grep -i easybuild/${EB_VERSION} &> ${ml_av_easybuild_out}
     if [[ $? -eq 0 ]]; then
         echo_green ">> Module for EasyBuild v${EB_VERSION} found!"
     else
-        eb_ec=EasyBuild-${EB_VERSION}.eb
-        echo_yellow ">> Still no module for EasyBuild v${EB_VERSION}, trying with easyconfig ${eb_ec}..."
-        ${EB} --search ${eb_ec} | grep ${eb_ec} > /dev/null
+        module --ignore_cache avail 2>&1 | grep -i easybuild/${EB_VERSION} &> ${ml_av_easybuild_out}
         if [[ $? -eq 0 ]]; then
-            echo "Easyconfig ${eb_ec} found for EasyBuild v${EB_VERSION}, so installing it..."
-            ok_msg="EasyBuild v${EB_VERSION} installed, alright!"
-            fail_msg="Installing EasyBuild v${EB_VERSION}, yikes! (output: ${eb_install_out})"
-            ${EB} EasyBuild-${EB_VERSION}.eb 2>&1 | tee -a ${eb_install_out}
-            check_exit_code $? "${ok_msg}" "${fail_msg}"
+            echo_green ">> Module for EasyBuild v${EB_VERSION} found!"
+            IGNORE_CACHE='--ignore_cache'
         else
-            fatal_error "No easyconfig found for EasyBuild v${EB_VERSION}"
+            eb_ec=EasyBuild-${EB_VERSION}.eb
+            echo_yellow ">> Still no module for EasyBuild v${EB_VERSION}, trying with easyconfig ${eb_ec}..."
+            ${EB} --search ${eb_ec} | grep ${eb_ec} > /dev/null
+            if [[ $? -eq 0 ]]; then
+                echo "Easyconfig ${eb_ec} found for EasyBuild v${EB_VERSION}, so installing it..."
+                ok_msg="EasyBuild v${EB_VERSION} installed, alright!"
+                fail_msg="Installing EasyBuild v${EB_VERSION}, yikes! (output: ${eb_install_out})"
+                ${EB} EasyBuild-${EB_VERSION}.eb 2>&1 | tee -a ${eb_install_out}
+                check_exit_code $? "${ok_msg}" "${fail_msg}"
+            else
+                fatal_error "No easyconfig found for EasyBuild v${EB_VERSION}"
+            fi
         fi
     fi
 
@@ -103,7 +110,7 @@ else
 fi
 
 echo ">> Loading EasyBuild v${EB_VERSION} module..."
-module load EasyBuild/${EB_VERSION}
+module ${IGNORE_CACHE} load EasyBuild/${EB_VERSION}
 eb_show_system_info_out=${TMPDIR}/eb_show_system_info.out
 ${EB} --show-system-info > ${eb_show_system_info_out}
 if [[ $? -eq 0 ]]; then

From 465cdca7a4af629ba5f0974cc2fd7847ee20ee9f Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 13:21:25 +0000
Subject: [PATCH 10/19] added missed modifications

---
 README.md                       | 2 +-
 init/Magic_Castle/bash          | 2 +-
 init/Magic_Castle/eessi_python3 | 2 +-
 init/bash                       | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 07ec32e495..31c08db348 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@ Using x86_64/intel/broadwell subdirectory for software layer
 Initializing Lmod...
 Prepending /cvmfs/pilot.nessi.no/versions/2023.06/software/x86_64/intel/broadwell/modules/all to $MODULEPATH...
 Environment set up to use EESSI (2023.06), have fun!
-[EESSI pilot 2023.06] $
+[EESSI 2023.06] $
 ```
 
 ### Accessing EESSI via a container
diff --git a/init/Magic_Castle/bash b/init/Magic_Castle/bash
index 896a6b1810..fdeda20e3b 100644
--- a/init/Magic_Castle/bash
+++ b/init/Magic_Castle/bash
@@ -36,4 +36,4 @@ else
    module reload
 fi
 
-echo "Environment set up to use EESSI pilot software stack (${EESSI_VERSION}), have fun!"
+echo "Environment set up to use EESSI (${EESSI_VERSION}), have fun!"
diff --git a/init/Magic_Castle/eessi_python3 b/init/Magic_Castle/eessi_python3
index 8fd37e9c87..b2f7fd4d66 100755
--- a/init/Magic_Castle/eessi_python3
+++ b/init/Magic_Castle/eessi_python3
@@ -16,6 +16,6 @@ eessi_python=$(ls ${EESSI_SOFTWARE_PATH}/software/Python/3*GCCcore*/bin/python |
 if [ -f "$eessi_python" ]; then
   $eessi_python "$@"
 else
-  echo "ERROR: No EESSI python 3 available."
