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JunCEEEJunCEEE
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update docker for master branch
1 parent 0bc32a2 commit 04b4dca

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11 files changed

+246
-93
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11 files changed

+246
-93
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‎Docker/run_docker.sh‎

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#!/usr/bin/env bash
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containername="cloudbusting/simex"
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J_PORT=8897
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TRASIT_HOST=max-exfl-display.desy.de
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HOST_PATH=/gpfs/exfel/data/user/
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MOUNT_PATH=/home/xfeluser
7+
JUPYTER_START_PATH=/home/xfeluser/juncheng
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9+
# To forward to external host
10+
DISPHOST=`dig +short $TRASIT_HOST |head -1`
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DISPHOST=${DISPHOST%.}
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echo "Transit host: " $DISPHOST
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ssh -f -N -T -R ${J_PORT}:localhost:$J_PORT $DISPHOST &
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docker run -v ${HOST_PATH}:${MOUNT_PATH} -e HOME=${JUPYTER_START_PATH} -u `id -u`:`id -g` --userns=host --security-opt no-new-privileges -ti -e JUPYTER_RUNTIME_DIR=/tmp -p ${J_PORT}:${J_PORT} $containername jupyter notebook --no-browser --ip 0.0.0.0 --port ${J_PORT} ${JUPYTER_START_PATH}

‎Docker/simex/Dockerfile‎

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@@ -1,19 +1,28 @@
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# [email protected] - Daniel Webster
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FROM chuckie82/centos_env
2-
MAINTAINER Chunhong Yoon <[email protected]>
3+
LABEL maintainer="Chunhong Yoon <[email protected]>"
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45
ADD requirements.txt /opt/requirements.txt
56
ADD python_install.sh /opt/python_install.sh
6-
RUN ["bash", "/opt/python_install.sh"]
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RUN yum remove -y cmake && yum install -y cmake3 hdf5-devel flex bison && \
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yum clean all && rm -rf /var/cache/yum && \
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update-alternatives --install /usr/bin/cmake cmake /usr/bin/cmake3 3 && \
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/opt/python_install.sh
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ENV PATH /opt/miniconda/bin:$PATH
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913
ARG simex_script=simex_install.sh
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ADD $simex_script /opt/simex_install.sh
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1216
RUN ["bash", "/opt/simex_install.sh"]
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14-
ENV SIMEX_ROOT=/opt/simex_platform
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ENV MKLROOT=/opt/miniconda
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ENV MKL_ROOT=/opt/miniconda
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ENV PYPATH=/opt/miniconda
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ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/miniconda/lib
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ENV SIMEX_ROOT=/opt/SimEx-master
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ENV PATH=$SIMEX_ROOT/bin:$PATH
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ENV PYTHONPATH=$SIMEX_ROOT/Sources/python:$SIMEX_ROOT/lib/python3.6:$PYTHONPATH
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ENV PYTHONPATH=$SIMEX_ROOT/Sources/python:$SIMEX_ROOT/lib/python3.7:$PYTHONPATH:/opt/SimEx-master/build/Modules/Others/sdf/sdf-prefix/src/sdf-build/lib/python3.7/site-packages/lib/python
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ENV SIMEX_TESTS=$SIMEX_ROOT/Tests
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ENV PYFAI_TESTIMAGES=/tmp
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RUN useradd -m jovyan

‎Docker/simex/build_image‎

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@@ -1,4 +1,4 @@
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cp ../../requirements.txt .
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3-
docker build --no-cache -t cfgrote/simex .
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buildah bud -t cloudbusting/simex -f Dockerfile .
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‎Docker/simex/python_install.sh‎

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@@ -1,6 +1,7 @@
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#!/usr/bin/env bash
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3-
export myminiconda=Miniconda3-4.4.10-Linux-x86_64.sh
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#export myminiconda=Miniconda3-4.4.10-Linux-x86_64.sh
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export myminiconda=Miniconda3-py37_4.8.3-Linux-x86_64.sh
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URL=https://repo.continuum.io/miniconda/$myminiconda
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# Install dir
@@ -21,7 +22,7 @@ export PATH=$PREFIX/bin:$PATH
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conda config --set always_yes True
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# pip cannot install pyqt
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conda install --no-update-deps pyqt=4
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conda install --no-update-deps pyqt=5.9.2
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# delete tests
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find . -type d -name tests -depth -exec rm -rf {} \;

