Remove hh5

README.md

@@ -4,7 +4,7 @@ Helpful scripts for working at NCI
 To use these scripts on NCI infrastructure do the following:
 
 ```
-module use /g/data/hh5/public/modules
+module use /g/data/xp65/public/modules
 module load nci-scripts
 ```
 
@@ -22,7 +22,7 @@ $ uqstat
 qcost
 ------
 
-Calculates what it would cost, in SU, for a job submitted to the PBS system with the same configuration. 
+Calculates what it would cost, in SU, for a job submitted to the PBS system with the same configuration.
 The information is all contained in the [PBS queue information is provided by NCI](https://opus.nci.org.au/display/Help/Queue+Limits)
 but it can be tedious to determine which configuration of queue and memory request should be used
 to minimise job cost. `qcost` was created to make this process easier.
@@ -32,8 +32,8 @@ Usage:
 ./qcost -h
 usage: qcost [-h] -q QUEUE -n NCPUS -m MEM [-t TIME]
 
-Return what it would cost (in SUs) for a PBS job submitted on gadi with the same               
-configuration. No checking is done to ensure requests are within queue limits.                 
+Return what it would cost (in SUs) for a PBS job submitted on gadi with the same
+configuration. No checking is done to ensure requests are within queue limits.
 
 
 optional arguments:
@@ -59,15 +59,15 @@ $ qcost -q normal -n 4 -m 60GB -t 3:00:00
 gadi_jupyter
 ------------
 
-Run a Jupyter notebook on Gadi, displaying it in a local web browser. 
+Run a Jupyter notebook on Gadi, displaying it in a local web browser.
 
 **THIS MUST BE RUN FROM YOUR OWN COMPUTER**
 
 So the first step is to clone this repository to your local workstation. It
 works on mac/linux/windows (for windows using e.g. [git bash](https://gitforwindows.org/)
 or [Windows Ssubsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install)).
 
-By default the script will spawn a job with a single CPU, 4GB of memory 
+By default the script will spawn a job with a single CPU, 4GB of memory
 and a walltime of 1 hour.
 
