From 8684bd4e770aa730c3f83405fd23bf7681ac5aac Mon Sep 17 00:00:00 2001
From: Matthew K Defenderfer <mdefende@uab.edu>
Date: Fri, 30 Aug 2024 16:57:44 -0500
Subject: [PATCH] add python control script for submit-pol-job
---
src/exceptions.py | 21 ++++++
src/run-submit-pol-job.py | 140 ++++++++++++++++++++++++++++++++++++++
2 files changed, 161 insertions(+)
create mode 100644 src/exceptions.py
create mode 100755 src/run-submit-pol-job.py
diff --git a/src/exceptions.py b/src/exceptions.py
new file mode 100644
index 0000000..857be66
--- /dev/null
+++ b/src/exceptions.py
@@ -0,0 +1,21 @@
+# exceptions.py
+
+import sys
+
+class CustomException(Exception):
+ """Base class for other exceptions"""
+ def __init__(self, message):
+ super().__init__(message)
+ self.handle_exception(message)
+
+ def handle_exception(self, message):
+ print(f"Error: {message}")
+ sys.exit(1)
+
+class InvalidDeviceError(CustomException):
+ """Exception raised when an improper fileset or path is given as the device"""
+ pass
+
+class ValueError(CustomException):
+ """Overloaded exception to exit when improper value is given"""
+ pass
\ No newline at end of file
diff --git a/src/run-submit-pol-job.py b/src/run-submit-pol-job.py
new file mode 100755
index 0000000..be824cc
--- /dev/null
+++ b/src/run-submit-pol-job.py
@@ -0,0 +1,140 @@
+#!/bin/python3
+
+import argparse
+from pathlib import Path
+import subprocess
+import re
+from exceptions import InvalidDeviceError, ValueError
+
+description = """
+Interface for non-privileged users to execute the run-mmpol.sh script with elevated permissions. Calls the
+submit-pol-job wrapper
+"""
+
+def parse_args():
+ parser = argparse.ArgumentParser(description=description,
+ formatter_class=argparse.RawTextHelpFormatter
+ )
+ parser.add_argument('-o','--outdir', type=str,
+ help="Directory to store the policy output in",
+ default='/data/rc/gpfs-policy/data')
+ parser.add_argument('-f','--outfile', type=str,
+ help="Base name of the output file. Defaults to 'list-policy_[device-id]' where 'device-id'"
+ "is the device stem when device is a path or just device when it is a fileset. The final"
+ "file name will have the policy type, the job ID, and the run date tagged on the end")
+ parser.add_argument('--with-dirs', action='store_true',
+ help="Include directories as entries in the policy output (Default: false)")
+ sbatch = parser.add_argument_group('sbatch parameters')
+ sbatch.add_argument('-N','--nodes',type=int,default=1,
+ help='Number of nodes to run job across')
+ sbatch.add_argument('-n','--ntasks',type=int,default=16,
+ help='Number of cores to request')
+ sbatch.add_argument('-p','--partition',type=str,default='amd-hdr100,medium',
+ help='Partition to submit job to. Can be a comma-separated list of multiple partitions')
+ sbatch.add_argument('-t','--time',type=str,default='24:00:00',
+ help='Time limit for job formatted as [D-]HH:MM:SS')
+ sbatch.add_argument('-m','--mem-per-cpu',type=str,default='8G',
+ help='Amount of RAM to allocate per core')
+ parser.add_argument('device',type=str,
+ help="GPFS fileset/directory apply the policy to. Can be specified as either the name of the"
+ "fileset or the full path to the directory. (Examples: scratch, /data/user/[username])')")
+ args = parser.parse_args()
+ return args
+
+# Validate that the string supplied to 'device' is either the name of a valid, predefined fileset (only 'scratch'
+# for now) or is a valid path in GPFS. Will not accept 'data' alone. Only valid top-levels in /data are /data/user,
+# /home, and /data/project
+def validate_device(device):
+ device = device.strip()
+ if device in ['data','/data']:
+ raise InvalidDeviceError("A policy run cannot be performed on the full 'data' fileset. Choose a valid subdirectory such as '/data/user' or '/data/project'")
+
+ if device in ['scratch','home']:
+ return Path('/').joinpath(device).resolve()
+
+ if device in ['/scratch','/home','/data/user','/data/project']:
+ return Path(device).resolve()
+
+ p = Path(device).resolve() # resolve given path into absolute path
+
+ # check if p is a valid path and is located in /data or /scratch. If not, raise an exception
+ valid_parents = [Path(parent).resolve() for parent in ['/data','/home','/scratch']]
+ if p.exists() and any([parent in p.parents for parent in valid_parents]):
+ return p
+ else:
+ raise InvalidDeviceError('The path or fileset must be within /data or /scratch')
+
+def validate_time(time):
+ if not re.match(r'^(?:[0-6]-\d{2}|\d{1,3}):\d{2}:\d{2}$',time):
+ raise ValueError("Time must have format [[H]H]H:MM:SS or D-HH:MM:SS")
+
+def validate_mem(mem):
+ if not re.match(r'[\d]+[GM]?', mem):
+ raise ValueError("Mem per CPU must be an integer. May be followed by M or G to denote units")
+
+def validate_partition(partition):
+ if len(partition.split('\s')) > 1 and not re.search(',',partition):
+ raise ValueError("Multiple partitions should be given as a comma-separated list")
+
+ partition = re.sub(r'\s',r'',partition)
+ partitions = [partition.split(r',')]
+ cmd=r'sinfo -h -o "%R"'
+ avail_partitions=subprocess.run(cmd, shell=True, stdout=subprocess.PIPE, text=True).stdout.splitlines()
+
+ if ([p for p in partitions if p not in avail_partitions]):
+ incorrect = [p for p in partitions if p not in avail_partitions]
+ raise ValueError(f"The following partition(s) do not exist: {', '.join(incorrect)}. To see a list of valid partitions, visit https://rc.uab.edu/")
+
+ return partition
+
+def validate_nodes(n):
+ if not isinstance(n,int) and n >= 1 and n <= 4:
+ raise ValueError('Nodes must be an integer between 1 and 4')
+
+def validate_ntasks(n):
+ if not isinstance(n,int) and n >= 1 and n <= 48:
+ raise ValueError('Ntasks must be an integer between 1 and 48')
+
+def validate_sbatch_options(args):
+ validate_nodes(args['nodes'])
+ validate_ntasks(args['ntasks'])
+ validate_mem(args['mem_per_cpu'])
+ validate_time(args['time'])
+ args['partition'] = validate_partition(args['partition'])
+ return args
+
+# Need to validate that the output directory exists. This will not create a directory that does not already exist.
+def validate_output_directory(outdir):
+ p = Path(outdir).resolve()
+
+ if not p.is_dir():
+ raise ValueError(f"{p} is not a valid output directory")
+ return p
+
+def create_default_outfile(device):
+ if device.match('/data/user'):
+ outfile = 'list-policy_data_user'
+ else:
+ outfile = f'list-policy_{device.stem}'
+ return outfile
+
+def main():
+ args = parse_args()
+ args_dict = vars(args)
+
+ args['device'] = validate_device(args['device'])
+
+ sbatch_args = {(k,v) for k,v in args_dict.items() if k in ['nodes','ntasks','partition','time','mem_per_cpu'] and v is not None}
+ sbatch_args = validate_sbatch_options(sbatch_args)
+
+ args['outdir'] = validate_output_directory(args['outdir'])
+
+ if 'outfile' not in args.keys():
+ args['outfile'] = create_default_outfile(args['device'])
+
+ cmd = f"./submit-pol-job "
+
+ exit()
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
--
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