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Accepting request 931785 from home:mslacken:sp

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- updated to version 0.17.0
  (Upstream feature/bug references (<ID>) are relative to
   https://github.com/spack/spack/issues/<ID>).
  * New concretizer is now default
    The new concretizer introduced as an experimental feature in v0.16.0
    is now the default (#25502). The new concretizer is based on the
    clingo logic programming system,
    and it enables us to do much higher quality and faster dependency solving
    The old concretizer is still available via the concretizer: original
    setting, but it is deprecated and will be removed in v0.18.0.
  * Binary Bootstrapping
    To make it easier to use the new concretizer and binary packages,
    Spack now bootstraps clingo and GnuPG from public binaries. If it
    is not able to bootstrap them from binaries, it installs them from
    source code. With these changes, you should still be able to clone Spack
    and start using it almost immediately.
  * Reuse existing packages (experimental)
    The most wanted feature from our
    2020 user survey and
    the most wanted Spack feature of all time (#25310). spack install,
    spack spec, and spack concretize now have a --reuse option, which
    causes Spack to minimize the number of rebuilds it does. The --reuse
    option will try to find existing installations and binary packages locally
    and in registered mirrors, and will prefer to use them over building new
    versions. This will allow users to build from source far less than in
    prior versions of Spack. This feature will continue to be improved, with
    configuration options and better CLI expected in v0.17.1. It will become
    the default concretization mode in v0.18.0.
  * Better error messages
    We have improved the error messages generated by the new concretizer by

OBS-URL: https://build.opensuse.org/request/show/931785
OBS-URL: https://build.opensuse.org/package/show/network:cluster/spack?expand=0&rev=35
This commit is contained in:
Christian Goll 2021-11-16 14:32:55 +00:00 committed by Git OBS Bridge
parent 732e3a6699
commit 1399716433
16 changed files with 366 additions and 320 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.gitattributes vendored
View File

@ -21,3 +21,5 @@
*.xz filter=lfs diff=lfs merge=lfs -text
*.zip filter=lfs diff=lfs merge=lfs -text
*.zst filter=lfs diff=lfs merge=lfs -text
## Specific LFS patterns
objects.inv filter=lfs diff=lfs merge=lfs -text

