Merge branch '21-new-container-job-failed-30516' into 'master'

Fix acts build for #21

Closes #21

See merge request !27

containers/builder/Dockerfile

 # Builder with Argonne EIC software
 #
-FROM eicweb.phy.anl.gov:4567/containers/image_recipes/debian_spack:snapshot-20201117
+FROM eicweb.phy.anl.gov:4567/containers/image_recipes/debian_spack:snapshot-20210111
 
 LABEL maintainer="Sylvester Joosten <sjoosten@anl.gov>" \
       name="eic_builder" \
@@ -11,7 +11,7 @@ LABEL maintainer="Sylvester Joosten <sjoosten@anl.gov>" \
 
 ENV DOCKERFILE_BASE=debian            \
     DOCKERFILE_DISTRO=debian          \
-    DOCKERFILE_DISTRO_VERSION=20201117-testing \
+    DOCKERFILE_DISTRO_VERSION=20210111-testing \
     SPACK_ROOT=/opt/spack             \
     DEBIAN_FRONTEND=noninteractive    \
     CURRENTLY_BUILDING_DOCKER_IMAGE=1 \
@@ -28,10 +28,6 @@ RUN apt-get -yqq update \
 ## Setup our environment definition
 COPY spack.yaml /opt/spack-environment/spack.yaml
 
-## Utility script to update the build cache
-## TODO: move this upstream to debian_spack
-COPY update_buildcache.sh /usr/sbin/update_buildcache
-
 ## Ensure an up-to-date custom package list
 ## TODO: We should just remove this from the upstream container
 ##       and only initialize the custom packages here for more

containers/builder/spack.yaml

 spack:
   specs:
-    - cmake@3.18.4
+    - cmake@3.18.1
     - fmt@7.1.2 cxxstd=17
     - spdlog@1.5.0
     - nlohmann-json@3.9.1
@@ -23,7 +23,7 @@ spack:
     - podio@0.13
     - geant4@10.6.2 cxxstd=17 +opengl +vecgeom +x11 +qt ^qt +opengl
     - dd4hep@1.14.1 +geant4 +assimp +hepmc3 +ipo
-    - acts@1.02.0 +dd4hep +digitization +identification +json +tgeo +ipo ^eigen@3.3.7
+    - acts@1.02.0 +dd4hep +digitization +identification +json +tgeo +ipo
     - gaudi@34.0
     - dawn@3_91a
     - dawncut@1_54a

containers/builder/update_buildcache.sh

-#!/bin/bash
-
-## Update the spack buildcache with the contents of this image
-## Note: this needs to be run manually from the CI machine with
-##       all relevant directories mounted into the image.
-
-## info of spack installation on CI machine
-GLOBAL_SPACK_ROOT=/lab/opt/spack
-LOCAL_SPACK_ROOT=/opt/spack
-SPACK_MIRROR=$GLOBAL_SPACK_ROOT/var/mirror
-
-## two use cases:
-## 1. arguments supplied --> update the packages in the arguments
-## 2. no arguments supplied --> update all packages
-
-function print_the_help() {
-  echo "USAGE: $0 [-h] [packages ...]"
-  echo ""
-  echo "        Update the spack buildcache with contents of this image."
-  echo "        If no packages are supplied on the command line, create"
-  echo "        cache for *all* packages in this image"
-  exit
-}
-
-
-positional=("$@")
-while [ $# -gt 0 ]; do
-  key="$1"
-  case $key in
-    *-h|--help) 
-      print_the_help
-      exit 0
-      shift
-      ;;
-    *)    # unknown option, do nothing
-      shift
-      ;;
-  esac
-done
-set -- "${positional[@]}"
-
-## setup GPG to sign packages
-rm -rf $LOCAL_SPACK_ROOT/opt/spack/gpg
-cp -r $GLOBAL_SPACK_ROOT/opt/spack/gpg $LOCAL_SPACK_ROOT/opt/spack/gpg
-
-## case 1: no argument --> export all
-if [ $# -eq 0 ]; then
-  ## list all available packages
-  spack find > tmp.manifest.txt
-
-  ## trim off the first line, trim off the version info 
-  ## and replace newlines with spaces
-  tail -n +2 tmp.manifest.txt | sed "s/@.+//" | tr '\n' ' ' > tmp.packages.txt
-  rm tmp.manifest.txt
-## case 2: update requested packages only
-else
-  echo $@ > tmp.packages.txt
-fi
-
-## now generate the buildcache (this will take a while)
-cat tmp.packages.txt | xargs spack buildcache create -a -f -d $SPACK_MIRROR
-spack buildcache update-index -d /lab/opt/spack/var/mirror
-rm tmp.packages.txt
-
-## That's all!

