Dockerfile-build-env

FROM ubuntu:18.10

MAINTAINER Lukasz.Kaczmarczyk@glasgow.ac.uk

# Confif apt-get
RUN echo 'APT::Install-Recommends "0";' > /etc/apt/apt.conf.d/99local

# ENV http_proxy="http://wwwcache.gla.ac.uk:8080/"
# ENV ftp_proxy="ftp://wwwcache.gla.ac.uk:8080/"
# ENV https_proxy="https://wwwcache.gla.ac.uk:8080/"

ENV DEBIAN_FRONTEND=noninteractive

# Install packages
RUN apt-get update && \
apt-get install -y \
file \
zlib1g-dev \
openssh-server \
wget \
valgrind \
git \
g++ \
gfortran \
gdb \
m4 \
automake \
build-essential \
libtool \
libblas-dev \
liblapack-dev \
libsigsegv2 \
libjpeg-dev \
graphviz \
doxygen \
cmake \
gnuplot \
pstack \
ca-certificates \
python \
bison \
flex \
libx11-dev \
libboost-all-dev \
libopenmpi-dev \
openmpi-bin \
xauth \
xterm \
unzip \
tk8.6-dev \
libfreetype6-dev \
mesa-common-dev \
libglu1-mesa-dev \
libxmu-dev \
libxi-dev \
libssl-dev \
&& rm -rf /var/lib/apt/lists/*

#libadolc-dev 

# CMake
RUN cd /opt \
&& wget https://cmake.org/files/v3.8/cmake-3.8.2.tar.gz \
&& tar -xzf cmake-3.8.2.tar.gz && rm cmake-3.8.2.tar.gz \
&& cd cmake-3.8.2 && cmake -DCMAKE_USE_OPENSSL=ON -DCMAKE_INSTALL_PREFIX=/opt/local \
&& make install \
&& cd /opt && rm -rf cmake-3.8.2*

# Set petesc version
ENV PETSC_VERSION 3.7.7
ENV PETSC_ARCH arch-linux2-c-opt
ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/opt/petsc/arch-linux2-c-opt/lib
ENV MESHKIT_DIR /opt/petsc/arch-linux2-c-opt/
ENV CASROOT /opt/petsc/arch-linux2-c-opt/

# Install petsc opt
RUN cd /opt && git clone --branch v$PETSC_VERSION --depth 1 https://gitlab.com/petsc/petsc.git

RUN cd /opt/petsc \
&& wget https://bitbucket.org/likask/mofem-joseph/downloads/netcdf-4.3.3.1.tar.gz \
&& ./configure \
--with-debugging=0 \
--with-mpi=1 \
--download-metis=1 \
--download-parmetis=1 \
--download-hypre=1 \
--download-mumps=1 \
--download-superlu_dist=1 \
--download-blacs=1 \
--download-hdf5=1 \
--download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz  \
--download-scalapack=1 \
--with-shared-libraries=1 \
&& make PETSC_DIR=/opt/petsc PETSC_ARCH=$PETSC_ARCH all \
&& rm -rvf /opt/petsc/$PETSC_ARCH/externalpackages/*

# ADOL-C
RUN cd /opt \
&& wget http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.5.2.tgz \
&& tar -xzf ADOL-C-2.5.2.tgz \
&& cd ADOL-C-2.5.2 \
&& ./configure  --prefix=/opt/petsc/$PETSC_ARCH \
&& make && make install

