Commit dbf83dfb authored by sfux's avatar sfux
Browse files

Update README.md

parent f25e258e
......@@ -90,8 +90,8 @@ Required options:
Optional arguments:
-b | --batch_sys BATCHSYS Batch system to use (LSF or SLURM)
-c | --config CONFIG_FILE Configuration file for specifying options
-e | --environment ENV Python virtual environment
-g | --numgpu NUM_GPU Number of GPUs to be used on the cluster
-h | --help Display help for this script and quit
-i | --interval INTERVAL Time interval for checking if the job on the cluster already started
......@@ -103,21 +103,26 @@ Optional arguments:
-s | --softwarestack SOFTWARE_STACK Software stack to be used (old, new)
-v | --version Display version of the script and exit
-w | --workdir WORKING_DIR Working directory for the jupyter notebook/lab
--extra-modules EXTRA_MODULES Load additional cluster modules before starting
--module-use MODULE_USE Use additional cluster module collection before starting
--pythonpath PYTHONPATH Set PYTHONPATH before starting
-W | --runtime RUN_TIME Run time limit for jupyter notebook/lab in hours and minutes HH:MM
Examples:
./start_jupyter_nb.sh -u sfux -n 4 -W 04:00 -m 2048 -w /cluster/scratch/sfux
./start_jupyter_nb.sh -u sfux -b SLURM -n 4 -W 04:00 -m 2048 -w /cluster/scratch/sfux
./start_jupyter_nb.sh -u sfxu -n 1 -W 01:00 -m 1024 -j TRUE
./start_jupyter_nb.sh -u sfux -b SLURM -n 1 -W 01:00 -m 1024 -j TRUE
./start_jupyter_nb.sh --username sfux --numcores 2 --runtime 01:30 --memory 2048 --softwarestack new
./start_jupyter_nb.sh --username sfux --batch_sys SLURM --numcores 2 --runtime 01:30 --memory 2048 --softwarestack new
./start_jupyter_nb.sh -c /c/Users/sfux/.jnb_config
Format of configuration file:
JNB_USERNAME="" # ETH username for SSH connection to Euler
JNB_BATCH="SLURM" # Choose SLURM or LSF as batch system
JNB_EXTRA_MODULES # Additional modules to be loaded
JNB_NUM_CPU=1 # Number of CPU cores to be used on the cluster
JNB_NUM_GPU=0 # Number of GPUs to be used on the cluster
JNB_RUN_TIME="01:00" # Run time limit for jupyter notebook/lab in hours and minutes HH:MM
......@@ -130,7 +135,6 @@ JNB_ENV="" # Path to virtual environment
JNB_JLAB="" # "lab" -> start jupyter lab; "" -> start jupyter notebook
JNB_JKERNEL="FALSE" # "FALSE" -> no Julia kernel; "TRUE" -> Julia kernel
```
### Reconnect to a Jupyter notebook
......@@ -192,15 +196,6 @@ Then follow the instructions provided on our wiki:
https://scicomp.ethz.ch/wiki/R#Extensions
```
### Running with a Python Virtual Environment
You can create your own [virtual environment](https://scicomp.ethz.ch/wiki/Python_virtual_environment) in the cluster and run your jupyter notebook with that environment. Please make sure that the Python version used to create your virtual environment is compatible with the one used in the jupyter script.
```
./start_jupyter_nb.sh -u sfux -n 4 -W 04:00 -m 2048 -w /cluster/scratch/sfux -e sample_env
```
## Main author
* Samuel Fux
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment