diff --git a/002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/Catalyst_Example.ipynb b/002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/Catalyst_Example.ipynb
index 772dc7f2fc4a045a8e0223e2770e684a234d1185..1eb84fdac0094baae300bd5a2b057a730d8964e4 100644
--- a/002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/Catalyst_Example.ipynb
+++ b/002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/Catalyst_Example.ipynb
@@ -24,6 +24,7 @@
"source": [
"## Table of contents\n",
"\n",
+ "- Requirements \n",
"- Start pvserver\n",
"- Start Catalyst enabled simulation\n",
"- Setup Render Window in Browser\n",
@@ -33,6 +34,61 @@
"- Additional usefull functions for using Catalyst in Notebook"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Requirements\n",
+ "- The bash variable JUPYTER_LOG_DIR needs to be set to a folder, where logs can be written. It can be set, before starting jupyter by executing `export JUPYTER_LOG_DIR=\"/your/path\"` before running `jupyter-lab`. The two following lines allows to check the value that was set when starting jupyter:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from os import environ\n",
+ "print(environ.get('JUPYTER_LOG_DIR'))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Additional files are needed. They can be obtained by cloning the git repo, or copying the files in the folder `001-Catalyst2JupyterLab-Tutorial`. Afterwards the path to the folder needs to be written into the file `${JUPYTER_LAB_DIR}/catalystTutorialPath.txt`. This can be done with the following commands:\n",
+ "\n",
+ "```\n",
+ "git init repo j4j_notebooks\n",
+ "cd j4j_notebooks\n",
+ "git remote add origin https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_notebooks.git\n",
+ "git config core.sparseCheckout true\n",
+ "echo \"002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/*\" >> .git/info/sparse-checkout\n",
+ "git pull --depth=1 origin master\n",
+ "cd 002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/\n",
+ "pwd >${JUPYTER_LOG_DIR}/catalystTutorialPath.txt\n",
+ "```"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import glob\n",
+ "file = open(environ.get('JUPYTER_LOG_DIR') + \"/catalystTutorialPath.txt\",\"r\")\n",
+ "catalystTutorialPath = file.readline().rstrip()\n",
+ "file.close()\n",
+ "if len(catalystTutorialPath) < 30:\n",
+ " import sys\n",
+ " print(\"Path is short: '\" + catalystTutorialPath + \"' is it the right path?\", file=sys.stderr)\n",
+ " \n",
+ "if len(glob.glob(catalystTutorialPath+ \"/*\")) < 4:\n",
+ " import sys\n",
+ " print(\"Not enough files in '\" + catalystTutorialPath + \"' is it the right path?\", file=sys.stderr)"
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
@@ -210,9 +266,7 @@
"simple.SetActiveSource(extract)\n",
"extractDisplay = simple.Show(extract, view)\n",
"\n",
- "#ResetCamera(view, renderer)\n",
- "view.ResetCamera()\n",
- "view.CenterOfRotation = view.GetActiveCamera().GetFocalPoint()"
+ "ResetCamera(view, renderer)"
]
},
{
diff --git a/002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/Catalyst_Example_minimal.ipynb b/002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/Catalyst_Example_minimal.ipynb
index 74eadb9d0e6e57201b66097931ef652c51de8cc5..6d76b151ce3fa187c656ab1575b87bbab5358526 100644
--- a/002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/Catalyst_Example_minimal.ipynb
+++ b/002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/Catalyst_Example_minimal.ipynb
@@ -24,12 +24,68 @@
"source": [
"## Table of contents\n",
"\n",
+ "- Requirements \n",
"- Start Catalyst enabled simulation\n",
"- Setup Render Window in Browser\n",
"- Establish Catalyst Connection\n",
"- Setup render pipeline using ParaView Python Commands"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Requirements\n",
+ "- The bash variable JUPYTER_LOG_DIR needs to be set to a folder, where logs can be written. It can be set, before starting jupyter by executing `export JUPYTER_LOG_DIR=\"/your/path\"` before running `jupyter-lab`. The two following lines allows to check the value that was set when starting jupyter:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from os import environ\n",
+ "print(environ.get('JUPYTER_LOG_DIR'))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Additional files are needed. They can be obtained by cloning the git repo, or copying the files in the folder `001-Catalyst2JupyterLab-Tutorial`. Afterwards the path to the folder needs to be written into the file `${JUPYTER_LAB_DIR}/catalystTutorialPath.txt`. This can be done with the following commands:\n",
+ "\n",
+ "```\n",
+ "git init repo j4j_notebooks\n",
+ "cd j4j_notebooks\n",
+ "git remote add origin https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_notebooks.git\n",
+ "git config core.sparseCheckout true\n",
+ "echo \"002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/*\" >> .git/info/sparse-checkout\n",
+ "git pull --depth=1 origin master\n",
+ "cd 002-Methods/003-Visualization/001-InSitu/001-Catalyst2JupyterLab-Tutorial/\n",
+ "pwd >${JUPYTER_LOG_DIR}/catalystTutorialPath.txt\n",
+ "```"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import glob\n",
+ "file = open(environ.get('JUPYTER_LOG_DIR') + \"/catalystTutorialPath.txt\",\"r\")\n",
+ "catalystTutorialPath = file.readline().rstrip()\n",
+ "file.close()\n",
+ "if len(catalystTutorialPath) < 30:\n",
+ " import sys\n",
+ " print(\"Path is short: '\" + catalystTutorialPath + \"' is it the right path?\", file=sys.stderr)\n",
+ " \n",
+ "if len(glob.glob(catalystTutorialPath+ \"/*\")) < 4:\n",
+ " import sys\n",
+ " print(\"Not enough files in '\" + catalystTutorialPath + \"' is it the right path?\", file=sys.stderr)"
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
@@ -45,6 +101,7 @@
"outputs": [],
"source": [
"%%script bash --bg --proc catalyst_process\n",
+ "cd `cat ${JUPYTER_LOG_DIR}/catalystTutorialPath.txt`\n",
"export OMP_NUM_THREADS=1\n",
"pvpython CatalystEnabledSimulation/fedriver.py CatalystEnabledSimulation/cpscript.py > ${JUPYTER_LOG_DIR}/simulation.log 2>&1"
]
@@ -145,9 +202,7 @@
"simple.SetActiveSource(extract)\n",
"extractDisplay = simple.Show(extract, view)\n",
"\n",
- "#ResetCamera(view, renderer)\n",
- "view.ResetCamera()\n",
- "view.CenterOfRotation = view.GetActiveCamera().GetFocalPoint()"
+ "ResetCamera(view, renderer)"
]
},
{