From 1bbe56f6c4fd628944d0d8402938c0221f307f75 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 7 Jun 2021 22:50:49 +0200
Subject: [PATCH 01/35] add step that changes gentoo overlay from using rsync
 to git

---
 .../compatibility_layer/tasks/add_overlay.yml | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 28a81364..e6f69337 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -58,6 +58,28 @@
         selectattr('eclass-overrides', 'equalto', True) | map(attribute='name') | join(' ')
       }}
 
+- name: Use git instead of rsync for the Gentoo overlay
+  copy:
+    dest: "{{ gentoo_prefix_path }}/etc/portage/repos.conf/gentoo.conf"
+    mode: "0644"
+    content: |
+      [DEFAULT]
+      main-repo = gentoo
+      sync-git-pull-extra-opts = --quiet
+      
+      [gentoo]
+      priority  = 1
+      location  = {{ gentoo_prefix_path }}/var/db/repos/gentoo
+      sync-uri  = https://github.com/gentoo/gentoo.git
+      sync-type = git
+      auto-sync = Yes
+      clone-depth = 1
+
+- name: Remove the old contents of the Gentoo overlay
+  file:
+    state: absent
+    path: "{{ gentoo_prefix_path }}/var/db/repos/gentoo"
+
 - name: Sync the repositories
   portage:
     sync: 'yes'

From 9baff727e677a1fab73d88312c76f48223d97109 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 13:58:57 +0200
Subject: [PATCH 02/35] use latest version of gentoo prefix bootstrap script

---
 bootstrap-prefix.sh | 36 +++++++++++++++++++++++++-----------
 1 file changed, 25 insertions(+), 11 deletions(-)

diff --git a/bootstrap-prefix.sh b/bootstrap-prefix.sh
index 26ea17fd..d7204e6a 100755
--- a/bootstrap-prefix.sh
+++ b/bootstrap-prefix.sh
@@ -282,7 +282,7 @@ configure_toolchain() {
 			;;
 	esac
 
-	return
+	return 0
 }
 
 bootstrap_setup() {
@@ -450,6 +450,12 @@ bootstrap_setup() {
 	ACCEPT_KEYWORDS="~${ARCH}-linux"
 	EOF
 
+	# bug #788613 avoid gcc-11 during stage 2/3 prior sync/emerge -e
+	is-rap && cat >> "${ROOT}"/etc/portage/make.profile/package.mask <<-EOF
+	# during bootstrap mask, bug #788613
+	>=sys-devel/gcc-11
+	EOF
+
 	# Use package.use to disable in the portage tree to be shared between
 	# stage2 and stage3. The hack will be undone during tree sync in stage3.
 	cat >> "${ROOT}"/etc/portage/make.profile/package.use <<-EOF
@@ -1355,8 +1361,8 @@ bootstrap_libressl() {
 
 bootstrap_stage_host_gentoo() {
 	if ! is-rap ; then
-		einfo "Shortcut only supports prefix-standalone, but we are bootstrapping"
-		einfo "prefix-rpath. Do nothing."
+		einfo "Shortcut only supports prefix-standalone, but we "
+		einfo "are bootstrapping prefix-rpath.  Do nothing."
 		return 0
 	fi
 	
@@ -1447,6 +1453,7 @@ bootstrap_stage1() {
 	# we're working with now, bug #650284
 	[[ -x ${ROOT}/tmp/usr/bin/bash ]] \
 		|| (bootstrap_bash) || return 1
+
 	# Some host tools need to be wrapped to be useful for us.
 	# We put them in tmp/usr/local/bin, to not accidentally
 	# be identified as stage1-installed like in bug #615410.
@@ -1475,10 +1482,14 @@ bootstrap_stage1() {
 				# We need to direct the system gcc to find the system binutils.
 				cat >> "${ROOT}"/tmp/usr/local/bin/gcc <<-EOF
 					#! /bin/sh
-					PATH="${STAGE1_PATH}" export PATH
-					exec "\${0##*/}" "\$@"
+					PATH="${ORIGINAL_PATH}" export PATH
+					exec "$(type -P gcc)" "\$@"
+				EOF
+				cat >> "${ROOT}"/tmp/usr/local/bin/g++ <<-EOF
+					#! /bin/sh
+					PATH="${ORIGINAL_PATH}" export PATH
+					exec "$(type -P g++)" "\$@"
 				EOF
-				cp "${ROOT}"/tmp/usr/local/bin/g{cc,++}
 				chmod 755 "${ROOT}"/tmp/usr/local/bin/g{cc,++}
 			fi
 			;;
@@ -1905,7 +1916,11 @@ bootstrap_stage3() {
 	}
 
 	# pre_emerge_pkgs relies on stage 2 portage.
-	pre_emerge_pkgs() { is-rap && without_stack_emerge_pkgs "$@" || with_stack_emerge_pkgs "$@"; }
+	pre_emerge_pkgs() {
+		is-rap \
+			&& without_stack_emerge_pkgs "$@" \
+			|| with_stack_emerge_pkgs "$@"
+	}
 
 	# Some packages fail to properly depend on sys-apps/texinfo.
 	# We don't really need that package, so we fake it instead,
@@ -2768,7 +2783,6 @@ EOF
 		# location seems ok
 		break
 	done
-	export STAGE1_PATH=${PATH}
 	export PATH="$EPREFIX/usr/bin:$EPREFIX/bin:$EPREFIX/tmp/usr/bin:$EPREFIX/tmp/bin:$EPREFIX/tmp/usr/local/bin:${PATH}"
 
 	cat << EOF
@@ -3078,9 +3092,6 @@ case ${CHOST} in
 	powerpc-*darwin*)
 		DARWIN_USE_GCC=1  # must use GCC, Clang is impossible
 		;;
-#	arm64-*darwin*)
-#		DARWIN_USE_GCC=0  # cannot use GCC yet (needs silicon support)
-#		;;
 	*-darwin*)
 		# normalise value of DARWIN_USE_GCC
 		case ${DARWIN_USE_GCC} in
@@ -3116,6 +3127,9 @@ case ${CHOST}:${LC_ALL}:${LANG} in
 	;;
 esac
 
+# save original path, need this before interactive, #788334
+ORIGINAL_PATH="${PATH}"
+
 # Just guessing a prefix is kind of scary.  Hence, to make it a bit less
 # scary, we force the user to give the prefix location here.  This also
 # makes the script a bit less dangerous as it will die when just run to