containers/release/Dockerfile.in

@@ -11,7 +11,7 @@ RUN cd /opt/spack-environment && spack env activate . && spack gc -y
     #grep 'x-executable\|x-archive\|x-sharedlib' | \
     #awk -F: '{print $1}' | xargs strip -s
 
-FROM eicweb.phy.anl.gov:4567/containers/image_recipes/debian_minimal:testing-20201117
+FROM eicweb.phy.anl.gov:4567/containers/image_recipes/debian_minimal:testing-20210111
 LABEL maintainer="Sylvester Joosten <sjoosten@anl.gov>" \
       name="eic" \
       group="eic" \
@@ -22,7 +22,7 @@ LABEL maintainer="Sylvester Joosten <sjoosten@anl.gov>" \
 ## @ENV@ will be automatically expanded to auto-load the 
 ## runtime environment
 ENV DOCKERFILE_DISTRO=debian          \
-    DOCKERFILE_DISTRO_VERSION=20201117-testing   \
+    DOCKERFILE_DISTRO_VERSION=20210111-testing   \
     DEBIAN_FRONTEND=noninteractive    \
 @ENV@
 

gitlab-ci/docker/Makefile

@@ -55,21 +55,25 @@ publish-stable: login
 	@echo 'publish $(STABLE) to $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME)'
 	docker tag $(APP_NAME):$(VERSION) $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(STABLE)
 	docker push $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(STABLE)
+	docker rmi $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(STABLE)
 
 publish-latest: login 
 	@echo 'publish latest to $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME)'
 	docker tag $(APP_NAME):$(VERSION) $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):latest
 	docker push $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):latest
+	docker rmi $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):latest
 
 publish-version: login 
 	@echo 'publish $(STABLE) to $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME)'
 	docker tag $(APP_NAME):$(VERSION) $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(VERSION)
 	docker push $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(VERSION)
+	docker rmi $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(VERSION)
 
 publish-unstable: login 
 	@echo 'publish unstable to $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME)'
 	docker tag $(APP_NAME):$(VERSION)-unstable $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):unstable
 	docker push $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):unstable
+	docker rmi $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):unstable
 
 version: ## Output the current version
 	@echo $(VERSION)

spack/packages/acts/README.md

-This is merely an older version of the spack file to fix an issue where the older version
-of acts somehow does not correctly build anymore with the new package file. This should be
-removed when we upgrade acts.

