Add mongod into Dockerfile.

- Fix eblocbroker init to constantly print folder_setup.sh output.

- Add venv installation from Dockerfile.

.gitignore

@@ -174,4 +174,5 @@ slurm-*.out
 README.html
 _slurm/example/hello
 alper.csv
-helloWorld.txt
+helloWorld.txt
+volumes

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "orcid-authentication-php"]
-	path = orcid-authentication-php
-	url = https://github.com/avatar-lavventura/orcid-authentication-php.git
+[submodule "orcid-authentication"]
+	path = orcid-authentication
+	url = https://github.com/avatar-lavventura/orcid-authentication

Dockerfile

@@ -13,29 +13,20 @@ WORKDIR /workspace/gdrive
 RUN go env -w GO111MODULE=auto \
  && go get github.com/prasmussen/gdrive
 
-# Instal SLURM
-# ============
-FROM python:3.7
-WORKDIR /workspace
-RUN git config --global advice.detachedHead false \
- && git clone --depth 1 --branch slurm-19-05-8-1 https://github.com/SchedMD/slurm.git
-WORKDIR slurm
-RUN ./configure --enable-debug --enable-front-end \
- && make \
- && make install \
- && slurmctld -V
-
 FROM python:3.7
-RUN python -m venv /opt/venv
-ENV PATH="/opt/venv/bin:$PATH"
 ENV PYTHONDONTWRITEBYTECODE 1
 ENV PYTHONUNBUFFERED 1
-
+ENV PATH="/root/.pyenv/shims:/root/.pyenv/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:$PATH"
 ARG DEBIAN_FRONTEND=noninteractive
 ARG DEBCONF_NOWARNINGS="yes"
+EXPOSE 6817 6818 6819 6820 3306
+
+## ebloc-broker -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
 RUN apt-get update \
- && apt-get install -y --no-install-recommends apt-utils \
- && apt-get install -y --no-install-recommends libdbus-1-dev \
+ && apt-get install -y --no-install-recommends --assume-yes apt-utils \
+ && apt-get install -y --no-install-recommends --assume-yes \
+    build-essential \
+    libdbus-1-dev \
     libdbus-glib-1-dev \
     libgirepository1.0-dev \
     libssl-dev \
@@ -45,24 +36,29 @@ RUN apt-get update \
     pigz \
     zlib1g-dev \
     make \
+    default-mysql-server \
+    npm \
+    nodejs \
+    python3-venv \
+    # sudo \
+    # slurm-packages
+    gcc \
     munge \
     libmunge-dev \
     libboost-all-dev \
     libmunge2 \
     default-mysql-client \
     default-mysql-server \
+    software-properties-common \
     default-libmysqlclient-dev \
     mailutils \
-    npm \
-    nodejs \
+    unzip \
     libmariadbd-dev \
-    mariadb-server
-    # build-essential \
-    # software-properties-common \
-    # tree \
-    # python-setuptools \
-    # default-libmariadbclient-dev \
-    # libmariadb-dev \
+    mariadb-server \
+    supervisor \
+    nano \
+    less \
+ && apt-get clean
 
 RUN npm config set fund false \
  && npm config set update-notifier false \
@@ -72,66 +68,112 @@ RUN npm config set fund false \
  && npm install -g npm@latest \
  && npm install -g ganache
 
+RUN python3 -m venv /opt/venv
+#: enable venv
+ENV PATH="/opt/venv/bin:$PATH"
+
 WORKDIR /workspace
 RUN git clone https://github.com/ebloc/ebloc-broker.git
 WORKDIR /workspace/ebloc-broker
-#: pip install takes few minutes
-RUN git checkout dev \
+#: `pip install -e .` takes few minutes
+RUN git checkout dev >/dev/null 2>&1 \
  && git fetch --all --quiet >/dev/null 2>&1 \
  && git pull --all -r -v >/dev/null 2>&1 \
- && pip install -U pip wheel \
- && pip install -e .  \
- && eblocbroker >/dev/null 2>&1
+ && pip install --upgrade pip \
+ && pip install -U pip wheel setuptools \
+ && pip install -e . --use-deprecated=legacy-resolver \
+ && eblocbroker >/dev/null 2>&1 \
+ && ./broker/_utils/yaml.py >/dev/null 2>&1
 
