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Accepting request 1084588 from network:cluster

Browse Source 
OBS-URL: https://build.opensuse.org/request/show/1084588
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/spack?expand=0&rev=32
This commit is contained in:
Dominique Leuenberger 2023-05-04 15:11:12 +00:00 committed by Git OBS Bridge
commit b4ba70e162
7 changed files with 234 additions and 46 deletions
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39
Add-zypper-to-the-valid-container.os_packages-commands.patch Normal file
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@ -0,0 +1,39 @@
From: Egbert Eich <eich@suse.com>
Date: Thu Apr 6 11:29:30 2023 +0200
Subject: Add 'zypper' to the valid container.os_packages commands
Patch-mainline: Not yet
Git-commit: 0614150f86a3554118f60614e9b0cfaf8fb2aa12
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
lib/spack/docs/containers.rst | 2 +-
lib/spack/spack/schema/container.py | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/lib/spack/docs/containers.rst b/lib/spack/docs/containers.rst
index 9c6f8a26..1452b6a0 100644
--- a/lib/spack/docs/containers.rst
+++ b/lib/spack/docs/containers.rst
@@ -498,7 +498,7 @@ to customize the generation of container recipes:
- No
* - ``os_packages:command``
- Tool used to manage system packages
- - ``apt``, ``yum``
+ - ``apt``, ``yum``, ``zypper``
- Only with custom base images
* - ``os_packages:update``
- Whether or not to update the list of available packages
diff --git a/lib/spack/spack/schema/container.py b/lib/spack/spack/schema/container.py
index b05199f8..7c98a1db 100644
--- a/lib/spack/spack/schema/container.py
+++ b/lib/spack/spack/schema/container.py
@@ -54,7 +54,7 @@
"os_packages": {
"type": "object",
"properties": {
- "command": {"type": "string", "enum": ["apt", "yum"]},
+ "command": {"type": "string", "enum": ["apt", "yum", "zypper"]},
"update": {"type": "boolean"},
"build": _list_of_packages,
"final": _list_of_packages,

40
Make-sure-spack-environment-is-set-up-in-Dockerfile-template.patch
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@ -1,40 +0,0 @@
From: Egbert Eich <eich@suse.com>
Date: Tue Jan 31 09:24:46 2023 +0100
Subject: Make sure spack environment is set up in Dockerfile template
Patch-mainline: Not yet
Git-commit: 865116877fe2536485326aa0fb53943160fa5e25
References:
The Dockerfile template did source the script
/opt/spack/share/spack/setup-env.sh
which lead to the binary 'spack' not being found and the
environment not being set up properly for `spack env activate .`.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
share/spack/templates/container/Dockerfile | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/share/spack/templates/container/Dockerfile b/share/spack/templates/container/Dockerfile
index b10dcf08..dc9b91e5 100644
--- a/share/spack/templates/container/Dockerfile
+++ b/share/spack/templates/container/Dockerfile
@@ -19,7 +19,8 @@ RUN mkdir {{ paths.environment }} \
{{ manifest }} > {{ paths.environment }}/spack.yaml
# Install the software, remove unnecessary deps
-RUN cd {{ paths.environment }} && spack env activate . && spack install --fail-fast && spack gc -y
+RUN . /opt/spack/share/spack/setup-env.sh && \
+ cd {{ paths.environment }} && spack env activate . && spack install --fail-fast && spack gc -y
{% if strip %}
# Strip all the binaries
@@ -31,7 +32,7 @@ RUN find -L {{ paths.view }}/* -type f -exec readlink -f '{}' \; | \
{% endif %}
# Modifications to the environment that are necessary to run
-RUN cd {{ paths.environment }} && \
+RUN . /opt/spack/share/spack/setup-env.sh && cd {{ paths.environment }} && \
spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
{% if extra_instructions.build %}

3
spack-0.19.1.tar.gz
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:c9666f0b22ccf3cbda2736104d5d4e3b9cad5b4b4f01874a501e97d2c9477452
size 9420035

3
spack-0.19.2.tar.gz Normal file
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@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:4978b37da50f5690f4e1aa0cfe3975a89ccef85d96c68d417ea0716a8ce3aa98
size 9424447