From 68c88d71cf601daf86c9092d7de321e58a34d85c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 14:12:02 +0200
Subject: [PATCH 03/35] bump version to 2021.06

---
 ansible/playbooks/roles/compatibility_layer/defaults/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index 4b32a311..b92e595b 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -1,6 +1,6 @@
 # Defaults file for the compatibility layer role.
 ---
-eessi_version: "2021.03"
+eessi_version: "2021.06"
 
 custom_overlays:
   - name: eessi

From 122022d3f3d6af13504409323e0f73741adf72fb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 14:16:06 +0200
Subject: [PATCH 04/35] change snapshot host url, bump snapshot version

---
 ansible/playbooks/roles/compatibility_layer/defaults/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index b92e595b..922029b7 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -17,8 +17,8 @@ gentoo_prefix_path: /cvmfs/{{ cvmfs_repository }}/{{ eessi_version }}/compat/{{
 
 # How to build the prefix
 prefix_required_space: 15 GB
-prefix_snapshot_url: http://cvmfs-s0.eessi-hpc.org/snapshots
-prefix_snapshot_version: 20210322
+prefix_snapshot_url: https://eessi-gentoo-snapshot.s3-eu-west-1.amazonaws.com
+prefix_snapshot_version: 20210607
 prefix_python_targets: python3_8
 prefix_user_defined_trusted_dirs:
   - "/cvmfs/{{ cvmfs_repository }}/host_injections/{{ eessi_version }}/compat/{{ eessi_host_os }}/{{ eessi_host_arch }}/lib"

From a1c31829ff171f96eb8311f35eeb951d4554f56c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 17:13:52 +0200
Subject: [PATCH 05/35] add step for generating post-sync hooks

---
 .../roles/compatibility_layer/tasks/add_overlay.yml  | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index e6f69337..363a1a4d 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -75,6 +75,18 @@
       auto-sync = Yes
       clone-depth = 1
 
+- name: Add post-sync hooks for Gentoo overlay
+  template:
+    src: "{{ item }}.j2"
+    dest: "{{ gentoo_prefix_path }}/etc/portage/repo.postsync.d/{{ item }}"
+  with_items:
+    - sync_gentoo_cache
+    - sync_gentoo_dtd
+    - sync_gentoo_glsa
+    - sync_gentoo_news
+    - sync_gentoo_projects_xml
+    - sync_overlay_cache
+
 - name: Remove the old contents of the Gentoo overlay
   file:
     state: absent

From 6f2ff40cb00e028508cedd92880731f27c1dc85c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 17:15:41 +0200
Subject: [PATCH 06/35] extra step for creating postsync dir

---
 .../roles/compatibility_layer/tasks/add_overlay.yml         | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 363a1a4d..7ae73129 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -75,6 +75,12 @@
       auto-sync = Yes
       clone-depth = 1
 
+- name: Create repo.postsync.d directory
+  file:
+    path: "{{ gentoo_prefix_path }}/etc/portage/repo.postsync.d"
+    state: directory
+    mode: '0755'
+
 - name: Add post-sync hooks for Gentoo overlay
   template:
     src: "{{ item }}.j2"

From bf7c37c9f698a7a8686d6b6f64c58b6ed1101cd7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 17:16:40 +0200
Subject: [PATCH 07/35] rename step

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 7ae73129..cae02a86 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -93,7 +93,7 @@
     - sync_gentoo_projects_xml
     - sync_overlay_cache
 
-- name: Remove the old contents of the Gentoo overlay
+- name: Remove the old Gentoo overlay directory
   file:
     state: absent
     path: "{{ gentoo_prefix_path }}/var/db/repos/gentoo"

From 66482ca5fdaaabebbd74a3c6ab3cf702f6b63ffd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 17:23:23 +0200
Subject: [PATCH 08/35] add mode for template task

---
 .../roles/compatibility_layer/tasks/add_overlay.yml        | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index cae02a86..14fdb6ea 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -66,7 +66,7 @@
       [DEFAULT]
       main-repo = gentoo
       sync-git-pull-extra-opts = --quiet
-      
+
       [gentoo]
       priority  = 1
       location  = {{ gentoo_prefix_path }}/var/db/repos/gentoo
@@ -85,13 +85,14 @@
   template:
     src: "{{ item }}.j2"
     dest: "{{ gentoo_prefix_path }}/etc/portage/repo.postsync.d/{{ item }}"
+    mode: 0755
   with_items:
     - sync_gentoo_cache
     - sync_gentoo_dtd
     - sync_gentoo_glsa
     - sync_gentoo_news
-    - sync_gentoo_projects_xml
-    - sync_overlay_cache
+    #- sync_gentoo_projects_xml
+    #- sync_overlay_cache
 
 - name: Remove the old Gentoo overlay directory
   file:

From fd52eb74ebc5bb4d456fcbf8ac9c2243254396ba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 17:33:24 +0200
Subject: [PATCH 09/35] also generate metadata for custom overlays

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 14fdb6ea..534be4d7 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -91,8 +91,8 @@
     - sync_gentoo_dtd
     - sync_gentoo_glsa
     - sync_gentoo_news
-    #- sync_gentoo_projects_xml
-    #- sync_overlay_cache
+    - sync_gentoo_projects_xml
+    - sync_overlay_cache
 
 - name: Remove the old Gentoo overlay directory
   file:

From d98d6ed6d9f22db0a639c62f49aa1e2f3211b7bc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 17:36:46 +0200
Subject: [PATCH 10/35] add postsync scripts

---
 .../templates/sync_gentoo_cache.j2            | 34 +++++++++++++++++++
 .../templates/sync_gentoo_dtd.j2              | 17 ++++++++++
 .../templates/sync_gentoo_glsa.j2             | 17 ++++++++++
 .../templates/sync_gentoo_news.j2             | 17 ++++++++++
 .../templates/sync_overlay_cache.j2           | 14 ++++++++
 5 files changed, 99 insertions(+)
 create mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_cache.j2
 create mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_dtd.j2
 create mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_glsa.j2
 create mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_news.j2
 create mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_overlay_cache.j2

diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_cache.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_cache.j2
new file mode 100755
index 00000000..f1f572d2
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_cache.j2
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
+
+# Number of jobs for egencache, default is number or processors.
+parallel_jobs="$(nproc)"
+
+if [[ -f ${repository_path}/metadata/timestamp.x ]]; then
+	portage_current_timestamp=$(cut -f 1 -d " " "${repository_path}/metadata/timestamp.x" )
+else
+	portage_current_timestamp=0
+fi
+
+ebegin "Fetching metadata timestamp for ${repository_name}"
+rsync -aq rsync://rsync.gentoo.org/gentoo-portage/metadata/timestamp.x "${repository_path}"/metadata/timestamp.x
+eend $?
+portage_new_timestamp=$(cut -f 1 -d " " "${repository_path}/metadata/timestamp.x" )
+
+if [[ ${portage_current_timestamp} -lt ${portage_new_timestamp} ]]; then
+	ebegin "Fetching pre-generated metadata cache for ${repository_name}"
+	rsync -aq rsync://rsync.gentoo.org/gentoo-portage/metadata/md5-cache/ "${repository_path}"/metadata/md5-cache/
+	eend $?
+else
+	einfo "Metadata cache for ${repository_name} already recent, no need to fetch it :-)"
+fi
+
+ebegin "Updating metadata cache for ${repository_name}"
+egencache --jobs="${parallel_jobs}" --repo="${repository_name}" --update --update-use-local-desc
+eend $?
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_dtd.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_dtd.j2
new file mode 100755
index 00000000..81d8ff0f
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_dtd.j2
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
+
+DTDDIR="${repository_path}"/metadata/dtd
+ebegin "Updating DTDs"
+if [[ -e ${DTDDIR} ]]; then
+	git -C "${DTDDIR}" pull -q --ff-only
+else
+	git clone -q https://anongit.gentoo.org/git/data/dtd.git "${DTDDIR}"
+fi
+eend "$?"
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_glsa.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_glsa.j2
new file mode 100755
index 00000000..220e3aea
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_glsa.j2
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
+
+GLSADIR="${repository_path}"/metadata/glsa
+ebegin "Updating GLSAs"
+if [[ -e ${GLSADIR} ]]; then
+	git -C "${GLSADIR}" pull -q --ff-only
+else
+	git clone -q https://anongit.gentoo.org/git/data/glsa.git "${GLSADIR}"
+fi
+eend "$?"
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_news.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_news.j2
new file mode 100755
index 00000000..dbab56ca
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_news.j2
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
+
+NEWSDIR="${repository_path}"/metadata/news
+ebegin "Updating news items"
+if [[ -e ${NEWSDIR} ]]; then
+	git -C "${NEWSDIR}" pull -q --ff-only
+else
+	git clone -q https://anongit.gentoo.org/git/data/gentoo-news.git "${NEWSDIR}"
+fi
+eend $? "Try to remove ${NEWSDIR}"
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_overlay_cache.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_overlay_cache.j2
new file mode 100755
index 00000000..e373c810
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/templates/sync_overlay_cache.j2
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+repository_name="${1}"
+
+[[ ${repository_name} == "gentoo" ]] && exit 0
+
+source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
+
+# Number of jobs for egencache, default is number or processors.
+parallel_jobs="$(nproc)"
+
+ebegin "Updating metadata cache for ${repository_name}"
+egencache --jobs="${parallel_jobs}" --repo="${repository_name}" --update --update-use-local-desc
+eend $?

From e433003bd98541b677f049ca1452c167f84335fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 17:38:50 +0200
Subject: [PATCH 11/35] add other script, which we won't use for now

---
 .../templates/sync_gentoo_projects_xml.j2            | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_projects_xml.j2

diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_projects_xml.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_projects_xml.j2
new file mode 100644
index 00000000..07067e5b
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_projects_xml.j2
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
+
+ebegin "Updating projects.xml"
+wget -q -P "${repository_path}"/metadata/ -N https://api.gentoo.org/metastructure/projects.xml
+eend $?

From 2f1b85e1339058438ef78f49ad9fa221e2f0a31a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 9 Jun 2021 17:39:25 +0200
Subject: [PATCH 12/35] dont run sync_gentoo_projects_xml for now

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 534be4d7..aabc0f90 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -91,8 +91,8 @@
     - sync_gentoo_dtd
     - sync_gentoo_glsa
     - sync_gentoo_news
-    - sync_gentoo_projects_xml
     - sync_overlay_cache
+    #- sync_gentoo_projects_xml
 
 - name: Remove the old Gentoo overlay directory
   file:

From 1a3448867e0c580cb20a48770aa62722cf3c581b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 10 Jun 2021 00:12:46 +0200
Subject: [PATCH 13/35] bump python to 3.9

---
 ansible/playbooks/roles/compatibility_layer/defaults/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index 922029b7..4b0528c6 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -19,7 +19,7 @@ gentoo_prefix_path: /cvmfs/{{ cvmfs_repository }}/{{ eessi_version }}/compat/{{
 prefix_required_space: 15 GB
 prefix_snapshot_url: https://eessi-gentoo-snapshot.s3-eu-west-1.amazonaws.com
 prefix_snapshot_version: 20210607
-prefix_python_targets: python3_8
+prefix_python_targets: python3_9
 prefix_user_defined_trusted_dirs:
   - "/cvmfs/{{ cvmfs_repository }}/host_injections/{{ eessi_version }}/compat/{{ eessi_host_os }}/{{ eessi_host_arch }}/lib"
 prefix_singularity_command: "singularity run -B {{ gentoo_prefix_path }}:{{ gentoo_prefix_path }}"

From bd8ca8ed20cafcd8a56be444f8ec80310a9b8c25 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 10 Jun 2021 09:19:35 +0200
Subject: [PATCH 14/35] move glibc steps to a separate task

---
 .../tasks/install_packages.yml                | 22 ----------
 .../roles/compatibility_layer/tasks/main.yml  |  2 +
 .../tasks/set_glibc_trusted_dirs.yml          | 44 +++++++++++++++++++
 3 files changed, 46 insertions(+), 22 deletions(-)
 create mode 100644 ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/install_packages.yml b/ansible/playbooks/roles/compatibility_layer/tasks/install_packages.yml
index 78a5c8b6..7d245297 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/install_packages.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/install_packages.yml
@@ -1,27 +1,5 @@
 # Install a specified list of sets and packages.
 ---
-- name: Find all strings in libc library
-  command: "strings {{ gentoo_prefix_path }}/usr/lib64/libc.a"
-  register: libc_strings
-  when: eessi_host_os == "linux"
-
-- name: Find user defined trusted dirs in libc strings output
-  set_fact: match='{{ libc_strings.stdout | regex_search("\n" + item + "/?\n") | default('', True) | string | length>0 }}'
-  with_items: "{{ prefix_user_defined_trusted_dirs }}"
-  register: trusted_dirs_in_libc
-
-- name: (Re)install glibc with the user-defined-trusted-dirs option
-  portage:
-    package: sys-libs/glibc
-    noreplace: no
-    oneshot: yes
-  become: no
-  environment:
-    EXTRA_EMAKE: "user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
-  when:
-    - eessi_host_os == "linux"
-    - trusted_dirs_in_libc.results | selectattr('ansible_facts.match', 'equalto', False) | list | length>0
-
 - name: Install package set {{ package_sets }}
   portage:
     package: "@{{ item }}"
diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/main.yml b/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
index 402c9d11..0fc0e4b8 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
@@ -27,6 +27,8 @@
         environment:
           PYTHON_TARGETS: "{{ prefix_python_targets }}"
 
