From d769f1a808fc291674f656ea12cc54b55ddcdc03 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 18 Nov 2021 14:35:53 +0100
Subject: [PATCH 01/22] merge latest upstream changes

---
 bootstrap-prefix.sh | 125 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 98 insertions(+), 27 deletions(-)
 mode change 100755 => 100644 bootstrap-prefix.sh

diff --git a/bootstrap-prefix.sh b/bootstrap-prefix.sh
old mode 100755
new mode 100644
index d7204e6a..9a6aaa04
--- a/bootstrap-prefix.sh
+++ b/bootstrap-prefix.sh
@@ -105,7 +105,7 @@ efetch() {
 
 configure_cflags() {
 	export CPPFLAGS="-I${ROOT}/tmp/usr/include"
-	
+
 	case ${CHOST} in
 		*-darwin*)
 			export LDFLAGS="-Wl,-search_paths_first -L${ROOT}/tmp/usr/lib"
@@ -203,9 +203,9 @@ configure_toolchain() {
 					;;
 				*"Apple clang version "*|*"Apple LLVM version "*)
 					# recent binutils-apple are hard to build (C++11
-					# features, and cmake buildsystem) so avoid going
+					# features, and cmake build system) so avoid going
 					# there, the system ld is good enough to bring us to
-					# stage3, after which system set will take care of
+					# stage3, after which the @system set will take care of
 					# the rest
 					linker=sys-devel/native-cctools
 					;;
@@ -319,8 +319,15 @@ bootstrap_setup() {
 			echo "CONFIG_SHELL=\"${ROOT}/bin/bash\""
 			echo "DISTDIR=\"${DISTDIR:-${ROOT}/var/cache/distfiles}\""
 			if is-rap ; then
-				echo "# sandbox does not work well on Prefix, bug 490246"
+				echo "# sandbox does not work well on Prefix, bug #490246"
 				echo 'FEATURES="${FEATURES} -usersandbox -sandbox"'
+				# bug #759424
+				[[ -n ${STABLE_PREFIX} ]] && \
+					echo 'ACCEPT_KEYWORDS="${ARCH} -~${ARCH}"'
+			else
+				echo "# last mirror is for Prefix specific distfiles, you"
+				echo "# might experience fetch failures if you remove it"
+				echo "GENTOO_MIRRORS=\"${GENTOO_MIRRORS} ${DISTFILES_PFX}\""
 			fi
 			if [[ ${FS_INSENSITIVE} == 1 ]] ; then
 				echo
@@ -337,10 +344,24 @@ bootstrap_setup() {
 	fi
 
