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Dockerfile-batch-dev
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Dockerfile-batch-dev
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#FROM ubuntu:xenial as build
#
#RUN apt-get -y update && apt-get install -y apt-utils && \
# apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran zlib1g-dev \
# libhdf5-dev libcurl4-openssl-dev libboost-dev cmake wget python
#
##
## build PETSc with mpich for static linking
##
#RUN mkdir /usr/local/petsc && \
# cd /usr/local/petsc && \
# wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.7.7.tar.gz && \
# tar xzf petsc-3.7.7.tar.gz && \
# cd petsc-3.7.7 && \
# ./configure --with-shared-libraries=0 --download-fblaslapack=1 --with-debugging=1 --download-mpich && \
# make PETSC_DIR=/usr/local/petsc/petsc-3.7.7 PETSC_ARCH=arch-linux2-c-debug all
#
#ENV PETSC_DIR=/usr/local/petsc/petsc-3.7.7 \
# PETSC_ARCH=arch-linux2-c-debug
#
#COPY . /vcellroot
#
##
## build most solvers, and FiniteVolume without PETSc (FiniteVolume_x64)
##
#RUN mkdir -p /vcellroot/build/bin
#WORKDIR /vcellroot/build
#
#RUN /usr/bin/cmake \
# -DOPTION_TARGET_MESSAGING=ON \
# -DOPTION_TARGET_PARALLEL=OFF \
# -DOPTION_TARGET_PETSC=OFF \
# -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
# -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
# -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
# -DOPTION_TARGET_FV_SOLVER=ON \
# -DOPTION_TARGET_STOCHASTIC_SOLVER=ON \
# -DOPTION_TARGET_NFSIM_SOLVER=ON \
# -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=ON \
# -DOPTION_TARGET_SUNDIALS_SOLVER=ON \
# -DOPTION_TARGET_HY3S_SOLVERS=OFF \
# .. && \
# make
#
##
## build FiniteVolume with PETSc (FiniteVolume_PETSc_x64)
##
#RUN mkdir -p /vcellroot/build_PETSc/bin
#WORKDIR /vcellroot/build_PETSc
#
#RUN /usr/bin/cmake \
# -DOPTION_TARGET_MESSAGING=ON \
# -DOPTION_TARGET_PARALLEL=OFF \
# -DOPTION_TARGET_PETSC=ON \
# -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
# -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
# -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
# -DOPTION_TARGET_FV_SOLVER=ON \
# -DOPTION_TARGET_STOCHASTIC_SOLVER=OFF \
# -DOPTION_TARGET_NFSIM_SOLVER=OFF \
# -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
# -DOPTION_TARGET_SUNDIALS_SOLVER=OFF \
# -DOPTION_TARGET_HY3S_SOLVERS=OFF \
# .. && \
# make
#
#
#FROM ubuntu:xenial
#
#RUN apt-get -y update && apt-get install -y apt-utils && \
# apt-get install -y -qq -o=Dpkg::Use-Pty=0 gcc gfortran zlib1g \
# libhdf5-10 libhdf5-cpp-11 libcurl4-openssl-dev zip
#
#COPY --from=build /vcellroot/build/bin /vcellbin
#COPY --from=build /vcellroot/build_PETSc/bin/FiniteVolume_PETSc_x64 /vcellbin/
#WORKDIR /vcellbin
#ENV PATH=/vcellbin:$PATH
FROM virtualcell/vcell-solvers:v0.0.24
RUN apt-get -y update && \
apt-get install -y openjdk-8-jre-headless curl && \
apt-get install -y python python-pip wget gdebi-core && \
pip install thrift python-libsbml && \
wget https://download.opensuse.org/repositories/home:/fbergman:/COPASI/xUbuntu_17.10/amd64/python-copasi_4.22.170-1_amd64.deb && \
gdebi -n -q python-copasi_4.22.170-1_amd64.deb
RUN mkdir -p /usr/local/app/localsolvers && ln -s /vcellbin /usr/local/app/localsolvers/linux64
WORKDIR /usr/local/app
COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
./vcell-server/target/maven-jars/*.jar \
./lib/
COPY ./nativelibs/linux64 ./nativelibs/linux64
COPY ./docker/build/batch/JavaPreprocessor64 \
./docker/build/batch/JavaPostprocessor64 \
./docker/build/batch/JavaSimExe64 \
./docker/build/batch/entrypoint.sh \
./pythonScripts \
/vcellscripts/
ENV PATH=/vcellscripts:$PATH \
CLASSPATH=/usr/local/app/lib/*
ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
serverid=SITE \
installdir=/usr/local/app \
jmshost_sim_internal="jms-host-not-set" \
jmsport_sim_internal="jms-port-not-set" \
jmsrestport_sim_internal="jms-restport-not-set" \
jmsuser="jms-user-not-set" \
jmspswd="jms-pswd-not-set" \
blob_message_use_mongo=true \
datadir_internal=/simdata \
datadir_external=/path/to/external/simdata \
htclogdir_internal=/htclogs \
htclogdir_external=/path/to/external/htclogs \
mongodbhost_internal="mongo-host-not-set" \
mongodbport_internal="mongo-port-not-set" \
mongodb_database=test \
TMPDIR=/solvertmp/ \
java_mem_Xmx=200M \
jmsblob_minsize=100000
VOLUME /simdata
VOLUME /share/apps/vcell10/users
VOLUME /htclogs
VOLUME /solvertmp
ENTRYPOINT [ "/vcellscripts/entrypoint.sh" ]