73
Adapt-shell-scripts-that-set-up-the-environment-for-different-shells.patch
View File

@ -1,18 +1,20 @@
From fbbddf93f0715830a6ae9842c91f89ae40973619 Mon Sep 17 00:00:00 2001
From: Egbert Eich <eich@suse.com>
Date: Sat, 21 Nov 2020 21:46:02 +0100
Subject: [PATCH 4/4] Adapt shell scripts that set up the environment for
different shells
Date: Wed Nov 10 13:01:17 2021 +0100
Subject: Adapt shell scripts that set up the environment for different shells
Patch-mainline: Not yet
Git-repo: https://github.com/spack/spack
Git-commit: 565c91f4e3a40495fc470a8887df7dee9ced8c09
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
share/spack/setup-env.csh | 5 +++-
share/spack/setup-env.fish | 15 +---------
share/spack/setup-env.sh | 57 +++-----------------------------------
3 files changed, 9 insertions(+), 68 deletions(-)
share/spack/setup-env.fish | 15 +-----------
share/spack/setup-env.sh | 61 ++--------------------------------------------
3 files changed, 7 insertions(+), 74 deletions(-)
diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh
index b70036456..ab3d941ef 100755
index 4ac0503947..67fad7516c 100755
--- a/share/spack/setup-env.csh
+++ b/share/spack/setup-env.csh
@@ -12,6 +12,10 @@
@ -26,8 +28,8 @@ index b70036456..ab3d941ef 100755
if ($?_sp_initializing) then
exit 0
endif
@@ -59,7 +63,6 @@ alias spacktivate 'spack env activate'
alias _spack_pathadd 'set _pa_args = (\!*) && source $_spack_share_dir/csh/pathadd.csh'
@@ -71,7 +75,6 @@ foreach cmd ("$SPACK_PYTHON" python3 python python2)
end
# Set variables needed by this script
-_spack_pathadd PATH "$SPACK_ROOT/bin"
@ -35,10 +37,10 @@ index b70036456..ab3d941ef 100755
# Set up module search paths in the user environment
diff --git a/share/spack/setup-env.fish b/share/spack/setup-env.fish
index b74eae34d..decb718e1 100755
index d16ee617df..84e3a9e044 100755
--- a/share/spack/setup-env.fish
+++ b/share/spack/setup-env.fish
@@ -660,20 +660,7 @@ end
@@ -671,12 +671,6 @@ end
@ -48,7 +50,13 @@ index b74eae34d..decb718e1 100755
-set -l sp_source_file (status -f) # name of current file
-
-
-
#
# Identify and lock the python interpreter
@@ -691,14 +685,7 @@ end
-#
-# Find root directory and add bin to path.
-#
@ -56,15 +64,16 @@ index b74eae34d..decb718e1 100755
-set -l sp_prefix (realpath (dirname (dirname $sp_share_dir)))
-spack_pathadd PATH "$sp_prefix/bin"
-set -xg SPACK_ROOT $sp_prefix
-
+set -xg SPACK_ROOT @@_prefix@@
#
diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index 5761d1636..768866abe 100755
index 5136e8a58a..6aef191129 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -246,58 +246,6 @@ _sp_shell=$(_spack_determine_shell)
@@ -249,64 +249,6 @@ _sp_shell=$(_spack_determine_shell)
alias spacktivate="spack env activate"
@ -98,8 +107,13 @@ index 5761d1636..768866abe 100755
-#
-# We send cd output to /dev/null to avoid because a lot of users set up
-# their shell so that cd prints things out to the tty.
-_sp_share_dir="$(cd "$(dirname $_sp_source_file)" > /dev/null && pwd)"
-_sp_prefix="$(cd "$(dirname $(dirname $_sp_share_dir))" > /dev/null && pwd)"
-if [ "$_sp_shell" = zsh ]; then
- _sp_share_dir="${_sp_source_file:A:h}"
- _sp_prefix="${_sp_share_dir:h:h}"
-else
- _sp_share_dir="$(cd "$(dirname $_sp_source_file)" > /dev/null && pwd)"
- _sp_prefix="$(cd "$(dirname $(dirname $_sp_share_dir))" > /dev/null && pwd)"
-fi
-if [ -x "$_sp_prefix/bin/spack" ]; then
- export SPACK_ROOT="${_sp_prefix}"
-else
@ -120,24 +134,21 @@ index 5761d1636..768866abe 100755
- fi
-fi
-_spack_pathadd PATH "${_sp_prefix%/}/bin"
-
#
# Check whether a function of the given name is defined
@@ -369,10 +317,13 @@ _sp_multi_pathadd() {
}
_sp_multi_pathadd MODULEPATH "$_sp_tcl_roots"
#
@@ -387,11 +329,12 @@ if [ -z "${SPACK_SKIP_MODULES+x}" ]; then
}
_sp_multi_pathadd MODULEPATH "$_sp_tcl_roots"
fi
+export SPACK_ROOT=@@_prefix@@
+
+
# Add programmable tab completion for Bash
#
if [ "$_sp_shell" = bash ]; then
if test "$_sp_shell" = bash || test -n "${ZSH_VERSION:-}"; then
- source $_sp_share_dir/spack-completion.bash
+ source $SPACK_ROOT/share/spack/spack-completion.bash
+ source $SPACK_ROOT/share/spack/spack-completion.bash
fi
# done: unset sentinel variable as we're no longer initializing
--
2.26.2

56
Fix-Spinx-configuration-to-avoid-throwing-errors.patch Normal file
View File

@ -0,0 +1,56 @@
From: Egbert Eich <eich@suse.com>
Date: Wed Nov 10 16:30:14 2021 +0100
Subject: Fix Spinx configuration to avoid throwing errors
Patch-mainline: Not yet
Git-repo: https://github.com/spack/spack
Git-commit: f8be4e346441f8d33b760ddfdc5fad360edf055d
References:
- Ignore certain variables
- Don't attempt downloading ntersphinx inventory
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
lib/spack/docs/conf.py | 24 +++++++++++++++++++++++-
1 file changed, 23 insertions(+), 1 deletion(-)
diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py
index 2b58223e1d..95888cf5d4 100644
--- a/lib/spack/docs/conf.py
+++ b/lib/spack/docs/conf.py
@@ -179,6 +179,28 @@ def setup(sphinx):
('py:class', '_frozen_importlib_external.SourceFileLoader'),
# Spack classes that are private and we don't want to expose
('py:class', 'spack.provider_index._IndexBase'),
+ ('py:class', 'datetime.datetime'),
+ ('py:class', 'argparse.ArgumentParser'),
+ ('py:class', 'argparse.RawTextHelpFormatter'),
+ ('py:class', 'argparse.Namespace'),
+ ('py:class', 'argparse.Action'),
+ ('py:class', 'ast.NodeVisitor'),
+ ('py:class', 'ast.NodeTransformer'),
+ ('py:class', 'ast.AST'),
+ ('py:class', 'collections.abc.MutableMapping'),
+ ('py:class', 'collections.abc.Sequence'),
+ ('py:class', 'collections.abc.Mapping'),
+ ('py:class', 'html.parser.HTMLParser'),
+ ('py:class', 'typing.IO'),
+ ('py:class', 'urllib.request.HTTPSHandler'),
+ ('py:obj', 'typing.Callable'),
+ ('py:obj', 'typing.IO'),
+ ('py:obj', 'bool'),
+ ('py:obj', 'dict'),
+ ('py:obj', 'int'),
+ ('py:obj', 'list'),
+ ('py:obj', 're'),
+ ('py:obj', 'str')
]
# The reST default role (used for this markup: `text`) to use for all documents.
@@ -381,5 +403,5 @@ class SpackStyle(DefaultStyle):
# sphinx.ext.intersphinx
intersphinx_mapping = {
- "python": ("https://docs.python.org/3", None),
+ "python": ("https://docs.python.org/3", "objects.inv"),
}