## OpenCascade & CGM
#RUN cd /opt && git clone --branch master --depth 1 https://bitbucket.org/fathomteam/cgm && \
#cd /opt && wget http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/OpenCASCADE660.tgz && \
#tar -xzf OpenCASCADE660.tgz && rm OpenCASCADE660.tgz && \
#cd /opt/ros && \
#patch -p1 < ../cgm/src/geom/OCC/occ_patches_6.6.0; true && \
#autoreconf -fi && \
#./configure --prefix=/opt/petsc/arch-linux2-c-opt/ && \
#make install && make clean && \
#cd /opt/cgm && \
#autoreconf -fi && \
#./configure --prefix=/opt/petsc/$PETSC_ARCH --libdir=/opt/petsc/$PETSC_ARCH/lib \
#CC=mpicc CFLAGS="-fPIC -g -O" \
#AR=/usr/bin/ar ARFLAGS=cr \
#CXX=mpicxx CXXFLAGS="-g -fPIC" F90=mpif90 \
#F90FLAGS="-fPIC -ffree-line-length-0 -g -O" \
#F77=mpif90 FFLAGS="-fPIC -ffree-line-length-0 -g -O" \
#FC=mpif90 FCFLAGS="-fPIC -ffree-line-length-0 -g -O" \
#--with-occ=/opt/petsc/$PETSC_ARCH \
#--enable-shared \
#&& make install && make clean && \
#rm -rf /opt/ros

# Install moab
RUN cd /opt && git clone --branch master --depth 1  https://bitbucket.org/likask/moab.git

RUN cd /opt/moab && \
autoreconf -fi && \
./configure --prefix=/opt/petsc/$PETSC_ARCH --libdir=/opt/petsc/$PETSC_ARCH/lib \
CC=mpicc CFLAGS="-fPIC -g -O" \
AR=/usr/bin/ar ARFLAGS=cr \
CXX=mpicxx CXXFLAGS="-g -fPIC" F90=mpif90 \
F90FLAGS="-fPIC -ffree-line-length-0 -g -O" \
F77=mpif90 FFLAGS="-fPIC -ffree-line-length-0 -g -O" \
FC=mpif90 FCFLAGS="-fPIC -ffree-line-length-0 -g -O" \
LDFLAGS="-L/opt/petsc/arch-linux2-c-opt/lin64/gcc/lib" \
--enable-shared --with-mpi= \
--with-hdf5=/opt/petsc/$PETSC_ARCH \
--with-netcdf=/opt/petsc/$PETSC_ARCH \
--with-parmetis=/opt/petsc/$PETSC_ARCH \
--with-metis=/opt/petsc/$PETSC_ARCH \
&& make install && make clean

#--with-cgm=/opt/petsc/$PETSC_ARCH \
#--enable-irel --enable-fbigeom \

# SLEP opt solve eigen value problem
#RUN cd /opt && git clone https://bitbucket.org/slepc/slepc && cd /opt/slepc && git checkout tags/v$PETSC_VERSION
#RUN cd /opt/slepc && PETSC_DIR=/opt/petsc PETSC_ARCH=$PETSC_ARCH ./configure && make SLEPC_DIR=$PWD PETSC_DIR=/opt/petsc PETSC_ARCH=$PETSC_ARCH

# MED
RUN cd /opt && wget http://files.salome-platform.org/Salome/other/med-3.2.0.tar.gz && \
tar -xzf med-3.2.0.tar.gz && rm med-3.2.0.tar.gz && \
cd med-3.2.0/ && \
./configure --disable-python --disable-fortran --prefix=/opt/med --with-hdf5=/opt/petsc/$PETSC_ARCH && \
make install && make clean && rm -rf /opt/med-3.2.0

# TETGEN
RUN cd /opt && wget https://bitbucket.org/likask/mofem-joseph/downloads/tetgen1.5.0.tgz && \
tar -xf tetgen1.5.0.tgz && rm tetgen1.5.0.tgz && \
cd tetgen1.5.0 && \
/opt/local/bin/cmake . && \
make && \
cp libtet.a lib/

