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address pio issues #4925

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1679740
address pio issues
jedwards4b Jan 30, 2026
3f41b69
Update CIME/XML/env_run.py
jedwards4b Feb 2, 2026
5882bd5
Update CIME/XML/env_run.py
jedwards4b Feb 2, 2026
4c84023
Update CIME/case/preview_namelists.py
jedwards4b Feb 2, 2026
20ffc33
Update CIME/case/preview_namelists.py
jedwards4b Feb 2, 2026
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41 changes: 41 additions & 0 deletions CIME/XML/env_run.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
"""
Interface to the env_run.xml file. This class inherits from EnvBase
"""
from itertools import zip_longest
from CIME.XML.standard_module_setup import *

from CIME.XML.env_base import EnvBase
Expand Down Expand Up @@ -66,5 +67,45 @@ def set_value(self, vid, value, subgroup=None, ignore_type=False):
self._pio_async_interface[comp] = convert_to_type(
value, "logical", vid
)
# PIO_NETCDF_FORMAT=64bit_data is not compatible with PIO_TYPENAME=netcdf4p
# make sure that this combination of options is not set
if "PIO_TYPENAME" in vid or "PIO_NETCDF_FORMAT" in vid:
nvid, comp, iscompvar = self.check_if_comp_var(vid, None)
pio_netcdf_formats = []
pio_typenames = []

if nvid == "PIO_TYPENAME":
if comp:
pio_netcdf_formats = [
self.get_value("PIO_NETCDF_FORMAT_{}".format(comp.upper()))
]
else:
pio_netcdf_formats = self.get_values("PIO_NETCDF_FORMAT")
pio_typenames = [value]
elif nvid == "PIO_NETCDF_FORMAT":
if comp:
pio_typenames = [
self.get_value("PIO_TYPENAME_{}".format(comp.upper()))
]
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Copilot AI Jan 30, 2026

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If get_value() returns None (which can happen if the entry is not found), this will create a list containing None [None]. Later when the validation tries to check "64bit_data" in pio_netcdf_format (line 105), it will raise a TypeError because the in operator cannot be used with None. Consider adding a check to handle the case where get_value returns None, or provide a default value.

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else:
pio_typenames = self.get_values("PIO_TYPENAME")
pio_netcdf_formats = [value]

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This code will raise an IndexError if either pio_netcdf_formats or pio_typenames is an empty list, since it tries to access [-1] index. This could happen if get_values() returns an empty list when the variable is not found or has no values. Consider adding a check to ensure the lists are not empty before accessing the last element, or handle the case where no values are found.

Suggested change
# If either list is empty, we cannot perform a meaningful compatibility
# check. In that case, skip the check and proceed with setting the value.
if not pio_netcdf_formats or not pio_typenames:
return EnvBase.set_value(self, vid, value, subgroup, ignore_type)

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last_format = pio_netcdf_formats[-1]
last_typename = pio_typenames[-1]
for pio_typename, pio_netcdf_format in zip_longest(
pio_typenames, pio_netcdf_formats
):
if pio_typename is None:
pio_typename = last_typename
if pio_netcdf_format is None:
pio_netcdf_format = last_format

expect(
not ("4" in pio_typename and "64bit_data" in pio_netcdf_format),
"pio_typename {} is not compatible with pio_netcdf_format {}".format(
pio_typename, pio_netcdf_format
),
)
Comment on lines +72 to +119
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The new validation logic for incompatible PIO_TYPENAME and PIO_NETCDF_FORMAT combinations lacks test coverage. Given that this repo has comprehensive automated testing (as seen in the CIME/tests directory), consider adding unit tests to verify that:

  1. The validation correctly prevents setting netcdf4p/netcdf4c with 64bit_data format
  2. The validation works for both component-specific and general PIO settings
  3. Edge cases like None values or empty lists are handled properly
  4. The validation allows valid combinations to pass through

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return EnvBase.set_value(self, vid, value, subgroup, ignore_type)
6 changes: 4 additions & 2 deletions CIME/build_scripts/buildlib.pio
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Original file line number Diff line number Diff line change
Expand Up @@ -191,9 +191,9 @@ def buildlib(bldroot, installpath, case):
installed_file_time = os.path.getmtime(installed_file)
if item_time > installed_file_time:
safe_copy(item, installed_file)
expect_string = "NetCDF_C_LIBRARY-ADVANCED"
expect_string = "NetCDF_C_FOUND:BOOL=TRUE"
pnetcdf_string = "WITH_PNETCDF:BOOL=ON"
netcdf4_string = "NetCDF_C_HAS_PARALLEL:BOOL=TRUE"
netcdf4_string = "HAVE_NETCDF_PAR:INTERNAL=1"

# make sure case pio_typename valid_values is set correctly
expect_string_found = False
Expand All @@ -204,6 +204,8 @@ def buildlib(bldroot, installpath, case):
for line in cache_file:
if re.search(expect_string, line):
expect_string_found = True
elif re.search("NetCDF_C_LIBRARY-ADVANCED", line):
expect_string_found = True
if re.search(pnetcdf_string, line):
pnetcdf_found = True
if re.search(netcdf4_string, line):
Expand Down
11 changes: 10 additions & 1 deletion CIME/case/preview_namelists.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,16 @@ def create_namelists(self, component=None):
compname,
case=self,
)

pio_typename = self.get_value("PIO_TYPENAME_{}".format(model_str.upper()))
pio_netcdf_format = self.get_value(
"PIO_NETCDF_FORMAT_{}".format(model_str.upper())
)
expect(
not ("4" in pio_typename and pio_netcdf_format == "64bit_data"),
"Cannot use pio_netcdf_format {} with pio_typename {}".format(
pio_netcdf_format, pio_typename
),
)
logger.debug(
"Finished creating component namelists, component {} models = {}".format(
component, models
Expand Down
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