├── etcldap.conf ├── setup-user.sh ├── docker-compose.yml ├── nsswitch.conf ├── start-notebook.sh ├── start-singleuser.sh ├── Dockerfile ├── jupyter_notebook_config.py ├── start.sh └── CactusTutorial.ipynb /etcldap.conf: -------------------------------------------------------------------------------- 1 | base dc=hub 2 | uri ldap://hub 3 | ldap_version 3 4 | rootbinddn cn=admin,dc=hub 5 | pam_password clear 6 | 7 | -------------------------------------------------------------------------------- /setup-user.sh: -------------------------------------------------------------------------------- 1 | export USER=$(python3 -c 'import pwd, os; print(pwd.getpwuid(os.getuid()).pw_name)') 2 | cp -nr /etc/skel/* $HOME/ 3 | -------------------------------------------------------------------------------- /docker-compose.yml: -------------------------------------------------------------------------------- 1 | version: '3' 2 | 3 | services: 4 | 5 | perimeter-workspace: 6 | build: 7 | context: . 8 | dockerfile: Dockerfile 9 | image: einsteintoolkit/et-workshop 10 | -------------------------------------------------------------------------------- /nsswitch.conf: -------------------------------------------------------------------------------- 1 | passwd: files ldap 2 | group: files ldap 3 | shadow: files ldap 4 | gshadow: files ldap 5 | hosts: files dns 6 | networks: files 7 | protocols: db files 8 | services: db files 9 | ethers: db files 10 | rpc: db files 11 | netgroup: nis 12 | -------------------------------------------------------------------------------- /start-notebook.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Copyright (c) Jupyter Development Team. 3 | # Distributed under the terms of the Modified BSD License. 4 | 5 | set -e 6 | 7 | #set 8 | #echo "start-notebook.sh: $@" 9 | #echo "I am: $(whoami)" 10 | export HOME=/nfs/home/$(whoami) 11 | cd 12 | echo "pwd: $(pwd)" 13 | echo "restartable: $RESTARTABLE" 14 | echo "api token: $JUPYTERHUB_API_TOKEN" 15 | echo "lab: $JUPYTER_ENABLE_LAB" 16 | 17 | mkdir -p /tmp/$(whoami)/jupyter-runtime 18 | export JUPYTER_RUNTIME_DIR=/tmp/$(whoami)/jupyter-runtime 19 | 20 | # Special setup 21 | if [ -r /usr/local/bin/setup-user.sh ]; then source /usr/local/bin/setup-user.sh; fi 22 | 23 | wrapper="" 24 | if [[ "${RESTARTABLE}" == "yes" ]]; then 25 | wrapper="run-one-constantly" 26 | fi 27 | 28 | if [[ ! -z "${JUPYTERHUB_API_TOKEN}" ]]; then 29 | # launched by JupyterHub, use single-user entrypoint 30 | exec /usr/local/bin/start-singleuser.sh "$@" 31 | elif [[ ! -z "${JUPYTER_ENABLE_LAB}" ]]; then 32 | #. /usr/local/bin/start.sh $wrapper jupyter lab "$@" 33 | $wrapper jupyter lab "$@" 34 | else 35 | #. /usr/local/bin/start.sh $wrapper jupyter notebook "$@" 36 | $wrapper jupyter notebook --allow-root "$@" 37 | fi 38 | -------------------------------------------------------------------------------- /start-singleuser.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Copyright (c) Jupyter Development Team. 3 | # Distributed under the terms of the Modified BSD License. 4 | 5 | set -e 6 | 7 | # set default ip to 0.0.0.0 8 | if [[ "$NOTEBOOK_ARGS $@" != *"--ip="* ]]; then 9 | NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS" 10 | fi 11 | 12 | # handle some deprecated environment variables 13 | # from DockerSpawner < 0.8. 