## NETGEN
#RUN cd /opt && wget http://downloads.sourceforge.net/project/netgen-mesher/netgen-mesher/5.3/netgen-5.3.0.tar.gz && \
#tar -xzf netgen-5.3.0.tar.gz && rm netgen-5.3.0.tar.gz && \
#cd netgen-5.3.0 && \
#./configure --prefix=/opt/petsc/$PETSC_ARCH --libdir=/opt/petsc/$PETSC_ARCH/lib \
#CC=mpicc CFLAGS="-fPIC -g -O" \
#AR=/usr/bin/ar ARFLAGS=cr \
#CXX=mpicxx CXXFLAGS="-g -fPIC" F90=mpif90 \
#F90FLAGS="-fPIC -ffree-line-length-0 -g -O" \
#F77=mpif90 FFLAGS="-fPIC -ffree-line-length-0 -g -O" \
#FC=mpif90 FCFLAGS="-fPIC -ffree-line-length-0 -g -O" \
#--disable-gui --enable-nglib && \
#make install && make clean && rm -rf /opt/netgen-5.3.0

## Triangle
#RUN cd /opt && mkdir /opt/triangle && \
#cd triangle && wget http://www.netlib.org/voronoi/triangle.zip && \
#unzip triangle.zip && rm triangle.zip && \
#mpicc -O -o triangle triangle.c -lm && \
#mpicc -DTRILIBRARY -O -c triangle.c && \
#mkdir lib && mkdir include && \
#cp triangle.h include/ && \
#ar rcs lib/libtriangle.a triangle.o

## MeshKit
#RUN cd /opt && git clone --branch master --depth 1 https://bitbucket.org/fathomteam/meshkit && \
#cd /opt/meshkit && \
#autoreconf -fi && \
#./configure --prefix=/opt/petsc/$PETSC_ARCH --libdir=/opt/petsc/$PETSC_ARCH/lib \
#CC=mpicc CFLAGS="-fPIC -g -O" \
#AR=/usr/bin/ar ARFLAGS=cr \
#CXX=mpicxx CXXFLAGS="-g -fPIC" F90=mpif90 \
#F90FLAGS="-fPIC -ffree-line-length-0 -g -O" \
#F77=mpif90 FFLAGS="-fPIC -ffree-line-length-0 -g -O" \
#FC=mpif90 FCFLAGS="-fPIC -ffree-line-length-0 -g -O" \
#--with-igeom=/opt/petsc/$PETSC_ARCH \
#--with-imesh=/opt/petsc/$PETSC_ARCH \
#--with-tetgen=/opt/tetgen1.5.0 \
#--with-netgen=/opt/petsc/$PETSC_ARCH \
#--with-triangle=/opt/triangle \
#&& make install && make clean

ENV PETSC_DIR=/opt/petsc
ENV PETSC_ARCH=$PETSC_ARCH
ENV PATH $PATH:$PETSC_DIR/$PETSC_ARCH/bin
ENV MOFEM_SRC_DIR=/mofem
ENV MOFEM_ROOT_DIR=/mofem_build
ENV MOFEM_INSTALL_DIR=/mofem_build/um
ENV MOFEM_BUILD_DIR=/mofem_build/lib

# Set mpirun alias
ENV OMPI_MCA_btl_vader_single_copy_mechanism=none
RUN echo "alias mpirun='mpirun --allow-run-as-root'" >> /root/.bash_aliases

# SSH
RUN mkdir /var/run/sshd
RUN echo 'root:mofem' | chpasswd
RUN sed -i 's/PermitRootLogin prohibit-password/PermitRootLogin yes/' /etc/ssh/sshd_config

# SSH login fix. Otherwise user is kicked off after login
RUN sed 's@session\s*required\s*pam_loginuid.so@session optional pam_loginuid.so@g' -i /etc/pam.d/sshd

ENV NOTVISIBLE "in users profile"
RUN echo "export VISIBLE=now" >> /etc/profile

# SSH .ssh dir
RUN mkdir root/.ssh

# Allow to trace child procsses needed for debuging
RUN sed  -i 's/kernel.yama.ptrace_scope = 1/kernel.yama.ptrace_scope = 0/' /etc/sysctl.d/10-ptrace.conf

EXPOSE 22
CMD ["/usr/sbin/sshd", "-D"]