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Merged
zaihuaji merged 1 commit into from
Jan 8, 2026
Merged

save #10

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34 changes: 16 additions & 18 deletions src/rda_python_miscs/bashqsub.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,26 +20,25 @@ class BashQsub(PgLOG):
def __init__(self):
super().__init__()
self.DEFMODS = {
'default' : "ncarenv,netcdf,ncl,nco,cdo,conda,grib-util,wgrib2",
'default': "ncarenv,netcdf,ncl,nco,cdo,conda,grib-util,wgrib2"
}
self.DEFLIBS = {
'default' : "conda activate /glade/work/gdexdata/conda-envs/pg-gdex",
}
self.SWAPMODS = {
'default': "conda activate /glade/work/gdexdata/conda-envs/pg-gdex"
}
self.SWAPMODS = {}
self.RESOURCES = { # resource list for option -l
'walltime' : '6:00:00', # if this is changed, change defpbstime in PgCheck.py too
'select' : '1:ncpus=1:mem=1gb'
'walltime': '6:00:00', # if this is changed, change defpbstime in PgCheck.py too
'select': '1:ncpus=1:mem=1gb'
}
self.SOPTIONS = { # single-dash option values
'o' : None, # will set to default if not provided
'e' : None,
'A' : "P43713000",
'q' : "gdex@casper-pbs",
# 'm' : 'a',
'm' : 'n',
'o': None, # will set to default if not provided
'e': None,
'A': "P43713000",
'q': "gdex@casper-pbs",
# 'm': 'a',
'm': 'n',
}
self.coptions = {'cmd' : None, 'cwd' : None, 'env' : None, 'mod' : None, 'res' : 'default'} # customized options
self.coptions = {'cmd': None, 'cwd': None, 'env': None, 'mod': None, 'res': 'default'} # customized options
self.gdexsub = self.BCHCMDS['PBS']
self.args = None

Expand All @@ -50,7 +49,6 @@ def read_parameters(self):
self.set_help_path(__file__)
copts = '|'.join(self.coptions)
option = None
dcount = 0
argv = sys.argv[1:]
if not argv: self.show_usage(aname)
self.PGLOG['LOGFILE'] = pname + ".log"
Expand Down Expand Up @@ -92,7 +90,7 @@ def read_parameters(self):
if self.coptions['cwd']:
if 's' in self.coptions['cwd']: self.coptions['cwd'] = self.replace_environments(self.coptions['cwd'], '', self.LGWNEX)
os.chdir(self.coptions['cwd'])

# function to start actions
def start_actions(self):
cmd = self.valid_command(self.coptions['cmd'])
Expand Down Expand Up @@ -129,7 +127,7 @@ def build_bash_script(self, cmd):
buf += self.set_vm_libs(self.coptions['res'])
buf += "\necho {}\n{}\n\ndate\n".format(cmd, cmd)
return buf

# check and add resource options
def add_resources(self):
for res in re.split(',', self.SOPTIONS['l']):
Expand All @@ -139,7 +137,7 @@ def add_resources(self):
else:
self.pglog(res + ": use '=' to separate resource name & value", self.LGEREX)
del self.SOPTIONS['l']

# add module loads for modules provided
def add_modules(self, res, mods):
mbuf = "\n"
Expand All @@ -162,7 +160,7 @@ def add_modules(self, res, mods):
if smod in self.SWAPMODS: mbuf += "module unload {}\n".format(self.SWAPMODS[smod])
mbuf += "module load {}\n".format(amod)
return mbuf

# set virtual machine libraries
def set_vm_libs(self, res):
deflibs = self.DEFLIBS[res] if res in self.DEFLIBS else self.DEFLIBS['default']
Expand Down
36 changes: 18 additions & 18 deletions src/rda_python_miscs/gdexls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,24 +27,24 @@ def __init__(self):
self.WIDTHS = [0, 0, 0] # WIDTHS for formated display
self.ALIGNS = [0, 1, 1] # alignment, 0 - left; 1 - right
self.GDEXLS = {
'd' : 0, # 1 to list directory information only
'f' : 0, # 1 to list file information only
'N' : 0, # 1 to list files unformatted
'r' : 0, # 1 if recursive all
'R' : 0, # > 0 to set recursive limit
'D' : None, # specify delimiting symbols, default to ' '
'd': 0, # 1 to list directory information only
'f': 0, # 1 to list file information only
'N': 0, # 1 to list files unformatted
'r': 0, # 1 if recursive all
'R': 0, # > 0 to set recursive limit
'D': None, # specify delimiting symbols, default to ' '
}
self.LINFO = {
'files' : [],
'curdir' : None,
'tpath' : None,
'dhome' : None,
'dsid' : None,
'dcnt' : 0,
'gcnt' : 0,
'fcnt' : 0,
'pcnt' : 0,
'pgrecs' : []
'files': [],
'curdir': None,
'tpath': None,
'dhome': None,
'dsid': None,
'dcnt': 0,
'gcnt': 0,
'fcnt': 0,
'pcnt': 0,
'pgrecs': []
}

# function to read parameters
Expand Down Expand Up @@ -75,7 +75,7 @@ def read_parameters(self):
else:
self.GDEXLS[option] = arg
option = defopt

# functio to start actions
def start_actions(self):
self.view_dbinfo()
Expand Down Expand Up @@ -149,7 +149,7 @@ def display_line(self, file, isdir):
getwfile = 0
if getwfile:
self.LINFO['dsid'] = self.find_dataset_id(file)
if self.LINFO['dsid'] == None: return # skip for missing dsid
if self.LINFO['dsid'] is None: return # skip for missing dsid
pgrec = self.pgget("dataset", "title, (dwebcnt + nwebcnt) nc, (dweb_size + nweb_size) ns", "dsid = '{}'".format(self.LINFO['dsid']), self.LGEREX)
if not pgrec: return None
self.LINFO['dhome'] = "{}/{}".format(self.PGLOG['DSDHOME'], self.LINFO['dsid'])
Expand Down
42 changes: 21 additions & 21 deletions src/rda_python_miscs/rdacp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,29 +19,29 @@ class RdaCp(PgFile):
def __init__(self):
super().__init__()
self.RDACP = {
'fh' : None, # from host name, default to localhost
'th' : None, # to host name, defaul to localhost
'fb' : None, # from bucket name for a from file in Object Store
'tb' : None, # to bucket name for a to file in Object Store
'fp' : None, # from Globus endpoint
'tp' : None, # to Globus endpoint
'f' : [], # from file names
't' : None, # to file name
'r' : 0, # 1 if recursive all
'R' : 0, # > 0 to set recursive limit
'F' : 0o664, # to file mode, default to 664
'D' : 0o775, # to directory mode, default to 775
'fh': None, # from host name, default to localhost
'th': None, # to host name, defaul to localhost
'fb': None, # from bucket name for a from file in Object Store
'tb': None, # to bucket name for a to file in Object Store
'fp': None, # from Globus endpoint
'tp': None, # to Globus endpoint
'f': [], # from file names
't': None, # to file name
'r': 0, # 1 if recursive all
'R': 0, # > 0 to set recursive limit
'F': 0o664, # to file mode, default to 664
'D': 0o775, # to directory mode, default to 775
}
self.CINFO = {
'tcnt' : 0,
'htcnt' : 0,
'cpflag' : 0, # 1 file only, 2 directory only, 3 both
'cpstr' : ['', 'Files', 'Directories', 'Files/Directories'],
'fpath' : None,
'tpath' : None,
'fhost' : '',
'thost' : '',
'curdir' : os.getcwd()
'tcnt': 0,
'htcnt': 0,
'cpflag': 0, # 1 file only, 2 directory only, 3 both
'cpstr': ['', 'Files', 'Directories', 'Files/Directories'],
'fpath': None,
'tpath': None,
'fhost': '',
'thost': '',
'curdir': os.getcwd()
}