 	if is-rap ; then
-		[[ -f ${ROOT}/etc/passwd ]] || getent passwd > "${ROOT}"/etc/passwd || \
-			ln -sf {,"${ROOT}"}/etc/passwd
-		[[ -f ${ROOT}/etc/group ]] || getent group > "${ROOT}"/etc/group || \
-			ln -sf {,"${ROOT}"}/etc/group
+		if [[ ! -f ${ROOT}/etc/passwd ]]; then
+			if grep -q $(id -un) /etc/passwd; then
+				ln -sf {,"${ROOT}"}/etc/passwd
+			else
+				getent passwd > "${ROOT}"/etc/passwd
+				# add user if it's not in /etc/passwd, bug #766417
+				getent passwd $(id -un) >> "${ROOT}"/etc/passwd
+			fi
+		fi
+		if [[ ! -f ${ROOT}/etc/group ]]; then
+			if grep -q $(id -gn) /etc/group; then
+				ln -sf {,"${ROOT}"}/etc/group
+			else
+				getent group > "${ROOT}"/etc/group
+				# add group if it's not in /etc/group, bug #766417
+				getent group $(id -gn) >> "${ROOT}"/etc/group
+			fi
+		fi
 		[[ -f ${ROOT}/etc/resolv.conf ]] || ln -s {,"${ROOT}"}/etc/resolv.conf
 		[[ -f ${ROOT}/etc/hosts ]] || cp {,"${ROOT}"}/etc/hosts
 		local profile_linux=default/linux/ARCH/17.0/prefix/$(profile-kernel)
@@ -361,15 +382,31 @@ bootstrap_setup() {
 			rev=${CHOST##*darwin}
 			profile="prefix/darwin/macos/10.$((rev - 4))/x64"
 			;;
-		x86_64-apple-darwin2[0123456789])
+		x86_64-apple-darwin20)
 			# Big Sur is 11.0
 			rev=${CHOST##*darwin}
 			profile="prefix/darwin/macos/11.$((rev - 20))/x64"
 			;;
-		arm64-apple-darwin2[0123456789])
+		x86_64-apple-darwin2[123456789])
+			# Monterey is 12.0
+			rev=${CHOST##*darwin}
+			profile="prefix/darwin/macos/12.$((rev - 21))/x64"
+			;;
+		arm64-apple-darwin20)
 			rev=${CHOST##*darwin}
 			profile="prefix/darwin/macos/11.$((rev - 20))/arm64"
 			;;
+		# TODO: Come up with something better for macOS 11+
+		x86_64-apple-darwin2[123456789])
+			# Monterey is 12.0
+			rev=${CHOST##*darwin}
+			profile="prefix/darwin/macos/12.$((rev - 21))/x64"
+			;;
+		arm64-apple-darwin2[123456789])
+			# Monterey is 12.0
+			rev=${CHOST##*darwin}
+			profile="prefix/darwin/macos/12.$((rev - 21))/arm64"
+			;;
 		i*86-pc-linux-gnu)
 			profile=${profile_linux/ARCH/x86}
 			;;
@@ -410,7 +447,7 @@ bootstrap_setup() {
 		x86_64-pc-cygwin*)
 			profile="prefix/windows/cygwin/x64"
 			;;
-		*)	
+		*)
 			eerror "UNKNOWN ARCH: You need to set up a make.profile symlink to a"
 			eerror "profile in ${PORTDIR} for your CHOST ${CHOST}"
 			exit 1
@@ -440,7 +477,7 @@ bootstrap_setup() {
 	profile=${PROFILE_BASE:-prefix}/${profile#prefix/}${PROFILE_VARIANT:+/${PROFILE_VARIANT}}
 	if [[ -n ${profile} && ! -e ${ROOT}/etc/portage/make.profile ]] ; then
 		local fullprofile="${PORTDIR}/profiles/${profile}"
-		
+
 		ln -s "${fullprofile}" "${ROOT}"/etc/portage/make.profile
 		einfo "Your profile is set to ${fullprofile}."
 	fi
@@ -540,7 +577,7 @@ do_tree() {
 bootstrap_tree() {
 	# RAP uses the latest gentoo main repo snapshot to bootstrap.
 	is-rap && LATEST_TREE_YES=1
-	local PV="20210213"
+	local PV="20211105"
 	if is-rap ; then
 		do_tree "${CUSTOM_SNAPSHOT_URL:-$SNAPSHOT_URL}" portage-${CUSTOM_SNAPSHOT_VERSION:-latest}.tar.bz2
 	else
@@ -607,12 +644,12 @@ bootstrap_portage() {
 	# STABLE_PV that is known to work. Intended for power users only.
 	## It is critical that STABLE_PV is the lastest (non-masked) version that is
 	## included in the snapshot for bootstrap_tree.
-	STABLE_PV="3.0.12.0.2"
-	[[ ${TESTING_PV} == latest ]] && TESTING_PV="3.0.12.0.2"
+	STABLE_PV="3.0.21"
+	[[ ${TESTING_PV} == latest ]] && TESTING_PV="3.0.21"
 	PV="${TESTING_PV:-${STABLE_PV}}"
 	A=prefix-portage-${PV}.tar.bz2
 	einfo "Bootstrapping ${A%.tar.*}"
-		
+
 	efetch ${DISTFILES_URL}/${A} || return 1
 
 	einfo "Unpacking ${A%.tar.*}"
@@ -661,7 +698,7 @@ bootstrap_portage() {
 	cd "${ROOT}"
 	rm -Rf ${ptmp} >& /dev/null
 
-	# Some people will skip the tree() step and hence var/log is not created 
+	# Some people will skip the tree() step and hence var/log is not created
 	# As such, portage complains..
 	mkdir -p "${ROOT}"/tmp/var/log
 
@@ -942,9 +979,9 @@ bootstrap_gnu() {
 	einfo "${A%.tar.*} successfully bootstrapped"
 }
 
-PYTHONMAJMIN=3.8   # keep this number in line with PV below for stage1,2
+PYTHONMAJMIN=3.9   # keep this number in line with PV below for stage1,2
 bootstrap_python() {
-	PV=3.8.6
+	PV=3.9.6
 	A=Python-${PV}.tar.xz
 	einfo "Bootstrapping ${A%.tar.*}"
 
@@ -1010,8 +1047,8 @@ bootstrap_python() {
 			-e 's/KQUEUE/KQUEUE_DISABLED/' \
 			configure
 		# fixup thread id detection
-		efetch "http://dev.gentoo.org/~grobian/distfiles/python-3.8.6-darwin9.patch"
-		patch -p1 < "${DISTDIR}"/python-3.8.6-darwin9.patch
+		efetch "https://dev.gentoo.org/~sam/distfiles/dev-lang/python/python-3.9.6-darwin9_pthreadid.patch"
+		patch -p1 < "${DISTDIR}"/python-3.9.6-darwin9_pthreadid.patch
 		;;
 	(arm64-*-darwin*)
 		# Teach Python a new trick (arm64)
@@ -1153,7 +1190,7 @@ bootstrap_cmake_core() {
 	emake install || return 1
 
