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#92 modified R kernel installation to fix permissions errors #93

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125 changes: 65 additions & 60 deletions docker/Dockerfile
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Expand Up @@ -33,54 +33,55 @@ RUN cd /home/jovyan/libs/hs_restclient/hs_restclient && patch < hs_restclient.pa

# install DHSVM (need to modify UFconfig.mk for linux)
RUN git clone -b glacier https://github.com/pnnl/DHSVM-PNNL.git /home/jovyan/libs/DHSVM-PNNL
RUN sed -i '/# CC = gcc/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
RUN sed -i '/# CFLAGS = -O3 -fexceptions/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
RUN sed -i '/# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
RUN sed -i 's/F77 = gfortran/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
RUN sed -i 's/CFLAGS = -O3 -fno-common -no-cpp-precomp -fexception/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
RUN sed -i 's/BLAS = -framework Accelerate/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
RUN sed -i 's/LAPACK = -framework Accelerate/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
RUN sed -i 's/DEFS = -DHAVE_X11 -DHAVE_GLACIER/DEFS = -DHAVE_X11/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/sourcecode/makefile
RUN rm /home/jovyan/libs/DHSVM-PNNL/DHSVM/Lib/libcxsparse.a
RUN cd /home/jovyan/libs/DHSVM-PNNL/DHSVM/Lib && make
RUN cd /home/jovyan/libs/DHSVM-PNNL/DHSVM/sourcecode && make
RUN sed -i '/# CC = gcc/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk \
&& sed -i '/# CFLAGS = -O3 -fexceptions/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk \
&& sed -i '/# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk \
&& sed -i 's/F77 = gfortran/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk \
&& sed -i 's/CFLAGS = -O3 -fno-common -no-cpp-precomp -fexception/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk \
&& sed -i 's/BLAS = -framework Accelerate/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk \
&& sed -i 's/LAPACK = -framework Accelerate/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk \
&& sed -i 's/DEFS = -DHAVE_X11 -DHAVE_GLACIER/DEFS = -DHAVE_X11/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/sourcecode/makefile \
&& rm /home/jovyan/libs/DHSVM-PNNL/DHSVM/Lib/libcxsparse.a \
&& cd /home/jovyan/libs/DHSVM-PNNL/DHSVM/Lib && make \
&& cd /home/jovyan/libs/DHSVM-PNNL/DHSVM/sourcecode && make

# install Boost and Dakota
RUN wget -O /home/jovyan/libs/boost.tar.gz https://sourceforge.net/projects/boost/files/boost/1.53.0/boost_1_53_0.tar.gz/download
RUN mkdir /home/jovyan/libs/boost && tar xzfv /home/jovyan/libs/boost.tar.gz -C /home/jovyan/libs/boost --strip-components 1
RUN wget -O /home/jovyan/libs/boost.tar.gz https://sourceforge.net/projects/boost/files/boost/1.53.0/boost_1_53_0.tar.gz/download \
&& mkdir /home/jovyan/libs/boost \
&& tar xzfv /home/jovyan/libs/boost.tar.gz -C /home/jovyan/libs/boost --strip-components 1

###### BEGIN ROOT #######
USER root

RUN cd /home/jovyan/libs/boost && ./bootstrap.sh --prefix=/usr/local
RUN echo "using mpi ;" >> /home/jovyan/libs/boost/tools/build/v2/user-config.jam
RUN cd /home/jovyan/libs/boost && ./b2 --with=all -j 4 install; exit 0
RUN sh -c 'echo "/usr/local/lib" >> /etc/ld.so.conf.d/local.conf'
RUN ldconfig
RUN apt-get install -y libblas-dev liblapack-dev cmake

RUN apt-get install -y libblas-dev liblapack-dev cmake \
&& cd /home/jovyan/libs/boost && ./bootstrap.sh --prefix=/usr/local \
&& echo "using mpi ;" >> /home/jovyan/libs/boost/tools/build/v2/user-config.jam \
&& cd /home/jovyan/libs/boost && ./b2 --with=all -j 4 install; exit 0 \
&& sh -c 'echo "/usr/local/lib" >> /etc/ld.so.conf.d/local.conf' \
&& ldconfig
USER jovyan
####### END ROOT ########