40
Fix-documentation-so-that-parser-doesn-t-stumble.patch
View File

@ -1,40 +0,0 @@
From: Egbert Eich <eich@suse.com>
Date: Thu Feb 4 07:51:10 2021 +0100
Subject: Fix documentation so that parser doesn't stumble
Patch-mainline: Not yet
Git-commit: 7e787fef5e2c87c53166ee71670f1787300cced3
References:
Add argument to code-block::
Signed-off-by: Egbert Eich <eich@suse.com>
---
lib/spack/docs/build_systems/autotoolspackage.rst | 2 +-
lib/spack/docs/build_systems/pythonpackage.rst | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/lib/spack/docs/build_systems/autotoolspackage.rst b/lib/spack/docs/build_systems/autotoolspackage.rst
index a4c15e5..21913a6 100644
--- a/lib/spack/docs/build_systems/autotoolspackage.rst
+++ b/lib/spack/docs/build_systems/autotoolspackage.rst
@@ -348,7 +348,7 @@ Defining ``with_or_without_verbs`` overrides the behavior of a
``--with-openib`` for older versions of the package and specifying an
alternative dependency name:
-.. code-block::
+.. code-block:: console
--with-openib=</path/to/rdma-core>
diff --git a/lib/spack/docs/build_systems/pythonpackage.rst b/lib/spack/docs/build_systems/pythonpackage.rst
index c2da028..695b446 100644
--- a/lib/spack/docs/build_systems/pythonpackage.rst
+++ b/lib/spack/docs/build_systems/pythonpackage.rst
@@ -90,7 +90,7 @@ Instead of using the ``PythonPackage`` base class, you should extend
the ``Package`` base class and implement the following custom installation
procedure:
-.. code-block::
+.. code-block:: python
def install(self, spec, prefix):
pip = which('pip')

76
Fix-error-during-documentation-build-due-to-recursive-module-inclusion.patch
View File

@ -1,70 +1,72 @@
From: Egbert Eich <eich@suse.com>
Date: Thu Feb 4 09:17:55 2021 +0100
Date: Wed Nov 10 09:40:47 2021 +0100
Subject: Fix error during documentation build due to recursive module inclusion
Patch-mainline: Not yet
Git-commit: 0239763866f506f34357b30e9d882d1e8a87211e
Git-repo: https://github.com/spack/spack
Git-commit: ffc7c32398d3aad53a2f5700b6d6ddee9f0d8ef2
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
lib/spack/spack/build_environment.py | 3 ++-
lib/spack/spack/environment.py | 3 ++-
lib/spack/spack/main.py | 3 ++-
lib/spack/spack/user_environment.py | 3 ++-
lib/spack/spack/build_environment.py | 3 ++-
lib/spack/spack/environment/environment.py | 3 ++-
lib/spack/spack/main.py | 3 ++-
lib/spack/spack/user_environment.py | 3 ++-
4 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 3cf02dc..afd34c0 100644
index 83aa634276..3f32ed39cf 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -51,7 +51,8 @@
import spack.build_systems.cmake
@@ -53,7 +53,8 @@
import spack.build_systems.meson
import spack.config
import spack.install_test
-import spack.main
+if not ( "spack.main" in sys.modules ):
+ import spack.main
import spack.paths
import spack.package
import spack.repo
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 7f7625f..e48929e 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -30,7 +30,8 @@
import spack.util.spack_json as sjson
import spack.util.spack_yaml as syaml
import spack.config
import spack.paths
import spack.platforms
diff --git a/lib/spack/spack/environment/environment.py b/lib/spack/spack/environment/environment.py
index a6be5d1c50..a8d1008c46 100644
--- a/lib/spack/spack/environment/environment.py
+++ b/lib/spack/spack/environment/environment.py
@@ -32,7 +32,8 @@
import spack.stage
import spack.store
import spack.subprocess_context
-import spack.user_environment as uenv
+if not ( "spack.user_environment" in sys.modules ):
+ import spack.user_environment as uenv
from spack.filesystem_view import YamlFilesystemView
import spack.util.cpus
import spack.util.environment
import spack.architecture as architecture
import spack.util.hash
diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py
index f4265a5..494a9ce 100644
index 31a4bfe4ed..dfb2078d4f 100644
--- a/lib/spack/spack/main.py
+++ b/lib/spack/spack/main.py
@@ -31,7 +31,8 @@
import spack.architecture
import spack.config
@@ -36,7 +36,8 @@
import spack
import spack.cmd
import spack.config
-import spack.environment as ev
+if not ( "spack.environment" in sys.modules ):
+ import spack.environment as ev
import spack.modules
import spack.paths
import spack.repo
import spack.store
import spack.platforms
diff --git a/lib/spack/spack/user_environment.py b/lib/spack/spack/user_environment.py
index f08f21e..8925246 100644
index 55f516b732..824583d2ef 100644
--- a/lib/spack/spack/user_environment.py
+++ b/lib/spack/spack/user_environment.py
@@ -8,7 +8,8 @@
import spack.config
import spack.util.prefix as prefix
import spack.util.environment as environment
-import spack.build_environment as build_env
+if not ( "spack.build_environment" in sys.modules ):
+ import spack.build_environment as build_env
@@ -5,7 +5,8 @@
import os
import sys
#: Environment variable name Spack uses to track individually loaded packages
spack_loaded_hashes_var = 'SPACK_LOADED_HASHES'
-import spack.build_environment
+if not ( "spack.build_environment" in sys.modules ):
+ import spack.build_environment
import spack.config
import spack.util.environment as environment
import spack.util.prefix as prefix

