diff --git a/day2/3-hpc-environment/1-hpc-environment.ipynb b/day2/3-hpc-environment/1-hpc-environment.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..9de9ff92a2ab4cab997fe1c689bbffb821676dd1 --- /dev/null +++ b/day2/3-hpc-environment/1-hpc-environment.ipynb @@ -0,0 +1,175 @@ +{ + "cells": [ + { + "attachments": { + "67258d94-84e6-4a0c-ae8f-c74332ec082e.jpg": { + "image/jpeg": 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" + } + }, + "cell_type": "markdown", + "id": "relevant-coverage", + "metadata": { + "toc-hr-collapsed": false + }, + "source": [ + "\n", + "Author: [Jens Henrik Göbbert](mailto:j.goebbert@fz-juelich.de)\n", + "------------------------------------" + ] + }, + { + "cell_type": "markdown", + "id": "greatest-cannon", + "metadata": {}, + "source": [ + "### Exploring the HPC environment\n", + "\n", + "---------------------------------------------" + ] + }, + { + "cell_type": "markdown", + "id": "everyday-cannon", + "metadata": {}, + "source": [ + "#### Exercise 1: Terminal\n", + "1. Open the JupyterLab Terminal\n", + " - `A=10`\n", + " - CLose it and check the \"Running Panel\" -> Terminal keeps running\n", + " - Click on \"terminal/1\" and `echo $A`" + ] + }, + { + "cell_type": "markdown", + "id": "czech-vienna", + "metadata": {}, + "source": [ + "#### Exercise 2:\n", + "Use a terminal to check some files\n", + "1. `echo $JUPYTER_LOG_DIR`\n", + "2. `cd $JUPYTER_LOG_DIR`\n", + "3. `vim stderr`\n", + " - explore file\n", + "4. `vim .start`\n", + " - explore file" + ] + }, + { + "cell_type": "markdown", + "id": "chubby-photography", + "metadata": {}, + "source": [ + "#### Exercise 3:\n", + "**ONLY FOR HDF-CLOUD** \n", + "**!!DANGEROUS!! YOU ARE MOUNTING WRITEABLE** \n", + "Mount the $HOMEs from GPFS on the HDF Cloud" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "other-gilbert", + "metadata": {}, + "outputs": [], + "source": [ + "import pyunicore.client as unicore_client\n", + "import json, os" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "turkish-ozone", + "metadata": {}, + "outputs": [], + "source": [ + "_auth = \"https://uftp.fz-juelich.de:9112/UFTP_Auth/rest/auth/\"\n", + "_tr = unicore_client.Transport(os.getenv(\"UNITYJSCACCESSTOKEN\"))\n", + "\n", + "# check access\n", + "_info = _tr.get(url=_auth)\n", + "_uid = _info[\"JUDAC\"]['uid']" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "sapphire-reduction", + "metadata": {}, + "outputs": [], + "source": [ + "remote_base_dir = \"/p/home/jusers/%s\" % _uid # $HOME" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "italian-accuracy", + "metadata": {}, + "outputs": [], + "source": [ + "# auhenticate\n", + "_req = {\"persistent\": \"true\", \"serverPath\": \"%s/___UFTP___MULTI___FILE___SESSION___MODE___\" % remote_base_dir}\n", + "_reply = _tr.post(url = _auth+\"/JUDAC\", json=_req).json()\n", + "uftp_pwd = _reply['secret']\n", + "uftp_host = _reply['serverHost']\n", + "uftp_port = _reply['serverPort']" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "beginning-sensitivity", + "metadata": {}, + "outputs": [], + "source": [ + "# mount\n", + "!mkdir -p uftp-mount\n", + "!curlftpfs -v -s -o ftp_method=singlecwd,enable_epsv,big_writes,ipv4,user=anonymous:$uftp_pwd $uftp_host:$uftp_port uftp-mount" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "coated-packaging", + "metadata": {}, + "outputs": [], + "source": [ + "# ...\n", + "!ls -l uftp-mount" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "accredited-jersey", + "metadata": {}, + "outputs": [], + "source": [ + "# unmount\n", + "!fusermount -u uftp-mount" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/day2/4-build-your-kernel/Create_JupyterKernel_conda.ipynb b/day2/4-build-your-kernel/Create_JupyterKernel_conda.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..44860543c2f3bbcfff8a1a8b0e89d8296a4ae9b8 --- /dev/null +++ b/day2/4-build-your-kernel/Create_JupyterKernel_conda.ipynb @@ -0,0 +1,319 @@ +{ + "cells": [ + { + "attachments": { + "500ad0ee-8923-43bb-9336-e838a26dc2f1.jpg": { + "image/jpeg": 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" + } + }, + "cell_type": "markdown", + "metadata": { + "toc-hr-collapsed": false + }, + "source": [ + " \n", + "Author: [Sebastian Lührs](mailto:s.luehrs@fz-juelich.de)\n", + "--------------------------------------" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Create your own Jupyter CONDA-Kernel\n", + "\n", + "Often the standard kernel do not provide all features you need for your work. This might be that certain modules are not loaded or packages are not installed.