+  echo "ERROR: No EESSI Python 3 available."
   false
 fi
diff --git a/init/bash b/init/bash
index ae2ff40526..13bd9ffad8 100644
--- a/init/bash
+++ b/init/bash
@@ -13,7 +13,7 @@ source $(dirname "$BASH_SOURCE")/eessi_environment_variables
 # only continue if setting EESSI environment variables worked fine
 if [ $? -eq 0 ]; then
 
-    export PS1="[EESSI $EESSI_PILOT_VERSION] $ "
+    export PS1="[EESSI $EESSI_VERSION] $ "
 
     # add location of commands provided by compat layer to $PATH;
     # see https://github.com/EESSI/software-layer/issues/52

From 78de89918e159179f08c634b8c108ab10b4c525b Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 13:46:51 +0000
Subject: [PATCH 11/19] changed EB version in
 .github/workflows/tests_scripts.yml

---
 .github/workflows/tests_scripts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 74e2ebcffe..84b8c912d8 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -43,7 +43,7 @@ jobs:
         # can't test with EasyBuild versions older than v4.5.2 when using EESSI pilot 2023.06,
         # since Python in compat layer is Python 3.11.x;
         # testing with a single EasyBuild version takes a while in GitHub Actions, so stick to a single sensible version
-        for EB_VERSION in '4.6.0'; do
+        for EB_VERSION in '4.8.0'; do
           # Create script that uses load_easybuild_module.sh which we can run in compat layer environment
           # note: Be careful with single vs double quotes below!
           #       ${EB_VERSION} should be expanded, so use double quotes;

From 86ffb28209eded1e4d4a92aec5de3058edcac94b Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 11 Jan 2024 14:05:03 +0000
Subject: [PATCH 12/19] applied changes to .github/workflows/tests_scripts.yml

---
 .github/workflows/tests_scripts.yml | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 84b8c912d8..3acf52476c 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -43,7 +43,7 @@ jobs:
         # can't test with EasyBuild versions older than v4.5.2 when using EESSI pilot 2023.06,
         # since Python in compat layer is Python 3.11.x;
         # testing with a single EasyBuild version takes a while in GitHub Actions, so stick to a single sensible version
-        for EB_VERSION in '4.8.0'; do
+        for EB_VERSION in '4.6.0'; do
           # Create script that uses load_easybuild_module.sh which we can run in compat layer environment
           # note: Be careful with single vs double quotes below!
           #       ${EB_VERSION} should be expanded, so use double quotes;
@@ -79,20 +79,18 @@ jobs:
 
     - name: test install_software_layer.sh script
       run: |
-          # scripts need to be copied to /tmp,
-          # since install_software_layer.sh must be accessible from within build container
-          cp -a * /tmp/
-          cd /tmp
+          # bind current directory into container as /software-layer
+          export SINGULARITY_BIND="${PWD}:/software-layer"
           # force using x86_64/generic, to avoid triggering an installation from scratch
-          sed -i "s@./EESSI-pilot-install-software.sh@\"export EESSI_SOFTWARE_SUBDIR_OVERRIDE='x86_64/generic'; ./EESSI-pilot-install-software.sh\"@g" install_software_layer.sh
+          sed -i "s@./EESSI-install-software.sh@\"export EESSI_SOFTWARE_SUBDIR_OVERRIDE='x86_64/generic'; ./EESSI-install-software.sh\"@g" install_software_layer.sh
           ./build_container.sh run /tmp/$USER/EESSI /tmp/install_software_layer.sh
 
     - name: test create_directory_tarballs.sh script
       run: |
+          # bind current directory into container as /software-layer
+          export SINGULARITY_BIND="${PWD}:/software-layer"
           # scripts need to be copied to /tmp,
           # since create_directory_tarballs.sh must be accessible from within build container
-          cp -a * /tmp/
-          cd /tmp
-          ./build_container.sh run /tmp/$USER/EESSI /tmp/create_directory_tarballs.sh 2023.06
