Add intel mkl (#69)

* add nomkl for paddle
* Update script-setup.sh

Author: haobibo

.github/workflows/docker.yml

@@ -38,7 +38,7 @@ jobs:
       - run: |
           source ./tool.sh
           build_image core latest  docker_core/Dockerfile \
-            --build-arg "ARG_PROFILE_PYTHON=base,datascience,database,nlp,cv,chem,tf2,torch" \
+            --build-arg "ARG_PROFILE_PYTHON=base,datascience,mkl,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" \
@@ -51,31 +51,31 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - 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
+      - run: source ./tool.sh && build_image py-data latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,mkl,database" && push_image
 
   qpod_py-chem:
     name: qpod/py-chem
     needs: qpod_base
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - run: source ./tool.sh && build_image py-chem latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,chem" && push_image
+      - run: source ./tool.sh && build_image py-chem latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,mkl,chem" && push_image
 
   qpod_py-std:
     name: qpod/py-std
     needs: qpod_base
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - run: source ./tool.sh && build_image py-std  latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,database,nlp,cv,chem" && push_image
+      - run: source ./tool.sh && build_image py-std  latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,mkl,database,nlp,cv,chem" && push_image
 
   qpod_py-jdk:
     name: qpod/py-jdk
     needs: qpod_base
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - run: source ./tool.sh && build_image py-jdk  latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,database,nlp,cv,chem" --build-arg "ARG_PROFILE_JAVA=base" && push_image
+      - run: source ./tool.sh && build_image py-jdk  latest docker_core/Dockerfile --build-arg "ARG_PROFILE_PYTHON=datascience,mkl,database,nlp,cv,chem" --build-arg "ARG_PROFILE_JAVA=base" && push_image
 
   qpod_r-base:
     name: qpod/r-base
@@ -263,7 +263,7 @@ jobs:
       - uses: actions/checkout@v2
       - run: |
           source ./tool.sh
-          build_image paddle-cuda116 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.6" --build-arg "ARG_PROFILE_PYTHON=paddle"
+          build_image paddle-cuda116 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.6" --build-arg "ARG_PROFILE_PYTHON=paddle,mkl"
           alias_image paddle-cuda116 latest paddle latest
           push_image
 
@@ -275,7 +275,7 @@ jobs:
       - uses: actions/checkout@v2
       - run: |
           source ./tool.sh
-          build_image paddle-cuda102 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_10.2" --build-arg "ARG_PROFILE_PYTHON=paddle"
+          build_image paddle-cuda102 latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_10.2" --build-arg "ARG_PROFILE_PYTHON=paddle,mkl"
           push_image
 
 
@@ -287,7 +287,7 @@ jobs:
       - 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"
+          build_image py-nlp latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.6" --build-arg "ARG_PROFILE_PYTHON=datascience,mkl,torch,nlp"
           push_image
 
   qpod_py-cv:
@@ -298,7 +298,7 @@ jobs:
       - 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"
+          build_image py-cv   latest docker_core/Dockerfile --build-arg "BASE_IMG=cuda_11.6" --build-arg "ARG_PROFILE_PYTHON=datascience,mkl,torch,cv"
           push_image
 
 
@@ -312,7 +312,7 @@ jobs:
           source ./tool.sh && free_diskspace
           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_PYTHON=base,datascience,mkl,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" \

docker_atom/work/script-setup.sh

@@ -16,14 +16,23 @@ setup_mamba() {
 
 
 setup_conda_postprocess() {
+  # If python exists, set pypi source
+  if [ -f "$(which python)" ]; then
+    cat >/etc/pip.conf <<EOF
+[global]
+progress_bar=off
+root-user-action=ignore
+EOF
+  fi
+
      conda config --system --prepend channels conda-forge \
   && conda config --system --set auto_update_conda false  \
   && conda config --system --set show_channel_urls true   \
   && conda config --system --set report_errors false \
   && conda config --system --set channel_priority strict \
   && conda update --all --quiet --yes
 
-  # These conda pkgs shouldn't be removed (otherwise will cause RemoveError) since they are directly reqiuired by conda: pip setuptools pycosat pyopenssl requests ruamel_yaml
+  # These conda pkgs shouldn't be removed (otherwise will cause RemoveError) since they are directly required by conda: pip setuptools pycosat pyopenssl requests ruamel_yaml
      CONDA_PY_PKGS=$(conda list | grep "py3" | cut -d " " -f 1 | sed "/#/d;/conda/d;/pip/d;/setuptools/d;/pycosat/d;/pyopenssl/d;/requests/d;/ruamel_yaml/d;") \
   && conda remove --force -yq "${CONDA_PY_PKGS}" \
   && pip install -UIq pip setuptools "${CONDA_PY_PKGS}"

docker_core/Dockerfile

@@ -44,8 +44,13 @@ RUN source /opt/utils/script-utils.sh \
 RUN source /opt/utils/script-setup.sh \
  && for profile in $(echo $ARG_PROFILE_R | tr "," "\n") ; do ( setup_R_${profile} ) ; done
 
-# If on a x86_64 architecture and install data science pkgs, install MKL for acceleration; Installing conda packages if provided.
-RUN $(grep -q "x86_64" <<< `arch`) && $(grep -q "datascience" <<< "${ARG_PROFILE_PYTHON}") && ( echo "mkl" >> /opt/utils/install_list.conda ) || echo "Skip MLK install." \
+# If on a x86_64 architecture: 1) if mkl specified, install nomkl; 2) install conda packages as specified.
+RUN $(grep -q "x86_64" <<< `arch`) && ( \
+      ( $(grep -q "mkl" <<< "${ARG_PROFILE_PYTHON}") && \
+        ( echo "mkl"   >> /opt/utils/install_list_core.conda && echo "Install mkl.") || \
+        ( echo "nomkl" >> /opt/utils/install_list_core.conda && echo "Install nomkl.") \
+      ) \
+    ) \
  && source /opt/utils/script-utils.sh && install_conda /opt/utils/install_list_core.conda
 
 # If installing Python packages