Update package versions (#67)

* add paddle docker image
* pin ubuntu version to focal
* upgrade cuda 116

Author: QPod0

.gitattributes

@@ -1 +1,25 @@
-* text=auto eol=lf
+# Ignore all differences in line endings
+*               text=auto eol=lf
+*.md            text eol=lf
+*.py            text eol=lf
+*.sh            text eol=lf
+*.yml           text eol=lf
+*.yaml          text eol=lf
+*.json          text eol=lf
+*.properties    text eol=lf
+*.conf          text eol=lf
+*.ipynb         text eol=lf
+Dockerfile*     text eol=lf
+.gitattributes  text eol=lf
+.gitignore      text eol=lf
+.dockerignore   text eol=lf
+
+# Files using LFS to track
+*.tgz   filter=lfs diff=lfs merge=lfs -text
+*.h5    filter=lfs diff=lfs merge=lfs -text
+*.jsonl filter=lfs diff=lfs merge=lfs -text
+*.xlsx  filter=lfs diff=lfs merge=lfs -text
+*.bin   filter=lfs diff=lfs merge=lfs -text
+*.png   filter=lfs diff=lfs merge=lfs -text
+*.jpg   filter=lfs diff=lfs merge=lfs -text
+*.jpeg  filter=lfs diff=lfs merge=lfs -text

.github/workflows/docker.yml

@@ -29,44 +29,6 @@ jobs:
           build_image atom latest docker_atom/Dockerfile && push_image
           build_image base latest docker_base/Dockerfile && alias_image base latest  python latest && push_image
 
-  # latest cuda supported by torch: https://pytorch.org/get-started/locally/
-  qpod_cuda_11_5:
-    name: qpod/cuda_11.5
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - run: |
-          source ./tool.sh
-          build_image cuda_11.5 latest docker_atom/Dockerfile --build-arg "BASE_IMG=nvidia/cuda:11.5.2-cudnn8-devel-ubuntu20.04"
-          build_image cuda_11.5 latest docker_base/Dockerfile --build-arg "BASE_IMG=cuda_11.5"
-          build_image cuda_11.5 latest docker_cuda/Dockerfile --build-arg "BASE_IMG=cuda_11.5"
-          alias_image cuda_11.5 latest cuda latest
-          push_image
-
-  # For legacy torch support
-  qpod_cuda_10_2:
-    name: qpod/cuda_10.2
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - run: |
-          source ./tool.sh
-          build_image cuda_10.2 latest docker_atom/Dockerfile --build-arg "BASE_IMG=nvidia/cuda:10.2-cudnn8-devel-ubuntu18.04"
-          build_image cuda_10.2 latest docker_base/Dockerfile --build-arg "BASE_IMG=cuda_10.2"
-          build_image cuda_10.2 latest docker_cuda/Dockerfile --build-arg "BASE_IMG=cuda_10.2" && push_image
-
-  # cuda_10.0 - for legacy tensorflow 1.15 support
-  qpod_cuda_10_0:
-    name: qpod/cuda_10.0
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - run: |
-          source ./tool.sh        
-          build_image cuda_10.0 latest docker_atom/Dockerfile --build-arg "BASE_IMG=nvidia/cuda:10.0-cudnn7-devel-ubuntu18.04"
-          build_image cuda_10.0 latest docker_base/Dockerfile --build-arg "BASE_IMG=cuda_10.0"
-          build_image cuda_10.0 latest docker_cuda/Dockerfile --build-arg "BASE_IMG=cuda_10.0" && push_image
-
   qpod_core:
     name: qpod/core
     needs: qpod_base
@@ -91,22 +53,6 @@ jobs:
       - uses: actions/checkout@v2
       - run: source ./tool.sh && build_image py-data latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,database" && push_image
 
-  qpod_py-nlp:
-    name: qpod/py-nlp
-    needs: qpod_base
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - run: source ./tool.sh && build_image py-nlp  latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,nlp" && push_image
-
-  qpod_py-cv:
-    name: qpod/py-cv
-    needs: qpod_base
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - run: source ./tool.sh && build_image py-cv   latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,cv" && push_image
-
   qpod_py-chem:
     name: qpod/py-chem
     needs: qpod_base
@@ -207,6 +153,61 @@ jobs:
       - uses: actions/checkout@v2
       - run: source ./tool.sh && build_image go latest docker_core/Dockerfile --build-arg "ARG_PROFILE_GO=base"     && push_image
 