\n", + "With your own kernel you can overcome that problem easily and define your own environment, in which you work.\n", + "\n", + "This notebook shows you how you can build your own kernel for a **conda environment**.\n", + "\n", + "--------------------------------------" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Building your own Jupyter CONDA-kernel is a three step process\n", + "Download Minconda installer\n", + "1. Download/Install Miniconda\n", + " * Miniconda3.sh\n", + "2. Create Conda Environment\n", + " * conda create\n", + "2. Create/Edit launch script for the Jupyter kernel\n", + " * kernel.sh\n", + "3. Create/Edit Jupyter kernel configuration\n", + " * kernel.json" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Settings" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Selectable **CONDA_TARGET_DIR** path for the central conda installation, should be in the project filesystem" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "export CONDA_TARGET_DIR=${HOME}/PROJECT_training2005/testdir/miniconda3" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Selectable **CONDA_ENV** name, will be used to specify the environment name\n", + " - must be lowercase" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "CONDA_ENV=my_env\n", + "\n", + "export CONDA_ENV=$(echo \"${CONDA_ENV}\" | awk '{print tolower($0)}')\n", + "echo ${KERNEL_NAME} # double check" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---\n", + "## 1. Download/Install Miniconda" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Start here if you want to run the full installation.\n", + "If you want to create another environment in an existing conda setup go to **create environment**. If you want to attach yourself to an existing environment go to **create user kernel**." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.1 - Download Minconda installer" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "wget --output-document=$HOME/Miniconda3.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.2 - Create target directory" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "mkdir -p ${CONDA_TARGET_DIR}" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.3 - Install Miniconda" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "bash $HOME/Miniconda3.sh -b -u -p ${CONDA_TARGET_DIR}" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "${CONDA_TARGET_DIR}/bin/conda init bash" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.4 - Disable automatic activation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "${CONDA_TARGET_DIR}/bin/conda config --set auto_activate_base false" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---\n", + "## 2. Create conda environment" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Create new conda environment. The following steps can be repeated if multiple environments should be created. If the Python version differ towards the external Python version, a mix of Conda modules and external modules will not be possible" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "${CONDA_TARGET_DIR}/bin/conda create -n ${CONDA_ENV} -y python=3.6.8 ipykernel" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---\n", + "## 3. Create/Edit launch script for the Jupyter kernel" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 3.1 - Create kernel to allow access to the conda environment. Adapte `module purge` and `PYTHONPATH` according to the comments." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "echo '#!