14 | # These won't be passed from DockerSpawner 0.9, 15 | # so avoid specifying --arg=empty-string 16 | if [ ! -z "$NOTEBOOK_DIR" ]; then 17 | NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS" 18 | fi 19 | if [ ! -z "$JPY_PORT" ]; then 20 | NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS" 21 | fi 22 | if [ ! -z "$JPY_USER" ]; then 23 | NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS" 24 | fi 25 | if [ ! -z "$JPY_COOKIE_NAME" ]; then 26 | NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS" 27 | fi 28 | if [ ! -z "$JPY_BASE_URL" ]; then 29 | NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS" 30 | fi 31 | if [ ! -z "$JPY_HUB_PREFIX" ]; then 32 | NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS" 33 | fi 34 | if [ ! -z "$JPY_HUB_API_URL" ]; then 35 | NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS" 36 | fi 37 | if [ ! -z "$JUPYTER_ENABLE_LAB" ]; then 38 | NOTEBOOK_BIN="jupyter labhub" 39 | else 40 | NOTEBOOK_BIN="jupyterhub-singleuser" 41 | fi 42 | 43 | #. /usr/local/bin/start.sh $NOTEBOOK_BIN $NOTEBOOK_ARGS "$@" 44 | $NOTEBOOK_BIN $NOTEBOOK_ARGS "$@" 45 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | # FROM ubuntu:18.04 2 | # FROM nvidia/cuda:11.5.2-devel-ubuntu20.04 3 | #FROM nvidia/cuda:11.0.3-devel-ubuntu20.04 4 | FROM einsteintoolkit/et-notebook 5 | USER root 6 | 7 | ENV DEBIAN_FRONTEND=noninteractive 8 | RUN apt update && apt -yq dist-upgrade && \ 9 | apt install -yq --no-install-recommends apt-utils && \ 10 | apt install -yq --no-install-recommends \ 11 | wget \ 12 | bzip2 \ 13 | ca-certificates \ 14 | sudo \ 15 | locales \ 16 | fonts-liberation \ 17 | run-one \ 18 | python3 python3-pip python3-dev \ 19 | openssh-client libssl-dev \ 20 | gnupg policycoreutils imagemagick curl vim \ 21 | iputils-ping git less \ 22 | patch gcc make libc6-dev \ 23 | nfs-common rpcbind libnss-ldap ldap-utils ldap-auth-config \ 24 | libpam-ldap \ 25 | libbz2-dev \ 26 | && rm -rf /var/lib/apt/lists/* 27 | 28 | # Make python3 the default 29 | RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && \ 30 | update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1 31 | 32 | RUN pip install --no-cache-dir setuptools && \ 33 | pip install --no-cache-dir \ 34 | oauthenticator==0.9.0 \ 35 | jupyter==1.0.0 \ 36 | jupyterhub==1.0.0 \ 37 | python-oauth2==1.1.1 \ 38 | notebook==6.0.2 \ 39 | matplotlib numpy scipy scikit-learn astropy pandas fitsio pyephem \ 40 | asdf h5py emcee corner cython 41 | 42 | # RUN wget -nv https://julialang-s3.julialang.org/bin/linux/x64/1.5/julia-1.5.2-linux-x86_64.tar.gz && \ 43 | # tar xvz -C /usr/local --strip-components 1 -f julia-1.5.2-linux-x86_64.tar.gz && \ 44 | # rm julia-1.5.2-linux-x86_64.tar.gz 45 | 46 | COPY nsswitch.conf /etc 47 | COPY etcldap.conf /etc/ldap.conf 48 | 49 | RUN echo "libpam-runtime libpam-runtime/profiles multiselect unix, ldap" | debconf-set-selections && \ 50 | dpkg-reconfigure libpam-runtime 51 | 52 | RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen 53 | 54 | ENV SHELL=/bin/bash \ 55 | LC_ALL=en_US.UTF-8 \ 56 | LANG=en_US.UTF-8 \ 57 | LANGUAGE=en_US.UTF-8 58 | 59 | EXPOSE 8888 60 | CMD ["start-notebook.sh"] 61 | 62 | # From https://github.com/jupyter/docker-stacks 63 | COPY start-notebook.sh /usr/local/bin/ 64 | COPY start-singleuser.sh /usr/local/bin/ 65 | COPY setup-user.sh /usr/local/bin/ 66 | COPY jupyter_notebook_config.py /etc/jupyter/ 67 | COPY CactusTutorial.ipynb /etck/skel/ 68 | -------------------------------------------------------------------------------- /jupyter_notebook_config.py: -------------------------------------------------------------------------------- 1 | # Copyright (c) Jupyter Development Team. 2 | # Distributed under the terms of the Modified BSD License. 