RUN wget https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.5-public.src.tar.gz -P /home/jovyan/libs
RUN tar xzf /home/jovyan/libs/dakota-6.5-public.src.tar.gz -C /home/jovyan/libs
RUN mkdir /home/jovyan/libs/dakota-6.5.0.src/build
RUN wget https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.5-public.src.tar.gz -P /home/jovyan/libs \
&& tar xzf /home/jovyan/libs/dakota-6.5-public.src.tar.gz -C /home/jovyan/libs \
&& mkdir /home/jovyan/libs/dakota-6.5.0.src/build
ADD docker/dakota_template.cmake /home/jovyan/libs/dakota-6.5.0.src/build/BuildDakota.cmake
RUN cd /home/jovyan/libs/dakota*.src/build && cmake -C BuildDakota.cmake /home/jovyan/libs/dakota*.src
RUN cd /home/jovyan/libs/dakota*.src/build \
&& cmake -C BuildDakota.cmake /home/jovyan/libs/dakota*.src

###### BEGIN ROOT #######
USER root
RUN cd /home/jovyan/libs/dakota*.src/build && make clean
RUN cd /home/jovyan/libs/dakota*.src/build && make
RUN cd /home/jovyan/libs/dakota*.src/build && make install
ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
RUN cd /home/jovyan/libs/dakota*.src/build \
&& make clean \
&& make \
&& make install
USER jovyan
####### END ROOT ########

ADD docker/icommands.sh /home/jovyan/libs/icommands.sh
USER root
RUN chmod +x /home/jovyan/libs/icommands.sh
RUN echo "/home/jovyan/libs" | /home/jovyan/libs/icommands.sh
RUN chmod +x /home/jovyan/libs/icommands.sh \
&& echo "/home/jovyan/libs" | /home/jovyan/libs/icommands.sh
USER jovyan

ENV \
Expand All @@ -89,41 +90,45 @@ IRODS_PLUGINS_HOME=/home/jovyan/libs/icommands/plugins/ \
IRODS_ENVIRONMENT_FILE=/home/jovyan/work/notebooks/data/.irods/irods_environment.json \
IRODS_AUTHENTICATION_FILE=/home/jovyan/work/notebooks/data/.irods/.irodsA

RUN pip install git+https://github.com/cybergis/jupyterlib.git
RUN pip3 install git+https://github.com/cybergis/jupyterlib.git
RUN pip install git+https://github.com/cybergis/jupyterlib.git \
&& pip3 install git+https://github.com/cybergis/jupyterlib.git

###### BEGIN ROOT #######
USER root

# register the kernel in the current R installation
RUN sh -c 'echo "deb http://cran.rstudio.com/bin/linux/debian jessie-cran3/" >> /etc/apt/sources.list'
RUN gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
RUN gpg -a --export E084DAB9 | apt-key add -
RUN apt-key update
RUN apt-get update

# required libs for installing R packages
RUN apt-get -y install \
libcurl4-openssl-dev \
libssl-dev \
make \
gcc \
g++

# install R-base packages (including IRKernel)
RUN apt-get install --allow-unauthenticated --no-install-recommends -y r-base=3.3*
RUN Rscript -e "install.packages('devtools', repos='http://archive.linux.duke.edu/cran')"
RUN Rscript -e "devtools::install_github('IRkernel/IRkernel')"
USER jovyan
####### END ROOT ########
#RUN Rscript -e "IRkernel::installspec(name = 'ir33', displayname = 'R 3.3')" \
ENV R_LIBS_SITE=/home/jovyan/.userRLib
RUN mkdir /home/jovyan/.userRLib

RUN conda create -y -n R
RUN conda update conda -y #(conda update --all)

RUN conda install -n R -c r \
r-essentials
r-xml \
r-rjsonio

# ###### BEGIN ROOT #######
USER root
RUN ln -s /opt/conda/envs/R/bin/R /usr/bin/R
RUN ln -s /opt/conda/envs/R/bin/Rscript /usr/bin/Rscript
USER jovyan
# ####### END ROOT ########

RUN echo "options(repos=structure(c(CRAN=\"http://archive.linux.duke.edu/cran\")))" >> /home/jovyan/.Rprofile \
&& Rscript -e "install.packages('devtools', repos='http://archive.linux.duke.edu/cran')" \
&& Rscript -e "IRkernel::installspec(name = 'ir33', displayname = 'R 3.3')" \
&& Rscript -e "install.packages('WaterML')"

RUN Rscript -e "IRkernel::installspec(name = 'ir33', displayname = 'R 3.3')"
RUN pip install geopandas graphviz \
&& pip3 install geopandas graphviz

RUN pip install geopandas
RUN pip3 install geopandas
# celery
ENV PATH=/home/jovyan/libs:$PATH
RUN pip install celery \
&& pip3 install celery

RUN pip install graphviz
RUN pip3 install graphviz
RUN mkdir /home/jovyan/libs/celeryworker
ADD docker/celery/celeryworker /home/jovyan/libs/celeryworker/
ENV PYTHONPATH=/home/jovyan/libs:$PYTHONPATH

###################################################
## End - JupyterHub Development Image Additions ###
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