 COPY --from=0 /go /go
 COPY --from=0 /usr/local/bin /usr/local/bin
 COPY --from=0 /usr/local/go /usr/local/go
 COPY --from=0 /workspace/gdrive /workspace/gdrive
 
-COPY --from=1 /usr/local/sbin/ /usr/local/sbin/
-COPY --from=1 /usr/local/bin /usr/local/bin
-COPY --from=1 /usr/local/lib /usr/local/lib
-
-# COPY --from=1 /opt/venv /opt/venv
-# COPY --from=1 /usr/local/lib/node_modules /usr/local/lib/node_modules
-# COPY --from=1 /usr/local/bin /usr/local/bin
-# COPY --from=1 /workspace/ebloc-broker /workspace/ebloc-broker
-
 ENV GOPATH=/go
 ENV GOROOT=/usr/local/go
-ENV PATH /opt/venv/bin:/go/bin:/usr/local/go/bin:$PATH
+ENV PATH /go/bin:/usr/local/go/bin:$PATH
 
+# Instal SLURM
+# -=-=-=-=-=-=
+# Add Tini
+ENV TINI_VERSION v0.19.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+
+RUN git config --global advice.detachedHead false
+WORKDIR /workspace
+ARG JOBS=4
+RUN git clone -b slurm-19-05-8-1 --single-branch --depth 1 https://github.com/SchedMD/slurm.git \
+ && cd slurm \
+ && ./configure --prefix=/usr --sysconfdir=/etc/slurm --enable-slurmrestd \
+   --with-mysql_config=/usr/bin --libdir=/usr/lib64 \
+ && make \
+ && make -j ${JOBS} install \
+ && install -D -m644 etc/cgroup.conf.example /etc/slurm/cgroup.conf.example \
+ && install -D -m644 etc/slurm.conf.example /etc/slurm/slurm.conf.example \
+ && install -D -m600 etc/slurmdbd.conf.example /etc/slurm/slurmdbd.conf.example \
+ && install -D -m644 contribs/slurm_completion_help/slurm_completion.sh /etc/profile.d/slurm_completion.sh \
+ && cd .. \
+ && rm -rf slurm \
+ && slurmctld -V \
+ && groupadd -r slurm  \
+ && useradd -r -g slurm slurm \
+ && mkdir -p /etc/sysconfig/slurm \
+     /var/spool/slurmd \
+     /var/spool/slurmctld \
+     /var/log/slurm \
+     /var/run/slurm \
+ && chown -R slurm:slurm /var/spool/slurmd \
+    /var/spool/slurmctld \
+    /var/log/slurm \
+    /var/run/slurm
+
+RUN chown root:munge -R /etc/munge /etc/munge/munge.key /var/lib/munge  # works but root is alright?
 WORKDIR /var/log/slurm
-WORKDIR /workspace/ebloc-broker
+WORKDIR /var/run/supervisor
+COPY broker/_slurm/files/supervisord.conf /etc/
+
+# Mark externally mounted volumes
+VOLUME ["/var/lib/mysql", "/var/lib/slurmd", "/var/spool/slurm", "/var/log/slurm", "/run/munge"]
+
+COPY --chown=slurm broker/_slurm/files/slurm/slurm.conf /etc/slurm/slurm.conf
+COPY --chown=slurm broker/_slurm/files/slurm/gres.conf /etc/slurm/gres.conf
+COPY --chown=slurm broker/_slurm/files/slurm/slurmdbd.conf /etc/slurm/slurmdbd.conf
+RUN chmod 0600 /etc/slurm/slurmdbd.conf
+
+## mongodb
+RUN curl -fsSL https://www.mongodb.org/static/pgp/server-4.4.asc | apt-key add - \
+ && echo "deb [ arch=amd64,arm64 ] https://repo.mongodb.org/apt/ubuntu focal/mongodb-org/4.4 multiverse" | \
+    tee /etc/apt/sources.list.d/mongodb-org-4.4.list \
+ && apt-get update \
+ && apt-get install -y mongodb-org \
+ && mkdir -p /data/db \
+ && chown -R mongodb. /var/log/mongodb \
+ && chown -R mongodb. /var/lib/mongodb \
+ && chown mongodb:mongodb /data/db
+
+# RUN git clone --depth=1 https://github.com/romkatv/powerlevel10k.git ~/powerlevel10k \
+#  && echo "source ~/powerlevel10k/powerlevel10k.zsh-theme" >> ~/.zshrc \
 