3 | 4 | from jupyter_core.paths import jupyter_data_dir 5 | import subprocess 6 | import os 7 | import errno 8 | import stat 9 | 10 | c = get_config() 11 | c.NotebookApp.ip = '0.0.0.0' 12 | c.NotebookApp.port = 8888 13 | #c.NotebookApp.open_browser = False 14 | 15 | # Auto-shutdown -- 16 | # shutdown the server after no activity for an hour 17 | c.NotebookApp.shutdown_no_activity_timeout = 60 * 60 18 | # shutdown kernels after no activity for 20 minutes 19 | c.MappingKernelManager.cull_idle_timeout = 20 * 60 20 | # check for idle kernels every two minutes 21 | c.MappingKernelManager.cull_interval = 2 * 60 22 | 23 | 24 | # https://github.com/jupyter/notebook/issues/3130 25 | c.FileContentsManager.delete_to_trash = False 26 | 27 | # https://stackoverflow.com/questions/55245895/jupyter-notebook-ssh-tunneling-error-the-signatures-database-cannot-be-opened 28 | c.NotebookNotary.db_file = ':memory:' 29 | 30 | # Generate a self-signed certificate 31 | if 'GEN_CERT' in os.environ: 32 | dir_name = jupyter_data_dir() 33 | pem_file = os.path.join(dir_name, 'notebook.pem') 34 | try: 35 | os.makedirs(dir_name) 36 | except OSError as exc: # Python >2.5 37 | if exc.errno == errno.EEXIST and os.path.isdir(dir_name): 38 | pass 39 | else: 40 | raise 41 | 42 | # Generate an openssl.cnf file to set the distinguished name 43 | cnf_file = os.path.join(os.getenv('CONDA_DIR', '/usr/lib'), 'ssl', 'openssl.cnf') 44 | if not os.path.isfile(cnf_file): 45 | with open(cnf_file, 'w') as fh: 46 | fh.write('''\ 47 | [req] 48 | distinguished_name = req_distinguished_name 49 | [req_distinguished_name] 50 | ''') 51 | 52 | # Generate a certificate if one doesn't exist on disk 53 | subprocess.check_call(['openssl', 'req', '-new', 54 | '-newkey', 'rsa:2048', 55 | '-days', '365', 56 | '-nodes', '-x509', 57 | '-subj', '/C=XX/ST=XX/L=XX/O=generated/CN=generated', 58 | '-keyout', pem_file, 59 | '-out', pem_file]) 60 | # Restrict access to the file 61 | os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR) 62 | c.NotebookApp.certfile = pem_file 63 | 64 | # Change default umask for all subprocesses of the notebook server if set in 65 | # the environment 66 | if 'NB_UMASK' in os.environ: 67 | os.umask(int(os.environ['NB_UMASK'], 8)) 68 | -------------------------------------------------------------------------------- /start.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Copyright (c) Jupyter Development Team. 3 | # Distributed under the terms of the Modified BSD License. 4 | 5 | set -e 6 | 7 | # Exec the specified command or fall back on bash 8 | if [ $# -eq 0 ]; then 9 | cmd=( "bash" ) 10 | else 11 | cmd=( "$@" ) 12 | fi 13 | 14 | run-hooks () { 15 | # Source scripts or run executable files in a directory 16 | if [[ ! -d "$1" ]] ; then 17 | return 18 | fi 19 | echo "$0: running hooks in $1" 20 | for f in "$1/"*; do 21 | case "$f" in 22 | *.sh) 23 | echo "$0: running $f" 24 | source "$f" 25 | ;; 26 | *) 27 | if [[ -x "$f" ]] ; then 28 | echo "$0: running $f" 29 | "$f" 30 | else 31 | echo "$0: ignoring $f" 32 | fi 33 | ;; 34 | esac 35 | done 36 | echo "$0: done running hooks in $1" 37 | } 38 | 39 | run-hooks /usr/local/bin/start-notebook.d 40 | 41 | # Handle special flags if we're root 42 | if [ $(id -u) == 0 ] ; then 43 | 44 | # Only attempt to change the jovyan username if it exists 45 | if id jovyan &> /dev/null ; then 46 | echo "Set username to: $NB_USER" 47 | usermod -d /home/$NB_USER -l $NB_USER jovyan 48 | fi 49 | 50 | # Handle case where provisioned storage does not have the correct permissions by default 51 | # Ex: default NFS/EFS (no auto-uid/gid) 52 | if [[ "$CHOWN_HOME" == "1" || "$CHOWN_HOME" == 'yes' ]]; then 53 | echo "Changing ownership of /home/$NB_USER to $NB_UID:$NB_GID with options '${CHOWN_HOME_OPTS}'" 54 | chown $CHOWN_HOME_OPTS $NB_UID:$NB_GID /home/$NB_USER 55 | fi 56 | if [ ! -z "$CHOWN_EXTRA" ]; then 57 | for extra_dir in $(echo $CHOWN_EXTRA | tr ',' ' '); do 58 | echo "Changing ownership of ${extra_dir} to $NB_UID:$NB_GID with options '${CHOWN_EXTRA_OPTS}'" 59 | chown $CHOWN_EXTRA_OPTS $NB_UID:$NB_GID $extra_dir 60 | done 61 | fi 62 | 63 | # handle home and working directory if the username changed 64 | if [[ "$NB_USER" != "jovyan" ]]; then 