 	# we need sysroot crap to build cmake itself, but it makes trouble
-	# lateron, so kill it in the installed version
+	# later on, so kill it in the installed version
 	ver=${A%-*} ; ver=${ver%.*}
 	sed -i -e '/cmake_gnu_set_sysroot_flag/d' \
 		"${ROOT}"/tmp/usr/share/${ver}/Modules/Platform/Apple-GNU-*.cmake || die
@@ -1365,7 +1402,7 @@ bootstrap_stage_host_gentoo() {
 		einfo "are bootstrapping prefix-rpath.  Do nothing."
 		return 0
 	fi
-	
+
 	if [[ ! -L ${ROOT}/tmp ]] ; then
 		if [[ -e ${ROOT}/tmp ]] ; then
 			einfo "${ROOT}/tmp exists and is not a symlink to ${HOST_GENTOO_EROOT}"
@@ -1602,6 +1639,7 @@ do_emerge_pkgs() {
 			-python
 			-qmanifest -qtegrity
 			-readline
+			-sanitize
 			bootstrap
 			clang
 			internal-glib
@@ -2002,6 +2040,7 @@ bootstrap_stage3() {
 		pkgs=(
 			sys-apps/attr
 			sys-libs/libcap
+			sys-libs/libxcrypt
 		)
 		BOOTSTRAP_RAP=yes \
 		USE="${USE} -pam" \
@@ -2041,7 +2080,7 @@ bootstrap_stage3() {
 	# in addition, avoid collisions
 	rm -Rf "${ROOT}"/tmp/usr/lib/python${PYTHONMAJMIN}/site-packages/clang
 
-	# try to get ourself out of the mudd, bug #575324
+	# try to get ourself out of the mud, bug #575324
 	EXTRA_ECONF="--disable-compiler-version-checks $(rapx '--disable-lto --disable-bootstrap')" \
 	GCC_MAKE_TARGET=$(rapx all) \
 	MYCMAKEARGS="-DCMAKE_USE_SYSTEM_LIBRARY_LIBUV=OFF" \
@@ -2129,10 +2168,10 @@ bootstrap_stage3() {
 	# Avoid glib compiling for Cocoa libs if it finds them, since we're
 	# still with an old llvm that may not understand the system headers
 	# very well on Darwin (-DGNUSTEP_BASE_VERSION hack)
-	einfo "running emerge -u system"
-	estatus "stage3: emerge -u system"
+	einfo "running emerge -uDNav system"
+	estatus "stage3: emerge -uDNav system"
 	CPPFLAGS="-DGNUSTEP_BASE_VERSION" \
-	CFLAGS= CXXFLAGS= emerge --color n -u -v system || return 1
+	CFLAGS= CXXFLAGS= emerge --color n -uDNav system || return 1
 
 	# remove anything that we don't need (compilers most likely)
 	einfo "running emerge --depclean"
@@ -2694,6 +2733,38 @@ EOF
 		esac
 	fi
 
+	# The experimental support for Stable Prefix.
+	# When expanding this to other CHOSTs, don't forget to update
+	# make.conf generation in bootstrap_setup().
+	# TODO: Consider at some point removing the ~ARCH override from
+	# profiles/features/prefix/standalone/make.defaults.
+	# https://bugs.gentoo.org/759424
+	if is-rap ; then
+		if [[ "${CHOST}" == x86_64-pc-linux-gnu ]]; then
+			cat <<EOF
+
+Normally I can only give you ~amd64 packages, and you would be exposed
+to all the bugs of the newest untested software.  Well, ok, sometimes
+it also has new features, but who needs those.  But as you are a VIP
+customer who uses Linux on x86_64, I have a one-time offer for you!
+I can limit your Prefix to use only packages keyworded for stable amd64
+by default.  Of course, you can still enable testing ~amd64 for
+the packages you want, when the need arises.
+EOF
+			[[ ${TODO} == 'noninteractive' ]] && ans=yes ||
+			read -p "  Do you want to use stable Prefix? [Yn] " ans
+			case "${ans}" in
+				[Yy][Ee][Ss]|[Yy]|"")
+					echo "Okay, I'll disable ~amd64 by default."
+					export STABLE_PREFIX="yes"
+					;;
+				*)
+					echo "Fine, I will not disable ~amd64, no problem."
+					;;
+			esac
+		fi
+	fi
+
 	# choose EPREFIX, we do this last, since we have to actually write
 	# to the filesystem here to check that the EPREFIX is sane
 	cat << EOF

