[to #45915958]feat: v1.0.2 docker file update, add deepspeed, apex, uncore

Link: https://code.alibaba-inc.com/Ali-MaaS/MaaS-lib/codereview/10617428

docker/Dockerfile.ubuntu

@@ -71,14 +71,13 @@ RUN pip install --no-cache-dir --upgrade pip && \
     pip install --no-cache-dir -r /var/modelscope/cv.txt -f https://modelscope.oss-cn-beijing.aliyuncs.com/releases/repo.html && \
     pip install --no-cache-dir -r /var/modelscope/multi-modal.txt -f https://modelscope.oss-cn-beijing.aliyuncs.com/releases/repo.html && \
     pip install --no-cache-dir -r /var/modelscope/nlp.txt -f https://modelscope.oss-cn-beijing.aliyuncs.com/releases/repo.html && \
+    pip install --no-cache-dir -r /var/modelscope/science.txt -f https://modelscope.oss-cn-beijing.aliyuncs.com/releases/repo.html && \
     pip cache purge
 
 # default shell bash
 ENV SHELL=/bin/bash
 
 # install special package
-RUN pip install --no-cache-dir mmcls>=0.21.0 mmdet>=2.25.0 decord>=0.6.0 datasets==2.1.0 numpy==1.18.5 ipykernel fairseq fasttext https://modelscope.oss-cn-beijing.aliyuncs.com/releases/dependencies/xtcocotools-1.12-cp37-cp37m-linux_x86_64.whl
-
 RUN if [ "$USE_GPU" = "True" ] ; then \
         pip install --no-cache-dir dgl-cu113 dglgo -f https://data.dgl.ai/wheels/repo.html; \
     else \
@@ -88,3 +87,22 @@ RUN if [ "$USE_GPU" = "True" ] ; then \
 # install  jupyter plugin
 RUN mkdir -p /root/.local/share/jupyter/labextensions/ && \
     cp -r  /tmp/resources/jupyter_plugins/*  /root/.local/share/jupyter/labextensions/
+
+COPY docker/scripts/modelscope_env_init.sh /usr/local/bin/ms_env_init.sh
+RUN pip install --no-cache-dir https://modelscope.oss-cn-beijing.aliyuncs.com/releases/dependencies/xtcocotools-1.12-cp37-cp37m-linux_x86_64.whl --force
+
+# for uniford
+COPY docker/scripts/install_unifold.sh /tmp/install_unifold.sh
+RUN if [ "$USE_GPU" = "True" ] ; then \
+        bash /tmp/install_unifold.sh; \
+    else \
+     echo 'cpu unsupport uniford'; \
+    fi
+
+RUN pip install --no-cache-dir mmcls>=0.21.0 mmdet>=2.25.0 decord>=0.6.0 datasets==2.1.0 numpy==1.18.5 ipykernel fairseq fasttext deepspeed
+COPY docker/scripts/install_apex.sh /tmp/install_apex.sh
+RUN if [ "$USE_GPU" = "True" ] ; then \
+        bash /tmp/install_apex.sh; \
+    else \
+     echo 'cpu unsupport uniford'; \
+    fi

docker/scripts/install_apex.sh

@@ -0,0 +1,5 @@
+git clone https://github.com/NVIDIA/apex
+cd apex
+TORCH_CUDA_ARCH_LIST="6.0;6.1;6.2;7.0;7.5;8.0;8.6" pip install -v --disable-pip-version-check --no-cache-dir --global-option="--cpp_ext" --global-option="--cuda_ext" ./
+cd ..
+rm -rf apex

docker/scripts/install_unifold.sh

@@ -0,0 +1,12 @@
+apt-get update && apt-get install -y  hmmer kalign curl cmake \
+        && apt-get clean && rm -rf /var/lib/apt/lists/* \
+        && git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
+        && mkdir /tmp/hh-suite/build \
+        && pushd /tmp/hh-suite/build \
+        && cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
+        && make -j 4 && make install \
+        && ln -s /opt/hhsuite/bin/* /usr/bin \
+        && popd \
+        && rm -rf /tmp/hh-suite \
+        && pip install --no-cache-dir unicore -f https://modelscope.oss-cn-beijing.aliyuncs.com/releases/repo.html \
+        && pip install --no-cache-dir  biopython ipdb

docker/scripts/modelscope_env_init.sh

@@ -0,0 +1,47 @@
+#!/bin/bash
+set -e
+set -o pipefail
+# chieck git is install
+git --version >/dev/null 2>&1 || { echo 'git not installed' ; exit 0; }
+
+if [ -z "$MODELSCOPE_USERNAME" ]  || [ -z "$MODELSCOPE_GITLAB_ACCESS_TOKEN" ]; then
+    :
+else
+    git config --global credential.helper store
+    echo "http://${MODELSCOPE_USERNAME}:${MODELSCOPE_GITLAB_ACCESS_TOKEN}@www.modelscope.cn">~/.git-credentials
+    echo "https://${MODELSCOPE_USERNAME}:${MODELSCOPE_GITLAB_ACCESS_TOKEN}@www.modelscope.cn">>~/.git-credentials
+    chmod go-rwx ~/.git-credentials
+fi
+if [ -z "$MODELSCOPE_USERNAME" ]  || [ -z "$MODELSCOPE_USEREMAIL" ]; then
+    :
+else
+    git config --system user.name ${MODELSCOPE_USERNAME}
+    git config --system user.email ${MODELSCOPE_USEREMAIL}
+fi
+if [ -z "$MODELSCOPE_ENVIRONMENT" ]; then
+    :
+else
+    git config --system --add http.http://www.modelscope.cn.extraHeader "Modelscope_Environment: $MODELSCOPE_ENVIRONMENT"
+    git config --system --add http.https://www.modelscope.cn.extraHeader "Modelscope_Environment: $MODELSCOPE_ENVIRONMENT"
+fi
+
+if [ -z "$MODELSCOPE_USERNAME" ]; then
+    :
+else
+    git config --system --add http.http://www.modelscope.cn.extraHeader "Modelscope_User: $MODELSCOPE_USERNAME"
+    git config --system --add http.https://www.modelscope.cn.extraHeader "Modelscope_User: $MODELSCOPE_USERNAME"
+fi
+
+if [ -z "$MODELSCOPE_USERID" ]; then
+    :
+else
+    git config --system --add http.http://www.modelscope.cn.extraHeader "Modelscope_Userid: $MODELSCOPE_USERID"
+    git config --system --add http.https://www.modelscope.cn.extraHeader "Modelscope_Userid: $MODELSCOPE_USERID"
+fi
+
+if [ -z "$MODELSCOPE_HAVANAID" ]; then
+    :
+else
+    git config --system --add http.http://www.modelscope.cn.extraHeader "Modelscope_Havanaid: $MODELSCOPE_HAVANAID"
+    git config --system --add http.https://www.modelscope.cn.extraHeader "Modelscope_Havanaid: $MODELSCOPE_HAVANAID"
+fi