/bin/bash\n", + "\n", + "# module purge # optional to disable the external environment, necessary, if python version is different\n", + " \n", + "# Activate your Python virtual environment\n", + "source '\"${CONDA_TARGET_DIR}\"'/bin/activate '\"${CONDA_ENV}\"'\n", + " \n", + "# Ensure python packages installed in conda are always prefered, not necessary if module purge is used\n", + "export PYTHONPATH=${CONDA_PREFIX}/lib/python3.6/site-packages:${PYTHONPATH}\n", + " \n", + "exec python -m ipykernel $@' > ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "chmod +x ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---\n", + "## 4. Create/Edit Jupyter kernel configuration" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 4.1 - Create user kernel, if you want to access the conda environment of a colleague, only these steps are necessary" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "mkdir -p $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 4.2 - Adjust kernel.json file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "echo '{\n", + " \"argv\": [\n", + " \"'\"${CONDA_TARGET_DIR}\"'/envs/'\"${CONDA_ENV}\"'/kernel.sh\",\n", + " \"-f\",\n", + " \"{connection_file}\"\n", + " ],\n", + " \"display_name\": \"conda_'\"${CONDA_ENV}\"'\",\n", + " \"language\": \"python\"\n", + "}' > $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}/kernel.json" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Restart of JupyterLab might be necessary to see the kernel in the kernel selection overview." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Bash", + "language": "bash", + "name": "bash" + }, + "language_info": { + "codemirror_mode": "shell", + "file_extension": ".sh", + "mimetype": "text/x-sh", + "name": "bash" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/day2/4-build-your-kernel/Create_JupyterKernel_general.ipynb b/day2/4-build-your-kernel/Create_JupyterKernel_general.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..206580d4066612fd2bbb5bb30324e664cade3072 --- /dev/null +++ b/day2/4-build-your-kernel/Create_JupyterKernel_general.ipynb @@ -0,0 +1,458 @@ +{ + "cells": [ + { + "attachments": { + "67258d94-84e6-4a0c-ae8f-c74332ec082e.jpg": { + "image/jpeg": 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" + } + }, + "cell_type": "markdown", + "metadata": { + "toc-hr-collapsed": false + }, + "source": [ + "\n", + "Author: [Jens Henrik Göbbert](mailto:j.goebbert@fz-juelich.de)\n", + "------------------------------------" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "toc-hr-collapsed": false + }, + "source": [ + "# Create your own Jupyter Kernel\n", + "\n", + "Often the standard kernel do not provide all features you need for your work. This might be that certain modules are not loaded or packages are not installed. \n", + "With your own kernel you can overcome that problem easily and define your own environment, in which you work.\n", + "\n", + "This notebook shows you how you can build your own kernel for a **python environment**.\n", + "\n", + "-------------------------" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Building your own Jupyter kernel is a three step process\n", + "1. Create/Pimp new virtual Python environment\n", + " * venv\n", + "2. Create/Edit launch script for the Jupyter kernel\n", + " * kernel.sh\n", + "3. Create/Edit Jupyter kernel configuration\n", + " * kernel.json" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Settings" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* Set kernel name\n", + " - must be lower case\n", + " - change if you like" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# INPUT NEEDED:\n", + "KERNEL_NAME=${USER}_kernel\n", + "\n", + "export KERNEL_NAME=$(echo \"${KERNEL_NAME}\" | awk '{print tolower($0)}')\n", + "echo ${KERNEL_NAME} # double check" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* List directories where JupyterLab will search for kernels" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# JUPYTER SEARCH PATH (for kernels-directory)\n", + "echo \"jupyter search paths for kernels-directories\"\n", + "if [ -z $JUPYTER_PATH ]; then\n", + " echo \"$HOME/.local/share/jupyter\"\n", + "else\n", + " tr ':' '\\n' <<< \"$JUPYTER_PATH\"\n", + "fi" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* Set kernel type\n", + " - private kernel = \"\\${HOME}/.local/\" \n", + " - project kernel = \"\\${PROJECT}/.local/\" \n", + " - other kernel = \"\\<your-path\\>\" (ensure it is part of $JUPYTER_PATH or your kernel will not be found by JuypterLab)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# INPUT NEEDED:\n", + "export KERNEL_TYPE=private # private, project or other\n", + "export KERNEL_SPECS_PREFIX=${HOME}/.local\n", + "\n", + "###################\n", + "# project