spack/packages/eigen/package.py

+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+class Eigen(CMakePackage):
+    """Eigen is a C++ template library for linear algebra matrices,
+    vectors, numerical solvers, and related algorithms.
+    """
+
+    homepage = 'http://eigen.tuxfamily.org/'
+    url = 'https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz'
+
+    version('3.3.8', sha256='146a480b8ed1fb6ac7cd33fec9eb5e8f8f62c3683b3f850094d9d5c35a92419a')
+    version('3.3.7', sha256='d56fbad95abf993f8af608484729e3d87ef611dd85b3380a8bad1d5cbc373a57')
+    version('3.3.6', sha256='e7cd8c94d6516d1ada9893ccc7c9a400fcee99927c902f15adba940787104dba')
+    version('3.3.5', sha256='383407ab3d0c268074e97a2cbba84ac197fd24532f014aa2adc522355c1aa2d0')
+    version('3.3.4', sha256='c5ca6e3442fb48ae75159ca7568854d9ba737bc351460f27ee91b6f3f9fd1f3d')
+    version('3.3.3', sha256='fd72694390bd8e81586205717d2cf823e718f584b779a155db747d1e68481a2e')
+    version('3.3.2', sha256='8d7611247fba1236da4dee7a64607017b6fb9ca5e3f0dc44d480e5d33d5663a5')
+    version('3.3.1', sha256='50dd21a8997fce0857b27a126811ae8ee7619984ab5425ecf33510cec649e642')
+    version('3.3.0', sha256='de82e01f97e1a95f121bd3ace87aa1237818353c14e38f630a65f5ba2c92f0e1')
+    version('3.2.10', sha256='0920cb60ec38de5fb509650014eff7cc6d26a097c7b38c7db4b1aa5df5c85042')
+    version('3.2.9', sha256='f683b20259ad72c3d384c00278166dd2a42d99b78dcd589ed4a6ca74bbb4ca07')
+    version('3.2.8', sha256='64c54781cfe9eefef2792003ab04b271d4b2ec32eda6e9cdf120d7aad4ebb282')
+    version('3.2.7', sha256='0ea9df884873275bf39c2965d486fa2d112f3a64b97b60b45b8bc4bb034a36c1')
+    version('3.2.6', sha256='e097b8dcc5ad30d40af4ad72d7052e3f78639469baf83cffaadc045459cda21f')
+    version('3.2.5', sha256='8068bd528a2ff3885eb55225c27237cf5cda834355599f05c2c85345db8338b4')
+
+    # there is a bug in 3.3.8 that provokes a compile error in dependent packages, see https://gitlab.com/libeigen/eigen/-/issues/2011
+    patch('https://gitlab.com/libeigen/eigen/-/commit/6d822a1052fc665f06dc51b4729f6a38e0da0546.diff', when='@3.3.8',
+          sha256='62590e9b33a8f72b608a72b87147a306e7cb20766ea53c6b8e0a183fa6cb7635')
+
+    # From http://eigen.tuxfamily.org/index.php?title=Main_Page#Requirements
+    # "Eigen doesn't have any dependencies other than the C++ standard
+    # library."
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo'))
+
+    # TODO: latex and doxygen needed to produce docs with make doc
+    # TODO: Other dependencies might be needed to test this package
+
+    def setup_run_environment(self, env):
+        env.prepend_path('CPATH', self.prefix.include.eigen3)
+
+    @property
+    def headers(self):
+        headers = find_all_headers(self.prefix.include)
+        headers.directories = [self.prefix.include.eigen3]
+        return headers

spack/packages/xcb-proto/package.py

+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class XcbProto(AutotoolsPackage):
+    """xcb-proto provides the XML-XCB protocol descriptions that libxcb uses to
+    generate the majority of its code and API."""
+
+    homepage = "http://xcb.freedesktop.org/"
+    url      = "http://xcb.freedesktop.org/dist/xcb-proto-1.13.tar.gz"
+
+    version('1.13', sha256='0698e8f596e4c0dbad71d3dc754d95eb0edbb42df5464e0f782621216fa33ba7')
+    version('1.12', sha256='cfa49e65dd390233d560ce4476575e4b76e505a0e0bacdfb5ba6f8d0af53fd59')
+    version('1.11', sha256='d12152193bd71aabbdbb97b029717ae6d5d0477ab239614e3d6193cc0385d906')
+
+    # TODO: uncomment once build deps can be resolved separately
+    # See #7646, #4145, #4063, and #2548 for details
+    # extends('python')
+
+    patch('xcb-proto-1.12-schema-1.patch', when='@1.12')
+
+    ## using fractions.gcd has been deprecated since python 3.5
+    ## always apply fix
+    patch('python-fix.patch')

