Upgrade the containers to the correct new setup.

dev_tools/containers/build_all_containers.sh

@@ -1,13 +1,22 @@
 #!/bin/bash
-
-hpccm --recipe ginkgo-nocuda-base.py --userarg gnu=8 llvm=6.0 papi=True > gko-nocuda-gnu8-llvm70.baseimage
-hpccm --recipe ginkgo-cuda-base.py --userarg cuda=10.0 gnu=7 llvm=6.0 > gko-cuda100-gnu7-llvm60.baseimage
-hpccm --recipe ginkgo-cuda-base.py --userarg cuda=9.2 gnu=7 llvm=5.0 > gko-cuda92-gnu7-llvm50.baseimage
-hpccm --recipe ginkgo-cuda-base.py --userarg cuda=9.1 gnu=6 llvm=4.0 > gko-cuda91-gnu6-llvm40.baseimage
-hpccm --recipe ginkgo-cuda-base.py --userarg cuda=9.0 gnu=5 llvm=3.9 > gko-cuda90-gnu5-llvm39.baseimage
-for i in $(ls *.baseimage)
+
+
+hpccm --recipe ginkgo-nocuda-base.py --userarg gnu=8 llvm=7 papi=True > gko-nocuda-gnu8-llvm70.baseimage
+list=('gko-nocuda-gnu8-llvm70.baseimage')
+if [ "$HOSTNAME" = "amdci" ]; then
+  list+=('gko-amd-gnu7-llvm60.baseimage')
+else
+  hpccm --recipe ginkgo-cuda-base.py --userarg cuda=10.1 gnu=8 llvm=7 > gko-cuda101-gnu8-llvm70.baseimage
+  hpccm --recipe ginkgo-cuda-base.py --userarg cuda=10.0 gnu=7 llvm=6.0 > gko-cuda100-gnu7-llvm60.baseimage
+  hpccm --recipe ginkgo-cuda-base.py --userarg cuda=9.2 gnu=7 llvm=5.0 > gko-cuda92-gnu7-llvm50.baseimage
+  hpccm --recipe ginkgo-cuda-base.py --userarg cuda=9.1 gnu=6 llvm=4.0 > gko-cuda91-gnu6-llvm40.baseimage
+  hpccm --recipe ginkgo-cuda-base.py --userarg cuda=9.0 gnu=5 llvm=3.9 > gko-cuda90-gnu5-llvm39.baseimage
+	list+=(gko-cuda*.baseimage)
+fi
+
+for i in "${list[@]}"
 do
-	name=$(echo $i | cut -d"." -f1)
-	docker build -t localhost:5000/$name -f $i .
-	docker push localhost:5000/$name
+  name=$(echo $i | cut -d"." -f1)
+  docker build -t localhost:5000/$name -f $i .
+  docker push localhost:5000/$name
 done

dev_tools/containers/ginkgo-cuda-base.py

@@ -11,13 +11,16 @@
     git, openssh, doxygen, curl, valgrind, graphviz, jq latest apt version
     build-essential, automake, pkg-config, libtool, latest apt version
     iwyu precompiled version 6.0
+    libthrust-dev latest apt version
+    gnupg-agent: latest apt version, for adding custom keys
 """
 # pylint: disable=invalid-name, undefined-variable, used-before-assignment
 
 import os
 
 cuda_version = USERARG.get('cuda', '10.0')
 
+release_name = 'xenial'
 image = 'nvidia/cuda:{}-devel-ubuntu16.04'.format(cuda_version)
 Stage0.baseimage(image)
 
@@ -39,20 +42,29 @@
 
 # Setup extra tools
 Stage0 += python()
-Stage0 += cmake(eula=True)
+Stage0 += cmake(eula=True, version='3.14.5')
 Stage0 += apt_get(ospackages=['git', 'openssh-client', 'doxygen', 'curl', 'valgrind', 'graphviz'])
 Stage0 += apt_get(ospackages=['jq', 'iwyu'])
 Stage0 += apt_get(ospackages=['build-essential', 'automake', 'pkg-config', 'libtool'])
-
+Stage0 += apt_get(ospackages=['libthrust-dev'])
+Stage0 += apt_get(ospackages=['gnupg-agent'])
+Stage0 += apt_get(ospackages=['ca-certificates']) # weird github certificates problem
 