+  - include_tasks: set_glibc_trusted_dirs.yml
+
   - include_tasks: install_packages.yml
 
   - include_tasks: create_host_symlinks.yml
diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
new file mode 100644
index 00000000..a2ee3361
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
@@ -0,0 +1,44 @@
+# Make sure that glibc is always compiled with a user-defined-trusted-dirs option
+---
+- name: Find all strings in libc library
+  command: "strings {{ gentoo_prefix_path }}/usr/lib64/libc.a"
+  register: libc_strings
+  when: eessi_host_os == "linux"
+
+- name: Find user defined trusted dirs in libc strings output
+  set_fact: match='{{ libc_strings.stdout | regex_search("\n" + item + "/?\n") | default('', True) | string | length>0 }}'
+  with_items: "{{ prefix_user_defined_trusted_dirs }}"
+  register: trusted_dirs_in_libc
+
+- name: (Re)install glibc with the user-defined-trusted-dirs option
+  portage:
+    package: sys-libs/glibc
+    noreplace: no
+    oneshot: yes
+  become: no
+  environment:
+    EXTRA_EMAKE: "user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
+  when:
+    - eessi_host_os == "linux"
+    - trusted_dirs_in_libc.results | selectattr('ansible_facts.match', 'equalto', False) | list | length>0
+
+- name: Create portage env directory
+  file:
+    path: "{{ gentoo_prefix_path }}/etc/portage/env"
+    state: directory
+    mode: '0755'
+
+- name: Add env file for glibc to make sure the user-defined-trusted-dirs is always used
+  copy:
+    dest: "{{ gentoo_prefix_path }}/etc/portage/env/glibc-user-defined-trusted-dirs.conf"
+    content: |
+      EXTRA_EMAKE: "user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
+
+- name: Add glibc env file to package.env
+  lineinfile:
+    path: "{{ gentoo_prefix_path }}/etc/portage/package.env"
+    create: yes
+    mode: 0644
+    line: sys-libs/glibc glibc-user-defined-trusted-dirs.conf
+    state: present
+

From 0d2ef192c6cc1eb8bbfb5c1902b5a0a658a79fec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 10 Jun 2021 09:23:57 +0200
Subject: [PATCH 15/35] add mode for new file

---
 .../roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
index a2ee3361..8d6de02e 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
@@ -31,6 +31,7 @@
 - name: Add env file for glibc to make sure the user-defined-trusted-dirs is always used
   copy:
     dest: "{{ gentoo_prefix_path }}/etc/portage/env/glibc-user-defined-trusted-dirs.conf"
+    mode: 0644
     content: |
       EXTRA_EMAKE: "user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
 

From abe38e4659abc4cfde5d64f5a22481fc063331c5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 10 Jun 2021 09:27:20 +0200
Subject: [PATCH 16/35] remove quotes

---
 .../roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
index 8d6de02e..6dc16917 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
@@ -26,7 +26,7 @@
   file:
     path: "{{ gentoo_prefix_path }}/etc/portage/env"
     state: directory
-    mode: '0755'
+    mode: 0755
 
 - name: Add env file for glibc to make sure the user-defined-trusted-dirs is always used
   copy:

From c88d68a9a93e3c342cff9e8b1b95527c9bc87081 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 10 Jun 2021 09:39:01 +0200
Subject: [PATCH 17/35] use copy instead of template for post-sync scripts

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index aabc0f90..e3d05bc8 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -82,8 +82,8 @@
     mode: '0755'
 
 - name: Add post-sync hooks for Gentoo overlay
-  template:
-    src: "{{ item }}.j2"
+  copy:
+    src: "{{ item }}"
     dest: "{{ gentoo_prefix_path }}/etc/portage/repo.postsync.d/{{ item }}"
     mode: 0755
   with_items:

From e2e694ef52b2449517fe4b8ebcff4a82a15e0759 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 10 Jun 2021 09:42:37 +0200
Subject: [PATCH 18/35] use portageq to find EPREFIX, remove .j2 extensions

---
 .../files/sync_gentoo_cache                   | 34 +++++++++++++++++++
 .../compatibility_layer/files/sync_gentoo_dtd | 17 ++++++++++
 .../files/sync_gentoo_glsa                    | 17 ++++++++++
 .../files/sync_gentoo_news                    | 17 ++++++++++
 .../files/sync_gentoo_projects_xml            | 12 +++++++
 .../files/sync_overlay_cache                  | 14 ++++++++
 6 files changed, 111 insertions(+)
 create mode 100755 ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_cache
 create mode 100755 ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_dtd
 create mode 100755 ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_glsa
 create mode 100755 ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_news
 create mode 100644 ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_projects_xml
 create mode 100755 ansible/playbooks/roles/compatibility_layer/files/sync_overlay_cache

