cape.cfdx.options.pbs: PBS script options

This portion of the options is universal, and so it is only encoded in the cape module. The cape.pycart module, for example, does not have a modified version. It contains options for specifying which architecture to use, how many nodes to request, etc.

class cape.cfdx.options.pbs.PBS

Dictionary-based options for PBS jobs

Call:

>>> opts = PBS(**kw)

Inputs:

kw: dict

Dictionary of PBS options

Outputs:

opts: cape.options.pbs.PBS

PBS options interface

Versions:

• 2014-12-01 @ddalle: First version

get_PBS_A(i=None)

Return PBS A setting, usually for “account”

Call:

>>> A = opts.get_PBS_A(i=None)

Inputs:

opts: cape.cfdx.options.Options

Options interface

i: {None} | int

Phase number

Outputs:

A: str

Account name

Versions:

• 2023-06-14 @ddalle: v1.0

get_PBS_S(i=None)

Return the PBS S setting, which determines the shell

Call:

>>> r = opts.get_PBS_S(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

S: str

PBS shell setting; '/bin/bash' in most cases

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_W(i=None)

Return PBS W setting, usually for setting groups

Call:

>>> W = opts.get_PBS_W(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

W: str

PBS W setting; usually 'group_list=$grp'

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_aoe(i=None)

Return the PBS operating environment

Call:

>>> s = opts.get_PBS_model(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

s: str

Name of (alternate) operating environment to use

Versions:

• 2017-04-05 @ddalle: First version

get_PBS_e(i=None)

Return the explicit STDERR file

Call:

>>> e = opts.get_PBS_o(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

e: str

PBS e setting; explicit STDERR file

Versions:

• 2017-01-11 @ddalle: First version

get_PBS_j(i=None)

Return the PBS j setting, which can be used to join STDIO and STDERR into a single file.

Call:

>>> j = opts.get_PBS_j(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

j: str

PBS j setting; 'oe' to join outputs

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_model(i=None)

Return the PBS model/architecture

Call:

>>> s = opts.get_PBS_model(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

s: str

Name of architecture/model to use

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_mpiprocs(i=None)

Return the number of CPUs per node

Call:

>>> n = opts.get_PBS_ncpus(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

n: int

PBS number of MPI processes per node

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_ncpus(i=None)

Return the number of CPUs per node

Call:

>>> n = opts.get_PBS_ncpus(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

n: int

PBS number of CPUs per node

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_o(i=None)

Return the explicit STDOUT file

Call:

>>> o = opts.get_PBS_o(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

o: str

PBS o setting; explicit STDOUT file

Versions:

• 2017-01-11 @ddalle: First version

get_PBS_ompthreads(i=None)

Return number of OMP threads

Call:

>>> n = opts.get_PBS_ompthreads(i=None)

Inputs:

opts: cape.options.Options

Options interface

i: {None} | int

Phase number

Outputs:

n: None | int

Number of OMP threads to select

Versions:

• 2017-05-01 @ddalle: First version

get_PBS_p(i=None)

Return the PBS priority

Call:

>>> p = opts.get_PBS_p(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

p: int

PBS priority level

Versions:

• 2017-05-30 @ddalle: First version

get_PBS_q(i=None)

Return PBS queue

Call:

>>> q = opts.get_PBS_q()

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

q: str

Name of PBS queue to submit to

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_r(i=None)

Return the PBS r setting, which determines if a job can be rerun

Call:

>>> r = opts.get_PBS_r(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

r: str

PBS r setting; 'n' for non-rerunable

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_select(i=None)

Return the number of nodes

Call:

>>> n = opts.get_PBS_select(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

n: int

PBS number of nodes

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_PBS_walltime(i=None)

Return maximum wall time

Call:

>>> t = opts.get_PBS_walltime(i)

Inputs:

opts: cape.options.Options

Options interface

i: int or None

Index to select

Outputs:

t: str

Maximum wall clock time (e.g. '8:00:00')

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

get_nPBS()

Return the maximum number of unique PBS inputs

For example, if a case is set up to be run in two parts, and the first phase needs only one node (select=1) while the second phase needs 10 nodes (select=10), then the input file should have "select": [1, 10], and the output of this function will be 2.