84
Make-spack-paths-compliant-to-distro-installation.patch
View File

@ -1,68 +1,42 @@
From f0ccc0fee51e272776af8b4f85f4b4d2d2854bf7 Mon Sep 17 00:00:00 2001
From: Egbert Eich <eich@suse.com>
Date: Tue, 22 Sep 2020 09:42:40 +0200
Subject: [PATCH 2/4] Make spack paths compliant to distro installation
Date: Wed Nov 10 09:40:07 2021 +0100
Subject: Make spack paths compliant to distro installation
Patch-mainline: Not yet
Git-repo: https://github.com/spack/spack
Git-commit: f91da8159ac285f41d215f0bf7d3a15461e63324
References:
Spack is particular about the choice of 'prefix' which will
replace $spack. 'prefix' is the 4th ancestor of paths.py, so
it is relative to the spack installation.
This will only change the coded setups of
var_path -> /var/lib/spack
opt_path -> /opt/spack
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
etc/spack/defaults/config.yaml | 8 ++++----
etc/spack/defaults/repos.yaml | 2 +-
lib/spack/spack/paths.py | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/etc/spack/defaults/config.yaml b/etc/spack/defaults/config.yaml
index d1a7f35a6..4813a8a0a 100644
--- a/etc/spack/defaults/config.yaml
+++ b/etc/spack/defaults/config.yaml
@@ -31,13 +31,13 @@ config:
# Locations where templates should be found
template_dirs:
- - $spack/share/spack/templates
+ - /usr/share/spack/templates
# Locations where different types of modules should be installed.
module_roots:
- tcl: $spack/share/spack/modules
- lmod: $spack/share/spack/lmod
+ tcl: /usr/share/spack/modules
+ lmod: /usr/share/spack/lmod
# Temporary locations Spack can try to use for builds.
@@ -77,7 +77,7 @@ config:
# Cache directory for already downloaded source tarballs and archived
# repositories. This can be purged with `spack clean --downloads`.
- source_cache: $spack/var/spack/cache
+ source_cache: /var/spack/cache
# Cache directory for miscellaneous files, like the package index.
diff --git a/etc/spack/defaults/repos.yaml b/etc/spack/defaults/repos.yaml
index f3e00653e..246919425 100644
--- a/etc/spack/defaults/repos.yaml
+++ b/etc/spack/defaults/repos.yaml
@@ -11,4 +11,4 @@
# ~/.spack/repos.yaml
# -------------------------------------------------------------------------
repos:
- - $spack/var/spack/repos/builtin
+ - /var/lib/spack/repos/builtin
lib/spack/spack/paths.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/lib/spack/spack/paths.py b/lib/spack/spack/paths.py
index 9c803cba7..f16e8ca54 100644
index 6b3543406b..bb16e14145 100644
--- a/lib/spack/spack/paths.py
+++ b/lib/spack/spack/paths.py
@@ -39,7 +39,7 @@
@@ -41,7 +41,7 @@
operating_system_path = os.path.join(module_path, 'operating_systems')
test_path = os.path.join(module_path, "test")
hooks_path = os.path.join(module_path, "hooks")
-opt_path = os.path.join(prefix, "opt")
+opt_path = os.path.join("/", "opt")
share_path = os.path.join(prefix, "share", "spack")
etc_path = os.path.join(prefix, "etc")
@@ -49,7 +49,7 @@
#
# Things in $spack/var/spack
#
-var_path = os.path.join(prefix, "var", "spack")
+var_path = os.path.join("/", "var", "lib", "spack")
# read-only things in $spack/var/spack
repos_path = os.path.join(var_path, "repos")
tests_path = os.path.join(var_path, "tests")
share_path = os.path.join(prefix, "share", "spack")
--
2.26.2