 # GNU compilers
 gnu_version = USERARG.get('gnu', '7')
 Stage0 += gnu(version=gnu_version, extra_repository=True)
+gcov_update = ['update-alternatives --install /usr/bin/gcov gcov /usr/bin/gcov-{} 90'.format(gnu_version)]
+Stage0 += shell(commands=gcov_update)
 
 # Clang compilers
-llvm_version = USERARG.get('llvm', '6.0')
-Stage0 += llvm(version=llvm_version, extra_repository=True)
-Stage0 += apt_get(ospackages=['libomp-dev']) #required for openmp+clang
+llvm_version = USERARG.get('llvm', '7')
+clang_ver = 'clang-{}'.format(llvm_version)
+repo_ver = ['deb http://apt.llvm.org/{}/ llvm-toolchain-{}-{} main'.format(release_name, release_name, llvm_version)]
+Stage0 += apt_get(ospackages=[clang_ver, 'libomp-dev'], repositories=repo_ver, keys=['https://apt.llvm.org/llvm-snapshot.gpg.key'])
+clang_update = 'update-alternatives --install /usr/bin/clang clang /usr/bin/clang-{} 90'.format(llvm_version)
+clangpp_update = 'update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang-{} 90'.format(llvm_version)
+Stage0 += shell(commands=[clang_update, clangpp_update])
+
 
 # clang-tidy
 clangtidy = ['clang-tidy-{}'.format(llvm_version)]
@@ -64,7 +76,7 @@
 if os.path.isdir('bin/'):
     Stage0 += copy(src='bin/*', dest='/usr/bin/')
 
-if os.path.isdir('sonar-scanner/'):
+if os.path.isdir('sonar-scanner/') and float(cuda_version) >= float(10.0):
     Stage0 += copy(src='sonar-scanner/', dest='/')
 
 # hwloc
@@ -73,6 +85,7 @@
                               'git clone https://github.com/open-mpi/hwloc.git hwloc'])
     Stage0 += shell(commands=['cd /var/tmp/hwloc', './autogen.sh',
                               './configure --prefix=/usr --disable-nvml', 'make -j10', 'make install'])
+    Stage0 += shell(commands=['rm -rf /var/tmp/hwloc'])
 
     # upload valid FineCI topology and set it for hwloc
     if os.path.isfile('topology/fineci.xml'):
@@ -85,11 +98,29 @@
 intel_versions = {'9.0' : '2017', '9.1' : '2017', '9.2' : '2017', '10.0' : '2018'}
 intel_path = 'intel/parallel_studio_xe_{}/compilers_and_libraries/linux/'.format(intel_versions.get(cuda_version))
 if os.path.isdir(intel_path):
-        Stage0 += copy(src=intel_path+'bin/intel64/', dest='/opt/intel/bin/')
-        Stage0 += copy(src=intel_path+'lib/intel64/', dest='/opt/intel/lib/')
-        Stage0 += copy(src=intel_path+'include/', dest='/opt/intel/include/')
-        Stage0 += environment(variables={'INTEL_LICENSE_FILE': '28518@scclic1.scc.kit.edu'})
-        Stage0 += environment(variables={'PATH': '$PATH:/opt/intel/bin'})
-        Stage0 += environment(variables={'LIBRARY_PATH': '$LIBRARY_PATH:/opt/intel/lib'})
-        Stage0 += environment(variables={'LD_LIBRARY_PATH': '$LD_LIBRARY_PATH:/opt/intel/lib'})
-        Stage0 += environment(variables={'LD_RUN_PATH': '$LD_RUN_PATH:/opt/intel/lib'})
+    Stage0 += copy(src=intel_path+'bin/intel64/', dest='/opt/intel/bin/')
+    Stage0 += copy(src=intel_path+'lib/intel64/', dest='/opt/intel/lib/')
+    Stage0 += copy(src=intel_path+'include/', dest='/opt/intel/include/')
+    Stage0 += environment(variables={'INTEL_LICENSE_FILE': '28518@scclic1.scc.kit.edu'})
+    Stage0 += environment(variables={'PATH': '$PATH:/opt/intel/bin'})
+    Stage0 += environment(variables={'LIBRARY_PATH': '$LIBRARY_PATH:/opt/intel/lib'})
+    Stage0 += environment(variables={'LD_LIBRARY_PATH': '$LD_LIBRARY_PATH:/opt/intel/lib'})
+    Stage0 += environment(variables={'LD_RUN_PATH': '$LD_RUN_PATH:/opt/intel/lib'})
+
+
+# HIP
+Stage0 += shell(commands=['cd /var/tmp',
+                          'git clone https://github.com/ROCm-Developer-Tools/HIP.git'])
+Stage0 += shell(commands=['cd /var/tmp/HIP', 'mkdir build', 'cd build',
+                          'cmake ..', 'make install'])
+Stage0 += shell(commands=['rm -rf /var/tmp/HIP'])
+Stage0 += shell(commands=['cd /var/tmp',
+                          'git clone https://github.com/tcojean/hipBLAS.git'])
+Stage0 += shell(commands=['cd /var/tmp/hipBLAS', 'mkdir build', 'cd build',
+                          'cmake ..', 'make install'])
+Stage0 += shell(commands=['rm -rf /var/tmp/hipBLAS'])
+Stage0 += shell(commands=['cd /var/tmp',
+                          'git clone https://github.com/tcojean/hipSPARSE.git'])
+Stage0 += shell(commands=['cd /var/tmp/hipSPARSE', 'mkdir build', 'cd build',
+                          'cmake -DBUILD_CUDA=on ..', 'make install'])
+Stage0 += shell(commands=['rm -rf /var/tmp/hipSPARSE'])