+
+  # cuda docker image tags: https://hub.docker.com/r/nvidia/cuda/tags
+  # latest cuda supported by torch: https://pytorch.org/get-started/locally/
+  # latest cuda supported by tensorflow: https://tensorflow.google.cn/install/source_windows?hl=en#gpu
+  qpod_cuda_11_6:
+    name: qpod/cuda_11.6
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          source ./tool.sh
+          build_image cuda_11.6 latest docker_atom/Dockerfile --build-arg "BASE_IMG=nvidia/cuda:11.6.2-cudnn8-devel-ubuntu20.04"
+          build_image cuda_11.6 latest docker_base/Dockerfile --build-arg "BASE_IMG=cuda_11.6"
+          build_image cuda_11.6 latest docker_cuda/Dockerfile --build-arg "BASE_IMG=cuda_11.6"
+          alias_image cuda_11.6 latest cuda latest
+          push_image
+
+  qpod_cuda_11_2:
+    name: qpod/cuda_11.2
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          source ./tool.sh
+          build_image cuda_11.2 latest docker_atom/Dockerfile --build-arg "BASE_IMG=nvidia/cuda:11.2.2-cudnn8-devel-ubuntu20.04"
+          build_image cuda_11.2 latest docker_base/Dockerfile --build-arg "BASE_IMG=cuda_11.2"
+          build_image cuda_11.2 latest docker_cuda/Dockerfile --build-arg "BASE_IMG=cuda_11.2"
+          alias_image cuda_11.2 latest cuda latest
+          push_image
+
+  # For legacy torch/paddle support
+  qpod_cuda_10_2:
+    name: qpod/cuda_10.2
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          source ./tool.sh
+          build_image cuda_10.2 latest docker_atom/Dockerfile --build-arg "BASE_IMG=nvidia/cuda:10.2-cudnn8-devel-ubuntu18.04"
+          build_image cuda_10.2 latest docker_base/Dockerfile --build-arg "BASE_IMG=cuda_10.2"
+          build_image cuda_10.2 latest docker_cuda/Dockerfile --build-arg "BASE_IMG=cuda_10.2" && push_image
+
+  # cuda_10.0 - for legacy tensorflow 1.15 support
+  qpod_cuda_10_0:
+    name: qpod/cuda_10.0
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          source ./tool.sh        
+          build_image cuda_10.0 latest docker_atom/Dockerfile --build-arg "BASE_IMG=nvidia/cuda:10.0-cudnn7-devel-ubuntu18.04"
+          build_image cuda_10.0 latest docker_base/Dockerfile --build-arg "BASE_IMG=cuda_10.0"
+          build_image cuda_10.0 latest docker_cuda/Dockerfile --build-arg "BASE_IMG=cuda_10.0" && push_image
+
+
   qpod_tf1:
     name: qpod/tf1
     needs: qpod_cuda_10_0
@@ -221,26 +222,26 @@ jobs:
 
   qpod_tf2:
     name: qpod/tf2
-    needs: qpod_cuda_11_5
+    needs: qpod_cuda_11_2
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - run: |
           source ./tool.sh
-          build_image tf2-cu115 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.5"  --build-arg "ARG_PROFILE_PYTHON=tf2"
-          alias_image tf2-cu115 latest torch latest
+          build_image tf2-cu112 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.2"  --build-arg "ARG_PROFILE_PYTHON=tf2"
+          alias_image tf2-cu112 latest torch latest
           push_image
 
-  qpod_torch_cu115:
-    name: qpod/torch-cuda115
-    needs: qpod_cuda_11_5
+  qpod_torch_cu116:
+    name: qpod/torch-cuda116
+    needs: qpod_cuda_11_6
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - run: |
           source ./tool.sh
-          build_image torch-cu115 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.5" --build-arg "ARG_PROFILE_PYTHON=torch"
-          alias_image torch-cu115 latest torch latest
+          build_image torch-cu116 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.6" --build-arg "ARG_PROFILE_PYTHON=torch"
+          alias_image torch-cu116 latest torch latest
           push_image
 
   qpod_torch_cu102:
@@ -254,22 +255,58 @@ jobs:
           build_image torch-cu102 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_10.2" --build-arg "ARG_PROFILE_PYTHON=torch"
           push_image
 