diff --git a/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_cache b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_cache
new file mode 100755
index 00000000..65b4f709
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_cache
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source $(portageq envvar EPREFIX)/lib/gentoo/functions.sh
+
+# Number of jobs for egencache, default is number or processors.
+parallel_jobs="$(nproc)"
+
+if [[ -f ${repository_path}/metadata/timestamp.x ]]; then
+	portage_current_timestamp=$(cut -f 1 -d " " "${repository_path}/metadata/timestamp.x" )
+else
+	portage_current_timestamp=0
+fi
+
+ebegin "Fetching metadata timestamp for ${repository_name}"
+rsync -aq rsync://rsync.gentoo.org/gentoo-portage/metadata/timestamp.x "${repository_path}"/metadata/timestamp.x
+eend $?
+portage_new_timestamp=$(cut -f 1 -d " " "${repository_path}/metadata/timestamp.x" )
+
+if [[ ${portage_current_timestamp} -lt ${portage_new_timestamp} ]]; then
+	ebegin "Fetching pre-generated metadata cache for ${repository_name}"
+	rsync -aq rsync://rsync.gentoo.org/gentoo-portage/metadata/md5-cache/ "${repository_path}"/metadata/md5-cache/
+	eend $?
+else
+	einfo "Metadata cache for ${repository_name} already recent, no need to fetch it :-)"
+fi
+
+ebegin "Updating metadata cache for ${repository_name}"
+egencache --jobs="${parallel_jobs}" --repo="${repository_name}" --update --update-use-local-desc
+eend $?
diff --git a/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_dtd b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_dtd
new file mode 100755
index 00000000..c12f6c3b
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_dtd
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source $(portageq envvar EPREFIX)/lib/gentoo/functions.sh
+
+DTDDIR="${repository_path}"/metadata/dtd
+ebegin "Updating DTDs"
+if [[ -e ${DTDDIR} ]]; then
+	git -C "${DTDDIR}" pull -q --ff-only
+else
+	git clone -q https://anongit.gentoo.org/git/data/dtd.git "${DTDDIR}"
+fi
+eend "$?"
diff --git a/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_glsa b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_glsa
new file mode 100755
index 00000000..e2a2face
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_glsa
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source $(portageq envvar EPREFIX)/lib/gentoo/functions.sh
+
+GLSADIR="${repository_path}"/metadata/glsa
+ebegin "Updating GLSAs"
+if [[ -e ${GLSADIR} ]]; then
+	git -C "${GLSADIR}" pull -q --ff-only
+else
+	git clone -q https://anongit.gentoo.org/git/data/glsa.git "${GLSADIR}"
+fi
+eend "$?"
diff --git a/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_news b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_news
new file mode 100755
index 00000000..92c69a63
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_news
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source $(portageq envvar EPREFIX)/lib/gentoo/functions.sh
+
+NEWSDIR="${repository_path}"/metadata/news
+ebegin "Updating news items"
+if [[ -e ${NEWSDIR} ]]; then
+	git -C "${NEWSDIR}" pull -q --ff-only
+else
+	git clone -q https://anongit.gentoo.org/git/data/gentoo-news.git "${NEWSDIR}"
+fi
+eend $? "Try to remove ${NEWSDIR}"
diff --git a/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_projects_xml b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_projects_xml
new file mode 100644
index 00000000..fe1ac0e9
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/files/sync_gentoo_projects_xml
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+repository_name="${1}"
+repository_path="${3}"
+
+[[ ${repository_name} == "gentoo" ]] || exit 0
+
+source $(portageq envvar EPREFIX)/lib/gentoo/functions.sh
+
+ebegin "Updating projects.xml"
+wget -q -P "${repository_path}"/metadata/ -N https://api.gentoo.org/metastructure/projects.xml
+eend $?
diff --git a/ansible/playbooks/roles/compatibility_layer/files/sync_overlay_cache b/ansible/playbooks/roles/compatibility_layer/files/sync_overlay_cache
new file mode 100755
index 00000000..e7f5ecf0
--- /dev/null
+++ b/ansible/playbooks/roles/compatibility_layer/files/sync_overlay_cache
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+repository_name="${1}"
+
+[[ ${repository_name} == "gentoo" ]] && exit 0
+
+source $(portageq envvar EPREFIX)/lib/gentoo/functions.sh
+
+# Number of jobs for egencache, default is number or processors.
+parallel_jobs="$(nproc)"
+
+ebegin "Updating metadata cache for ${repository_name}"
+egencache --jobs="${parallel_jobs}" --repo="${repository_name}" --update --update-use-local-desc
+eend $?

From 4ace650a2861cd81e086aa83784ea32d50ebfc16 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 10 Jun 2021 09:53:29 +0200
Subject: [PATCH 19/35] fix syntax error in env file

---
 .../roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
index 6dc16917..baaf36bb 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
@@ -17,7 +17,7 @@
     oneshot: yes
   become: no
   environment:
-    EXTRA_EMAKE: "user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
+    EXTRA_EMAKE="user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
   when:
     - eessi_host_os == "linux"
     - trusted_dirs_in_libc.results | selectattr('ansible_facts.match', 'equalto', False) | list | length>0

From cd5d3784eb7dd3fb535a2f2979260948a2b3a928 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 10 Jun 2021 10:35:33 +0200
Subject: [PATCH 20/35] fixed the wrong line...

---
 .../compatibility_layer/tasks/set_glibc_trusted_dirs.yml      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
index baaf36bb..0650d73d 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/set_glibc_trusted_dirs.yml
@@ -17,7 +17,7 @@
     oneshot: yes
   become: no
   environment:
-    EXTRA_EMAKE="user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
+    EXTRA_EMAKE: "user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
   when:
     - eessi_host_os == "linux"
     - trusted_dirs_in_libc.results | selectattr('ansible_facts.match', 'equalto', False) | list | length>0
@@ -33,7 +33,7 @@
     dest: "{{ gentoo_prefix_path }}/etc/portage/env/glibc-user-defined-trusted-dirs.conf"
     mode: 0644
     content: |
-      EXTRA_EMAKE: "user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
+      EXTRA_EMAKE="user-defined-trusted-dirs={{ prefix_user_defined_trusted_dirs | join(':') }}"
 
 - name: Add glibc env file to package.env
   lineinfile:

From 60e4addf678fdb6d597dd663fc04676fa30b296e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 11 Jun 2021 15:06:57 +0200
Subject: [PATCH 21/35] add test to verify that the glibc env file is used

---
 test/compat_layer.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/test/compat_layer.py b/test/compat_layer.py
index 132f2009..2e2fb745 100644
--- a/test/compat_layer.py
+++ b/test/compat_layer.py
@@ -182,3 +182,28 @@ def __init__(self):
             sn.assert_eq(self.exit_code, 0),
             sn.assert_found(f'\n/{self.symlink_to_host}\n', self.stdout),
         ])
+
+@rfm.simple_test
+class GlibcEnvFileTest(RunInGentooPrefixTest):
+    def __init__(self):
+        # the glibc env file was added in 2021.06
+        self.skip_if(self.eessi_version == '2021.03')
+
+        super().__init__()
+        self.descr = 'Verify that the env file for sys-libs/glibc was created and is picked up by emerge.'
+        self.command = 'equery has --package glibc EXTRA_EMAKE'
+
+        trusted_dir = os.path.join(
+            self.eessi_repo_dir,
+            'host_injections',
+            self.eessi_version,
+            'compat',
+            self.eessi_os,
+            self.eessi_arch,
+            'lib'
+        )
+
+        self.sanity_patterns = sn.assert_found(
+            f'user-defined-trusted-dirs={trusted_dir}',
+            self.stdout
+        )