kernel\n", + "if [ \"${KERNEL_TYPE}\" == \"project\" ]; then\n", + " export KERNEL_SPECS_PREFIX=${PROJECT}/.local\n", + " echo \"project kernel\"\n", + "# private kernel\n", + "elif [ \"${KERNEL_TYPE}\" == \"private\" ]; then\n", + " export KERNEL_SPECS_PREFIX=${HOME}/.local\n", + " echo \"private kernel\"\n", + "else\n", + " if [ ! -d \"$KERNEL_SPECS_PREFIX\" ]; then\n", + " echo \"ERROR: please create directory $KERNEL_SPECS_PREFIX\"\n", + " fi\n", + " echo \"other kernel\"\n", + "fi\n", + "export KERNEL_SPECS_DIR=${KERNEL_SPECS_PREFIX}/share/jupyter/kernels\n", + "\n", + "# check if kernel name is unique\n", + "if [ -d \"${KERNEL_SPECS_DIR}/${KERNEL_NAME}\" ]; then\n", + " echo \"ERROR: Kernel already exists in ${KERNEL_SPECS_DIR}/${KERNEL_NAME}\"\n", + " echo \" Rename kernel name or remove directory.\"\n", + "fi\n", + "\n", + "echo ${KERNEL_SPECS_DIR}/${KERNEL_NAME} # double check" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* Set directory for kernels virtual environment\n", + " - change if you like" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# INPUT NEEDED:\n", + "export KERNEL_VENVS_DIR=${PROJECT}/${USER}/jupyter/kernels\n", + "\n", + "###################\n", + "mkdir -p ${KERNEL_VENVS_DIR}\n", + "if [ \"${KERNEL_TYPE}\" != \"private\" ] && [ \"${KERNEL_TYPE}\" != \"other\" ]; then\n", + " echo \"Please check the permissions and ensure your project partners have read/execute permissions:\"\n", + " namei -l ${KERNEL_VENVS_DIR}\n", + "fi\n", + "\n", + "echo ${KERNEL_VENVS_DIR} # double check\n", + "ls -lt ${KERNEL_VENVS_DIR}" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Create/Pimp new virtual Python environment" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.1 - Load required modules" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "module -q purge\n", + "module -q use $OTHERSTAGES \n", + "module -q load Stages/2020 2> /dev/null # any stage can be used\n", + "module -q load GCCcore/.9.3.0 2> /dev/null\n", + "module -q load Python/3.8.5 # only Python is required\n", + "module list # double check" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.2 - Load extra modules you need for your kernel" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# module load <module you need>" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.3 - Create and activate a virtual environment for the kernel \n", + "and ensure python packages installed in the virtual environment are always prefered" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "if [ -d \"${KERNEL_VENVS_DIR}/${KERNEL_NAME}\" ]; then\n", + " echo \"ERROR: Directory for virtual environment already ${KERNEL_VENVS_DIR}/${KERNEL_NAME}\"\n", + " echo \" Rename kernel name or remove directory.\"\n", + "else\n", + " python -m venv --system-site-packages ${KERNEL_VENVS_DIR}/${KERNEL_NAME}\n", + " source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate\n", + " export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:${PYTHONPATH}\n", + " echo ${VIRTUAL_ENV} # double check\n", + "fi" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.4 - Install Python libraries required for communication with Jupyter" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "which pip\n", + "if [ -z \"${VIRTUAL_ENV}\" ]; then\n", + " echo \"ERROR: Virtual environment not successfully initialized.\"\n", + "else\n", + " pip install --ignore-installed ipykernel\n", + " ls ${VIRTUAL_ENV}/lib/python3.8/site-packages/ # double check\n", + "fi" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 1.5 - Install whatever else you need in your Python virtual environment (using pip)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#pip install <python-package you need>" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Create/Edit launch script for the Jupyter kernel" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 2.1 - Create launch script, which loads your Python virtual environment and starts the ipykernel process inside:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "echo '#!