From 8a28d398e191b6dcd43a2ed4a2d77bcc16286a04 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 18 Nov 2021 14:36:11 +0100
Subject: [PATCH 02/22] add execute permissions

---
 bootstrap-prefix.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 bootstrap-prefix.sh

diff --git a/bootstrap-prefix.sh b/bootstrap-prefix.sh
old mode 100644
new mode 100755

From 885c3f5b3cf6ba4c1f4fa3e0c0f5e74e4a46774e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 18 Nov 2021 16:10:18 +0100
Subject: [PATCH 03/22] bump version to 2021.12

---
 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 a5bd0895..696f6a6d 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: "2021.06"
+eessi_version: "2021.12"
 
 custom_overlays:
   - name: eessi

From ece202175316971ad6b7ae3c6348490d025e3e48 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 18 Nov 2021 16:10:53 +0100
Subject: [PATCH 04/22] use newer snapshot

---
 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 696f6a6d..ab88ad95 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -18,7 +18,7 @@ gentoo_prefix_path: /cvmfs/{{ cvmfs_repository }}/{{ eessi_version }}/compat/{{
 # How to build the prefix
 prefix_required_space: 15 GB
 prefix_snapshot_url: https://eessi-gentoo-snapshot.s3-eu-west-1.amazonaws.com
-prefix_snapshot_version: 20210607
+prefix_snapshot_version: 20211117
 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 abfbaa93d552e3babca00a0a39fdb4ed13d11524 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Nov 2021 16:13:44 +0100
Subject: [PATCH 05/22] remove the -a from emerge system

---
 bootstrap-prefix.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bootstrap-prefix.sh b/bootstrap-prefix.sh
index 9a6aaa04..0e0e58ea 100755
--- a/bootstrap-prefix.sh
+++ b/bootstrap-prefix.sh
@@ -2168,10 +2168,10 @@ bootstrap_stage3() {
 	# Avoid glib compiling for Cocoa libs if it finds them, since we're
 	# still with an old llvm that may not understand the system headers
 	# very well on Darwin (-DGNUSTEP_BASE_VERSION hack)
-	einfo "running emerge -uDNav system"
-	estatus "stage3: emerge -uDNav system"
+	einfo "running emerge -uDNv system"
+	estatus "stage3: emerge -uDNv system"
 	CPPFLAGS="-DGNUSTEP_BASE_VERSION" \
-	CFLAGS= CXXFLAGS= emerge --color n -uDNav system || return 1
+	CFLAGS= CXXFLAGS= emerge --color n -uDNv system || return 1
 
 	# remove anything that we don't need (compilers most likely)
 	einfo "running emerge --depclean"

From c76978276cbc3ad6583c77d42ada4f7d50127071 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 20 Nov 2021 12:08:00 +0100
Subject: [PATCH 06/22] add task step for copying custom bootstrap script

---
 .../compatibility_layer/tasks/install_prefix.yml      | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml b/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
index 531ee308..a96903e7 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
@@ -70,6 +70,17 @@
   tags:
     - build_prefix
 
+- name: debug
+  debug:
+    msg: "{{ prefix_custom_bootstrap_script.local }} {{ prefix_custom_bootstrap_script.remote }}"
+
+- name: "Copy custom bootstrap script"
+  copy:
+    src: "{{ prefix_custom_bootstrap_script.local }}"
+    dest: "{{ prefix_custom_bootstrap_script.remote }}"
+    mode: 0755
+  when: not prefix_use_builtin_bootstrap
+
 - name: "Install Gentoo prefix via {{ prefix_install }}"
   shell: set -o pipefail && ( {{ prefix_install }} | tee -a {{ prefix_build_log }} | grep -E '^(>>> Installing|\\* )' )
   become: no

From b1a449ef39d9f5a1531a319a9a8f0a5800fb4d12 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 20 Nov 2021 12:08:14 +0100
Subject: [PATCH 07/22] add options for using a custom bootstrap script

---
 .../roles/compatibility_layer/defaults/main.yml          | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index ab88ad95..92c74ae2 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -21,14 +21,19 @@ prefix_snapshot_url: https://eessi-gentoo-snapshot.s3-eu-west-1.amazonaws.com
 prefix_snapshot_version: 20211117
 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 }}"
+prefix_use_builtin_bootstrap: no
+prefix_custom_bootstrap_script:
+  local: "{{ playbook_dir }}/../../bootstrap-prefix.sh"
+  remote: /tmp/bootstrap-prefix.sh
+prefix_bootstrap_script_path: "{{ prefix_use_builtin_bootstrap | ternary('/usr/local/bin/bootstrap-prefix.sh', prefix_custom_bootstrap_script.remote) }}"
+prefix_singularity_command: "singularity exec -B {{ gentoo_prefix_path }}:{{ gentoo_prefix_path }}"
 prefix_source: "docker://ghcr.io/eessi/bootstrap-prefix:centos8"
 prefix_source_options: "{{ gentoo_prefix_path }} noninteractive"
 prefix_install: >-
     SINGULARITYENV_USE_CPU_CORES={{ ansible_processor_vcpus }}
     SINGULARITYENV_CUSTOM_SNAPSHOT_URL="{{ prefix_snapshot_url }}"
     SINGULARITYENV_CUSTOM_SNAPSHOT_VERSION="{{ prefix_snapshot_version }}"
-    {{ prefix_singularity_command }} {{ prefix_source }} {{ prefix_source_options }}
+    {{ prefix_singularity_command }} {{ prefix_source }} {{ prefix_bootstrap_script_path }} {{ prefix_source_options }}
 
