From 8e1e513e947dc4be353fd3663b2d3d0fc56fd10a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jens=20Henrik=20G=C3=B6bbert?= <goebbert1@jwlogin07.juwels>
Date: Tue, 2 Feb 2021 11:38:55 +0100
Subject: [PATCH] update to Stage/2020
---
.../Create_JupyterKernel_general.ipynb | 27 +++++++++++--------
1 file changed, 16 insertions(+), 11 deletions(-)
diff --git a/001-Jupyter/Create_JupyterKernel_general.ipynb b/001-Jupyter/Create_JupyterKernel_general.ipynb
index 8c6eb6e..206580d 100644
--- a/001-Jupyter/Create_JupyterKernel_general.ipynb
+++ b/001-Jupyter/Create_JupyterKernel_general.ipynb
@@ -114,7 +114,7 @@
"source": [
"# INPUT NEEDED:\n",
"export KERNEL_TYPE=private # private, project or other\n",
- "export KERNEL_SPECS_PREFIX=/p/home/jusers/$USER/jureca/.local\n",
+ "export KERNEL_SPECS_PREFIX=${HOME}/.local\n",
"\n",
"###################\n",
"# project kernel\n",
@@ -199,9 +199,9 @@
"source": [
"module -q purge\n",
"module -q use $OTHERSTAGES \n",
- "module -q load Stages/Devel-2019a 2> /dev/null # any stage can be used\n",
- "module -q load GCCcore/.8.3.0 2> /dev/null\n",
- "module -q load Python/3.6.8 # only Python is required\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"
]
},
@@ -241,7 +241,7 @@
"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=${VIRTUAL_ENV}/lib/python3.6/site-packages:${PYTHONPATH}\n",
+ " export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.8/site-packages:${PYTHONPATH}\n",
" echo ${VIRTUAL_ENV} # double check\n",
"fi"
]
@@ -260,8 +260,12 @@
"outputs": [],
"source": [
"which pip\n",
- "pip install --ignore-installed ipykernel\n",
- "ls ${VIRTUAL_ENV}/lib/python3.6/site-packages/ # double check"
+ "if [ -z \"${VIRTUAL_ENV}\" ]; then\n",
+ " echo \"ERROR: Virtual environment not successfully initialized.\"\n",
+ "else\n",
+ " pip install --ignore-installed ipykernel\n",
+ " ls ${VIRTUAL_ENV}/lib/python3.8/site-packages/ # double check\n",
+ "fi"
]
},
{
@@ -312,9 +316,9 @@
"# Load required modules\n",
"module purge\n",
"module use \"'$OTHERSTAGES'\"\n",
- "module load Stages/Devel-2019a\n",
- "module load GCCcore/.8.3.0\n",
- "module load Python/3.6.8\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",
@@ -323,7 +327,7 @@
"source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate\n",
" \n",
"# Ensure python packages installed in the virtual environment are always prefered\n",
- "export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.6/site-packages:\"'${PYTHONPATH}'\"\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",
@@ -408,6 +412,7 @@
"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"
]
},
--
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