65 | # changing username, make sure homedir exists 66 | # (it could be mounted, and we shouldn't create it if it already exists) 67 | if [[ ! -e "/home/$NB_USER" ]]; then 68 | echo "Relocating home dir to /home/$NB_USER" 69 | mv /home/jovyan "/home/$NB_USER" 70 | fi 71 | # if workdir is in /home/jovyan, cd to /home/$NB_USER 72 | if [[ "$PWD/" == "/home/jovyan/"* ]]; then 73 | newcwd="/home/$NB_USER/${PWD:13}" 74 | echo "Setting CWD to $newcwd" 75 | cd "$newcwd" 76 | fi 77 | fi 78 | 79 | # Change UID of NB_USER to NB_UID if it does not match 80 | if [ "$NB_UID" != $(id -u $NB_USER) ] ; then 81 | echo "Set $NB_USER UID to: $NB_UID" 82 | usermod -u $NB_UID $NB_USER 83 | fi 84 | 85 | # Set NB_USER primary gid to NB_GID (after making the group). Set 86 | # supplementary gids to NB_GID and 100. 87 | if [ "$NB_GID" != $(id -g $NB_USER) ] ; then 88 | echo "Add $NB_USER to group: $NB_GID" 89 | groupadd -g $NB_GID -o ${NB_GROUP:-${NB_USER}} 90 | usermod -g $NB_GID -aG 100 $NB_USER 91 | fi 92 | 93 | # Enable sudo if requested 94 | if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then 95 | echo "Granting $NB_USER sudo access and appending $CONDA_DIR/bin to sudo PATH" 96 | echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook 97 | fi 98 | 99 | # Add $CONDA_DIR/bin to sudo secure_path 100 | sed -r "s#Defaults\s+secure_path=\"([^\"]+)\"#Defaults secure_path=\"\1:$CONDA_DIR/bin\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path 101 | 102 | # Exec the command as NB_USER with the PATH and the rest of 103 | # the environment preserved 104 | run-hooks /usr/local/bin/before-notebook.d 105 | echo "Executing the command: ${cmd[@]}" 106 | exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=${PYTHONPATH:-} "${cmd[@]}" 107 | else 108 | if [[ "$NB_UID" == "$(id -u jovyan)" && "$NB_GID" == "$(id -g jovyan)" ]]; then 109 | # User is not attempting to override user/group via environment 110 | # variables, but they could still have overridden the uid/gid that 111 | # container runs as. Check that the user has an entry in the passwd 112 | # file and if not add an entry. 113 | STATUS=0 && whoami &> /dev/null || STATUS=$? && true 114 | if [[ "$STATUS" != "0" ]]; then 115 | if [[ -w /etc/passwd ]]; then 116 | echo "Adding passwd file entry for $(id -u)" 117 | cat /etc/passwd | sed -e "s/^jovyan:/nayvoj:/" > /tmp/passwd 118 | echo "jovyan:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd 119 | cat /tmp/passwd > /etc/passwd 120 | rm /tmp/passwd 121 | else 122 | echo 'Container must be run with group "root" to update passwd file' 123 | fi 124 | fi 125 | 126 | # Warn if the user isn't going to be able to write files to $HOME. 127 | if [[ ! -w /home/jovyan ]]; then 128 | echo 'Container must be run with group "users" to update files' 129 | fi 130 | else 131 | # Warn if looks like user want to override uid/gid but hasn't 132 | # run the container as root. 133 | if [[ ! -z "$NB_UID" && "$NB_UID" != "$(id -u)" ]]; then 134 | echo 'Container must be run as root to set $NB_UID' 135 | fi 136 | if [[ ! -z "$NB_GID" && "$NB_GID" != "$(id -g)" ]]; then 137 | echo 'Container must be run as root to set $NB_GID' 138 | fi 139 | fi 140 | 141 | # Warn if looks like user want to run in sudo mode but hasn't run 142 | # the container as root. 143 | if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then 144 | echo 'Container must be run as root to grant sudo permissions' 145 | fi 146 | 147 | # Execute the command 148 | run-hooks /usr/local/bin/before-notebook.d 149 | echo "Executing the command: ${cmd[@]}" 150 | exec "${cmd[@]}" 151 | fi 152 | -------------------------------------------------------------------------------- /CactusTutorial.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "

Introduction

\n", 8 | "\n", 9 | "Here you will find a step by step guide to downloading, configuring, and running the Einstein Toolkit. You may use this tutorial on a workstation or laptop, or on a supported cluster. Configuring the Einstein Toolkit on an unsupported cluster is beyond the scope of this tutorial. If you find something that does not work, please feel free to edit the wiki or mail users@einsteintoolkit.org." 10 | ] 11 | }, 12 | { 13 | "cell_type": "markdown", 14 | "metadata": {}, 15 | "source": [ 16 | "

Prerequisites

\n", 17 | "When using the Einstein Toolkit on a laptop or workstation you will need a number of packages installed in order to download, compile and use the Einstein Toolkit components.\n", 18 | "\n", 19 | "Before you build, type \"which mpirun\". If nothing is found, please load a version of mpi into your path before continuing. The Einstein Toolkit can build many of the dependencies it needs for itself. However, this can take time, and make a long build process even longer. If you have administrative priviliges on your machine, you would do well to install the following packages. Note that on Centos, you will have to do \"yum install -y epel-release\" for some of the important packages below to install.\n", 20 | "\n", 21 | "\n", 22 | "\n", 23 | "\n", 24 | "\n", 25 | "\n", 26 | "\n", 27 | "\n", 28 | "\n", 29 | "\n", 30 | "\n", 31 | "\n", 32 | "\n", 33 | "\n", 34 | "\n", 35 | "\n", 36 | "\n", 37 | "\n", 38 | "\n", 39 | "\n", 40 | "\n", 41 | "\n", 42 | "\n", 43 | "\n", 44 | "\n", 45 | "\n" 46 | ] 47 | }, 48 | { 49 | "cell_type": "markdown", 50 | "metadata": {}, 51 | "source": [ 52 | "

Download

\n", 53 | "\n", 54 | "A script called GetComponents is used to fetch the components of the Einstein Toolkit. GetComponents serves as convenient wrapper around lower level tools like git and svn to download the codes that make up the Einstein toolkit from their individual repositories. You may download and make it executable as follows:" 55 | ] 56 | }, 57 | { 58 | "cell_type": "code", 59 | "execution_count": null, 60 | "metadata": {}, 61 | "outputs": [], 62 | "source": [ 63 | "!curl -kLO https://raw.githubusercontent.com/gridaphobe/CRL/ET_2017_06/GetComponents\n", 64 | "!chmod a+x GetComponents" 65 | ] 66 | }, 67 | { 68 | "cell_type": "markdown", 69 | "metadata": {}, 70 | "source": [ 71 | "GetComponents accepts a thorn list as an argument. To check out the needed components:" 72 | ] 73 | }, 74 | { 75 | "cell_type": "code", 76 | "execution_count": null, 77 | "metadata": {}, 78 | "outputs": [], 79 | "source": [ 80 | "!./GetComponents --parallel https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2017_06/einsteintoolkit.th" 81 | ] 82 | }, 83 | { 84 | "cell_type": "code", 85 | "execution_count": null, 86 | "metadata": {}, 87 | "outputs": [], 88 | "source": [ 89 | "%cd ~/Cactus" 90 | ] 91 | }, 92 | { 93 | "cell_type": "markdown", 94 | "metadata": {}, 95 | "source": [ 96 | "