 # Logging
 eessi_log_dir: "/tmp/eessi-logs"

From 67df4bec37181735a5d94c5d894d21d3db61726b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 20 Nov 2021 12:22:39 +0100
Subject: [PATCH 08/22] update README

---
 ansible/playbooks/README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ansible/playbooks/README.md b/ansible/playbooks/README.md
index 12ddd783..7c6c819e 100644
--- a/ansible/playbooks/README.md
+++ b/ansible/playbooks/README.md
@@ -42,8 +42,9 @@ Before running the playbook, make sure the following settings are correct, and o
 | prefix_required_space | Minimal amount of disk space that is required for the Gentoo Prefix bootstrap |
 | prefix_snapshot_url | Directory (served over http(s)) containing snapshot files |
 | prefix_snapshot_version | Date (`YYYYMMDD`) of the Portage snapshot file for the Prefix installation |
-| prefix_python_targets | String consisting of [Gentoo Python targets](https://wiki.gentoo.org/wiki/Project:Python/PYTHON_TARGETS) Python targets used for the Prefix installation |
 | prefix_user_defined_trusted_dirs | List of paths to the user defined trusted dirs for glibc |
+| prefix_use_builtin_bootstrap | Use the container's built-in bootstrap script? |
+| prefix_custom_bootstrap_script | Dictionary with the `local` source and `remote` destination of the bootstrap script |
 | prefix_singularity_command | Singularity command for launching the container with the bootstrap script |
 | prefix_source | Singularity container path used for the Prefix installtion |
 | prefix_source_options | Arguments to be passed to the Prefix bootstrap script |

From f1026d6efd8c70990472c3b39d10715bb505c0e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 20 Nov 2021 12:24:19 +0100
Subject: [PATCH 09/22] remove debug step

---
 .../roles/compatibility_layer/tasks/install_prefix.yml        | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml b/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
index a96903e7..e5f64c44 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
@@ -70,10 +70,6 @@
   tags:
     - build_prefix
 
-- name: debug
-  debug:
-    msg: "{{ prefix_custom_bootstrap_script.local }} {{ prefix_custom_bootstrap_script.remote }}"
-
 - name: "Copy custom bootstrap script"
   copy:
     src: "{{ prefix_custom_bootstrap_script.local }}"

From 24641e1483f1a4dbb79857510760623a707b20f7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 20 Nov 2021 12:24:45 +0100
Subject: [PATCH 10/22] remove unnecessary variable

---
 ansible/playbooks/roles/compatibility_layer/defaults/main.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index 92c74ae2..79bfda6f 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -33,7 +33,9 @@ prefix_install: >-
     SINGULARITYENV_USE_CPU_CORES={{ ansible_processor_vcpus }}
     SINGULARITYENV_CUSTOM_SNAPSHOT_URL="{{ prefix_snapshot_url }}"
     SINGULARITYENV_CUSTOM_SNAPSHOT_VERSION="{{ prefix_snapshot_version }}"
-    {{ prefix_singularity_command }} {{ prefix_source }} {{ prefix_bootstrap_script_path }} {{ prefix_source_options }}
+    {{ prefix_singularity_command }} {{ prefix_source }}
+    {{ prefix_use_builtin_bootstrap | ternary('/usr/local/bin/bootstrap-prefix.sh', prefix_custom_bootstrap_script.remote) }}
+    {{ prefix_source_options }}
 
 # Logging
 eessi_log_dir: "/tmp/eessi-logs"

From 821c24b1c3b17fd0130a0a2e543d242ca10be50b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 20 Nov 2021 12:25:04 +0100
Subject: [PATCH 11/22] remove unnecessary variable