spack/packages/xcb-proto/python-fix.patch

+diff --git a/xcbgen/align.py b/xcbgen/align.py
+index d4c12ee..cc39764 100644
+--- a/xcbgen/align.py
++++ b/xcbgen/align.py
+@@ -2,7 +2,7 @@
+ This module contains helper classes for alignment arithmetic and checks
+ '''
+ 
+-from fractions import gcd
++import math
+ 
+ class Alignment(object):
+ 
+@@ -73,14 +73,14 @@ class Alignment(object):
+     def combine_with(self, other):
+         # returns the alignment that is guaranteed when
+         # both, self or other, can happen
+-        new_align = gcd(self.align, other.align)
++        new_align = math.gcd(self.align, other.align)
+         new_offset_candidate1 = self.offset % new_align
+         new_offset_candidate2 = other.offset % new_align
+         if new_offset_candidate1 == new_offset_candidate2:
+             new_offset = new_offset_candidate1
+         else:
+             offset_diff = abs(new_offset_candidate2 - new_offset_candidate1)
+-            new_align = gcd(new_align, offset_diff)
++            new_align = math.gcd(new_align, offset_diff)
+             new_offset_candidate1 = self.offset % new_align
+             new_offset_candidate2 = other.offset % new_align
+             assert new_offset_candidate1 == new_offset_candidate2

spack/packages/xcb-proto/xcb-proto-1.12-schema-1.patch

+Submitted By: Bruce Dubbs <bdubbs at linuxfromscratch dot org>
+Date: 2016-06-01
+Initial Package Version: 1.12
+Upstream Status: Not Committed
+Origin: https://lists.freedesktop.org/archives/xcb/2016-February/010676.html
+Description: Fixes make check
+
+
+--- a/src/xcb.xsd
++++ b/src/xcb.xsd
+@@ -44,6 +44,15 @@ authorization from the authors.
+     <xsd:complexType>
+       <xsd:attribute name="bytes" type="xsd:integer" use="optional" />
+       <xsd:attribute name="align" type="xsd:integer" use="optional" />
++      <xsd:attribute name="serialize" type="xsd:boolean" use="optional" />
++    </xsd:complexType>
++  </xsd:element>
++
++  <!-- Alignment -->
++  <xsd:element name="required_start_align" >
++    <xsd:complexType>
++      <xsd:attribute name="align" type="xsd:integer" use="required" />
++      <xsd:attribute name="offset" type="xsd:integer" use="optional" />
+     </xsd:complexType>
+   </xsd:element>
+ 
+@@ -76,14 +85,13 @@ authorization from the authors.
+     <xsd:sequence>
+       <!-- switch(expression) -->
+       <xsd:group ref="expression" minOccurs="1" maxOccurs="1" />
++      <xsd:element ref="required_start_align" minOccurs="0" maxOccurs="1" />
+       <xsd:choice>
+         <!-- bitcase expression - bit test -->
+         <xsd:element name="bitcase" type="caseexpr" minOccurs="0" maxOccurs="unbounded" />
+         <!-- case expression - value test -->
+         <xsd:element name="case" type="caseexpr" minOccurs="0" maxOccurs="unbounded" />
+       </xsd:choice>
+-      <!-- default: -->
+-      <xsd:group ref="fields" minOccurs="0" maxOccurs="1" />
+     </xsd:sequence>
+     <xsd:attribute name="name" type="xsd:string" use="required" />
+   </xsd:complexType>
+@@ -201,6 +209,7 @@ authorization from the authors.
+       <xsd:element ref="field" />
+       <xsd:element ref="list" />
+       <xsd:element ref="fd" />
++      <xsd:element ref="required_start_align" />
+     </xsd:choice>
+   </xsd:group>
+ 
+
+