Configure and build

\n", 97 | "\n", 98 | "The recommended way to compile the Einstein Toolkit is to use the Simulation Factory (\"SimFactory\").\n", 99 | "

Configuring SimFactory for your machine

\n", 100 | "\n", 101 | "The ET depends on various libraries, and needs to interact with machine-specific queueing systems and MPI implementations. As such, it needs to be configured for a given machine. For this, it uses SimFactory. Generally, configuring SimFactory means providing an optionlist, for specifying library locations and build options, a submit script for using the batch queueing system, and a runscript, for specifying how Cactus should be run, e.g. which mpirun command to use." 102 | ] 103 | }, 104 | { 105 | "cell_type": "code", 106 | "execution_count": null, 107 | "metadata": {}, 108 | "outputs": [], 109 | "source": [ 110 | "!./simfactory/bin/sim setup-silent" 111 | ] 112 | }, 113 | { 114 | "cell_type": "markdown", 115 | "metadata": {}, 116 | "source": [ 117 | "After this step is complete you will find your machine's default setup under ./simfactory/mdb/machines/<hostname >.ini\n", 118 | "You can edit some of these settings freely, such as \"description\", \"basedir\" etc. Some entry edits could result in simulation start-up warnings and/or errors such as \"ppn\" (processor-per-node meaning number of cores on your machine), \"num-threads\" (number of threads per core) so such edits must be done with some care." 119 | ] 120 | }, 121 | { 122 | "cell_type": "markdown", 123 | "metadata": {}, 124 | "source": [ 125 | "

Building the Einstein Toolkit

\n", 126 | "\n", 127 | "Assuming that SimFactory has been successfully set up on your machine, you should be able to build the Einstein Toolkit with the command below. Adjust -j2 to match the number of cores your machine possesses if you want to use more or less than 2 parallel build processes. This may take a while, as it compiles all the thorns specified in manifest/einsteintoolkit.th." 128 | ] 129 | }, 130 | { 131 | "cell_type": "code", 132 | "execution_count": null, 133 | "metadata": {}, 134 | "outputs": [], 135 | "source": [ 136 | "!./simfactory/bin/sim build --thornlist ../einsteintoolkit.th" 137 | ] 138 | }, 139 | { 140 | "cell_type": "markdown", 141 | "metadata": {}, 142 | "source": [ 143 | "