# function to read parameters
Expand Down
18 changes: 9 additions & 9 deletions src/rda_python_miscs/rdakill.py
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Expand Up @@ -19,14 +19,14 @@ class RdaKill(PgFile):
def __init__(self):
super().__init__()
self.RDAKILL = {
'a' : None, # application name
'h' : None, # hostname
'p' : 0, # process id to be killed
'P' : 0, # parent pid
'r' : 0, # 1 - reserved for exclusive, working with -s PEND only
'u' : None, # login user name
's' : None, # batch status to kill
'q' : None # batch partition/queue for SLURM/PBS, rda for default
'a': None, # application name
'h': None, # hostname
'p': 0, # process id to be killed
'P': 0, # parent pid
'r': 0, # 1 - reserved for exclusive, working with -s PEND only
'u': None, # login user name
's': None, # batch status to kill
'q': None # batch partition/queue for SLURM/PBS, rda for default
}

# function to read parameters
Expand Down Expand Up @@ -217,7 +217,7 @@ def rdakill_pbs_status(self, stat, queue, uname):
def record_dscheck_interrupt(self, pid, host):
pgrec = self.pgget("dscheck", "cindex", "pid = {} AND hostname = '{}'".format(pid, host), self.LOGERR)
if pgrec:
record = {'chktime' : int(time.time()), 'status' : 'I', 'pid' : 0} # release lock
record = {'chktime': int(time.time()), 'status': 'I', 'pid': 0} # release lock
self.pgupdt("dscheck", record, "cindex = {}".format(pgrec['cindex']), self.LGEREX)

# main function to excecute this script
Expand Down
24 changes: 12 additions & 12 deletions src/rda_python_miscs/rdamod.py
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Expand Up @@ -20,20 +20,20 @@ class RdaMod(PgFile):
def __init__(self):
super().__init__()
self.RDAMOD = {
'd' : 0, # 1 to change directory mode
'f' : 0, # 1 to change file mode
'h' : 0, # 1 to show help message
'r' : 0, # 1 if recursive all
'R' : 0, # > 0 to set recursive limit
'F' : 0o664, # to chnage file mode, default to 664
'D' : 0o775, # to chnge directory mode, default to 775
'd': 0, # 1 to change directory mode
'f': 0, # 1 to change file mode
'h': 0, # 1 to show help message
'r': 0, # 1 if recursive all
'R': 0, # > 0 to set recursive limit
'F': 0o664, # to chnage file mode, default to 664
'D': 0o775, # to chnge directory mode, default to 775
}
self.MINFO = {
'files' : [],
'curdir' : os.getcwd(),
'tpath' : None,
'dcnt' : 0,
'fcnt' : 0
'files': [],
'curdir': os.getcwd(),
'tpath': None,
'dcnt': 0,
'fcnt': 0
}

# function to read parameters
Expand Down
24 changes: 12 additions & 12 deletions src/rda_python_miscs/rdaown.py
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Expand Up @@ -22,20 +22,20 @@ class RdaOwn(PgFile):
def __init__(self):
super().__init__()
self.RDAOWN = {
'd' : 0, # 1 to change directory owner
'f' : 0, # 1 to change file owner
'h' : 0, # 1 to show help message
'r' : 0, # 1 if recursive all
'R' : 0, # > 0 to set recursive limit
'F' : 0o664, # to change file mode, default to 664
'D' : 0o775, # to change directory mode, default to 775
'd': 0, # 1 to change directory owner
'f': 0, # 1 to change file owner
'h': 0, # 1 to show help message
'r': 0, # 1 if recursive all
'R': 0, # > 0 to set recursive limit
'F': 0o664, # to change file mode, default to 664
'D': 0o775, # to change directory mode, default to 775
}
self.OINFO = {
'files' : [],
'curdir' : os.getcwd(),
'tpath' : None,
'dcnt' : 0,
'fcnt' : 0
'files': [],
'curdir': os.getcwd(),
'tpath': None,
'dcnt': 0,
'fcnt': 0
}

# function to read paramters
Expand Down
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