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Merged
lawrenceabird merged 2 commits into from
Nov 6, 2025
Merged

Sync upstream - 25.11.06 #9

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a403675
Update gadi cluster for more universal use
lawrenceabird Oct 24, 2025
52dcf15
Remove default modules from gadi cluster
lawrenceabird Nov 6, 2025
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39 changes: 21 additions & 18 deletions src/m/classes/clusters/gadi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,19 +22,13 @@ class gadi(object):
"""

def __init__(self, *args): # {{{
self.name = 'gadi.nci.org.au'
self.name = oshostname()
self.login = ''
# Adjust modules for Gadi as needed:
self.modules = [
# Example modules or spack loads:
'openmpi/4.1.2',
# 'python3/3.9.2',
# or just keep them empty if you handle externally:
]
# For Gadi, you usually specify the total ncpus. But if you still want
# to specify by numnodes & cpuspernode, that’s fine. Adjust as needed:
self.moduleload = []
self.moduleuse = []
self.numnodes = 1
self.cpuspernode = 4
self.memory = 40 # e.g. '40GB'
self.port = '' # typical SSH port
self.queue = 'normal' # or "hugemem", "express", etc.
self.time = 60 # total minutes of walltime, e.g. 60 => 1 hour
Expand All @@ -43,7 +37,8 @@ def __init__(self, *args): # {{{
self.extpkgpath = ''
self.codepath = ''
self.executionpath = ''
self.project = '' # Gadi uses -P <PROJECT>
self.project = ''
self.storage = ''
self.interactive = 0
self.bbftp = 0
self.numstreams = 8
Expand All @@ -68,12 +63,14 @@ def __init__(self, *args): # {{{
# }}}

def __repr__(self): # {{{
s = 'class Gadi object\n'
s = 'class gadi object\n'
s += ' name: {}\n'.format(self.name)
s += ' login: {}\n'.format(self.login)
s += ' modules: {}\n'.format(strjoin(self.modules, ', '))
s += ' moduleuse: {}\n'.format(', '.join(self.moduleuse) if getattr(self, 'moduleuse', None) else '')
s += ' moduleload: {}\n'.format(', '.join(self.moduleload) if getattr(self, 'moduleload', None) else '')
s += ' numnodes: {}\n'.format(self.numnodes)
s += ' cpuspernode: {}\n'.format(self.cpuspernode)
s += ' memory: {}GB\n'.format(self.memory)
s += ' np: {}\n'.format(self.nprocs())
s += ' port: {}\n'.format(self.port)
s += ' queue: {}\n'.format(self.queue)
Expand All @@ -84,6 +81,7 @@ def __repr__(self): # {{{
s += ' codepath: {}\n'.format(self.codepath)
s += ' executionpath: {}\n'.format(self.executionpath)
s += ' project: {}\n'.format(self.project)
s += ' storage: {}\n'.format(self.storage)
s += ' interactive: {}\n'.format(self.interactive)
s += ' bbftp: {}\n'.format(self.bbftp)
s += ' numstreams: {}\n'.format(self.numstreams)
Expand Down Expand Up @@ -114,6 +112,10 @@ def checkconsistency(self, md, solution, analyses): # {{{
md = md.checkmessage('executionpath is empty')
if not self.project:
md = md.checkmessage('project (PBS -P) is empty')
if not self.storage:
md = md.checkmessage('storage is empty')
if len(self.moduleload) != len(self.moduleuse):
raise ValueError("moduleload and moduleuse must have the same length")
return self
# }}}

Expand Down Expand Up @@ -155,20 +157,21 @@ def BuildQueueScript(
fid.write('#PBS -P {}\n'.format(self.project))
fid.write('#PBS -q {}\n'.format(self.queue))
fid.write('#PBS -l ncpus={}\n'.format(self.nprocs()))
# Optionally request memory (example: 4GB x nprocs):
# fid.write('#PBS -l mem={}GB\n'.format(4 * self.nprocs()))
fid.write('#PBS -l mem={}GB\n'.format(self.memory))
fid.write('#PBS -l walltime={}\n'.format(walltime_str))
fid.write('#PBS -l wd\n')
fid.write('#PBS -j oe\n')
fid.write('#PBS -l storage=scratch/{0}+gdata/{0}\n'.format(self.project))
fid.write('#PBS -l storage={}\n'.format(self.storage))
fid.write('#PBS -m bea\n')
fid.write('#PBS -o {}/{}/{}.outlog \n'.format(self.executionpath, dirname, modelname))
fid.write('#PBS -e {}/{}/{}.errlog \n\n'.format(self.executionpath, dirname, modelname))

fid.write('\n# Load modules as needed:\n')
fid.write('module purge\n')
for m in self.modules:
fid.write('module load {}\n'.format(m))
# Print alternating lines
for x, y in zip(self.moduleuse, self.moduleload):
fid.write(f"module use {x}\n")
fid.write(f"module load {y}\n")

# Optionally source environment scripts if needed:
# fid.write('source /g/data/...someSpackOrCondaEnv...\n')
Expand Down