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

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index 79bfda6f..5a733496 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -25,7 +25,6 @@ prefix_use_builtin_bootstrap: no
 prefix_custom_bootstrap_script:
   local: "{{ playbook_dir }}/../../bootstrap-prefix.sh"
   remote: /tmp/bootstrap-prefix.sh
-prefix_bootstrap_script_path: "{{ prefix_use_builtin_bootstrap | ternary('/usr/local/bin/bootstrap-prefix.sh', prefix_custom_bootstrap_script.remote) }}"
 prefix_singularity_command: "singularity exec -B {{ gentoo_prefix_path }}:{{ gentoo_prefix_path }}"
 prefix_source: "docker://ghcr.io/eessi/bootstrap-prefix:centos8"
 prefix_source_options: "{{ gentoo_prefix_path }} noninteractive"

From 16511c0a67e96e88ccbb0c5dce2bee17896769b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 20 Nov 2021 16:33:34 +0100
Subject: [PATCH 12/22] add note about which bootstrap script can/will be used
 by the playbook

---
 ansible/playbooks/README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/ansible/playbooks/README.md b/ansible/playbooks/README.md
index 7c6c819e..badbc177 100644
--- a/ansible/playbooks/README.md
+++ b/ansible/playbooks/README.md
@@ -76,3 +76,7 @@ ip-or-hostname-of-your-stratum0 eessi_host_arch=x86_64 eessi_host_os=linux
 
 The `eessi_host_arch` corresponds to the architecture of the machine that executes the playbook and for which this compatibility layer has to be built, e.g. `x86_64`, `aarch64`, or `ppc64le`.
 Similarly, `eessi_host_os` should refer to the operating system of the machine, and should be set to either `linux` or `macos`.
+
+Note that, by default, the bootstrap script from the root directory of this git repository will be used, unless you set `prefix_use_builtin_bootstrap` to `yes` 
+(in which case the bootstrap script included in the Prefix build container will be used).
+A different bootstrap script can be used by changing `prefix_custom_bootstrap_script.local` to a local path.

From 1ee7f64d7d7a7b21131530fbb79931074e223340 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 21 Nov 2021 16:08:22 +0100
Subject: [PATCH 13/22] update portage snapshot to 20211120 to pick up fix for
 sys-libs/libcap (see https://bugs.gentoo.org/825374) and masked
 sys-devel/binutils-2.37_p1-r1 (https://bugs.gentoo.org/824482)

---
 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 5a733496..4f96431e 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -18,7 +18,7 @@ gentoo_prefix_path: /cvmfs/{{ cvmfs_repository }}/{{ eessi_version }}/compat/{{
 # How to build the prefix
 prefix_required_space: 15 GB
 prefix_snapshot_url: https://eessi-gentoo-snapshot.s3-eu-west-1.amazonaws.com
-prefix_snapshot_version: 20211117
+prefix_snapshot_version: 20211120
 prefix_user_defined_trusted_dirs:
   - "/cvmfs/{{ cvmfs_repository }}/host_injections/{{ eessi_version }}/compat/{{ eessi_host_os }}/{{ eessi_host_arch }}/lib"
 prefix_use_builtin_bootstrap: no

From 7c87d658095bb1ec2dd58b656f42e75db6cd9a48 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 21 Nov 2021 22:36:58 +0100
Subject: [PATCH 14/22] disable 'stable mode' in Gentoo Prefix bootstrap
 script, since it's only used for x86_64 (cfr. #131)

---
 bootstrap-prefix.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bootstrap-prefix.sh b/bootstrap-prefix.sh
index 0e0e58ea..1776e0a0 100755
--- a/bootstrap-prefix.sh
+++ b/bootstrap-prefix.sh
@@ -2751,7 +2751,7 @@ I can limit your Prefix to use only packages keyworded for stable amd64
 by default.  Of course, you can still enable testing ~amd64 for
 the packages you want, when the need arises.
 EOF
-			[[ ${TODO} == 'noninteractive' ]] && ans=yes ||
+			[[ ${TODO} == 'noninteractive' ]] && ans=no ||
 			read -p "  Do you want to use stable Prefix? [Yn] " ans
 			case "${ans}" in
 				[Yy][Ee][Ss]|[Yy]|"")

From b94e4933e7a3a81649922b22d355a6f0b710a904 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 23 Nov 2021 09:52:51 +0100
Subject: [PATCH 15/22] use equery to find out if user_defined_trusted_dirs was
 used

---
 .../tasks/set_glibc_trusted_dirs.yml              | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 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 0650d73d..0f1ab4f9 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
@@ -1,15 +1,12 @@
 # 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
+- name: Check the EXTRA_EMAKE flags of glibc
+  command: "equery has --package glibc EXTRA_EMAKE"
+  changed_when: false
+  ignore_errors: yes
+  register: glibc_extra_emake
   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
@@ -20,7 +17,7 @@
     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
+    - glibc_extra_emake.stdout != "user-defined-trusted-dirs=" + ":".join(prefix_user_defined_trusted_dirs)
 