/bin/bash'\"\n", + "\n", + "# Load required modules\n", + "module purge\n", + "module use \"'$OTHERSTAGES'\"\n", + "module load Stages/2020\n", + "module load GCCcore/.9.3.0\n", + "module load Python/3.8.5\n", + "\n", + "# Load extra modules you need for your kernel (as you did in step 1.2)\n", + "#module load <module you need>\n", + " \n", + "# Activate your Python virtual environment\n", + "source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate\n", + " \n", + "# Ensure python packages installed in the virtual environment are always prefered\n", + "export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:\"'${PYTHONPATH}'\"\n", + " \n", + "exec python -m ipykernel \"'$@' > ${VIRTUAL_ENV}/kernel.sh\n", + "chmod +x ${VIRTUAL_ENV}/kernel.sh\n", + "\n", + "cat ${VIRTUAL_ENV}/kernel.sh # double check" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 3. Create/Edit Jupyter kernel configuration" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 3.1 - Create Jupyter kernel configuration directory and files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "python -m ipykernel install --name=${KERNEL_NAME} --prefix ${VIRTUAL_ENV}\n", + "export VIRTUAL_ENV_KERNELS=${VIRTUAL_ENV}/share/jupyter/kernels" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 3.2 - Adjust kernel.json file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "mv ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json.orig\n", + "\n", + "echo '{\n", + " \"argv\": [\n", + " \"'${KERNEL_VENVS_DIR}/${KERNEL_NAME}/kernel.sh'\",\n", + " \"-m\",\n", + " \"ipykernel_launcher\",\n", + " \"-f\",\n", + " \"{connection_file}\"\n", + " ],\n", + " \"display_name\": \"'${KERNEL_NAME}'\",\n", + " \"language\": \"python\"\n", + "}' > ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json\n", + "\n", + "cat ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json # double check" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* 3.3 - Create link to kernel specs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cd ${KERNEL_SPECS_DIR}\n", + "ln -s ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME} .\n", + "\n", + "echo -e \"\\n\\nThe new kernel '${KERNEL_NAME}' was added to your kernels in '${KERNEL_SPECS_DIR}/'\\n\"\n", + "ls ${KERNEL_SPECS_DIR} # double check" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "---" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 4. Cleanup" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "deactivate" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Bash", + "language": "bash", + "name": "bash" + }, + "language_info": { + "codemirror_mode": "shell", + "file_extension": ".sh", + "mimetype": "text/x-sh", + "name": "bash" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/day2/4-build-your-kernel/Modify_JupyterKernel_at_NotebookRuntime.ipynb b/day2/4-build-your-kernel/Modify_JupyterKernel_at_NotebookRuntime.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..9cfc5820408c691a4c4200a2025a1a7a9e646761 --- /dev/null +++ b/day2/4-build-your-kernel/Modify_JupyterKernel_at_NotebookRuntime.ipynb @@ -0,0 +1,153 @@ +{ + "cells": [ + { + "attachments": { + "f3736838-48a6-4450-9c91-5730ded4aca0.jpg": { + "image/jpeg": 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" + } + }, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "\n", + "Author: [Jonathan Windgassen](mailto:j.windgassen@fz-juelich.de)\n", + "------------------------------------" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# How to modify/extend a running Jupyter Kernel\n", + "\n", + "There are many cases where one needs modules from JupyterLab for a project. But building your own kernel is often a detour from the original idea or is annoying when publishing your project. \n", + "By adding these 4 cells to the top of your project you can load modules for the project \"on the fly\".\n", + "\n", + "Besides that this also adds a ways of installing python packages via pip without disrupting the uses packages or access to the system site-packages\n", + "\n", + "-------" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "- First we create to temp-folders in the */tmp* directory, who will contain the venv where we install the required packages and a folder that stores the PYTHONPATH and LD_LIBRARY_PATH environment variable. This is necessary because loading modules manipulates these variables but we can't access the changes from within python, so we store the changed variables in a folder.