+## Finally
+WORKDIR /workspace/ebloc-broker/broker
 RUN apt-get clean \
  && apt-get autoremove \
  && apt-get autoclean \
  && ipfs version \
  && ganache --version
 
- # Configure munge (for SLURM authentication)
-RUN mkdir /var/run/munge && \
-    chown root /var/lib/munge && \
-    chown root /etc/munge && chmod 600 /var/run/munge && \
-    chmod 755  /run/munge && \
-    chmod 600 /etc/munge/munge.key
-
-VOLUME ["/home", "/.secret"]
-
-#   22:         SSH
-# 3306:         MariaDB
-# 6817:         Slurm Ctl D
-# 6818:         Slurm D
-# 6819:         Slurm DBD
-EXPOSE 22 3306 6817 6818 6819
+COPY broker/_slurm/docker-entrypoint.sh /usr/local/bin/docker-entrypoint.sh
+ENTRYPOINT ["/tini", "--", "/usr/local/bin/docker-entrypoint.sh"]
+CMD ["/bin/bash"]
 
-# RUN git clone --depth=1 https://github.com/romkatv/powerlevel10k.git ~/powerlevel10k \
-#  && echo "source ~/powerlevel10k/powerlevel10k.zsh-theme" >> ~/.zshrc \
-#  && ipfs version \
-#  && ganache --version
+# -=-=-=-=-=-=-=-=-=-=-=-=- DELETE -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+# COPY --from=1 /opt/venv /opt/venv  # /opt/venv/bin
+# COPY --from=1 /usr/local/lib/node_modules /usr/local/lib/node_modules
+# COPY --from=1 /usr/local/bin /usr/local/bin
+# COPY --from=1 /workspace/ebloc-broker /workspace/ebloc-broker
 
-# https://github.com/GRomR1/docker-slurmbase/blob/master/Dockerfile
-# https://github.com/SciDAS/slurm-in-docker/blob/master/base/Dockerfile
-# https://stackoverflow.com/questions/42597739/accessing-docker-container-mysql-databases
-# https://github.com/giovtorres/docker-centos7-slurm/blob/main/Dockerfile
+# COPY --from=1 /usr/local/sbin/ /usr/local/sbin/
+# COPY --from=1 /usr/local/bin /usr/local/bin
+# COPY --from=1 /usr/local/lib /usr/local/lib

README.org

@@ -15,7 +15,6 @@ eBlocBroker is a blockchain based autonomous computational resource broker.
   [[https://github.com/eth-brownie/brownie][eth-brownie]],
   [[https://github.com/trufflesuite/ganache][ganache-cli]]
 
-
 ** Using Docker
 
 You can use a sandbox container provided in the [[./docker-compose.yml]] file for testing inside a Docker
@@ -26,14 +25,20 @@ This container provides everything you need to test using a Python 3.7 interpret
 Start the test environment:
 
 #+begin_src bash
-docker build -t ebloc-broker:latest --progress plain .
-docker-compose up -d --remove-orphans
+docker build -t ebb:latest . --progress plain
+docker-compose up -d
+#+end_src
+
+To enter the shell of the running container in interactive mode, run:
+
+#+begin_src bash
+docker exec -it ebloc-broker_slurm_1 /bin/bash
 #+end_src
 