 - name: Create portage env directory
   file:

From 46ee4c99e8d2b8410cd8611f5bf4da7a19754630 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 25 Nov 2021 11:45:27 +0100
Subject: [PATCH 16/22] Add steps for creating a package.mask right before the
 bootstrap, change order of some steps, add tags

---
 .../tasks/install_prefix.yml                  | 38 +++++++++++++++----
 1 file changed, 31 insertions(+), 7 deletions(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml b/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
index e5f64c44..4e9be26e 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
@@ -61,6 +61,33 @@
   tags:
     - build_prefix
 
+- name: "Copy custom bootstrap script"
+  copy:
+    src: "{{ prefix_custom_bootstrap_script.local }}"
+    dest: "{{ prefix_custom_bootstrap_script.remote }}"
+    mode: 0755
+  when: not prefix_use_builtin_bootstrap
+  tags:
+    - build_prefix
+
+- name: "Create $EPREFIX/etc/portage directory"
+  file:
+    path: "{{ gentoo_prefix_path }}/etc/portage"
+    state: directory
+    mode: 0755
+  when: prefix_mask_packages is defined and prefix_mask_packages | length > 0
+  tags:
+    - build_prefix
+    
+- name: "Mask packages for the bootstrap"
+  copy:
+    dest: "{{ gentoo_prefix_path }}/etc/portage/package.mask"
+    content: "{{ prefix_mask_packages }}"
+    mode: 0644
+  when: prefix_mask_packages is defined and prefix_mask_packages | length > 0
+  tags:
+    - build_prefix
+
 - name: "Give {{ username_on_host.stdout }} recursive user and group ownership of {{ gentoo_prefix_path }}"
   file:
     dest: "{{ gentoo_prefix_path }}"
@@ -70,13 +97,6 @@
   tags:
     - build_prefix
 
-- name: "Copy custom bootstrap script"
-  copy:
-    src: "{{ prefix_custom_bootstrap_script.local }}"
-    dest: "{{ prefix_custom_bootstrap_script.remote }}"
-    mode: 0755
-  when: not prefix_use_builtin_bootstrap
-
 - name: "Install Gentoo prefix via {{ prefix_install }}"
   shell: set -o pipefail && ( {{ prefix_install }} | tee -a {{ prefix_build_log }} | grep -E '^(>>> Installing|\\* )' )
   become: no
@@ -88,8 +108,12 @@
   stat:
     path: "{{ gentoo_prefix_path }}/startprefix"
   register: startprefix
+  tags:
+    - build_prefix
 
 - name: "Fail if startprefix script has not been created"
   fail:
     msg: "The resulting Gentoo Prefix installation does not have a startprefix script. Something went wrong!"
   when: not startprefix.stat.exists
+  tags:
+    - build_prefix

From 2cbd6154e235f332bfbcb70dee25acfde8d217c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 25 Nov 2021 11:46:44 +0100
Subject: [PATCH 17/22] Add variable for setting a package.mask for the
 bootstrap

---
 ansible/playbooks/roles/compatibility_layer/defaults/main.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index 4f96431e..d6cb7df3 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -21,6 +21,9 @@ prefix_snapshot_url: https://eessi-gentoo-snapshot.s3-eu-west-1.amazonaws.com
 prefix_snapshot_version: 20211120
 prefix_user_defined_trusted_dirs:
   - "/cvmfs/{{ cvmfs_repository }}/host_injections/{{ eessi_version }}/compat/{{ eessi_host_os }}/{{ eessi_host_arch }}/lib"
+prefix_mask_packages: |
+  # Mask glibc >= 2.34, as it's causing issues with the bootstrap, and it's not compatible with CUDA 11.
+  >=sys-libs/glibc-2.34
 prefix_use_builtin_bootstrap: no
 prefix_custom_bootstrap_script:
   local: "{{ playbook_dir }}/../../bootstrap-prefix.sh"

From 42caa87d144f2fb42e0056f395068882540714f7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 25 Nov 2021 11:50:42 +0100
Subject: [PATCH 18/22] remove tab on empty line

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

diff --git a/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml b/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
index 4e9be26e..8bf3d77e 100644
--- a/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
+++ b/ansible/playbooks/roles/compatibility_layer/tasks/install_prefix.yml
@@ -78,7 +78,7 @@
   when: prefix_mask_packages is defined and prefix_mask_packages | length > 0
   tags:
     - build_prefix
-    
+
 - name: "Mask packages for the bootstrap"
   copy:
     dest: "{{ gentoo_prefix_path }}/etc/portage/package.mask"

From e7597d4d57c70d74b4f53eda4a60593313a11c19 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 25 Nov 2021 11:54:57 +0100
Subject: [PATCH 19/22] add prefix_mask_packages to README