dev_tools/containers/ginkgo-nocuda-base.py

@@ -7,38 +7,68 @@
     OpenMP latest apt version for Clang+OpenMP
     Python 2 and 3 (upstream)
     cmake (upstream)
-    build-essential, git, openssh, doxygen, curl, valgrind latest apt version
-    jq, graphviz, ghostscript, texlive, texlive-latex-extra, latest apt version
-    texlive-science, texlive-fonts-extra, texlive-publishers latest apt version
+    build-essential, git, openssh, curl, valgrind latest apt version
+    jq, graphviz, ghostscript, latest apt version
+    bison, flex latest apt version, required for doxygen compilation
+    doxygen: install the latest release
+    texlive: install the latest release
     clang-tidy, iwyu: latest apt version
     hwloc, libhwloc-dev, pkg-config latest apt version
     papi: adds package libpfm4, and copy precompiled papi headers and files
           from a directory called 'papi'
+    gpg-agent: latest apt version, for adding custom keys
 """
 # pylint: disable=invalid-name, undefined-variable, used-before-assignment
 
 import os
 
 Stage0.baseimage('ubuntu:18.04')
-
+release_name = 'bionic'
 
 # Setup extra tools
 Stage0 += python()
 Stage0 += cmake(eula=True)
-Stage0 += apt_get(ospackages=['build-essential', 'git', 'openssh-client', 'doxygen', 'curl', 'valgrind'])
-Stage0 += apt_get(ospackages=['jq', 'graphviz', 'ghostscript', 'texlive', 'texlive-latex-extra'])
-Stage0 += apt_get(ospackages=['texlive-science', 'texlive-fonts-extra', 'texlive-publishers'])
+Stage0 += apt_get(ospackages=['build-essential', 'git', 'openssh-client', 'curl', 'valgrind'])
+Stage0 += apt_get(ospackages=['jq', 'graphviz', 'ghostscript'])
 Stage0 += apt_get(ospackages=['clang-tidy', 'iwyu'])
 Stage0 += apt_get(ospackages=['hwloc', 'libhwloc-dev', 'pkg-config'])
+Stage0 += apt_get(ospackages=['gpg-agent'])
+Stage0 += apt_get(ospackages=['ca-certificates']) # weird github certificates problem
+Stage0 += apt_get(ospackages=['bison', 'flex'])
 