+          ./eessi_container.sh --mode run --verbose /software-layer/create_directory_tarballs.sh 2023.06
           # check if tarballs have been produced
           ls -l *.tar.gz

From d675a50d9a087212282443406ba93fea84909e3f Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 12 Jan 2024 07:35:12 +0000
Subject: [PATCH 13/19] applied changes to .github/workflows/tests_scripts.yml

---
 .github/workflows/tests_scripts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 3acf52476c..607e5c0744 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -83,7 +83,7 @@ jobs:
           export SINGULARITY_BIND="${PWD}:/software-layer"
           # force using x86_64/generic, to avoid triggering an installation from scratch
           sed -i "s@./EESSI-install-software.sh@\"export EESSI_SOFTWARE_SUBDIR_OVERRIDE='x86_64/generic'; ./EESSI-install-software.sh\"@g" install_software_layer.sh
-          ./build_container.sh run /tmp/$USER/EESSI /tmp/install_software_layer.sh
+          ./eessi_container.sh --mode run --verbose /software-layer/install_software_layer.sh
 
     - name: test create_directory_tarballs.sh script
       run: |

From 41f8bc646ad5d69300886f8695262f9a284f15d5 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 12 Jan 2024 10:43:58 +0000
Subject: [PATCH 14/19] modified PS1 in init/bash

---
 init/bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/bash b/init/bash
index 13bd9ffad8..f552a7d897 100644
--- a/init/bash
+++ b/init/bash
@@ -13,7 +13,7 @@ source $(dirname "$BASH_SOURCE")/eessi_environment_variables
 # only continue if setting EESSI environment variables worked fine
 if [ $? -eq 0 ]; then
 
-    export PS1="[EESSI $EESSI_VERSION] $ "
+    export PS1="{EESSI $EESSI_VERSION} $PS1"
 
     # add location of commands provided by compat layer to $PATH;
     # see https://github.com/EESSI/software-layer/issues/52

From 5e2bb244351b78dcf9bb50b817c7930103e6065d Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 12 Jan 2024 13:32:26 +0000
Subject: [PATCH 15/19] applied changes to run_in_compat_layer_env.sh

---
 run_in_compat_layer_env.sh | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/run_in_compat_layer_env.sh b/run_in_compat_layer_env.sh
index c70077bf15..f57c4d0749 100755
--- a/run_in_compat_layer_env.sh
+++ b/run_in_compat_layer_env.sh
@@ -3,25 +3,28 @@
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
 
-if [ -z $EESSI_PILOT_VERSION ]; then
-    echo "ERROR: \$EESSI_PILOT_VERSION must be set!" >&2
+if [ -z $EESSI_VERSION ]; then
+    echo "ERROR: \$EESSI_VERSION must be set!" >&2
     exit 1
 fi
-EESSI_COMPAT_LAYER_DIR="${EESSI_CVMFS_REPO}/versions/${EESSI_PILOT_VERSION}/compat/linux/$(uname -m)"
+EESSI_COMPAT_LAYER_DIR="${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/compat/linux/$(uname -m)"
 if [ ! -d ${EESSI_COMPAT_LAYER_DIR} ]; then
     echo "ERROR: ${EESSI_COMPAT_LAYER_DIR} does not exist!" >&2
     exit 1
 fi
 
 INPUT=$(echo "$@")
+if [ ! -z ${SLURM_JOB_ID} ]; then
+    INPUT="export SLURM_JOB_ID=${SLURM_JOB_ID}; ${INPUT}"
+fi
 if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
     INPUT="export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}; ${INPUT}"
 fi
 if [ ! -z ${EESSI_CVMFS_REPO_OVERRIDE} ]; then
     INPUT="export EESSI_CVMFS_REPO_OVERRIDE=${EESSI_CVMFS_REPO_OVERRIDE}; ${INPUT}"
 fi
-if [ ! -z ${EESSI_PILOT_VERSION_OVERRIDE} ]; then
-    INPUT="export EESSI_PILOT_VERSION_OVERRIDE=${EESSI_PILOT_VERSION_OVERRIDE}; ${INPUT}"
+if [ ! -z ${EESSI_VERSION_OVERRIDE} ]; then
+    INPUT="export EESSI_VERSION_OVERRIDE=${EESSI_VERSION_OVERRIDE}; ${INPUT}"
 fi
 if [ ! -z ${http_proxy} ]; then
     INPUT="export http_proxy=${http_proxy}; ${INPUT}"
@@ -30,5 +33,5 @@ if [ ! -z ${https_proxy} ]; then
     INPUT="export https_proxy=${https_proxy}; ${INPUT}"
 fi
 
-echo "Running '${INPUT}' in EESSI (${EESSI_CVMFS_REPO}) ${EESSI_PILOT_VERSION} compatibility layer environment..."
+echo "Running '${INPUT}' in EESSI (${EESSI_CVMFS_REPO}) ${EESSI_VERSION} compatibility layer environment..."
 ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< "${INPUT}"

From a4a67f5f383a57b0bf3c89cb5656603378fefb75 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 12 Jan 2024 20:14:30 +0000
Subject: [PATCH 16/19] changed to eessi instead of nessi in init/defaults for
 test

---
 init/eessi_defaults | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/init/eessi_defaults b/init/eessi_defaults
index 3fdfa53976..934d08e918 100644
--- a/init/eessi_defaults
+++ b/init/eessi_defaults
@@ -8,7 +8,8 @@
 # license: GPLv2
 #
 
-export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/pilot.nessi.no}"
+export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/software.eessi.io}"
+# export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/pilot.nessi.no}"
 export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=2023.06}"
 # use archdetect by default, unless otherwise specified
 export EESSI_USE_ARCHDETECT="${EESSI_USE_ARCHDETECT:=1}"

From 312832263fd8174dd11af047f9b5e277e068eeb5 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 15 Jan 2024 08:20:39 +0000
Subject: [PATCH 17/19] changed nessi to eessi in README.md

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 31c08db348..6c608350f6 100644
--- a/README.md
+++ b/README.md
@@ -9,12 +9,12 @@ See also https://www.eessi.io/docs/software_layer .
 You can set up your environment by sourcing the init script:
 
 ```
-$ source /cvmfs/pilot.nessi.no/versions/2023.06/init/bash
-Found EESSI pilot repo @ /cvmfs/pilot.nessi.no/versions/2023.06!
+$ source /cvmfs/software.eessi.io/versions/2023.06/init/bash
+Found EESSI repo @ /cvmfs/software.eessi.io/versions/2023.06!
 Derived subdirectory for software layer: x86_64/intel/broadwell
-Using x86_64/intel/broadwell subdirectory for software layer
+Using x86_64/intel/haswell subdirectory for software layer
 Initializing Lmod...
-Prepending /cvmfs/pilot.nessi.no/versions/2023.06/software/x86_64/intel/broadwell/modules/all to $MODULEPATH...
+Prepending /cvmfs/software.eessi.io/versions/2023.06/software/x86_64/intel/haswell/modules/all to $MODULEPATH...
 Environment set up to use EESSI (2023.06), have fun!
 [EESSI 2023.06] $
 ```

From d7b8f07b6c477b63348d75975e6be825a18d3077 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 16 Jan 2024 07:28:34 +0000
Subject: [PATCH 18/19] reverted to default to check CI workflow results

---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 6c608350f6..1de326b3f3 100644
--- a/README.md
+++ b/README.md
@@ -9,14 +9,14 @@ See also https://www.eessi.io/docs/software_layer .
 You can set up your environment by sourcing the init script:
 
 ```
-$ source /cvmfs/software.eessi.io/versions/2023.06/init/bash
-Found EESSI repo @ /cvmfs/software.eessi.io/versions/2023.06!
+$ source /cvmfs/pilot.nessi.no/versions/2023.06/init/bash
+Found EESSI pilot repo @ /cvmfs/pilot.nessi.no/versions/2023.06!
 Derived subdirectory for software layer: x86_64/intel/broadwell
 Using x86_64/intel/haswell subdirectory for software layer
 Initializing Lmod...
-Prepending /cvmfs/software.eessi.io/versions/2023.06/software/x86_64/intel/haswell/modules/all to $MODULEPATH...
-Environment set up to use EESSI (2023.06), have fun!
-[EESSI 2023.06] $
+Prepending /cvmfs/pilot.nessi.no/versions/2023.06/software/x86_64/intel/broadwell/modules/all to $MODULEPATH...
+Environment set up to use EESSI pilot software stack, have fun!
+[EESSI pilot 2023.06] $
 ```
 
 ### Accessing EESSI via a container

From 25966471f0261aaccecbb3249e62a4f669357215 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 16 Jan 2024 07:33:14 +0000
Subject: [PATCH 19/19] reverted init/eessi_defaults to default to check CI
 workflow results

---
 init/eessi_defaults | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/init/eessi_defaults b/init/eessi_defaults
index 934d08e918..3fdfa53976 100644
--- a/init/eessi_defaults
+++ b/init/eessi_defaults
@@ -8,8 +8,7 @@
 # license: GPLv2
 #
 
-export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/software.eessi.io}"
-# export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/pilot.nessi.no}"
+export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/pilot.nessi.no}"
 export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=2023.06}"
 # use archdetect by default, unless otherwise specified
 export EESSI_USE_ARCHDETECT="${EESSI_USE_ARCHDETECT:=1}"