From c01cf2d321c01c99bccfc3f7bca701affb5c183a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 11 Jun 2021 16:26:31 +0200
Subject: [PATCH 22/35] add reframe test for validating that gentoo overlay
 uses git

---
 test/compat_layer.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/test/compat_layer.py b/test/compat_layer.py
index 132f2009..17e0f500 100644
--- a/test/compat_layer.py
+++ b/test/compat_layer.py
@@ -182,3 +182,21 @@ def __init__(self):
             sn.assert_eq(self.exit_code, 0),
             sn.assert_found(f'\n/{self.symlink_to_host}\n', self.stdout),
         ])
+
+
+@rfm.simple_test
+class GentooOverlayGitTest(RunInGentooPrefixTest):
+    def __init__(self):
+        # the switch to git was made in pilot version 2021.06
+        self.skip_if(self.eessi_version == '2021.03')
+
+        super().__init__()
+        self.descr = 'Verify that the Gentoo overlay is synced using git.'
+        self.command = f'emerge --info'
+
+        gentoo_git_repo_info = '''gentoo
+    location: /cvmfs/pilot.eessi-hpc.org/2021.06/compat/linux/x86_64/var/db/repos/gentoo
+    sync-type: git
+    sync-uri: https://github.com/gentoo/gentoo.git'''
+
+        self.sanity_patterns = sn.assert_found(gentoo_git_repo_info, self.stdout)

From 7a08570eb8bb54ea4e12b64545ba033dc02b70a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 11 Jun 2021 18:03:19 +0200
Subject: [PATCH 23/35] fix hardcoded path

---
 test/compat_layer.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/test/compat_layer.py b/test/compat_layer.py
index 17e0f500..dcd6f461 100644
--- a/test/compat_layer.py
+++ b/test/compat_layer.py
@@ -194,9 +194,10 @@ def __init__(self):
         self.descr = 'Verify that the Gentoo overlay is synced using git.'
         self.command = f'emerge --info'
 
+        gentoo_repo_dir = os.path.join(self.compat_dir, 'var', 'db', 'repos', 'gentoo')
         gentoo_git_repo_info = '''gentoo
-    location: /cvmfs/pilot.eessi-hpc.org/2021.06/compat/linux/x86_64/var/db/repos/gentoo
+    location: %s
     sync-type: git
-    sync-uri: https://github.com/gentoo/gentoo.git'''
+    sync-uri: https://github.com/gentoo/gentoo.git''' % gentoo_repo_dir
 
         self.sanity_patterns = sn.assert_found(gentoo_git_repo_info, self.stdout)

From b2fb15bb4a5d8e0bacbc309314927afdab38ae2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 15 Jun 2021 09:53:21 +0200
Subject: [PATCH 24/35] try without setting python targets

---
 ansible/playbooks/roles/compatibility_layer/defaults/main.yml | 4 ++--
 ansible/playbooks/roles/compatibility_layer/tasks/main.yml    | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index 4b0528c6..b5b3ecdc 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -19,7 +19,7 @@ gentoo_prefix_path: /cvmfs/{{ cvmfs_repository }}/{{ eessi_version }}/compat/{{
 prefix_required_space: 15 GB
 prefix_snapshot_url: https://eessi-gentoo-snapshot.s3-eu-west-1.amazonaws.com
 prefix_snapshot_version: 20210607
-prefix_python_targets: python3_9
+#prefix_python_targets: python3_9
 prefix_user_defined_trusted_dirs:
   - "/cvmfs/{{ cvmfs_repository }}/host_injections/{{ eessi_version }}/compat/{{ eessi_host_os }}/{{ eessi_host_arch }}/lib"
 prefix_singularity_command: "singularity run -B {{ gentoo_prefix_path }}:{{ gentoo_prefix_path }}"
@@ -27,7 +27,7 @@ prefix_source: "docker://eessi/bootstrap-prefix:centos8-{{ eessi_host_arch }}"
 prefix_source_options: "{{ gentoo_prefix_path }} noninteractive"
 prefix_install: >-
     SINGULARITYENV_USE_CPU_CORES={{ ansible_processor_vcpus }}
-    SINGULARITYENV_PYTHON_TARGETS="{{ prefix_python_targets }}"
+    #SINGULARITYENV_PYTHON_TARGETS="{{ prefix_python_targets }}"
     SINGULARITYENV_CUSTOM_SNAPSHOT_URL="{{ prefix_snapshot_url }}"
     SINGULARITYENV_CUSTOM_SNAPSHOT_VERSION="{{ prefix_snapshot_version }}"
     {{ prefix_singularity_command }} {{ prefix_source }} {{ prefix_source_options }}
diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/main.yml b/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
index 402c9d11..1e7ad13b 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
@@ -24,8 +24,8 @@
     args:
       apply:
         become: False
-        environment:
-          PYTHON_TARGETS: "{{ prefix_python_targets }}"
+        #environment:
+        #  PYTHON_TARGETS: "{{ prefix_python_targets }}"
 
   - include_tasks: install_packages.yml
 

From a6eefe99d71615cecf6afd5f0a27224721384fd1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 17 Jun 2021 13:28:56 +0200
Subject: [PATCH 25/35] Remove commented python targets lines

---
 ansible/playbooks/roles/compatibility_layer/defaults/main.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index b5b3ecdc..af6f3bea 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -19,7 +19,6 @@ gentoo_prefix_path: /cvmfs/{{ cvmfs_repository }}/{{ eessi_version }}/compat/{{
 prefix_required_space: 15 GB
 prefix_snapshot_url: https://eessi-gentoo-snapshot.s3-eu-west-1.amazonaws.com
 prefix_snapshot_version: 20210607
-#prefix_python_targets: python3_9
 prefix_user_defined_trusted_dirs:
   - "/cvmfs/{{ cvmfs_repository }}/host_injections/{{ eessi_version }}/compat/{{ eessi_host_os }}/{{ eessi_host_arch }}/lib"
 prefix_singularity_command: "singularity run -B {{ gentoo_prefix_path }}:{{ gentoo_prefix_path }}"
@@ -27,7 +26,6 @@ prefix_source: "docker://eessi/bootstrap-prefix:centos8-{{ eessi_host_arch }}"
 prefix_source_options: "{{ gentoo_prefix_path }} noninteractive"
 prefix_install: >-
     SINGULARITYENV_USE_CPU_CORES={{ ansible_processor_vcpus }}
-    #SINGULARITYENV_PYTHON_TARGETS="{{ prefix_python_targets }}"
     SINGULARITYENV_CUSTOM_SNAPSHOT_URL="{{ prefix_snapshot_url }}"
     SINGULARITYENV_CUSTOM_SNAPSHOT_VERSION="{{ prefix_snapshot_version }}"
     {{ prefix_singularity_command }} {{ prefix_source }} {{ prefix_source_options }}