\n", + "- Then we use a bash-shell to:\n", + " - Load the Modules\n", + " - Create a venv and installing ipykernel in there\n", + " - Write PYTHONPATH and LD_LIBRARY_PATH to the tempdir\n", + "- Beacause the Dynamic Linker of Python doesn't detect changes in LD_LIBRARY_PATH we need to reboot the Interpreter afterwards to carry these changes over. To gain access to the venv we will start Python from there.\n", + "- After that we install the required modules.\n", + "\n", + "**Note**: The third cell **won't** show that it's completed and the Notebook will show `Python 3 | Starting` at the bottom, although the interpreter already reloaded compeltely. You can savely ignore this and continue with the third shell. As soon as this has finished the Notebook will show `Python3 | Idle` again." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os, sys, tempfile\n", + "\n", + "tempdir = tempfile.mkdtemp()\n", + "venv_folder = tempfile.mkdtemp()\n", + "print(tempdir, venv_folder)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%bash -s \"$tempdir\" \"$venv_folder\" # Pass the paths to the bash-subshell\n", + "\n", + "######################################################################\n", + "## The modules go here ##\n", + "## We will use Stage/Devel-2020 with Python 3.8 as a example ##\n", + "######################################################################\n", + "\n", + "# Update to Stage Devel-2020\n", + "module --force purge\n", + "module use $OTHERSTAGES \n", + "module load Stages/Devel-2020\n", + "\n", + "module load GCC/9.3.0\n", + "module load Python/3.8.5\n", + "\n", + "# Create a venv with the python from Devel-2020 and install ipykernel there (needed for communicating with Jupyter)\n", + "# If you don't change Python above this should be a normal Python 3.6 venv\n", + "python -m venv --system-site-packages $2\n", + "source $2/bin/activate\n", + "pip install --quiet ipykernel\n", + "\n", + "# Store the new variables to the temp-folder\n", + "echo $PYTHONPATH > $1/pythonpath\n", + "echo $LD_LIBRARY_PATH > $1/librarypath" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# The arguments for the new python interpreter. We need to initialize ipykernel or JupyterLab will fail to integrate the new process\n", + "args = [f\"{venv_folder}/bin/python\", \"-m\", \"ipykernel\"]\n", + "args.extend(sys.argv)\n", + "\n", + "# Because we call \"execve\" instead of \"execv\" we get the option to set the environment variables in the process. We use this to smuggle in the changed LD_LIBRARY_PATH and PYTHONPATH.\n", + "# You also can pass the location of the 2 temp-folders as new environment variables if you want to delete them later for cleanup.\n", + "env = {\"PYTHONPATH\": open(f\"{tempdir}/pythonpath\").read(),\n", + " \"LD_LIBRARY_PATH\": open(f\"{tempdir}/librarypath\").read(),\n", + " \"tempdir\": tempdir,\n", + " \"venv_folder\": venv_folder}\n", + " \n", + "!echo Restarting Interpreter from $venv_folder/bin/python. Please execute the next cell\n", + "os.execve(f\"{venv_folder}/bin/python\", args, env)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Because we are in the venv now, we can safely install all packages that we need and don't come with the Python3-Kernel. No need to add --user\n", + "%pip install --quiet ..." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "-----\n", + "\n", + "After that you can import all you libraries (remember that the Interpreter restarted and you need to reimport os/sys/tempfile if you need them) and start with the notebook" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/day2/4-build-your-kernel/PRACE-Wrkshp_interactive-hpc-with-jupyter_build-kernel.pdf b/day2/4-build-your-kernel/PRACE-Wrkshp_interactive-hpc-with-jupyter_build-kernel.pdf new file mode 100644 index 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" + } + }, + "cell_type": "markdown", + "id": "diverse-activity", + "metadata": { + "toc-hr-collapsed": false + }, + "source": [ + "\n", + "Author: [Jens Henrik Göbbert](mailto:j.goebbert@fz-juelich.de)\n", + "------------------------------------" + ] + }, + { + "cell_type": "markdown", + "id": "hourly-valentine", + "metadata": {}, + "source": [ + "### Accessing Arbitrary Ports or