26
Set-modules-default-to-lmod.patch Normal file
View File

@ -0,0 +1,26 @@
From: Egbert Eich <eich@suse.com>
Date: Wed Nov 10 20:28:29 2021 +0100
Subject: Set modules default to lmod
Patch-mainline: Not yet
Git-repo: https://github.com/spack/spack
Git-commit: fc190d74554d93e1907a6d56aeaeb35d328c4e22
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
etc/spack/defaults/modules.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/etc/spack/defaults/modules.yaml b/etc/spack/defaults/modules.yaml
index 27b7c45f66..09e572067b 100644
--- a/etc/spack/defaults/modules.yaml
+++ b/etc/spack/defaults/modules.yaml
@@ -44,7 +44,7 @@ modules:
# lmod: $spack/share/spack/lmod
# What type of modules to use
enable:
- - tcl
+ - lmod
# Default configurations if lmod is enabled
lmod:

11
_constraints Normal file
View File

@ -0,0 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<constraints>
<hardware>
<memory>
<size unit="G">8</size>
</memory>
<disk>
<size unit="G">8</size>
</disk>
</hardware>
</constraints>

77
added-dockerfile-for-opensuse-leap-15.patch
View File

@ -1,77 +0,0 @@
From d9b88381189ca860cd63c48a53d2298fd8d206db Mon Sep 17 00:00:00 2001
From: Christian Goll <cgoll@suse.de>
Date: Tue, 24 Nov 2020 16:35:32 +0100
Subject: [PATCH 1/2] added dockerfile for opensuse leap 15
---
share/spack/docker/leap-15.dockerfile | 58 +++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
create mode 100644 share/spack/docker/leap-15.dockerfile
diff --git a/share/spack/docker/leap-15.dockerfile b/share/spack/docker/leap-15.dockerfile
new file mode 100644
index 000000000..36054cd44
--- /dev/null
+++ b/share/spack/docker/leap-15.dockerfile
@@ -0,0 +1,58 @@
+FROM opensuse/leap:15.2
+MAINTAINER SUSE HPC <suse-hpc@suse.de>
+
+ENV DOCKERFILE_BASE=opensuse \
+ DOCKERFILE_DISTRO=opensuse_leap \
+ DOCKERFILE_DISTRO_VERSION=15.2 \
+ SPACK_ROOT_DOCKER=/opt/spack \
+ DEBIAN_FRONTEND=noninteractive \
+ CURRENTLY_BUILDING_DOCKER_IMAGE=1 \
+ container=docker
+
+COPY bin $SPACK_ROOT/bin
+COPY etc $SPACK_ROOT/etc
+COPY lib $SPACK_ROOT/lib
+COPY share $SPACK_ROOT/share
+COPY var $SPACK_ROOT/var
+
+
+RUN mkdir -p $SPACK_ROOT/opt/spack
+
+RUN zypper ref && \
+ zypper up -y && \
+ zypper in -y python3-base \
+ xz gzip tar bzip2 curl patch \
+ gcc-c++ make cmake automake&&\
+ zypper clean
+
+# clean up manpages
+RUN rm -rf /var/cache/zypp/* \
+ rm -rf /usr/share/doc/packages/* \
+ rm -rf /usr/share/doc/manual/*
+
+
+RUN mkdir -p /root/.spack \
+ && cp $SPACK_ROOT/share/spack/docker/modules.yaml \
+ /root/.spack/modules.yaml \
+ && rm -rf /root/*.* /run/nologin $SPACK_ROOT/.git
+
+# [WORKAROUND]
+# https://superuser.com/questions/1241548/
+# xubuntu-16-04-ttyname-failed-inappropriate-ioctl-for-device#1253889
+RUN [ -f ~/.profile ] \
+ && sed -i 's/mesg n/( tty -s \\&\\& mesg n || true )/g' ~/.profile \
+ || true
+
+WORKDIR /root
+SHELL ["docker-shell"]
+
+# Find tools which are in distro
+RUN spack external find --scope system
+
+# TODO: add a command to Spack that (re)creates the package cache
+RUN spack spec hdf5+mpi
+
+ENTRYPOINT ["/bin/bash", "/opt/spack/share/spack/docker/entrypoint.bash"]
+CMD ["interactive-shell"]
+
+
--
2.26.2