From ecdc20d2bda30d3a940d872c94f8753edeade285 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 17 Jun 2021 13:29:25 +0200
Subject: [PATCH 26/35] Remove commented python targets env var

---
 ansible/playbooks/roles/compatibility_layer/tasks/main.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/main.yml b/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
index 1e7ad13b..616f1f4a 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/main.yml
@@ -24,8 +24,6 @@
     args:
       apply:
         become: False
-        #environment:
-        #  PYTHON_TARGETS: "{{ prefix_python_targets }}"
 
   - include_tasks: install_packages.yml
 

From 0e64d56a24580233942c58fe55c6dccbe3cdc7ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sun, 20 Jun 2021 14:21:59 +0200
Subject: [PATCH 27/35] remove old versions of scripts in template dir

---
 .../templates/sync_gentoo_cache.j2            | 34 -------------------
 .../templates/sync_gentoo_dtd.j2              | 17 ----------
 .../templates/sync_gentoo_glsa.j2             | 17 ----------
 .../templates/sync_gentoo_news.j2             | 17 ----------
 .../templates/sync_gentoo_projects_xml.j2     | 12 -------
 .../templates/sync_overlay_cache.j2           | 14 --------
 6 files changed, 111 deletions(-)
 delete mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_cache.j2
 delete mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_dtd.j2
 delete mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_glsa.j2
 delete mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_news.j2
 delete mode 100644 ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_projects_xml.j2
 delete mode 100755 ansible/playbooks/roles/compatibility_layer/templates/sync_overlay_cache.j2

diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_cache.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_cache.j2
deleted file mode 100755
index f1f572d2..00000000
--- a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_cache.j2
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-repository_name="${1}"
-repository_path="${3}"
-
-[[ ${repository_name} == "gentoo" ]] || exit 0
-
-source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
-
-# Number of jobs for egencache, default is number or processors.
-parallel_jobs="$(nproc)"
-
-if [[ -f ${repository_path}/metadata/timestamp.x ]]; then
-	portage_current_timestamp=$(cut -f 1 -d " " "${repository_path}/metadata/timestamp.x" )
-else
-	portage_current_timestamp=0
-fi
-
-ebegin "Fetching metadata timestamp for ${repository_name}"
-rsync -aq rsync://rsync.gentoo.org/gentoo-portage/metadata/timestamp.x "${repository_path}"/metadata/timestamp.x
-eend $?
-portage_new_timestamp=$(cut -f 1 -d " " "${repository_path}/metadata/timestamp.x" )
-
-if [[ ${portage_current_timestamp} -lt ${portage_new_timestamp} ]]; then
-	ebegin "Fetching pre-generated metadata cache for ${repository_name}"
-	rsync -aq rsync://rsync.gentoo.org/gentoo-portage/metadata/md5-cache/ "${repository_path}"/metadata/md5-cache/
-	eend $?
-else
-	einfo "Metadata cache for ${repository_name} already recent, no need to fetch it :-)"
-fi
-
-ebegin "Updating metadata cache for ${repository_name}"
-egencache --jobs="${parallel_jobs}" --repo="${repository_name}" --update --update-use-local-desc
-eend $?
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_dtd.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_dtd.j2
deleted file mode 100755
index 81d8ff0f..00000000
--- a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_dtd.j2
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-repository_name="${1}"
-repository_path="${3}"
-
-[[ ${repository_name} == "gentoo" ]] || exit 0
-
-source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
-
-DTDDIR="${repository_path}"/metadata/dtd
-ebegin "Updating DTDs"
-if [[ -e ${DTDDIR} ]]; then
-	git -C "${DTDDIR}" pull -q --ff-only
-else
-	git clone -q https://anongit.gentoo.org/git/data/dtd.git "${DTDDIR}"
-fi
-eend "$?"
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_glsa.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_glsa.j2
deleted file mode 100755
index 220e3aea..00000000
--- a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_glsa.j2
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-repository_name="${1}"
-repository_path="${3}"
-
-[[ ${repository_name} == "gentoo" ]] || exit 0
-
-source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
-
-GLSADIR="${repository_path}"/metadata/glsa
-ebegin "Updating GLSAs"
-if [[ -e ${GLSADIR} ]]; then
-	git -C "${GLSADIR}" pull -q --ff-only
-else
-	git clone -q https://anongit.gentoo.org/git/data/glsa.git "${GLSADIR}"
-fi
-eend "$?"
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_news.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_news.j2
deleted file mode 100755
index dbab56ca..00000000
--- a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_news.j2
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-repository_name="${1}"
-repository_path="${3}"
-
-[[ ${repository_name} == "gentoo" ]] || exit 0
-
-source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
-
-NEWSDIR="${repository_path}"/metadata/news
-ebegin "Updating news items"
-if [[ -e ${NEWSDIR} ]]; then
-	git -C "${NEWSDIR}" pull -q --ff-only
-else
-	git clone -q https://anongit.gentoo.org/git/data/gentoo-news.git "${NEWSDIR}"
-fi
-eend $? "Try to remove ${NEWSDIR}"
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_projects_xml.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_projects_xml.j2
deleted file mode 100644
index 07067e5b..00000000
--- a/ansible/playbooks/roles/compatibility_layer/templates/sync_gentoo_projects_xml.j2
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash
-
-repository_name="${1}"
-repository_path="${3}"
-
-[[ ${repository_name} == "gentoo" ]] || exit 0
-
-source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
-
-ebegin "Updating projects.xml"
-wget -q -P "${repository_path}"/metadata/ -N https://api.gentoo.org/metastructure/projects.xml
-eend $?
diff --git a/ansible/playbooks/roles/compatibility_layer/templates/sync_overlay_cache.j2 b/ansible/playbooks/roles/compatibility_layer/templates/sync_overlay_cache.j2
deleted file mode 100755
index e373c810..00000000
--- a/ansible/playbooks/roles/compatibility_layer/templates/sync_overlay_cache.j2
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/bash
-
-repository_name="${1}"
-
-[[ ${repository_name} == "gentoo" ]] && exit 0
-
-source {{ gentoo_prefix_path }}/lib/gentoo/functions.sh
-
-# Number of jobs for egencache, default is number or processors.
-parallel_jobs="$(nproc)"
-
-ebegin "Updating metadata cache for ${repository_name}"
-egencache --jobs="${parallel_jobs}" --repo="${repository_name}" --update --update-use-local-desc
-eend $?

