Adding Tacc specific startup script

Dockerfile

@@ -203,6 +203,7 @@ RUN chmod +x /usr/sbin/tini
 
 # Add startup script
 ADD scripts/start-mspass.sh /usr/sbin/start-mspass.sh
+ADD scripts/start-mspass-tacc.sh /usr/sbin/start-mspass-tacc.sh
 RUN chmod +x /usr/sbin/start-mspass.sh
 RUN chmod +x /usr/local/bin/docker-entrypoint.sh
 RUN sed -i '/set -- mongod "$@"/i [[ -d data ]] || mkdir data' /usr/local/bin/docker-entrypoint.sh

Dockerfile_tapis

@@ -0,0 +1,229 @@
+#Image: mspass/mspass
+#Version: 1.0.0
+
+FROM ghcr.io/seisscoped/container-base:ubuntu22.04_jupyterlab
+
+LABEL maintainer="Ian Wang <[email protected]>"
+
+# add our user and group first to make sure their IDs get assigned consistently, regardless of whatever dependencies get added
+RUN set -eux; \
+	groupadd --gid 999 --system mongodb; \
+	useradd --uid 999 --system --gid mongodb --home-dir /data/db mongodb; \
+	mkdir -p /data/db /data/configdb; \
+	chown -R mongodb:mongodb /data/db /data/configdb \
+	&& docker-clean
+
+RUN set -eux; \
+	apt-get update; \
+	apt-get install -y --no-install-recommends \
+		ca-certificates \
+		dirmngr \
+		gnupg \
+		jq \
+		numactl \
+		procps \
+	; \
+	rm -rf /var/lib/apt/lists/* \
+	&& docker-clean
+
+# grab "js-yaml" for parsing mongod's YAML config files (https://github.com/nodeca/js-yaml/releases)
+ENV JSYAML_VERSION 3.13.1
+
+RUN set -ex; \
+	\
+	savedAptMark="$(apt-mark showmanual)"; \
+	apt-get update; \
+	apt-get install -y --no-install-recommends \
+		wget \
+	; \
+	rm -rf /var/lib/apt/lists/*; \
+	\
+	dpkgArch="$(dpkg --print-architecture | awk -F- '{ print $NF }')"; \
+	export GNUPGHOME="$(mktemp -d)"; \
+	gpg --batch --keyserver hkps://keys.openpgp.org --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4; \
+	gpgconf --kill all; \
+	\
+	wget -O /js-yaml.js "https://github.com/nodeca/js-yaml/raw/${JSYAML_VERSION}/dist/js-yaml.js"; \
+# TODO some sort of download verification here
+	\
+	apt-mark auto '.*' > /dev/null; \
+	apt-mark manual $savedAptMark > /dev/null; \
+	apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false \
+	&& docker-clean
+
+RUN mkdir /docker-entrypoint-initdb.d
+
+RUN set -ex; \
+	export GNUPGHOME="$(mktemp -d)"; \
+	set -- '39BD841E4BE5FB195A65400E6A26B1AE64C3C388'; \
+	for key; do \
+		gpg --batch --keyserver keyserver.ubuntu.com --recv-keys "$key"; \
+	done; \
+	mkdir -p /etc/apt/keyrings; \
+	gpg --batch --export "$@" > /etc/apt/keyrings/mongodb.gpg; \
+	gpgconf --kill all; \
+	rm -rf "$GNUPGHOME" \
+	&& docker-clean
+
+# Allow build-time overrides (eg. to build image with MongoDB Enterprise version)
+# Options for MONGO_PACKAGE: mongodb-org OR mongodb-enterprise
+# Options for MONGO_REPO: repo.mongodb.org OR repo.mongodb.com
+# Example: docker build --build-arg MONGO_PACKAGE=mongodb-enterprise --build-arg MONGO_REPO=repo.mongodb.com .
+ARG MONGO_PACKAGE=mongodb-org
+ARG MONGO_REPO=repo.mongodb.org
+ENV MONGO_PACKAGE=${MONGO_PACKAGE} MONGO_REPO=${MONGO_REPO}
+
+ENV MONGO_MAJOR 6.0