 # GNU compilers
 gnu_version = USERARG.get('gnu', '8')
 Stage0 += gnu(version=gnu_version, extra_repository=True)
 
 # Clang compilers
 llvm_version = USERARG.get('llvm', '7')
-Stage0 += llvm(version=llvm_version, extra_repository=True)
-Stage0 += apt_get(ospackages=['libomp-dev']) #required for openmp+clang
+clang_ver = 'clang-{}'.format(llvm_version)
+repo_ver = ['deb http://apt.llvm.org/{}/ llvm-toolchain-{}-{} main'.format(release_name, release_name, llvm_version)]
+Stage0 += apt_get(ospackages=[clang_ver, 'libomp-dev'], repositories=repo_ver, keys=['https://apt.llvm.org/llvm-snapshot.gpg.key'])
+clang_update = 'update-alternatives --install /usr/bin/clang clang /usr/bin/clang-{} 90'.format(llvm_version)
+clangpp_update = 'update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang-{} 90'.format(llvm_version)
+Stage0 += shell(commands=[clang_update, clangpp_update])
+
+# Doxygen
+Stage0 += shell(commands=['cd /var/tmp', 'git clone https://github.com/doxygen/doxygen'])
+Stage0 += shell(commands=['cd /var/tmp/doxygen', 'git checkout Release_1_8_16',
+                          'mkdir build', 'cd build',
+                          'cmake ..', 'make -j10', 'make install'])
+Stage0 += shell(commands=['cd /var/tmp', 'rm -rf doxygen'])
+
+# Texlive
+if os.path.isdir('texlive/'):
+    Stage0 += copy(src='texlive/texlive.profile', dest='/var/tmp')
+    Stage0 += shell(commands=['cd /var/tmp', 'wget '
+                              'http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz',
+                              'tar -xvf install-tl-unx.tar.gz', 'cd install-tl-2*',
+                              './install-tl --profile=../texlive.profile'])
+    Stage0 += shell(commands=['cd /var/tmp', 'rm -rf install-tl*'])
+    Stage0 += shell(commands=['tlmgr install mathtools float xcolor varwidth '
+                              'fancyvrb multirow hanging adjustbox xkeyval '
+                              'collectbox stackengine etoolbox listofitems ulem '
+                              'wasysym sectsty tocloft newunicodechar caption etoc '
+                              'pgf ec helvetic courier wasy'])
 
 # Copy PAPI libs
 add_papi = USERARG.get('papi', 'False')

dev_tools/containers/gko-amd-gnu7-llvm60.baseimage

@@ -0,0 +1,75 @@
+FROM ubuntu:16.04
+MAINTAINER Terry Cojean <terry.cojean@kit.edu>
+
+# Initialize the image
+# Modify to pre-install dev tools and ROCm packages
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends curl && \
+  curl -sL http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key | apt-key add - && \
+  sh -c 'echo deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main > /etc/apt/sources.list.d/rocm.list' && \
+  apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+  libelf1 \
+  libnuma-dev \
+  build-essential \
+  git \
+  vim-nox \
+  cmake-curses-gui \
+  kmod \
+  rocm-dev \
+  hipsparse hipblas rocthrust && \
+  apt-get clean && \
+  rm -rf /var/lib/apt/lists/*
+
+
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        wget && \
+    rm -rf /var/lib/apt/lists/*
+RUN mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://cmake.org/files/v3.11/cmake-3.11.1-Linux-x86_64.sh && \
+    /bin/sh /var/tmp/cmake-3.11.1-Linux-x86_64.sh --prefix=/usr/local --skip-license && \
+    rm -rf /var/tmp/cmake-3.11.1-Linux-x86_64.sh
+
+
+# GNU compiler
+RUN apt-get update -y && \
+     apt-get install -y --no-install-recommends software-properties-common && \
+     apt-add-repository ppa:ubuntu-toolchain-r/test -y && \
+     apt-get update -y && \
+     apt-get install -y --no-install-recommends \
+     gcc-7 \
+     g++-7 \
+     gfortran-7 && \
+     rm -rf /var/lib/apt/lists/*
+
+RUN update-alternatives --install /usr/bin/gcc gcc $(which gcc-7) 30 && \
+    update-alternatives --install /usr/bin/g++ g++ $(which g++-7) 30 && \
+    update-alternatives --install /usr/bin/gfortran gfortran $(which gfortran-7) 30
+
+# LLVM compiler
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        clang-6.0 && \
+    rm -rf /var/lib/apt/lists/*
+RUN update-alternatives --install /usr/bin/clang clang $(which clang-6.0) 30 && \
+    update-alternatives --install /usr/bin/clang++ clang++ $(which clang++-6.0) 30
+
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        libomp-dev && \
+    rm -rf /var/lib/apt/lists/*
+
+
+#    sed --in-place=.rocm-backup 's|^\(PATH=.*\)"$|\1:/opt/rocm/bin"|' /etc/environment
+
+USER root
+WORKDIR /root
+ENV PATH "${PATH}:/opt/rocm/bin"
+
+# The following are optional enhancements for the command-line experience
+# Uncomment the following to install a pre-configured vim environment based on http://vim.spf13.com/
+# 1.  Sets up an enhanced command line dev environment within VIM
+# 2.  Aliases GDB to enable TUI mode by default
+#RUN curl -sL https://j.mp/spf13-vim3 | bash && \
+#    echo "alias gdb='gdb --tui'\n" >> ~/.bashrc
+
+# Default to a login shell
+CMD ["bash", "-l"]