From 2c5b58f14bc2cff6ecd2f62ee734aba6356e9e1f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sun, 20 Jun 2021 14:23:07 +0200
Subject: [PATCH 28/35] remove commented sync_gentoo_project_xml

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml    | 1 -
 1 file changed, 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index e3d05bc8..523782bd 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -92,7 +92,6 @@
     - sync_gentoo_glsa
     - sync_gentoo_news
     - sync_overlay_cache
-    #- sync_gentoo_projects_xml
 
 - name: Remove the old Gentoo overlay directory
   file:

From 2c1a333eb4f3780c0c7286ed5970559c3e5c2d29 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 21 Jun 2021 13:12:33 +0200
Subject: [PATCH 29/35] Add a system update step for existing Prefix

---
 .../roles/compatibility_layer/tasks/add_overlay.yml   | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 523782bd..0d22db1c 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -13,12 +13,21 @@
     path: /etc/group
     regexp: portage
     line: portage::250:portage
-
+    
 - name: Install equery command (dependency for the portage module)
   command:
     cmd: emerge gentoolkit
     creates: "{{ gentoo_prefix_path }}/usr/bin/equery"
 
+- name: Update system set if we are running in an existing Prefix installation
+  portage:
+    changed_use: yes
+    deep: yes
+    package: system
+    update: yes
+    
+  when: not startprefix.stat.exists
+
 - name: Create repos directory
   file:
     path: "{{ gentoo_prefix_path }}/etc/portage/repos.conf"

From 397ac8d8658058e36835b0056534e763b1e7478a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 21 Jun 2021 13:16:17 +0200
Subject: [PATCH 30/35] remove trailing spaces

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml  | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 0d22db1c..4e58a827 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -13,7 +13,7 @@
     path: /etc/group
     regexp: portage
     line: portage::250:portage
-    
+
 - name: Install equery command (dependency for the portage module)
   command:
     cmd: emerge gentoolkit
@@ -25,7 +25,6 @@
     deep: yes
     package: system
     update: yes
-    
   when: not startprefix.stat.exists
 
 - name: Create repos directory

From 9db7b4ba55e34955fe2883e40283465e1f05dd90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 21 Jun 2021 14:10:00 +0200
Subject: [PATCH 31/35] remove wrong 'not' operator

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 4e58a827..3339d979 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -25,7 +25,7 @@
     deep: yes
     package: system
     update: yes
-  when: not startprefix.stat.exists
+  when: startprefix.stat.exists
 
 - name: Create repos directory
   file:

From 973081fb887c4e1ae0580aae49c8713188c00854 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 21 Jun 2021 14:36:01 +0200
Subject: [PATCH 32/35] update world instead of system

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 3339d979..239dc860 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -19,11 +19,11 @@
     cmd: emerge gentoolkit
     creates: "{{ gentoo_prefix_path }}/usr/bin/equery"
 
-- name: Update system set if we are running in an existing Prefix installation
+- name: Update world set if we are running in an existing Prefix installation
   portage:
     changed_use: yes
     deep: yes
-    package: system
+    package: "@world"
     update: yes
   when: startprefix.stat.exists
 

From 3044dff1676188b7c8212e6edf36bca26cbe6ad4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 21 Jun 2021 15:00:23 +0200
Subject: [PATCH 33/35] verbose output for ansible-playbook

---
 .github/actions/install_compatibility_layer/entrypoint.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/install_compatibility_layer/entrypoint.sh b/.github/actions/install_compatibility_layer/entrypoint.sh
index aca33c96..b4904ddd 100755
--- a/.github/actions/install_compatibility_layer/entrypoint.sh
+++ b/.github/actions/install_compatibility_layer/entrypoint.sh
@@ -5,7 +5,7 @@ cat << EOF > hosts
 127.0.0.1 eessi_host_arch=$(uname -m) eessi_host_os=linux
 EOF
 
-ansible-playbook --connection=local --inventory=hosts -e ansible_python_interpreter=python3 -e gentoo_prefix_path=$1 ${GITHUB_WORKSPACE}/ansible/playbooks/install.yml
+ansible-playbook -v --connection=local --inventory=hosts -e ansible_python_interpreter=python3 -e gentoo_prefix_path=$1 ${GITHUB_WORKSPACE}/ansible/playbooks/install.yml
 
 # A successful installation should at least have Lmod and archspec,
 # so let's  check if we can use them.

From cdeb9e72c1c9d8878d72e9cc521f46d33a6f2321 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 21 Jun 2021 15:18:21 +0200
Subject: [PATCH 34/35] Update of system set should go after the sync...

---
 .../compatibility_layer/tasks/add_overlay.yml    | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 239dc860..3733afae 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -19,14 +19,6 @@
     cmd: emerge gentoolkit
     creates: "{{ gentoo_prefix_path }}/usr/bin/equery"
 
-- name: Update world set if we are running in an existing Prefix installation
-  portage:
-    changed_use: yes
-    deep: yes
-    package: "@world"
-    update: yes
-  when: startprefix.stat.exists
-
 - name: Create repos directory
   file:
     path: "{{ gentoo_prefix_path }}/etc/portage/repos.conf"
@@ -125,3 +117,11 @@
     force: yes
   with_items:
     "{{ find_configs.results | rejectattr('files', 'equalto', []) | map(attribute='files') | list }}"
+
+- name: Update system set if we are running in an existing Prefix installation
+  portage:
+    changed_use: yes
+    deep: yes
+    package: "@system"
+    update: yes
+  when: startprefix.stat.exists

From 254a1b82232e573d58fa50ef4e116d0b4b3b1879 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 21 Jun 2021 15:52:59 +0200
Subject: [PATCH 35/35] update world instead of system

---
 .../playbooks/roles/compatibility_layer/tasks/add_overlay.yml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
index 3733afae..0454e1aa 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/add_overlay.yml
@@ -122,6 +122,6 @@
   portage:
     changed_use: yes
     deep: yes
-    package: "@system"
+    package: "@world"
     update: yes
   when: startprefix.stat.exists