 Command line options can be used to alter the resources requested, the
@@ -106,25 +106,25 @@ Queue Options:
 
 ```
 
-You will need to have ssh keys setup for logging into gadi. There is a 
+You will need to have ssh keys setup for logging into gadi. There is a
 [guide on how to do this on the CMS Wiki](http://climate-cms.wikis.unsw.edu.au/CLEx_induction#Step_2:_Set_up_your_Connection).
 
 vdi_jupyter.py
 --------------
 
-Run a Jupyter notebook on 
+Run a Jupyter notebook on
 [NCI Virtual Desktop Infrastructure (VDI)](https://opus.nci.org.au/display/Help/VDI+User+Guide), displaying it in a local web browser (run from your own computer).
 
 To run:
 ```
 python nci_scripts/vdi_jupyter.py
 ```
 
-This script requires the `pexpect` package. To make a `conda` environment with the required 
+This script requires the `pexpect` package. To make a `conda` environment with the required
 packages:
 ```
 conda env create -f nci_scripts/vdi_environment.yml
-``` 
+```
 then activate the environment:
 ```
 conda activate jupyter_vdi

gadi_jupyter

@@ -177,9 +177,16 @@ set -eu
 WORKDIR="$WORKDIR"
 mkdir -p "\$WORKDIR"
 
-# Check if a hh5 member
-if [ ! -d /g/data/hh5 ]; then
-    echo "ERROR: \$USER is not a member of hh5. Join at https://my.nci.org.au/mancini/project/hh5/join" >&2
+# Check if an xp65 member
+if [ ! -d /g/data/xp65 ]; then
+    echo "ERROR: \$USER is not a member of xp65. Join at https://my.nci.org.au/mancini/project/xp65/join" >&2
+    echo "x x x x ERROR"
+    exit
+fi
+
+# Check if an ik11 member
+if [ ! -d /g/data/ik11 ]; then
+    echo "ERROR: \$USER is not a member of ik11. Join at https://my.nci.org.au/mancini/project/ik11/join" >&2
     echo "x x x x ERROR"
     exit
 fi
@@ -200,8 +207,8 @@ cat > "\$WORKDIR/runjp.sh" <<EOQ
 
 module purge
 
-eval "\\\$(/g/data/hh5/public/apps/miniconda3/bin/conda shell.bash hook)"
-conda activate "${CONDA_ENV}"
+module use /g/data/xp65/public/modules
+module load conda/analysis3
 
 set -eu
 
@@ -228,8 +235,8 @@ export DASK_TEMPORARY_DIRECTORY="\\\$TMPDIR"
 $STRACE jupyter lab --NotebookApp.token="\\\$TOKEN" --no-browser --ip="\\\$HOSTNAME" --port "\\\$PORT" --port-retries=0
 EOQ
 
-# Required for conda
-storage="gdata/hh5"
+# Required for conda + nci_scripts
+storage="gdata/xp65+gdata/ik11"
 
 if [ -n "$STORAGE" ]; then
     storage="$STORAGE+\$storage"
@@ -334,7 +341,7 @@ fi
 set -e
 echo
 
-$SSH "$LOGINNODE" /g/data/hh5/public/apps/nci_scripts/qmonitor $jobid
+$SSH "$LOGINNODE" /g/data/ik11/nci_scripts/qmonitor $jobid
 
 # Move the cursor past the progress bars
 echo

python-analysis3

@@ -2,4 +2,4 @@
 
 # Always the current stable analysis3 python
 
-/g/data/hh5/public/apps/miniconda3/envs/analysis3/bin/python "$@"
+/g/data/xp65/public/apps/miniconda3/envs/analysis3/bin/python "$@"

qcost

@@ -1,4 +1,4 @@
-#!/g/data3/hh5/public/apps/nci_scripts/python-analysis3
+#!/g/data/xp65/public/apps/nci_scripts/python-analysis3
 
 import pandas
 import argparse

qmonitor

@@ -1,4 +1,4 @@
-#!/g/data/hh5/public/apps/nci_scripts/python-analysis3
+#!/g/data/xp65/public/apps/nci_scripts/python-analysis3
 # Copyright 2020 Scott Wales
 # author: Scott Wales <scott.wales@unimelb.edu.au>
 #

qsubs

@@ -2,7 +2,7 @@
 
 set -eu
 
-storage="gdata/hh5"
+storage="gdata/xp65"
 for p in $(id -nG); do
     if [ $p = "access.dev" ]; then continue; fi
     if [ $p = "access.admin" ]; then continue; fi

qtools.py

@@ -1,4 +1,4 @@
-#!/g/data/hh5/public/apps/nci_scripts/python-analysis3
+#!/g/data/xp65/public/apps/nci_scripts/python-analysis3
 # Copyright 2020 Scott Wales
 # author: Scott Wales <scott.wales@unimelb.edu.au>
 #

uqstat

@@ -1,4 +1,4 @@
-#!/g/data3/hh5/public/apps/nci_scripts/python-analysis3
+#!/g/data/xp65/public/apps/nci_scripts/python-analysis3
 
 import pandas
 import subprocess
@@ -80,7 +80,7 @@ def nqstat_df(project):
     token = pymunge.encode().decode('utf-8')
     headers = { 'Authorization': "MUNGE %s" % (token) }
     params = {'project': project}
-    
+
     response = requests.get(url, params=params, headers=headers, timeout=120.0)
     response.raise_for_status()
 

vdi_jupyter.py

@@ -208,7 +208,7 @@ def main(args):
             logging.info('Unable to launch new VDI session:\n'+r.before.decode())
 
         params.update(m.groupdict())
-        time.sleep(2)   # TODO: instead of waiting, should check for confirmation 
+        time.sleep(2)   # TODO: instead of waiting, should check for confirmation
                         # use has-started
 
     logging.info("Determine jobid for VDI session...{jobid}".format(**params))
@@ -222,7 +222,7 @@ def main(args):
     logging.info("Running Jupyter on VDI...")
 
     setupconda = params.get('setupconda',
-              """module use /g/data3/hh5/public/modules
+              """module use /g/data/xp65/public/modules
                  && module load conda/analysis3-unstable
               """.replace('\n', ' '))
 
@@ -257,7 +257,7 @@ def main(args):
     # optional: terminate to close the vdi session?
 
 def main_argv():
-    
+
     args = parse_args(sys.argv[1:])
 
     main(args)