---
 ansible/playbooks/README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ansible/playbooks/README.md b/ansible/playbooks/README.md
index badbc177..8a4a235e 100644
--- a/ansible/playbooks/README.md
+++ b/ansible/playbooks/README.md
@@ -43,6 +43,7 @@ Before running the playbook, make sure the following settings are correct, and o
 | prefix_snapshot_url | Directory (served over http(s)) containing snapshot files |
 | prefix_snapshot_version | Date (`YYYYMMDD`) of the Portage snapshot file for the Prefix installation |
 | prefix_user_defined_trusted_dirs | List of paths to the user defined trusted dirs for glibc |
+| prefix_mask_packages | Contents of a [package.mask file](https://wiki.gentoo.org/wiki//etc/portage/package.mask) that should be used during the bootstrap |
 | prefix_use_builtin_bootstrap | Use the container's built-in bootstrap script? |
 | prefix_custom_bootstrap_script | Dictionary with the `local` source and `remote` destination of the bootstrap script |
 | prefix_singularity_command | Singularity command for launching the container with the bootstrap script |

From a38c421b3ea0c80def555d46cd7727f460fe40dc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 25 Nov 2021 18:52:11 +0100
Subject: [PATCH 20/22] also add dev-libs/libgcrypt to package.mask to work
 around compilation error on ppc64le during Prefix bootstrap

---
 .../playbooks/roles/compatibility_layer/defaults/main.yml   | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
index d6cb7df3..28703077 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -22,8 +22,12 @@ prefix_snapshot_version: 20211120
 prefix_user_defined_trusted_dirs:
   - "/cvmfs/{{ cvmfs_repository }}/host_injections/{{ eessi_version }}/compat/{{ eessi_host_os }}/{{ eessi_host_arch }}/lib"
 prefix_mask_packages: |
-  # Mask glibc >= 2.34, as it's causing issues with the bootstrap, and it's not compatible with CUDA 11.
+  # avoid glibc 2.34, as it's causing issues with the bootstrap, and it's not compatible with CUDA 11.
+  # see https://github.com/EESSI/compatibility-layer/issues/137 + https://bugs.gentoo.org/824482
   >=sys-libs/glibc-2.34
+  # avoid libgcrypt 1.9.4 due to compiler errros on ppc64le,
+  # see https://github.com/EESSI/compatibility-layer/issues/134 + https://bugs.gentoo.org/825722
+  >=dev-libs/libgcrypt-1.9.4
 prefix_use_builtin_bootstrap: no
 prefix_custom_bootstrap_script:
   local: "{{ playbook_dir }}/../../bootstrap-prefix.sh"

From 20206a53999737241cac6821afb10ad49a60b3f5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 25 Nov 2021 19:41:12 +0100
Subject: [PATCH 21/22] only mask specific versions of glibc and libgcrypt

---
 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 28703077..f699452c 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -24,10 +24,10 @@ prefix_user_defined_trusted_dirs:
 prefix_mask_packages: |
   # avoid glibc 2.34, as it's causing issues with the bootstrap, and it's not compatible with CUDA 11.
   # see https://github.com/EESSI/compatibility-layer/issues/137 + https://bugs.gentoo.org/824482
-  >=sys-libs/glibc-2.34
+  =sys-libs/glibc-2.34
   # avoid libgcrypt 1.9.4 due to compiler errros on ppc64le,
   # see https://github.com/EESSI/compatibility-layer/issues/134 + https://bugs.gentoo.org/825722
-  >=dev-libs/libgcrypt-1.9.4
+  =dev-libs/libgcrypt-1.9.4
 prefix_use_builtin_bootstrap: no
 prefix_custom_bootstrap_script:
   local: "{{ playbook_dir }}/../../bootstrap-prefix.sh"

From fbe11eeb18106bc412b99469bc5d9e295203d6e1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Nov 2021 08:33:23 +0100
Subject: [PATCH 22/22] mask glibc >= 2.34

---
 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 f699452c..866ee26b 100644
--- a/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
+++ b/ansible/playbooks/roles/compatibility_layer/defaults/main.yml
@@ -24,7 +24,7 @@ prefix_user_defined_trusted_dirs:
 prefix_mask_packages: |
   # avoid glibc 2.34, as it's causing issues with the bootstrap, and it's not compatible with CUDA 11.
   # see https://github.com/EESSI/compatibility-layer/issues/137 + https://bugs.gentoo.org/824482
-  =sys-libs/glibc-2.34
+  >=sys-libs/glibc-2.34
   # avoid libgcrypt 1.9.4 due to compiler errros on ppc64le,
   # see https://github.com/EESSI/compatibility-layer/issues/134 + https://bugs.gentoo.org/825722
   =dev-libs/libgcrypt-1.9.4