Hosts\n", + "[more](https://jupyter-server-proxy.readthedocs.io/en/latest/arbitrary-ports-hosts.html)\n", + "\n", + "---------------------------------------------" + ] + }, + { + "cell_type": "markdown", + "id": "potential-store", + "metadata": {}, + "source": [ + "#### Exercise 1:\n", + "1. Start a web-server\n", + "**ATTENTION: the code below fails, because Jupyter is already running a tornado event loop\n", + "2. Create a Python file and run it in the terminal" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "brutal-failing", + "metadata": {}, + "outputs": [], + "source": [ + "### WILL FAIL ####\n", + "import tornado.ioloop\n", + "import tornado.web\n", + "\n", + "class MainHandler(tornado.web.RequestHandler):\n", + " def get(self):\n", + " self.write(\"Hello, world\")\n", + "\n", + "def make_app():\n", + " return tornado.web.Application([\n", + " (r\"/\", MainHandler),\n", + " ])\n", + "\n", + "if __name__ == \"__main__\":\n", + " app = make_app()\n", + " app.listen(8888)\n", + " tornado.ioloop.IOLoop.current().start()" + ] + }, + { + "cell_type": "markdown", + "id": "dynamic-experience", + "metadata": {}, + "source": [ + "#### Exercise 2:\n", + "1. Connect to the running web-server from within your browser \n", + " - add `/proxy/<port>` to the Jupyter-Notebook-Server´s URL\n", + " - e.g. https://jupyter-jsc.fz-juelich.de/user/j.goebbert@fz-juelich.de/jusuf_login/proxy/8888" + ] + }, + { + "cell_type": "markdown", + "id": "computational-prime", + "metadata": {}, + "source": [ + "**Image what that allows you to do without the hassle of ssh-tunnels!**" + ] + }, + { + "cell_type": "markdown", + "id": "peripheral-leave", + "metadata": {}, + "source": [ + "#### Exercise 3:\n", + "1. Check how `jupyter-xprahtml5-proxy` is using the jupyter-server-proxy extension\n", + " - [more](https://github.com/FZJ-JSC/jupyter-xprahtml5-proxy)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "micro-strap", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/day2/5-server-proxy/PRACE-Wrkshp_interactive-hpc-with-jupyter_serverproxy.pdf b/day2/5-server-proxy/PRACE-Wrkshp_interactive-hpc-with-jupyter_serverproxy.pdf new file mode 100644 index 0000000000000000000000000000000000000000..1c31f5bc54808d7cced6c2eed710739b9d3bea53 Binary files /dev/null and b/day2/5-server-proxy/PRACE-Wrkshp_interactive-hpc-with-jupyter_serverproxy.pdf differ diff --git a/day2/6-interactive-widgets/voila_with_jupyter_jsc.ipynb b/day2/6-interactive-widgets/voila_with_jupyter_jsc.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..84b029b0d4979d932b4d4e4a6088c81707d85837 --- /dev/null +++ b/day2/6-interactive-widgets/voila_with_jupyter_jsc.ipynb @@ -0,0 +1,188 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "remarkable-performance", + "metadata": {}, + "outputs": [], + "source": [ + "port = 8866" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "taken-subject", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "voila --server_url=jupyter-jsc.fz-juelich.de --base_url=/user/a.grosch@fz-juelich.de/jusuf/proxy/8866/ 08.01-voila-basics.ipynb\n", + "\n" + ] + } + ], + "source": [ + "import os\n", + "print(\"\"\"\n", + "voila --server_url=/ --base_url={prefix}proxy/{port}/ 08.01-voila-basics.ipynb\n", + "\"\"\".format(prefix=os.environ['JUPYTERHUB_SERVICE_PREFIX'], port=port))" + ] + }, + { + "cell_type": "markdown", + "id": "encouraging-making", + "metadata": {}, + "source": [ + "#### All voila arguments:" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "entire-trustee", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "voila [OPTIONS] NOTEBOOK_FILENAME\n", + "\n", + "This launches a stand-alone server for read-only notebooks.\n", + "\n", + "Options\n", + "-------\n", + "\n", + "notebook_path:\n", + " File name of the Jupyter notebook to display.\n", + "\n", + "--debug\n", + " Set the log level to logging.DEBUG, and show exception tracebacks in output.\n", + "--no-browser\n", + " Don't open the notebook in a browser after startup.\n", + "--port=<Int> (Voila.port)\n", + " Default: 8866\n", + " Port of the Voilà server. Default 8866.\n", + "--static=<Unicode> (Voila.static_root)\n", + " Default: '/p/software/jusuf/stages/2020/software/Jupyter/2020.2.6-gccc...\n", + " Directory holding static assets (HTML, JS and CSS files).