Add script to run Jupyter Lab HPC natively #59
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
van-go
changed the title
Comment on lines
27
to
34
| { | ||
| "name": "launchParameters", | ||
| "arg": "echo 'Job is done.'", | ||
| "inputMode": "FIXED", | ||
| "notes": { | ||
| "isHidden": true | ||
| } | ||
| } |
There was a problem hiding this comment.
This is not needed with zip runtime.
Suggested change
| { | |
| "name": "launchParameters", | |
| "arg": "echo 'Job is done.'", | |
| "inputMode": "FIXED", | |
| "notes": { | |
| "isHidden": true | |
| } | |
| } |
chandra-tacc
approved these changes
Oct 31, 2024
rstijerina
reviewed
Nov 6, 2024
rstijerina
reviewed
Nov 6, 2024
rstijerina
reviewed
Nov 6, 2024
rstijerina
reviewed
Nov 6, 2024
rstijerina
reviewed
Nov 6, 2024
rstijerina
reviewed
Nov 6, 2024
rstijerina
reviewed
Nov 6, 2024
rstijerina
reviewed
Nov 7, 2024
| echo "TACC: ERROR - ssh tunnels failed to launch" | ||
| exit 1 | ||
| fi | ||
| echo "TACC: created reverse ports on Frontera logins" |
There was a problem hiding this comment.
Can remove system specific language
Suggested change
| echo "TACC: created reverse ports on Frontera logins" | |
| echo "TACC: created reverse ports on system logins" |
rstijerina
reviewed
Nov 7, 2024
Comment on lines
+124
to
+136
| # verify jupyter is up. if not, give one more try, then bail | ||
| if ! $(ps -fu ${USER} | grep ${JUPYTER_BIN} | grep -qv grep) ; then | ||
| echo "TACC: first jupyter launch failed. Retrying..." | ||
| nohup ${JUPYTER_BIN} ${JUPYTER_ARGS} &> ${JUPYTER_LOGFILE} && rm ${TAP_LOCKFILE} & | ||
| fi | ||
| if ! $(ps -fu ${USER} | grep ${JUPYTER_BIN} | grep -qv grep) ; then | ||
| echo "TACC: ERROR - jupyter failed to launch" | ||
| echo "TACC: ERROR - this is often due to an issue in your python or conda environment" | ||
| echo "TACC: ERROR - jupyter logfile contents:" | ||
| cat ${JUPYTER_LOGFILE} | ||
| echo "TACC: job ${SLURM_JOB_ID} execution finished at: $(date)" | ||
| exit 1 | ||
| fi |
There was a problem hiding this comment.
This can be simplified to the below, and moved to after curl on line 153
Suggested change
| # verify jupyter is up. if not, give one more try, then bail | |
| if ! $(ps -fu ${USER} | grep ${JUPYTER_BIN} | grep -qv grep) ; then | |
| echo "TACC: first jupyter launch failed. Retrying..." | |
| nohup ${JUPYTER_BIN} ${JUPYTER_ARGS} &> ${JUPYTER_LOGFILE} && rm ${TAP_LOCKFILE} & | |
| fi | |
| if ! $(ps -fu ${USER} | grep ${JUPYTER_BIN} | grep -qv grep) ; then | |
| echo "TACC: ERROR - jupyter failed to launch" | |
| echo "TACC: ERROR - this is often due to an issue in your python or conda environment" | |
| echo "TACC: ERROR - jupyter logfile contents:" | |
| cat ${JUPYTER_LOGFILE} | |
| echo "TACC: job ${SLURM_JOB_ID} execution finished at: $(date)" | |
| exit 1 | |
| fi | |
| ${JUPYTER_BIN} ${JUPYTER_ARGS} |
There was a problem hiding this comment.
We want to hang on the jupyter process after everything is setup, then do cleanup after
rstijerina
reviewed
Nov 7, 2024
Comment on lines
+124
to
+136
| # verify jupyter is up. if not, give one more try, then bail | ||
| if ! $(ps -fu ${USER} | grep ${JUPYTER_BIN} | grep -qv grep) ; then | ||
| echo "TACC: first jupyter launch failed. Retrying..." | ||
| nohup ${JUPYTER_BIN} ${JUPYTER_ARGS} &> ${JUPYTER_LOGFILE} && rm ${TAP_LOCKFILE} & | ||
| fi | ||
| if ! $(ps -fu ${USER} | grep ${JUPYTER_BIN} | grep -qv grep) ; then | ||
| echo "TACC: ERROR - jupyter failed to launch" | ||
| echo "TACC: ERROR - this is often due to an issue in your python or conda environment" | ||
| echo "TACC: ERROR - jupyter logfile contents:" | ||
| cat ${JUPYTER_LOGFILE} | ||
| echo "TACC: job ${SLURM_JOB_ID} execution finished at: $(date)" | ||
| exit 1 | ||
| fi |
There was a problem hiding this comment.
We want to hang on the jupyter process after everything is setup, then do cleanup after
| mkdir -p ${NB_SERVERDIR} | ||
| mkdir -p ${HOME}/.tap | ||
|
|
||
| TAP_LOCKFILE=${HOME}/.tap/.${SLURM_JOB_ID}.lock |
There was a problem hiding this comment.
@chandra-tacc what is TAP_LOCKFILE for?
| export JUPYTERLAB_SETTINGS_DIR="${HOME}/.jupyterlab" | ||
|
|
||
| # launch jupyter-lab | ||
| JUPYTER_LOGFILE=${NB_SERVERDIR}/${NODE_HOSTNAME_PREFIX}.log |
There was a problem hiding this comment.
No need for JUPYTER_LOGFILE, logs will be logged to tapisjob.out automatically
rstijerina
reviewed
Nov 7, 2024
| c = get_config() | ||
| c.IPKernelApp.pylab = "inline" | ||
| c.ServerApp.ip = "0.0.0.0" | ||
| c.ServerApp.port = 5902 |
There was a problem hiding this comment.
Suggested change
| c.ServerApp.port = 5902 | |
| c.ServerApp.port = ${LOCAL_PORT} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
[DesignSafe] Enable MPI in Jupyter Lab HPC (CPU)
Created app.json that uses a ZIP runtime to run an interactive JupyterLab session. It is not containerized, allowing users more flexibility.