‎Docker/simex/simex_install.sh‎

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@@ -2,27 +2,50 @@
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33
set -e
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5-
BRANCH=develop
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BRANCH=master
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URL=https://github.com/PaNOSC-ViNYL/SimEx/archive/${BRANCH}.zip
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88
cd /opt
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1010
wget $URL
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unzip ${BRANCH}.zip
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rm ${BRANCH}.zip
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cd simex_platform-${BRANCH}
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cd SimEx-${BRANCH}
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export PATH=/opt/miniconda/bin:$PATH
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export HDF5_ROOT=/opt/miniconda
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#export HDF5_ROOT=/opt/miniconda
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echo "###### DONE unzip ${BRANCH}.zip"
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conda install -c intel mkl
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export MKLROOT=/opt/miniconda
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# This is a dirty hack
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pushd ${MKLROOT}/lib
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ln -s . intel64
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popd
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echo "##### DONE install mkl"
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24-
ROOT_DIR=/opt/simex_platform
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mkdir -p $ROOT_DIR
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#ROOT_DIR=/opt/simex_platform
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#mkdir -p $ROOT_DIR
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33+
# PYPATH is necessary to facilitate the
34+
# install of sdf and s2e; otherwise the
35+
# modules are not installed outside of
36+
# the build tree -- dwebster.
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PYPATH=/opt/miniconda
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39+
CONDA_PREFIX=/opt/miniconda
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CONDA_BIN=`which conda`
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CONDA_BIN=${CONDA_BIN%/*}
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source ${CONDA_BIN%/*}/etc/profile.d/conda.sh
43+
INSTALL_PREFIX=$CONDA_PREFIX
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PYVERSION=`python -V | tr '[:upper:]' '[:lower:]' | tr -d ' '`
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PYLIB=${PYVERSION%.*}
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DEVELOPER_MODE=ON
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export ZLIB_ROOT=$CONDA_PREFIX
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export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
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# Create new build dir and cd into it.
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@@ -32,20 +55,27 @@ cd build
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# Uncomment the next line and specify the install dir for a custom user install.
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#cmake -DCMAKE_INSTALL_PREFIX=$ROOT_DIR $ROOT_DIR
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# Uncomment the next line and specify the install dir for a developer install.
35-
cmake -DXCSITPhotonDetector=OFF \
36-
-DGAPDPhotonDiffractor=OFF \
37-
-DCrystFELPhotonDiffractor=OFF \
58+
cmake -DUSE_XCSITPhotonDetector=OFF \
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-DUSE_GAPDPhotonDiffractor=OFF \
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-DUSE_CrystFELPhotonDiffractor=ON \
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-DUSE_SingFELPhotonDiffractor=ON \
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-DINSTALL_TESTS=OFF \
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-DSRW_OPTIMIZED=ON \
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-DDEVELOPER_INSTALL=OFF \
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-DCMAKE_INSTALL_PREFIX=$ROOT_DIR \
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$ROOT_DIR \
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..
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-DDEVELOPER_INSTALL=$DEVELOPER_MODE \
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-DCMAKE_INSTALL_PREFIX=/opt/miniconda \
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-DUSE_sdf=ON \
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-DUSE_s2e=ON \
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-DUSE_S2EReconstruction_EMC=ON \
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-DUSE_S2EReconstruction_DM=ON \
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-DUSE_wpg=ON \
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-DUSE_GenesisPhotonSource=ON \
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-DUSE_FEFFPhotonInteractor=ON \
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-DCMAKE_INSTALL_LOCAL_ONLY=0 \
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..
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45-
chmod og+rwX -R $ROOT_DIR
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4777
# Build the project.
48-
make
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make -j12
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5080
echo "######## done make"
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@@ -55,18 +85,10 @@ cd ../..
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5686
echo "####### done make install"
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58-
#rm -rf simex_platform-${BRANCH}
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60-
61-
#remove tests?
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#rm -rf $ROOT_DIR/Tests
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64-
echo "source /opt/simex_platform/bin/simex_vars.sh" > /etc/profile.d/scripts-simex.sh && \
89+
cp /opt/SimEx-${BRANCH}/build/simex_vars.sh ${CONDA_PREFIX}/bin
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echo "source ${CONDA_PREFIX}/bin/simex_vars.sh" > /etc/profile.d/scripts-simex.sh && \
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chmod 755 /etc/profile.d/scripts-simex.sh
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67-
6893
echo "export PYFAI_TESTIMAGES=/tmp" >> /etc/profile.d/scripts-simex.sh
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70-
71-
chmod og+rwX -R /opt/simex_platform
72-