+RUN echo "deb [ signed-by=/etc/apt/keyrings/mongodb.gpg ] http://$MONGO_REPO/apt/ubuntu jammy/${MONGO_PACKAGE%-unstable}/$MONGO_MAJOR multiverse" | tee "/etc/apt/sources.list.d/${MONGO_PACKAGE%-unstable}.list"
+
+# https://docs.mongodb.org/master/release-notes/6.0/
+ENV MONGO_VERSION 6.0.5
+# 03/08/2023, https://github.com/mongodb/mongo/tree/c9a99c120371d4d4c52cbb15dac34a36ce8d3b1d
+
+RUN set -x \
+# installing "mongodb-enterprise" pulls in "tzdata" which prompts for input
+	&& export DEBIAN_FRONTEND=noninteractive \
+	&& apt-get update \
+	&& apt-get install -y \
+		${MONGO_PACKAGE}=$MONGO_VERSION \
+		${MONGO_PACKAGE}-server=$MONGO_VERSION \
+		${MONGO_PACKAGE}-shell=$MONGO_VERSION \
+		${MONGO_PACKAGE}-mongos=$MONGO_VERSION \
+		${MONGO_PACKAGE}-tools=$MONGO_VERSION \
+	&& rm -rf /var/lib/apt/lists/* \
+	&& rm -rf /var/lib/mongodb \
+	&& mv /etc/mongod.conf /etc/mongod.conf.orig \
+	&& docker-clean
+
+VOLUME /data/db /data/configdb
+
+# ensure that if running as custom user that "mongosh" has a valid "HOME"
+# https://github.com/docker-library/mongo/issues/524
+ENV HOME /data/db
+
+COPY docker-entrypoint.sh /usr/local/bin/
+
+EXPOSE 27017
+
+RUN apt-get update \
+    && apt-get install -y wget ssh rsync vim-tiny less \
+       build-essential python3-setuptools \
+       python3-dev python3-pip \
+       openjdk-8-jdk \
+       git cmake gfortran gdb \
+       liblapack-dev libboost-dev libboost-serialization-dev libyaml-dev \
+       zip unzip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+	&& docker-clean
+
+ARG TARGETARCH
+
+# Prepare the environment
+ARG SPARK_VERSION=3.0.0
+
+ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-${TARGETARCH}
+ENV SPARK_HOME /usr/local/spark
+ENV PYSPARK_PYTHON python3
+
+ARG APACHE_MIRROR=https://archive.apache.org/dist
+ARG SPARK_URL=${APACHE_MIRROR}/spark/spark-${SPARK_VERSION}/spark-${SPARK_VERSION}-bin-hadoop2.7.tgz
+
+# Download & install Spark
+RUN wget -qO - ${SPARK_URL} | tar -xz -C /usr/local/ \
+    && cd /usr/local && ln -s spark-${SPARK_VERSION}-bin-hadoop2.7 spark \
+	&& docker-clean
+RUN ln -s /usr/local/spark/bin/pyspark /usr/bin/pyspark
+RUN python -c "import site; print(site.getsitepackages()[0])" > site_packages_path.txt && \
+	PYTHON_SITE_PACKAGES_PATH=$(cat site_packages_path.txt) && \
+	ln -s /usr/local/spark/python/pyspark ${PYTHON_SITE_PACKAGES_PATH}/pyspark && \
+	unzip /usr/local/spark/python/lib/py4j-0.10.9-src.zip -d ${PYTHON_SITE_PACKAGES_PATH}/  \
+	&& docker-clean
+
+# Patch pyspark for machines don't have localhost defined in /etc/hosts
+RUN sed -i 's/localhost/127.0.0.1/' /usr/local/spark/python/pyspark/accumulators.py
+RUN unzip /usr/local/spark/python/lib/pyspark.zip \
+    && sed -i 's/localhost/127.0.0.1/' ./pyspark/accumulators.py \
+    && zip /usr/local/spark/python/lib/pyspark.zip pyspark/accumulators.py \
+    && rm -r ./pyspark \
+	&& docker-clean
+
+# Install Python dependencies through pip
+ADD requirements.txt requirements.txt
+RUN pip3 --no-cache-dir install --upgrade pip \
+	&& docker-clean