65
basic-exclude-pattern-for-external-find.patch
View File

@ -1,65 +0,0 @@
From 03bf4e89802b626278a4b14b4349ee94aa722965 Mon Sep 17 00:00:00 2001
From: Christian Goll <cgoll@suse.de>
Date: Fri, 26 Feb 2021 14:21:04 +0100
Subject: [PATCH] basic exclude pattern for external find
---
lib/spack/spack/cmd/external.py | 18 +++++++++++++-----
1 file changed, 13 insertions(+), 5 deletions(-)
diff --git a/lib/spack/spack/cmd/external.py b/lib/spack/spack/cmd/external.py
index 52af72ed8f..ff583d9e87 100644
--- a/lib/spack/spack/cmd/external.py
+++ b/lib/spack/spack/cmd/external.py
@@ -42,6 +42,9 @@ def setup_parser(subparser):
'--scope', choices=scopes, metavar=scopes_metavar,
default=spack.config.default_modify_scope('packages'),
help="configuration scope to modify")
+ find_parser.add_argument(
+ '--exclude',
+ help="do not call binaries with this regular pattern for the search")
find_parser.add_argument('packages', nargs=argparse.REMAINDER)
sp.add_parser(
@@ -153,7 +156,7 @@ def external_find(args):
else:
packages_to_check = spack.repo.path.all_packages()
- pkg_to_entries = _get_external_packages(packages_to_check)
+ pkg_to_entries = _get_external_packages(packages_to_check,args.exclude)
new_entries = _update_pkg_config(
args.scope, pkg_to_entries, args.not_buildable
)
@@ -236,7 +239,7 @@ def _update_pkg_config(scope, pkg_to_entries, not_buildable):
return all_new_specs
-def _get_external_packages(packages_to_check, system_path_to_exe=None):
+def _get_external_packages(packages_to_check,exclude_binaries=None, system_path_to_exe=None):
if not system_path_to_exe:
system_path_to_exe = _get_system_executables()
@@ -247,12 +250,17 @@ def _get_external_packages(packages_to_check, system_path_to_exe=None):
exe_pattern_to_pkgs[exe].append(pkg)
pkg_to_found_exes = defaultdict(set)
+ if exclude_binaries:
+ compiled_exclude = re.compile(exclude_binaries)
+ else:
+ compiled_exclude = None
for exe_pattern, pkgs in exe_pattern_to_pkgs.items():
compiled_re = re.compile(exe_pattern)
for path, exe in system_path_to_exe.items():
- if compiled_re.search(exe):
- for pkg in pkgs:
- pkg_to_found_exes[pkg].add(path)
+ if not compiled_exclude or not compiled_exclude.search(exe):
+ if compiled_re.search(exe):
+ for pkg in pkgs:
+ pkg_to_found_exes[pkg].add(path)
pkg_to_entries = defaultdict(list)
resolved_specs = {} # spec -> exe found for the spec
--
2.26.2

3
objects.inv Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:9494d0f318cc65c0871829455a4a4c08948b557a585ac26d83216ac8a93f7bc1
size 112656

11
run-find-external.sh
View File

@ -19,11 +19,18 @@ mypath=/usr/lib64/mpi/gcc/openmpi2/bin:${mypath}
mypath=/usr/lib64/mpi/gcc/openmpi1/bin:${mypath}
mypath=/usr/lib64/mpi/gcc/mvapich2/bin:${mypath}
mypath=/usr/lib64/mpi/gcc/mpich/bin:${mypath}
mypath=/usr/lib/hpc/gnu?/mpi/openmpi/4.*/bin:${mypath}
mypath=/usr/lib/hpc/gnu?/mpi/openmpi/3.*/bin:${mypath}
mypath=/usr/lib/hpc/gnu?/mpi/openmpi/2.*/bin:${mypath}
mypath=/usr/lib/hpc/gnu?/mpi/mpich/3.*/bin:${mypath}
mypath=/usr/lib/hpc/gnu?/mpi/mvapich2/2.*/bin:${mypath}
# test if we can run as nobody
getent passwd nobody &> /dev/null
if [ "x$?" == "x0" ] ; then
# drop all root rights, when calling external find
sudo -u nobody PATH=${mypath}:${PATH} spack external find --scope user --exclude 'installdbgsymbols'
sudo -u nobody PATH=${mypath}:${PATH} spack external find --scope user #--exclude 'installdbgsymbols'
if [ -e /var/lib/nobody/.spack/packages.yaml ] ; then
mv -v /var/lib/nobody/.spack/packages.yaml /etc/spack/packages.yaml
chown root:root /etc/spack/packages.yaml
@ -31,5 +38,5 @@ if [ "x$?" == "x0" ] ; then
fi
else
# May run in a container...
PATH=${mypath}:${PATH} spack external find --scope system --exclude 'installdbgsymbols'
PATH=${mypath}:${PATH} spack external find --scope system #--exclude 'installdbgsymbols'
fi

3
spack-0.16.3.tar.gz
View File

@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:26636a2e2cc066184f12651ac6949f978fc041990dba73934960a4c9c1ea383d
size 5543891

3
spack-0.17.0.tar.gz Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:93df99256a892ceefb153d48e2080c01d18e58e27773da2c2a469063d67cb582
size 6747773

