From: Mark Abraham <mark.j.abraham@gmail.com>
Date: Mon, 7 Jun 2021 08:57:19 +0000 (+0000)
Subject: Update to Ubuntu 20.04 in CI
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=181b490c575ed1abce504e1fb948cfef4e6bb4cb;p=alexxy%2Fgromacs.git

Update to Ubuntu 20.04 in CI
---

diff --git a/admin/containers/buildall.sh b/admin/containers/buildall.sh
index b3e5c7739f..6c3b366b15 100755
--- a/admin/containers/buildall.sh
+++ b/admin/containers/buildall.sh
@@ -9,18 +9,17 @@ SCRIPT=$PWD/scripted_gmx_docker_builds.py
 # images needed, because the same one can test library,
 # thread and no MPI configurations.
 
-args[${#args[@]}]="--gcc 10 --clfft --mpi openmpi --ubuntu 20.04"
+args[${#args[@]}]="--gcc 10 --clfft --mpi openmpi"
 args[${#args[@]}]="--gcc 9 --clfft --mpi openmpi"
-args[${#args[@]}]="--gcc 10 --cuda 11.2.2 --clfft --mpi openmpi --ubuntu 20.04"
-args[${#args[@]}]="--gcc 7 --cuda 11.0 --clfft --mpi openmpi --ubuntu 20.04"
-args[${#args[@]}]="--llvm 8 --tsan"
+args[${#args[@]}]="--gcc 10 --cuda 11.2.2 --clfft --mpi openmpi"
+args[${#args[@]}]="--gcc 7 --cuda 11.0 --clfft --mpi openmpi"
 args[${#args[@]}]="--llvm 11 --tsan"
-args[${#args[@]}]="--llvm 8 --cuda 11.0 --clfft --mpi openmpi --ubuntu 20.04"
-args[${#args[@]}]="--llvm 9 --clfft --mpi openmpi --ubuntu 18.04"
+args[${#args[@]}]="--llvm 8 --cuda 11.0 --clfft --mpi openmpi"
+args[${#args[@]}]="--llvm 9 --clfft --mpi openmpi"
 args[${#args[@]}]="--oneapi 2021.1.1"
-args[${#args[@]}]="--oneapi 2021.2.0 --intel-compute-runtime 21.21.19914 --ubuntu 20.04"
+args[${#args[@]}]="--oneapi 2021.2.0 --intel-compute-runtime 21.21.19914"
 args[${#args[@]}]="--llvm --doxygen --mpi openmpi --venvs 3.7.7"
-args[${#args[@]}]="--llvm 11 --cuda 11.2.1 --hipsycl 2bc21b677a --ubuntu 20.04"
+args[${#args[@]}]="--llvm 11 --cuda 11.2.1 --hipsycl 2bc21b677a"
 
 echo "Building the following images."
 for arg_string in "${args[@]}"; do
diff --git a/admin/containers/scripted_gmx_docker_builds.py b/admin/containers/scripted_gmx_docker_builds.py
index 1a5c94ca7b..a341dd64b3 100755
--- a/admin/containers/scripted_gmx_docker_builds.py
+++ b/admin/containers/scripted_gmx_docker_builds.py
@@ -108,8 +108,8 @@ _opencl_extra_packages = [
     'ocl-icd-opencl-dev',
     'opencl-headers',
     # The following require
-    #             apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
-    #             apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main']
+    #             apt_keys=['http://repo.radeon.com/rocm/rocm.gpg.key'],
+    #             apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/4.0.1/ xenial main']
     'libelf1',
     'rocm-opencl',
     'rocm-dev',
@@ -162,7 +162,6 @@ _docs_extra_packages = ['autoconf',
                         'help2man',
                         'imagemagick',
                         'libtool',
-                        'linkchecker',
                         'mscgen',
                         'm4',
                         'openssh-client',
@@ -532,6 +531,8 @@ def add_documentation_dependencies(input_args,
     """Add appropriate layers according to doxygen input arguments."""
     if input_args.doxygen is None:
         return
+    # Always clone the same version of linkchecker (latest release at June 1, 2021)
+    output_stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['git+https://github.com/linkchecker/linkchecker.git@v10.0.1'])
     output_stages['main'] += hpccm.primitives.shell(
         commands=['sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
     if input_args.doxygen == '1.8.5':
@@ -612,8 +613,8 @@ def build_stages(args) -> typing.Iterable[hpccm.Stage]:
     building_blocks['extra_packages'] = hpccm.building_blocks.packages(
         ospackages=os_packages,
         apt_ppas=['ppa:intel-opencl/intel-opencl'],
-        apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
-        apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main']
+        apt_keys=['http://repo.radeon.com/rocm/rocm.gpg.key'],
+        apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/4.0.1/ xenial main']
     )
 
     if args.cuda is not None and args.llvm is not None:
diff --git a/admin/containers/utility.py b/admin/containers/utility.py
index 5ba2f652f7..f8f8b8ce72 100644
--- a/admin/containers/utility.py
+++ b/admin/containers/utility.py
@@ -41,7 +41,7 @@ CI pipeline jobs.
 Example::
 
     $ python3 -m utility --llvm --doxygen
-    gromacs/ci-ubuntu-18.04-llvm-7-docs
+    gromacs/ci-ubuntu-20.04-llvm-7-docs
 
 See Also:
     :file:`buildall.sh`
@@ -105,9 +105,8 @@ compiler_group.add_argument('--oneapi', type=str, nargs='?', const="2021.1.1", d
                             help='Select Intel oneAPI package version.')
 
 linux_group = parser.add_mutually_exclusive_group()
-# Ubuntu 20+ is not yet tested. See issue #3680
-linux_group.add_argument('--ubuntu', type=str, nargs='?', const='18.04', default='18.04',
-                         help='Select Ubuntu Linux base image. (default: ubuntu 18.04)')
+linux_group.add_argument('--ubuntu', type=str, nargs='?', const='20.04', default='20.04',
+                         help='Select Ubuntu Linux base image. (default: ubuntu 20.04)')
 linux_group.add_argument('--centos', type=str, nargs='?', const='7', default=None,
                          help='Select Centos Linux base image.')