From d6cd7e61ef08ca2d988f9c3d6ee9fce7a5c6f711 Mon Sep 17 00:00:00 2001
From: Daniel Peter <daniel.peter22@gmail.com>
Date: Thu, 9 Mar 2023 18:27:30 +0300
Subject: [PATCH] adds docker file

---
 .docker/Dockerfile.alpine_minimal | 129 ++++++++++++++++++++++++++++++
 .dockerignore                     |  66 +++++++++++++++
 2 files changed, 195 insertions(+)
 create mode 100644 .docker/Dockerfile.alpine_minimal
 create mode 100644 .dockerignore

diff --git a/.docker/Dockerfile.alpine_minimal b/.docker/Dockerfile.alpine_minimal
new file mode 100644
index 000000000..097faaec9
--- /dev/null
+++ b/.docker/Dockerfile.alpine_minimal
@@ -0,0 +1,129 @@
+#########################################################
+## Docker
+#########################################################
+#
+# minimal container example
+# installs SPECFEM w/out additional support (ADIOS,ASDF,CUDA,..)
+#
+# building container:
+# > docker build -f .docker/Dockerfile.alpine_minimal -t specfem3d_minimal:latest .
+#
+# running container (interactive):
+# > docker run -it --rm specfem3d_minimal
+#
+# running container executable only:
+# > docker run -v $(pwd)/DATA:/home/myuser/DATA \
+#              -v $(pwd)/OUTPUT_FILES:/home/myuser/OUTPUT_FILES \
+#              --rm --entrypoint='mpirun' specfem3d_minimal -np 4 xspecfem3D
+#
+#
+#########################################################
+## build stage
+#########################################################
+# alpine - minimal linux distro
+# https://www.alpinelinux.org
+FROM alpine:latest AS mybuildstage
+
+#########################################################
+## Installation
+#########################################################
+# Install Deps
+# GNU compilers
+RUN apk update \
+    && apk add --no-cache \
+           bash \
+           build-base \
+           gfortran \
+           git \
+           openmpi \
+           openmpi-dev
+
+# changes default shell from ash to bash (for configuration to work properly)
+# re-directs /bin/sh to /bin/bash
+RUN sed -i -e "s/bin\/ash/bin\/bash/" /etc/passwd \
+    && cd /bin && mv sh sh.org && ln -s ./bash sh
+
+ENV LC_ALL=en_US.UTF-8
+ENV SHELL=/bin/bash
+
+# Installing software
+#########################################################
+## SPECFEM
+#########################################################
+RUN mkdir /app
+WORKDIR /app
+
+# setup w/ git (shallow clone)
+RUN git clone --depth=1 --recursive --branch devel https://github.com/SPECFEM/specfem3d.git
+
+#########################################################
+## configuration / compilation
+#########################################################
+# variables
+ARG CC=gcc
+ARG FC=gfortran
+ARG MPIFC=mpif90
+ARG FLAGS="-O3"
+
+WORKDIR /app/specfem3d
+
+# parallel
+RUN ./configure CC=${CC} FC=${FC} MPIFC=${MPIFC} FLAGS_CHECK="${FLAGS}" --with-mpi --enable-vectorization \
+    && make -j4 all
+
+# cleanup/removes .git folder (to minimize container size)
+RUN rm -rf .git \
+    && rm -rf external_libs/ doc/ lib/ m4/ obj/ \
+    && rm -rf src/inverse_problem_for_source/ \
+    && rm -rf utils/ADJOINT_TOMOGRAPHY_TOOLS/ utils/dynamic_rupture/ utils/unused_routines/ utils/Visualization/ \
+    && find ./EXAMPLES -mindepth 1 -maxdepth 1 -type d -not -name "homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides" | xargs rm -rf
+
+#########################################################
+## user stage
+#########################################################
+FROM alpine:latest
+
+# required libraries
+RUN apk update \
+    && apk add --no-cache \
+           bash \
+           libgfortran \
+           openmpi \
+           openssh-client-default \
+           vim
+
+# creates a default user
+ENV USER myuser
+ENV HOME /home/${USER}
+
+RUN adduser ${USER} --disabled-password --gecos ""
+
+# we use user from here on
+USER ${USER}
+WORKDIR ${HOME}
+
+# copies specfem w/ binaries
+COPY --from=mybuildstage --chown=${USER} /app/specfem3d ./specfem3d
+
+#########################################################
+## container default entry
+#########################################################
+# container setup
+# alias/bash
+RUN echo "alias ll='ls -lh'" > ${HOME}/.alias \
+    && echo ". ~/.alias" > ${HOME}/.bashrc \
+    && echo "ulimit -S -s unlimited" >> ${HOME}/.bashrc
+
+# puts specfem binaries in PATH
+ENV PATH=$PATH:${HOME}/specfem3d/bin
+
+# avoids OpenMPI runtime messages
+# when calling mpirun -np 4 ./bin/xspecfem3d, errors like appear:
+#  [e4cdf18d39c1:00068] Read -1, expected 18980, errno = 1
+#  ..
+# see: https://github.com/open-mpi/ompi/issues/4948
+ENV OMPI_MCA_btl_vader_single_copy_mechanism=none
+
+# default shell
+CMD ["/bin/bash"]
+
diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 000000000..fe790e202
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,66 @@
+# Docker ignore folders/files
+
+## from .gitignore:
+# Configure time
+aclocal.m4
+autom4te.cache
+config.log
+config.status
+config.h
+/Makefile
+
+setup/config.fh
+setup/constants.h
+setup/constants_inverse_problem.h
+setup/constants_tomography.h
+setup/precision.h
+setup/version.fh
+
+external_libs/scotch_5.1.12b/src/libscotch/y.output
+
+# Build time
+bin/
+lib/
+obj/
+src/decompose_mesh/*.mod
+src/generate_databases/*.mod
+src/meshfem3D/*.mod
+src/specfem3D/*.mod
+*__genmod.f90
+
+# documentation
+manual_SPECFEM3D_Cartesian.aux
+manual_SPECFEM3D_Cartesian.bbl
+doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.blg
+doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.brf
+doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.log
+doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.out
+doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.synctex.gz
+doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.toc
+doc/USER_MANUAL/Schedule
+
+# Trash files
+.*swp
+.*swo
+.*swn
+*~
+
+# documentation
+wiki/
+gh-pages/
+
+# tests
+.azure-pipelines/
+.github/
+.travis/
+
+# git folder (to minimize image size)
+.git/branches
+.git/filter-repo
+.git/hooks
+.git/logs
+.git/modules
+.git/objects
+.git/refs
+
+