58
spack.changes
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@ -1,3 +1,61 @@
-------------------------------------------------------------------
Mon Apr 17 06:59:15 UTC 2023 - Egbert Eich <eich@suse.com>
- Update to version 0.19.2 with the following bug fixes:
* Ignore global variant requirement for packages that do not define it.
* Compiler wrapper: improved parsing of linker arguments.
* Views: fix support for optional Python extensions.
* Views: fix issue where Python executable gets symlinked instead of copied.
* Fix a bug where tests were not added when concretizing together.
* Increase db timeout from 3s to 60s to improve stability of parallel
installs.
* Buildcache: improve error handling in downloads.
* Module files for packages installed from buildcache have long placeholder
paths abbreviated in configure args section.
* Ensure file with build environment variables is truncated when writing
to it.
* spack config update now works on active environments;
- Add:
Add-zypper-to-the-valid-container.os_packages-commands.patch
This adds `zypper` to the valid OS package managers that can
be specified in a slack.yaml container description like:
spack:
...
container:
..
os_packages:
command: zypper
..
- Add: spack_get_libs.sh
This scripts obtains library and include paths for spack-build
libraries and outputs shell commands which set these as
environment variables.
Additionally, it generates a command line to prepend these lib
directories to LD_LIBRARY_PATH. Thus, the variables can be set
in the current shell by running `source $(spack_get_libs.sh foo)`.
When using `bash` this script may also be sourced directly.
The names of the environment variables are the upper-cased library
names with the strings 'LIB_' and 'INC_' prepended. Thus, for a
library 'foo', they would be 'INC_FOO' and 'LIB_FOO'.
These variables may be used at build time to point the compiler
to the include and library files (bsc#1208751).
- Drop:
Make-sure-spack-environment-is-set-up-in-Dockerfile-template.patch
This patch should not be needed. When building using `podman` use:
`podman build --format docker ...` to enable the non-OCI compliant
instructions in a Dockerfile.
- Add info, makeinfo, libcurl-devel, patchelf to the recommended
packages to add.
Fix: openssl-devel -> libopenssl-devel
-------------------------------------------------------------------
Thu Apr 6 09:30:50 UTC 2023 - Egbert Eich <eich@suse.com>
- Add 'zypper' as valid command to container.os_packages. This
allows to build SUSE container using non-default registries.
- Add 'awk', 'git', 'gzip' and 'gunzip' to the requires.
- Add 'patchelf' to the recommended packages.
-------------------------------------------------------------------
Thu Mar 30 09:34:39 UTC 2023 - Egbert Eich <eich@suse.com>

13
spack.spec
View File

@ -31,7 +31,7 @@ ExclusiveArch: do_not_build
# These packages are found and can be used by spack, %{_sysconfdir}/spack/packages-yaml
# needs to be updated when one of these packages is updated or uninstalled.
# Distinguish between packages we recommend and packages which
%define spack_trigger_recommended_packages autoconf bash bison bzip2 libzip-devel cmake-full ccache cpio diffutils findutils flex git-lfs make m4 ncurses-devel libtool openssl-devel perl-base pkgconf pkg-config python3-base tar info xz xz-devel
%define spack_trigger_recommended_packages autoconf bash bison bzip2 libzip-devel cmake-full ccache cpio diffutils findutils flex git-lfs info make makeinfo m4 ncurses-devel libtool libcurl-devel libopenssl-devel perl-base pkgconf pkg-config python3-base tar xz xz-devel patchelf
%define spack_trigger_recommended_compilers gcc gcc-c++ gcc-fortran
@ -43,7 +43,7 @@ ExclusiveArch: do_not_build
# non oss packages
%define spack_trigger_external cuda-nvcc
Name: spack
Version: 0.19.1
Version: 0.19.2
Release: 0
Summary: Package manager for HPC systems
License: Apache-2.0 AND MIT AND Python-2.0 AND BSD-3-Clause
@ -55,6 +55,7 @@ Source3: run-find-external.sh.in
Source4: https://en.opensuse.org/index.php?title=Spack&action=raw&ref=157522#/README-oo-wiki
# Source5 is from https://docs.python.org/3/objects.inv, but has permanent changes so using a static version
Source5: objects.inv
Source6: spack_get_libs.sh
Patch2: Adapt-shell-scripts-that-set-up-the-environment-for-different-shells.patch
Patch4: added-target-and-os-calls-to-output-of-spack-spec-co.patch
Patch5: Make-spack-paths-compliant-to-distro-installation.patch
@ -62,7 +63,7 @@ Patch6: Fix-error-during-documentation-build-due-to-recursive-module-inc
Patch7: Fix-Spinx-configuration-to-avoid-throwing-errors.patch
Patch8: Set-modules-default-to-lmod.patch
Patch9: Add-support-for-container-building-using-a-SLE-base-container.patch
Patch100: Make-sure-spack-environment-is-set-up-in-Dockerfile-template.patch
Patch10: Add-zypper-to-the-valid-container.os_packages-commands.patch
%if %{without doc}
BuildRequires: fdupes
BuildRequires: lua-lmod
@ -71,12 +72,15 @@ BuildRequires: python3-urllib3
BuildRequires: sudo
BuildRequires: sysuser-tools
Requires: %{name}-recipes = %{version}
Requires: awk
Requires: bzip2
Requires: coreutils
Requires: curl
Requires: gcc-c++
Requires: gcc-fortran
Requires: git
Requires: gpg2
Requires: gzip
Requires: libbz2-devel
Requires: lua-lmod
Requires: make
@ -85,6 +89,7 @@ Requires: polkit
Requires: python3-clingo
Requires: sudo
Requires: tar
Requires: unzip
Requires: xz
Recommends: %spack_trigger_recommended_packages %spack_trigger_recommended_compilers
%else
@ -304,6 +309,8 @@ cp -r var/spack/* %{buildroot}%{_localstatedir}/lib/spack
mv %{buildroot}%{_localstatedir}/lib/spack/repos %{buildroot}%{_datarootdir}/spack
cp -r bin/sbang %{buildroot}/%{_bindir}
cp -r bin/spack* %{buildroot}%{_bindir}/
cp %{S:6} %{buildroot}%{_bindir}/
chmod 0755 %{buildroot}%{_bindir}/%{basename:%{S:6}}
cp etc/spack/defaults/config.yaml %{buildroot}%{_sysconfdir}/skel/.spack/
install -m 755 %{S:3} %{buildroot}/%{spack_dir}/run-find-external.sh
sed -i -e 's#@@_sysconfdir@@#%{_sysconfdir}#' %{buildroot}/%{spack_dir}/run-find-external.sh