-To open a session to the container:
+To stop the cluster container, run:
 
 #+begin_src bash
-docker-compose exec sandbox bash
+docker-compose down
 #+end_src
 
 ** Cloud Storages
@@ -67,13 +72,11 @@ Next, type ~eblocbroker --help~ for basic usage information.
 *** Submit Job
 
 
-In order to submit your job each user should already registered into
-eBlocBroker.You can use [[./broker/eblocbroker/register_requester.py]] to register.
+In order to submit your job each user should already registered into eBlocBroker.
+You can use [[./broker/eblocbroker/register_requester.py]] to register.
 Please update following arguments inside ~register.yaml~.
 
-After registration is done, each user should authenticate their ORCID iD using
-the following [[http://ebloc.cmpe.boun.edu.tr/orcid-authentication/index.php]].
-
+After registration is done, each user should authenticate their ORCID iD using the following [[http://eblocbroker.duckdns.org/]].
 
 ~$ ./eblocbroker.py submit job.yaml~
 

broker/.TODO.org_archive

@@ -23,3 +23,16 @@ a = "this string needs compressing"
 a = zlib.compress(a.encode())
 print(zlib.decompress(a).decode())
 #+end_src
+
+* DONE
+CLOSED: [2022-05-26 Thu 09:56]
+:PROPERTIES:
+:ARCHIVE_TIME: 2022-05-26 Thu 09:56
+:ARCHIVE_FILE: ~/ebloc-broker/broker/TODO.org
+:ARCHIVE_OLPATH: TASKS
+:ARCHIVE_CATEGORY: TODO
+:ARCHIVE_TODO: DONE
+:END:
+carry `run_with_output` into tools
+
+convert all ~run(~ into ~run_with_output(~

broker/_cli/__main__.py

@@ -22,12 +22,11 @@ def driver():
 def init():
     import git
     from pathlib import Path
-
-    from broker._utils.tools import run
+    from broker._utils.tools import run_keep_print
 
     f = Path(__file__).parent.resolve()
     repo = git.Repo(f, search_parent_directories=True)
-    run(Path(repo.working_tree_dir) / "broker" / "bash_scripts" / "folder_setup.sh")
+    run_keep_print(Path(repo.working_tree_dir) / "broker" / "bash_scripts" / "folder_setup.sh")
 
 
 def about():
@@ -58,12 +57,11 @@ def daemon():
     if args.daemon_type[0] == "slurm":
         import git
         import pathlib
-
-        from broker._utils.tools import run
+        from broker._utils.tools import run_keep_print
 
         f = pathlib.Path(__file__).parent.resolve()
         repo = git.Repo(f, search_parent_directories=True)
-        run(repo.working_tree_dir / "broker" / "bash_scripts" / "run_slurm.sh")
+        run_keep_print(repo.working_tree_dir / "broker" / "bash_scripts" / "run_slurm.sh")
 
 
 def console():

broker/_daemons/ipfs.py

@@ -8,7 +8,7 @@
 
 from broker import cfg, config
 from broker._utils._log import ok
-from broker._utils.tools import print_tb
+from broker._utils.tools import print_tb, run
 from broker.utils import is_ipfs_on, log, popen_communicate
 
 
@@ -17,7 +17,7 @@ def mount_ipfs():
     log(run(["sudo", "ipfs", "mount", "-f", "/ipfs"]))
 
 
-def run():
+def _run():
     """Run ipfs daemon.
 
     cmd: ipfs daemon --enable-gc --routing=none  # --mount
@@ -52,7 +52,7 @@ def main():
 
     if not is_ipfs_on():
         cfg.ipfs.remove_lock_files()
-        run()
+        _run()
     else:
         log(f"## [green]IPFS[/green] daemon is already running{ok()}")
         sys.exit(100)