+RUN if [ "$TARGETARCH" == "arm64" ]; then export CFLAGS="-O3" \
+	&& export DISABLE_NUMCODECS_SSE2=true && export DISABLE_NUMCODECS_AVX2=true; fi\
+	&& pip3 --no-cache-dir install numpy \
+    && pip3 --no-cache-dir install -r requirements.txt \
+    && rm -f requirements.txt \
+	&& docker-clean
+
+# Download & install pybind11
+ARG PYBIND11_VERSION=2.6.0
+ARG PYBIND11_URL=https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz
+RUN wget -qO - ${PYBIND11_URL} | tar -xz -C /usr/local/ \
+    && cd /usr/local/pybind11-${PYBIND11_VERSION} \
+    && mkdir build && cd build && cmake .. -DPYBIND11_TEST=OFF && make install && docker-clean
+RUN rm -r /usr/local/pybind11-${PYBIND11_VERSION}
+
+# Upgrade setuptools to enable namespace package
+RUN pip3 --no-cache-dir install --upgrade setuptools \
+	&& docker-clean
+
+# Add cxx library
+ADD cxx /mspass/cxx
+RUN ln -s /opt/conda/include/yaml-cpp /usr/include/yaml-cpp && cd /mspass/cxx \
+    && mkdir build && cd build \
+    && cmake .. \
+    && make \
+    && make install \ 
+    && rm -rf ../build \
+	&& docker-clean
+
+# Add data and env variable for the MetadataDefinition class
+ADD data /mspass/data
+ENV MSPASS_HOME /mspass
+
+# Add setup.py to install python components
+ADD setup.py /mspass/setup.py
+ADD pyproject.toml /mspass/pyproject.toml
+ADD requirements.txt /mspass/requirements.txt
+ADD python /mspass/python
+RUN pip3 install /mspass -v \
+	&& rm -rf /mspass/build && docker-clean
+
+# Install jedi
+RUN pip3 --no-cache-dir install jedi==0.17.2 && docker-clean
+
+# Tini operates as a process subreaper for jupyter.
+ARG TINI_VERSION=v0.19.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini-${TARGETARCH} /usr/sbin/tini
+RUN chmod +x /usr/sbin/tini
+
+# Add startup script
+ADD scripts/start-mspass.sh /usr/sbin/start-mspass.sh
+RUN chmod +x /usr/sbin/start-mspass.sh
+RUN chmod +x /usr/local/bin/docker-entrypoint.sh
+RUN sed -i '/set -- mongod "$@"/i [[ -d data ]] || mkdir data' /usr/local/bin/docker-entrypoint.sh
+
+# replace localhost to 127.0.0.1 in pymongo to run on HPC
+RUN python -c "import site; print(site.getsitepackages()[0])" > site_packages_path.txt && \
+	PYTHON_SITE_PACKAGES_PATH=$(cat site_packages_path.txt) && \
+	sed -i "s/localhost:27020,/127.0.0.1:27020,/g" "${PYTHON_SITE_PACKAGES_PATH}/pymongo/encryption_options.py" && \
+	sed -i 's/HOST = "localhost"/HOST = "127.0.0.1"/g' "${PYTHON_SITE_PACKAGES_PATH}/pymongo/mongo_client.py" && \
+	sed -i "s/'localhost'/'127.0.0.1'/g" "${PYTHON_SITE_PACKAGES_PATH}/pymongo/settings.py" && \
+	sed -i "s/'localhost'/'127.0.0.1'/g" "${PYTHON_SITE_PACKAGES_PATH}/pymongo/pool.py" && \
+	rm site_packages_path.txt
+
+ENV PATH="${SPARK_HOME}/bin:${SPARK_HOME}/sbin:${PATH}"
+
+# Set the default behavior of this container
+ENV SPARK_MASTER_PORT 7077
+ENV DASK_SCHEDULER_PORT 8786
+ENV MONGODB_PORT 27017
+ENV JUPYTER_PORT 8888
+ENV MSPASS_ROLE all
+
+# ENV MSPASS_SCHEDULER dask
+ENTRYPOINT ["/usr/sbin/tini", "-s", "-g", "--", "/usr/sbin/start-mspass.sh"]