124
spack_get_libs.sh Normal file
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@ -0,0 +1,124 @@
#! /bin/bash
#set -x
spack_shtyp=bash
help() {
echo -e "$0 [--help][--csh] lib ...
Print set commands to set or set LD_LIBRARY_PATH to libraries
specified as arguments as well as variables holding each library
directory individually. These are usful when linking applications
against these libraries.
The variable names of the latter begin with 'LIB_' followed by
the upper cased library name."
}
error() {
echo -e "$1" >&2
}
contains() {
local a=$1
shift
local -a b=($@)
local i
for i in ${b[*]}; do
[ "$i" == "$a" ] && return 0
done
return 1
}
path_contains() {
local a=$1
local i
[ -n "$2" ] || return 1
OFS=$IFS
IFS=:
for i in $2; do
IFS=$OFS
[ "$i" == "$a" ] && return 0
done
return 1
}
print_env() {
case $spack_shtyp in
csh)
echo "setenv $1 $2" ;;
bash)
if $spack_srcd; then
eval $1=$2
export $1
else
echo -e "$1=$2\nexport $1"
fi ;;
esac
}
get_paths()
{
local -A libpaths includepaths
local OFS=$IFS
local ld_exist=$LD_LIBRARY_PATH
IFS="
"
local package_list="$1"
local format="> {hash:7} {name}{@version}{%compiler}{arch=architecture}"
local l i
for l in $(spack find --format "{name}" --paths $package_list); do
local lib=${l%% *}
local path=${l##* }
if contains $lib "${!libpaths[@]}"; then
error "$lib matches multiple packages\n Matching packages:"
spack find --format ${format} ${lib} >&2
error " Use a more specific spec (e.g., prepend '/' to the hash)."
$spack_srcd || exit 1
fi
for i in lib64 lib; do
if [ -d $path/$i ]; then
libpaths[$lib]="$path/$i"
break
fi
done
if [ -d $path/include ]; then
includepaths[$lib]="$path/include"
fi
done
IFS=$OFS
local -A libs
local ld_library_path
for i in ${!libpaths[@]}; do
libs[LIB_${i^^*}]="${libpaths[$i]}"
path_contains ${libpaths[$i]} "${ld_exist}" || \
ld_library_path+="${libpaths[$i]}:"
done
for i in ${!includepaths[@]}; do
eval [ "unset" = "\${INC_${i}:-unset}" ] &&
print_env "INC_${i^^*}" "${includepaths[$i]}"
done
for i in ${!libs[@]}; do
eval [ "unset" = "\${${i}:-unset}" ] && print_env $i "${libs[$i]}"
done
[ -n "$ld_library_path" ] && \
print_env LD_LIBRARY_PATH "${ld_library_path}\$LD_LIBRARY_PATH"
}
spack_srcd=false
(
[[ -n $ZSH_VERSION && $ZSH_EVAL_CONTEXT =~ :file$ ]] ||
[[ -n $BASH_VERSION ]] && (return 0 2>/dev/null)
) && spack_srcd=true
while [ -n "$1" ]; do
case $1 in
*-help|*-h) help; $spack_srcd || exit 0 ;;
*-csh|*-tcsh)
spack_shtyp=csh ;;
*) package_list+=" $1" ;;
esac
shift
done
get_paths "$package_list"