94
spack.changes
View File

@ -1,3 +1,97 @@
-------------------------------------------------------------------
Mon Nov 8 14:55:34 UTC 2021 - Christian Goll <cgoll@suse.com>
- updated to version 0.17.0
(Upstream feature/bug references (<ID>) are relative to
https://github.com/spack/spack/issues/<ID>).
* New concretizer is now default
The new concretizer introduced as an experimental feature in v0.16.0
is now the default (#25502). The new concretizer is based on the
clingo logic programming system,
and it enables us to do much higher quality and faster dependency solving
The old concretizer is still available via the concretizer: original
setting, but it is deprecated and will be removed in v0.18.0.
* Binary Bootstrapping
To make it easier to use the new concretizer and binary packages,
Spack now bootstraps clingo and GnuPG from public binaries. If it
is not able to bootstrap them from binaries, it installs them from
source code. With these changes, you should still be able to clone Spack
and start using it almost immediately.
* Reuse existing packages (experimental)
The most wanted feature from our
2020 user survey and
the most wanted Spack feature of all time (#25310). spack install,
spack spec, and spack concretize now have a --reuse option, which
causes Spack to minimize the number of rebuilds it does. The --reuse
option will try to find existing installations and binary packages locally
and in registered mirrors, and will prefer to use them over building new
versions. This will allow users to build from source far less than in
prior versions of Spack. This feature will continue to be improved, with
configuration options and better CLI expected in v0.17.1. It will become
the default concretization mode in v0.18.0.
* Better error messages
We have improved the error messages generated by the new concretizer by
using unsatisfiable cores. Spack will now print a summary of the types
of constraints that were violated to make a spec unsatisfiable (#26719).
* Conditional variants
Variants can now have a when="<spec>" clause, allowing them to be
conditional based on the version or other attributes of a package (#24858).
* Git commit versions
In an environment and on the command-line, you can now provide a full,
40-character git commit as a version for any package with a top-level
git URL. e.g., spack install hdf5@45bb27f58240a8da7ebb4efc821a1a964d7712a8.
Spack will compare the commit to tags in the git repository to understand
what versions it is ahead of or behind.
* Override local config and cache directories
You can now set SPACK_DISABLE_LOCAL_CONFIG to disable the ~/.spack and
/etc/spack configuration scopes. SPACK_USER_CACHE_PATH allows you to
move caches out of ~/.spack, as well (#27022, #26735). This addresses
common problems where users could not isolate CI environments from local
configuration.
* Improvements to Spack Containerize
For added reproducibility, you can now pin the Spack version used by
spack containerize (#21910). The container build will only build
with the Spack version pinned at build recipe creation instead of the
latest Spack version.
* New commands for dealing with tags
The spack tags command allows you to list tags on packages (#26136), and you
can list tests and filter tags with spack test list (#26842).
* Copy and relocate environment views as stand-alone installations (#24832)
* spack diff command can diff two installed specs (#22283, #25169)
* spack -c <config> can set one-off config parameters on CLI (#22251)
* spack load --list is an alias for spack find --loaded (#27184)
* spack gpg can export private key with --secret (#22557)
* spack style automatically bootstraps dependencies (#24819)
* spack style --fix automatically invokes isort (#24071)
* build dependencies can be installed from build caches with --include-build-deps (#19955)
* spack audit command for checking package constraints (#23053)
* spack can now fetch from CVS repositories (yep, really) (#23212)
* spack monitor lets you upload analysis about installations to a
* spack monitor server (#23804, #24321, #23777, #25928))
* spack python --path shows which python Spack is using (#22006)
* spack env activate --temp can create temporary environments (#25388)
* --preferred and --latest options for spack checksum (#25830)
* SPACK_PYTHON environment variable sets which python spack uses (#21222)
* SPACK_SKIP_MODULES lets you source setup-env.sh faster if you don't need modules (#24545)
- removed following patches as incomperated upstream:
* added-dockerfile-for-opensuse-leap-15.patch
- removed as not needed any more:
* basic-exclude-pattern-for-external-find.patch
* Fix-documentation-so-that-parser-doesn-t-stumble.patch
- updated patches:
* Adapt-shell-scripts-that-set-up-the-environment-for-different-shells.patch
* added-target-and-os-calls-to-output-of-spack-spec-co.patch
* Fix-error-during-documentation-build-due-to-recursive-module-inclusion.patch
* fix-tumbleweed-naming.patch
* Make-spack-paths-compliant-to-distro-installation.patch
- added:
* Fix-Spinx-configuration-to-avoid-throwing-errors.patch
* Set-modules-default-to-lmod.patch
- updated requires to actual sphinx version, so that the documentation
builds
- Included source:
objects.inv
-------------------------------------------------------------------
Fri Oct 15 17:00:57 UTC 2021 - Egbert Eich <eich@suse.com>