Call:

>>> n = opts.get_nPBS()

Inputs:

opts: cape.options.Options

Options interface

Outputs:

n: int

Number of unique PBS scripts

Versions:

• 2014-12-01 @ddalle: First version

set_PBS_A(A, i=None)

Set PBS A setting, usually for account

Call:

>>> opts.set_PBS_A(A, i=None)

Inputs:

opts: cape.cfdx.options.Options

Options interface

A: str

Account name

i: {None} | int

Phase number

Versions:

• 2023-06-14 @ddalle: v1.0

set_PBS_S(S='/bin/bash', i=None)

Set the PBS S setting, which determines the shell

Call:

>>> opts.set_PBS_S(S, i=None)

Inputs:

opts: cape.options.Options

Options interface

S: str

PBS shell setting; '/bin/bash' in most cases

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_W(W='', i=None)

Set PBS W setting, usually for setting groups

Call:

>>> opts.set_PBS_W(W, i=None)

Inputs:

opts: cape.options.Options

Options interface

W: str

PBS W setting; usually 'group_list=$grp'

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_aoe(s=None, i=None)

Set the PBS model/architecture

Call:

>>> opts.set_PBS_aoe(s, i=None)

Inputs:

opts: cape.options.Options

Options interface

s: str

Name of (alternate) operating environment to use

i: int or None

Index to select

Versions:

• 2017-04-05 @ddalle: First version

set_PBS_e(e=None, i=None)

Set PBS file for STDERR

Call:

>>> opts.set_PBS_e(e, i=None)

Inputs:

opts: cape.options.Options

Options interface

e: str

PBS o setting; explicit STDERR file

i: int or None

Index to select

Versions:

• 2017-01-11 @ddalle: First version

set_PBS_j(j='oe', i=None)

Set PBS join setting

Call:

>>> opts.set_PBS_j(j, i=None)

Inputs:

opts: cape.options.Options

Options interface

j: str

PBS j setting; 'oe' to join outputs

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_model(s='ivy', i=None)

Set the PBS model/architecture

Call:

>>> opts.set_PBS_model(s, i=None)

Inputs:

opts: cape.options.Options

Options interface

s: str

Name of architecture/model to use

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_mpiprocs(n=20, i=None)

Set PBS number of cpus per node

Call:

>>> opts.set_PBS_ncpus(n, i=None)

Inputs:

opts: cape.options.Options

Options interface

n: int

PBS number of MPI processes per node

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_ncpus(n=20, i=None)

Set PBS number of CPUs per node

Call:

>>> opts.set_PBS_ncpus(n, i=None)

Inputs:

opts: cape.options.Options

Options interface

n: int

PBS number of CPUs per node

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_o(o=None, i=None)

Set PBS file for STDOUT

Call:

>>> opts.set_PBS_o(o, i=None)

Inputs:

opts: cape.options.Options

Options interface

o: str

PBS o setting; explicit STDOUT file

i: int or None

Index to select

Versions:

• 2017-01-11 @ddalle: First version

set_PBS_ompthreads(n=None, i=None)

Set number of OMP threads

Call:

>>> n = opts.get_PBS_ompthreads(n=None, i=None)

Inputs:

opts: cape.options.Options

Options interface

n: None | int

Number of OMP threads to select

i: {None} | int

Phase number

Versions:

• 2017-05-01 @ddalle: First version

set_PBS_p(p=None, i=None)

Set the PBS priority

Call:

>>> opts.set_PBS_p(p, i=None)

Inputs:

opts: cape.options.Options

Options interface

p: int

PBS priority level

i: int or None

Index to select

Versions:

• 2017-04-05 @ddalle: First version

set_PBS_q(q='normal', i=None)

Set PBS W setting, usually for setting groups

Call:

>>> opts.set_PBS_q(q, i=None)

Inputs:

opts: cape.options.Options

Options interface

q: str

Name of PBS queue to submit to

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_r(r='n', i=None)

Set PBS rerun setting

Call:

>>> opts.set_PBS_r(r, i=None)

Inputs:

opts: cape.options.Options

Options interface

r: str

PBS r setting; 'n' for non-rerunable

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_select(n=1, i=None)

Set PBS join setting

Call:

>>> opts.set_PBS_select(n, i=None)

Inputs:

opts: cape.options.Options

Options interface

n: int

PBS number of nodes

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index

set_PBS_walltime(t='8:00:00', i=None)

Set the maximum wall time

Call:

>>> opts.set_PBS_walltime(t, i=None)

Inputs:

opts: cape.options.Options

Options interface

t: str

Maximum wall clock time (e.g. '8:00:00')

i: int or None

Index to select

Versions:

• 2014-09-29 @ddalle: First version

• 2014-12-01 @ddalle: Added index