‎Docker/simex_devel/Dockerfile‎

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@@ -1,12 +1,28 @@
1-
FROM yakser/simex_3rdparty
2-
MAINTAINER Sergey Yakubov <[email protected]>
1+
# [email protected] - Daniel Webster
2+
FROM chuckie82/centos_env
3+
LABEL maintainer="Chunhong Yoon <[email protected]>"
34

4-
ARG simex_script=simex_install_devel.sh
5+
ADD requirements.txt /opt/requirements.txt
6+
ADD python_install.sh /opt/python_install.sh
7+
RUN yum remove -y cmake && yum install -y cmake3 hdf5-devel flex bison && \
8+
yum clean all && rm -rf /var/cache/yum && \
9+
update-alternatives --install /usr/bin/cmake cmake /usr/bin/cmake3 3 && \
10+
/opt/python_install.sh
11+
ENV PATH /opt/miniconda/bin:$PATH
12+
13+
ARG simex_script=simex_install.sh
514
ADD $simex_script /opt/simex_install.sh
15+
616
RUN ["bash", "/opt/simex_install.sh"]
7-
ENV SIMEX_ROOT=/opt/simex_platform
17+
18+
ENV MKLROOT=/opt/miniconda
19+
ENV MKL_ROOT=/opt/miniconda
20+
ENV PYPATH=/opt/miniconda
21+
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/miniconda/lib
22+
ENV SIMEX_ROOT=/opt/SimEx-master
823
ENV PATH=$SIMEX_ROOT/bin:$PATH
9-
ENV PYTHONPATH=$SIMEX_ROOT/Sources/python:$SIMEX_ROOT/lib/python2.7:$PYTHONPATH
24+
ENV PYTHONPATH=$SIMEX_ROOT/Sources/python:$SIMEX_ROOT/lib/python3.7:$PYTHONPATH:/opt/SimEx-master/build/Modules/Others/sdf/sdf-prefix/src/sdf-build/lib/python3.7/site-packages/lib/python
1025
ENV SIMEX_TESTS=$SIMEX_ROOT/Tests
1126
ENV PYFAI_TESTIMAGES=/tmp
12-
ENTRYPOINT ["python"]
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28+
RUN useradd -m jovyan

‎Docker/simex_devel/build_image‎

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cp ../../requirements.txt .
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3+
buildah bud -t cloudbusting/simex:devel -f Dockerfile .
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‎Docker/simex_devel/build_image_develop‎

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This file was deleted.

‎Docker/simex_devel/python_install.sh‎

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#!/usr/bin/env bash
2+
3+
#export myminiconda=Miniconda3-4.4.10-Linux-x86_64.sh
4+
export myminiconda=Miniconda3-py37_4.8.3-Linux-x86_64.sh
5+
URL=https://repo.continuum.io/miniconda/$myminiconda
6+
7+
# Install dir
8+
PREFIX=/opt/miniconda
9+
10+
# Download Miniconda
11+
wget -q $URL
12+
13+
# Extract packages
14+
15+
chmod +x $myminiconda
16+
./$myminiconda -b -p $PREFIX
17+
rm ./$myminiconda
18+
cd $PREFIX
19+
20+
# config
21+
export PATH=$PREFIX/bin:$PATH
22+
conda config --set always_yes True
23+
24+
# pip cannot install pyqt
25+
conda install --no-update-deps pyqt=5.9.2
26+
27+
# delete tests
28+
find . -type d -name tests -depth -exec rm -rf {} \;
29+
find . -type d -name test -depth -exec rm -rf {} \;
30+
31+
conda clean --tarballs
32+
33+
# install requirements from file (in given order)
34+
#$PREFIX/bin/pip install -r /opt/requirements.txt
35+
xargs -L 1 pip install < /opt/requirements.txt
36+
37+
# remove .pyc
38+
find . -name \__pycache__ -depth -exec rm -rf {} \;
39+
find . -name "*.pyc" -exec rm -rf {} \;
40+
41+
42+
# remove cache
43+
rm -r pkgs/*
44+
rm -rf /root/.cache/pip
45+
46+
47+
echo "export PATH=/opt/miniconda/bin:${PATH}" >> /etc/profile.d/scripts-path.sh
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‎Docker/simex_devel/simex_install.sh‎