+  qpod_paddle_cu116:
+    name: qpod/paddle-cuda116
+    needs: qpod_cuda_11_6
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          source ./tool.sh
+          build_image paddle-cu116 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.6" --build-arg "ARG_PROFILE_PYTHON=paddle"
+          alias_image paddle-cu116 latest paddle latest
+          push_image
+
+
+  qpod_py-nlp:
+    name: qpod/py-nlp
+    needs: qpod_base
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          source ./tool.sh
+          build_image py-nlp latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.6" --build-arg "ARG_PROFILE_PYTHON=datascience,torch,nlp"
+          push_image
+
+  qpod_py-cv:
+    name: qpod/py-cv
+    needs: qpod_base
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          source ./tool.sh 
+          build_image py-cv   latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.6" --build-arg "ARG_PROFILE_PYTHON=datascience,torch,cv"
+          push_image
+
+
   qpod_core-cuda:
     name: qpod/core-cuda
-    needs: qpod_cuda_11_5
+    needs: qpod_cuda_11_6
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - run: |
           source ./tool.sh && free_diskspace
-          build_image full-cuda-11.5 latest docker_core/Dockerfile \
-            --build-arg "BASE_IMG=cuda_11.5" \
+          build_image full-cuda-11.6 latest docker_core/Dockerfile \
+            --build-arg "BASE_IMG=cuda_11.6" \
             --build-arg "ARG_PROFILE_PYTHON=base,datascience,database,nlp,cv,chem,tf2,torch" \
             --build-arg "ARG_PROFILE_R=base,datascience,rstudio,rshiny" \
             --build-arg "ARG_PROFILE_NODEJS=base" \
             --build-arg "ARG_PROFILE_JAVA=base,maven" \
             --build-arg "ARG_PROFILE_LATEX=base,cjk"
-          alias_image full-cuda-11.5 latest core-cuda latest && push_image
+          alias_image full-cuda-11.6 latest core-cuda latest && push_image
 
   qpod_core-dev:
     name: qpod/core-dev

.gitignore

@@ -46,6 +46,10 @@ nosetests.xml
 coverage.xml
 *,cover
 
+# IDE
+.vscode/
+.idea/
+
 # Sphinx documentation
 docs/_build/
 

docker_atom/Dockerfile

@@ -2,7 +2,7 @@
 
 # default value: Latest LTS version of Ubuntu (https://hub.docker.com/_/ubuntu)
 
-ARG BASE_IMG="ubuntu:latest"
+ARG BASE_IMG="ubuntu:focal" # latest
 FROM ${BASE_IMG}
 
 LABEL maintainer="haobibo@gmail.com"

docker_atom/work/install_list_base.apt

@@ -1,11 +1,11 @@
 % This file contains apt packages to be installed with apt-get install line by line.
 % Use percent char as line comment separator.
 
-htop vim git jq tree    % Process Management, Editor, Version Control
-build-essential cmake   % build essentials
-wget iputils-ping       % download, network (ping)
-unzip bzip2 p7zip-full  % zip/unzip
-rsync                   % file transfer
-openssh-client          % Provide ssh client and generate keys
-openssh-server          % Provide ssh server (sshd)
-% tini                  % tini - which will be entry point later; not avaliable on ubuntu<=18
+htop vim git jq tree     % Process Management, Editor, Version Control
+build-essential cmake    % build essentials
+wget iputils-ping telnet % download, network (ping)
+unzip bzip2 p7zip-full   % zip/unzip
+rsync                    % file transfer
+openssh-client           % Provide ssh client and generate keys
+openssh-server           % Provide ssh server (sshd)
+% tini                   % tini - which will be entry point later; not available on ubuntu<=18

docker_atom/work/script-setup.sh

@@ -34,7 +34,7 @@ setup_conda_postprocess() {
 
 setup_conda_with_mamba() {
   VERSION_PTYHON=$1; shift 1;
-  mamba install -y --root-prefix="${CONDA_PREFIX}" --prefix="${CONDA_PREFIX}" -c "conda-forge" conda pip python="${VERSION_PTYHON:-3.9}"
+  mamba install -y --root-prefix="${CONDA_PREFIX}" --prefix="${CONDA_PREFIX}" -c "conda-forge" conda pip python="${VERSION_PTYHON:-3.10}"
   rm -rf /opt/conda/pkgs/*
   setup_conda_postprocess
 }
@@ -111,7 +111,7 @@ setup_node() {
 
 setup_R_base() {
      apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
-  && echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/cran.list \
+  && echo "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" > /etc/apt/sources.list.d/cran.list \
   && install_apt  /opt/utils/install_list_R_base.apt \
   && echo "options(repos=structure(c(CRAN=\"https://cloud.r-project.org\")))" >> /etc/R/Rprofile.site \
   && R -e "install.packages(c('devtools'),clean=T,quiet=T);" \

docker_atom/work/script-utils.sh

@@ -48,11 +48,12 @@ install__clean(){
   find /opt/conda/lib | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf
   which npm     && npm cache clean --force
   rm -rf /opt/conda/share/jupyter/lab/staging
-  ( rm -rf /root/.* /tmp/.* /tmp/* /var/log/* /var/cache/* || true )
+  ( rm -rf /tmp/.* /tmp/* /var/log/* /var/cache/* /root/.cache /root/.* || true )
   chmod ugo+rwXt /tmp
   ls -alh /root /tmp
-  echo "@ System environment variables:" && for e in $(echo $(printenv) | tr " " "\n") ; do echo $e ; done
-  echo "@ Version of image: building finished at:" `date` `uname -a`
+  echo "@ System release info:" && cat /etc/*release*
+  echo "@ System environment variables:" && printenv | sort
+  echo "@ Version of image: building finished at:" $(date)
   true
 }