62
spack.spec
View File

@ -36,7 +36,7 @@ ExclusiveArch: do_not_build
# non oss packages
%define spack_trigger_external cuda-nvcc
Name: spack
Version: 0.16.3
Version: 0.17.0
Release: 0
Summary: Package manager for HPC systems
License: Apache-2.0 AND MIT AND Python-2.0 AND BSD-3-Clause
@ -46,16 +46,14 @@ Source1: README.SUSE
Source2: spack-rpmlintrc
Source3: run-find-external.sh
Source4: https://en.opensuse.org/index.php?title=Spack&action=raw&ref=157522#/README-oo-wiki
Patch0: Make-spack-paths-compliant-to-distro-installation.patch
Source5: https://docs.python.org/3/objects.inv
Patch1: fix-tumbleweed-naming.patch
Patch2: Adapt-shell-scripts-that-set-up-the-environment-for-different-shells.patch
Patch3: added-dockerfile-for-opensuse-leap-15.patch
Patch4: added-target-and-os-calls-to-output-of-spack-spec-co.patch
Patch5: Fix-documentation-so-that-parser-doesn-t-stumble.patch
Patch5: Make-spack-paths-compliant-to-distro-installation.patch
Patch6: Fix-error-during-documentation-build-due-to-recursive-module-inclusion.patch
Patch7: basic-exclude-pattern-for-external-find.patch
# upstream patch removes also problemtatic binaries
#Patch4: spack-test-15702.patch
Patch7: Fix-Spinx-configuration-to-avoid-throwing-errors.patch
Patch8: Set-modules-default-to-lmod.patch
%if %{without doc}
BuildRequires: fdupes
BuildRequires: lua-lmod
@ -66,6 +64,7 @@ BuildRequires: sudo
BuildRequires: sysuser-tools
Requires: %{name}-recipes = %{version}
Requires: bzip2
Requires: coreutils
Requires: curl
Requires: gcc-c++
Requires: gcc-fortran
@ -75,16 +74,18 @@ Requires: lua-lmod
Requires: make
Requires: patch
Requires: polkit
Requires: python3-clingo
Requires: sudo
Requires: tar
Requires: xz
Recommends: %spack_trigger_recommended
Recommends: spack-recipes = %version
%else
BuildRequires: %{python_module Sphinx >= 1.8}
BuildRequires: %{python_module sphinxcontrib-programoutput}
BuildRequires: git
BuildRequires: makeinfo
# Hardcode this - there is no python2 version of this around any more.
BuildRequires: python3-Sphinx >= 3.4
BuildRequires: python3-sphinxcontrib-programoutput
BuildRequires: spack
# html
BuildRequires: graphviz
@ -164,12 +165,48 @@ This package contains the info page.
for i in share/spack/setup-env.*; do
sed -i -e "s;@@_prefix@@;%_prefix;g" $i
done
%else
cp %{S:5} lib/spack/docs/
%endif
for file in $(find . -type f); do
sed -e 's@$spack/opt@/opt@g' \
-e 's@$spack/share/spack/modules@/opt/spack/modules@g' \
-e 's@$spack/share/spack/lmod@/opt/spack/modules@g' \
-e 's@$spack/var@/var/lib@g' \
-i $file
done
%build
# Nothing to build
%if %{with doc}
mkdir -p ${HOME}/.spack
cat > ${HOME}/.spack/config.yaml <<EOF
config:
install_tree:
root: /tmp/spack
projections:
all: "${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}"
EOF
# Don't really run spack when building documentation!
tmpdir=$(mktemp -d %{_sourcedir}/tmpd-XXXXXXXXX)
echo -e '#! /bin/sh
args=${1+"$@"}
while [ -n "$1" ]; do
case $1 in
--*) shift ;;
graph|spec) exit 0 ;;
*) exec /usr/bin/spack ${args} ;;
esac;
done
exit 0' > $tmpdir/spack
chmod 0755 $tmpdir/spack
PATH=$tmpdir:${PATH}
export PATH
mkdir -p /tmp/spack
cd lib/spack/docs
# fix Makefile of sphinx and ignore warnings due to offline build
sed -i 's/\(^SPHINXOPTS\).*/\1 = --keep-going /' Makefile
# Causes issues building texinfo as a suitable image cannot be found
grep -rl ":target:" | xargs sed -i -e "/:target:/s/^/#/" -e "/figure::/s/^/#/"
# Fix path to var - we install this to the 'real' /var
@ -194,7 +231,9 @@ compilers:
unset: []
extra_rpaths: []
EOF
make man info #text dirhtml
source /usr/share/spack/setup-env.sh
make man info || { cat /tmp/sphinx-err-*.log; exit 1; } #text dirhtml
rm -rf $tmpdir
gzip _build/texinfo/Spack.info _build/man/spack.1
%endif
@ -393,6 +432,9 @@ fi
sed -i "s@HOSTTYPE@$HOSTTYPE@" %{spack_dir}/etc/spack/compilers.yaml
# find installed programms
/usr/lib/spack/run-find-external.sh
mkdir -p /opt/spack
chgrp spack /opt/spack
chmod 0775 /opt/spack
%triggerin -- %{?spack_trigger_recommended} %{?spack_trigger_packages} %{?spack_trigger_external}
/usr/lib/spack/run-find-external.sh