\n", + "--strip_sources=<Bool> (VoilaConfiguration.strip_sources)\n", + " Default: True\n", + " Strip sources from rendered html\n", + "--autoreload=<Bool> (Voila.autoreload)\n", + " Default: False\n", + " Will autoreload to server and the page when a template, js file or Python\n", + " code changes\n", + "--template=<Unicode> (VoilaConfiguration.template)\n", + " Default: 'lab'\n", + " template name to be used by voila.\n", + "--theme=<Unicode> (VoilaConfiguration.theme)\n", + " Default: 'light'\n", + "--base_url=<Unicode> (Voila.base_url)\n", + " Default: '/'\n", + " Path for Voilà API calls. If server_url is unset, this will be\n", + " used for both the base route of the server and the client. If\n", + " server_url is set, the server will server the routes prefixed by\n", + " server_url, while the client will prefix by base_url (this is\n", + " useful in reverse proxies).\n", + "--server_url=<Unicode> (Voila.server_url)\n", + " Default: None\n", + " Path to prefix to Voilà API handlers. Leave unset to default to base_url\n", + "--enable_nbextensions=<Bool> (VoilaConfiguration.enable_nbextensions)\n", + " Default: False\n", + " Set to True for Voilà to load notebook extensions\n", + "\n", + "To see all available configurables, use `--help-all`\n", + "\n", + "Examples\n", + "--------\n", + "\n", + " voila example.ipynb --port 8888\n", + "\n" + ] + } + ], + "source": [ + "!voila --help" + ] + }, + { + "cell_type": "markdown", + "id": "supposed-stupid", + "metadata": {}, + "source": [ + "#### With template:" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "chicken-scanning", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "voila --template vuetify-default --server_url=/ --base_url=/user/a.grosch@fz-juelich.de/jusuf/proxy/8866/ 08.01-voila-basics.ipynb\n", + "\n" + ] + } + ], + "source": [ + "print(\"\"\"\n", + "voila --template vuetify-default --server_url=/ --base_url={prefix}proxy/{port}/ 08.01-voila-basics.ipynb\n", + "\"\"\".format(prefix=os.environ['JUPYTERHUB_SERVICE_PREFIX'], port=port))" + ] + }, + { + "cell_type": "markdown", + "id": "alpha-badge", + "metadata": {}, + "source": [ + "#### With notenook extensions: \n", + "`Set to True for Voilà to load notebook extensions` \n", + "Needed when wanting to display plots from plotting libary for example." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "independent-examination", + "metadata": {}, + "outputs": [], + "source": [ + "print(\"\"\"\n", + "voila --enable_nbextensions=True --server_url=/ --base_url={prefix}proxy/{port}/ 08.01-voila-basics.ipynb\n", + "\"\"\".format(prefix=os.environ['JUPYTERHUB_SERVICE_PREFIX'], port=port))" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/day2/6-interactive-widgets/widget_tutorial.ipynb b/day2/6-interactive-widgets/widget_tutorial.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..e08ed6d94c298526dde473a3dd346a5ce65a6c7c --- /dev/null +++ b/day2/6-interactive-widgets/widget_tutorial.ipynb @@ -0,0 +1,66 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "national-cologne", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Cloning into 'tutorial'...\n", + "remote: Enumerating objects: 2007, done. \n", + "remote: Counting objects: 100% (85/85), done. \n", + "remote: Compressing objects: 100% (65/65), done. \n", + "remote: Total 2007 (delta 37), reused 37 (delta 20), pack-reused 1922 \n", + "Receiving objects: 100% (2007/2007), 7.18 MiB | 26.53 MiB/s, done.\n", + "Resolving deltas: 100% (1321/1321), done.\n" + ] + } + ], + "source": [ + "git clone https://github.com/jupyter-widgets/tutorial.git" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "induced-family", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "id": "equivalent-determination", + "metadata": {}, + "source": [ + "**Example Dashboards**:\n", + "\n", + "https://cosimo.fz-juelich.de/ \n", + "https://covid19-bayesian.fz-juelich.de/\n", + "\n", + "**Dashboards for Science**:\n", + "\n", + "https://www.fz-juelich.de/SharedDocs/Termine/IAS/JSC/DE/Kurse/2021/dashboards-2021.html" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Bash", + "language": "bash", + "name": "bash" + }, + "language_info": { + "codemirror_mode": "shell", + "file_extension": ".sh", + "mimetype": "text/x-sh", + "name": "bash" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}