Running

\n", 144 | "\n", 145 | "You can now run the Einstein Toolkit with a simple test parameter file." 146 | ] 147 | }, 148 | { 149 | "cell_type": "code", 150 | "execution_count": null, 151 | "metadata": {}, 152 | "outputs": [], 153 | "source": [ 154 | "!./simfactory/bin/sim create-submit helloworld \\\n", 155 | " --parfile arrangements/CactusExamples/HelloWorld/par/HelloWorld.par --walltime 0:5:0" 156 | ] 157 | }, 158 | { 159 | "cell_type": "markdown", 160 | "metadata": {}, 161 | "source": [ 162 | "The above command will submit the simulation to the queue naming it \"helloworld\" and ask for a 5 minutes long job time, if you are running on a cluster, or run it immediately in the background if you are on a personal laptop or workstation. You can check the status of the simulation with the command below. You can run this command repeatedly until the job shows 
[ACTIVE (FINISHED)...
as it's state. Prior to that, it may show up as QUEUED or RUNNING." 163 | ] 164 | }, 165 | { 166 | "cell_type": "code", 167 | "execution_count": null, 168 | "metadata": {}, 169 | "outputs": [], 170 | "source": [ 171 | "!simfactory/bin/sim list-simulations helloworld" 172 | ] 173 | }, 174 | { 175 | "cell_type": "markdown", 176 | "metadata": {}, 177 | "source": [ 178 | "Once it finished you can look at the output with the command below." 179 | ] 180 | }, 181 | { 182 | "cell_type": "code", 183 | "execution_count": null, 184 | "metadata": {}, 185 | "outputs": [], 186 | "source": [ 187 | "!simfactory/bin/sim show-output helloworld" 188 | ] 189 | }, 190 | { 191 | "cell_type": "markdown", 192 | "metadata": {}, 193 | "source": [ 194 | "If you see 
INFO (HelloWorld): Hello World!
anywhere in the above output, then congratulations, you have successfully downloaded, compiled and run the Einstein Toolkit! You may now want to try some of the other tutorials to explore some interesting physics examples." 195 | ] 196 | }, 197 | { 198 | "cell_type": "code", 199 | "execution_count": null, 200 | "metadata": {}, 201 | "outputs": [], 202 | "source": [] 203 | } 204 | ], 205 | "metadata": { 206 | "kernelspec": { 207 | "display_name": "Python 3", 208 | "language": "python", 209 | "name": "python3" 210 | }, 211 | "language_info": { 212 | "codemirror_mode": { 213 | "name": "ipython", 214 | "version": 3 215 | }, 216 | "file_extension": ".py", 217 | "mimetype": "text/x-python", 218 | "name": "python", 219 | "nbconvert_exporter": "python", 220 | "pygments_lexer": "ipython3", 221 | "version": "3.4.5" 222 | } 223 | }, 224 | "nbformat": 4, 225 | "nbformat_minor": 2 226 | } 227 | --------------------------------------------------------------------------------
PackageDebian /Ubuntufedoracentosopensuse
jpegapt-get install -y libjpeg-turbo?-devdnf install -y libjpeg-turbo-develyum install -y libjpeg-turbo-devel 
curlapt-get install -y curldnf install -y curlyum install -y curlzypper install -y curl
gccapt-get install -y gccdnf install -y gccyum install -y gcczypper install -y gcc
gitapt-get install -y gitdnf install -y gityum install -y gitzypper install -y git
lapackapt-get install -y liblapack-devdnf install -y lapack-develyum install -y lapack-develzypper install -y lapack-devel
makeapt-get install -y makednf install -y makeyum install -y makezypper install -y make
subversionapt-get install -y subversiondnf install -y subversionyum install -y subversionzypper install -y subversion
g++apt-get install -y g++dnf install -y gcc-c++yum install -y gcc-c++zypper install -y gcc-c++
which dnf install -y whichyum install -y whichzypper install -y which
papiapt-get install -y libpapi-devdnf install -y papi-develyum install -y papi-develzypper install -y papi-devel
pythonapt-get install -y pythondnf install -y pythonyum install -y pythonzypper install -y python
hwlocapt-get install -y libhwloc-devdnf install -y hwloc-develyum install -y hwloc-develzypper install -y hwloc-devel
mpilibopenmpi-dev libhdf5-openmpi-devopenmpi-devel hdf5-openmpi-developenmpi-devel hdf5-openmpi-develzypper install -y openmpi-devel
sslapt-get install -y libssl-devdnf install -y openssl-develyum install -y openssl-develzypper install -y libopenssl-devel
libtool dnf install -y libtool-ltdl-develyum install -y libtool-ltdl-devel 
numaapt-get install -y numactldnf install -y numactl-develyum install -y numactl-develzypper install -y libnuma-devel
gfortranapt-get install -y gfortrandnf install -y gcc-gfortranyum install -y gcc-gfortranzypper install -y gcc-fortran
xargs dnf install -y findutilsyum install -y findutils 
hdf5apt-get install -y libhdf5-devdnf install -y hdf5-develyum install -y hdf5-develzypper install -y hdf5-devel
fftwapt-get install -y libfftw3-devdnf install -y fftw-develyum install -y fftw-develzypper install -y libfftw3-3
patchapt-get install -y patchdnf install -y patchyum install -y patchzypper install -y patch
gslapt-get install -y libgsl-devdnf install -y gsl-develyum install -y gsl-develzypper install -y gsl-devel
pkg-configapt-get install -y pkg-configdnf install -y pkgconfigyum install -y pkgconfigzypper install -y pkg-config