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#!/usr/bin/env bash
2+
3+
set -e
4+
5+
BRANCH=develop
6+
URL=https://github.com/PaNOSC-ViNYL/SimEx/archive/${BRANCH}.zip
7+
8+
cd /opt
9+
10+
wget $URL
11+
unzip ${BRANCH}.zip
12+
rm ${BRANCH}.zip
13+
cd SimEx-${BRANCH}
14+
15+
export PATH=/opt/miniconda/bin:$PATH
16+
#export HDF5_ROOT=/opt/miniconda
17+
18+
echo "###### DONE unzip ${BRANCH}.zip"
19+
20+
conda install -c intel mkl
21+
export MKLROOT=/opt/miniconda
22+
23+
# This is a dirty hack
24+
pushd ${MKLROOT}/lib
25+
ln -s . intel64
26+
popd
27+
28+
echo "##### DONE install mkl"
29+
30+
#ROOT_DIR=/opt/simex_platform
31+
#mkdir -p $ROOT_DIR
32+
33+
# PYPATH is necessary to facilitate the
34+
# install of sdf and s2e; otherwise the
35+
# modules are not installed outside of
36+
# the build tree -- dwebster.
37+
PYPATH=/opt/miniconda
38+
39+
CONDA_PREFIX=/opt/miniconda
40+
CONDA_BIN=`which conda`
41+
CONDA_BIN=${CONDA_BIN%/*}
42+
source ${CONDA_BIN%/*}/etc/profile.d/conda.sh
43+
INSTALL_PREFIX=$CONDA_PREFIX
44+
PYVERSION=`python -V | tr '[:upper:]' '[:lower:]' | tr -d ' '`
45+
PYLIB=${PYVERSION%.*}
46+
DEVELOPER_MODE=ON
47+
export ZLIB_ROOT=$CONDA_PREFIX
48+
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
49+
50+
# Create new build dir and cd into it.
51+
52+
mkdir -v build
53+
cd build
54+
55+
# Uncomment the next line and specify the install dir for a custom user install.
56+
#cmake -DCMAKE_INSTALL_PREFIX=$ROOT_DIR $ROOT_DIR
57+
# Uncomment the next line and specify the install dir for a developer install.
58+
cmake -DUSE_XCSITPhotonDetector=OFF \
59+
-DUSE_GAPDPhotonDiffractor=OFF \
60+
-DUSE_CrystFELPhotonDiffractor=ON \
61+
-DUSE_SingFELPhotonDiffractor=ON \
62+
-DINSTALL_TESTS=OFF \
63+
-DSRW_OPTIMIZED=ON \
64+
-DDEVELOPER_INSTALL=$DEVELOPER_MODE \
65+
-DCMAKE_INSTALL_PREFIX=/opt/miniconda \
66+
-DUSE_sdf=ON \
67+
-DUSE_s2e=ON \
68+
-DUSE_S2EReconstruction_EMC=ON \
69+
-DUSE_S2EReconstruction_DM=ON \
70+
-DUSE_wpg=ON \
71+
-DUSE_GenesisPhotonSource=ON \
72+
-DUSE_FEFFPhotonInteractor=ON \
73+
-DCMAKE_INSTALL_LOCAL_ONLY=0 \
74+
..
75+
76+
77+
# Build the project.
78+
make -j12
79+
80+
echo "######## done make"
81+
82+
# Install the project.
83+
make install
84+
cd ../..
85+
86+
echo "####### done make install"
87+
88+
89+
cp /opt/SimEx-${BRANCH}/build/simex_vars.sh ${CONDA_PREFIX}/bin
90+
echo "source ${CONDA_PREFIX}/bin/simex_vars.sh" > /etc/profile.d/scripts-simex.sh && \
91+
chmod 755 /etc/profile.d/scripts-simex.sh
92+
93+
echo "export PYFAI_TESTIMAGES=/tmp" >> /etc/profile.d/scripts-simex.sh
94+

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