Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

move case clone to its own file #1879

Merged
merged 1 commit into from
Sep 11, 2017
Merged

move case clone to its own file #1879

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
140 changes: 1 addition & 139 deletions scripts/lib/CIME/case.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
through the Case module.
"""
from copy import deepcopy
import glob, os, shutil, math, string
import glob, os, shutil, math
from CIME.XML.standard_module_setup import *

from CIME.utils import expect, get_cime_root, append_status
Expand All @@ -32,8 +32,6 @@
from CIME.XML.env_batch import EnvBatch
from CIME.XML.generic_xml import GenericXML
from CIME.user_mod_support import apply_user_mods
from CIME.simple_compare import compare_files
from CIME.case_setup import case_setup
from CIME.aprun import get_aprun_cmd_for_case

logger = logging.getLogger(__name__)
Expand Down Expand Up @@ -1148,142 +1146,6 @@ def _get_comp_user_mods(self, component):
else:
return comp_user_mods

def create_clone(self, newcase, keepexe=False, mach_dir=None, project=None, cime_output_root=None,
user_mods_dir=None):
"""
Create a case clone
"""
if cime_output_root is None:
cime_output_root = self.get_value("CIME_OUTPUT_ROOT")

newcaseroot = os.path.abspath(newcase)
expect(not os.path.isdir(newcaseroot),
"New caseroot directory {} already exists".format(newcaseroot))
newcasename = os.path.basename(newcaseroot)
newcase_cimeroot = os.path.abspath(get_cime_root())

# create clone from self to case
clone_cimeroot = self.get_value("CIMEROOT")
if newcase_cimeroot != clone_cimeroot:
logger.warning(" case CIMEROOT is {} ".format(newcase_cimeroot))
logger.warning(" clone CIMEROOT is {} ".format(clone_cimeroot))
logger.warning(" It is NOT recommended to clone cases from different versions of CIME.")

# *** create case object as deepcopy of clone object ***
srcroot = os.path.join(newcase_cimeroot,"..")
newcase = self.copy(newcasename, newcaseroot, newsrcroot=srcroot)
newcase.set_value("CIMEROOT", newcase_cimeroot)

# if we are cloning to a different user modify the output directory
olduser = self.get_value("USER")
newuser = os.environ.get("USER")
if olduser != newuser:
cime_output_root = string.replace(cime_output_root, olduser, newuser)
newcase.set_value("USER", newuser)
newcase.set_value("CIME_OUTPUT_ROOT", cime_output_root)

# try to make the new output directory and raise an exception
# on any error other than directory already exists.
if os.path.isdir(cime_output_root):
expect(os.access(cime_output_root, os.W_OK), "Directory {} is not writable"
"by this user. Use the --cime-output-root flag to provide a writable "
"scratch directory".format(cime_output_root))
else:
try:
os.makedirs(cime_output_root)
except:
if not os.path.isdir(cime_output_root):
raise

# determine if will use clone executable or not
if keepexe:
orig_exeroot = self.get_value("EXEROOT")
newcase.set_value("EXEROOT", orig_exeroot)
newcase.set_value("BUILD_COMPLETE","TRUE")
orig_bld_complete = self.get_value("BUILD_COMPLETE")
if not orig_bld_complete:
logger.warn("\nWARNING: Creating a clone with --keepexe before building the original case may cause PIO_TYPENAME to be invalid in the clone")
logger.warn("Avoid this message by building case one before you clone.\n")
else:
newcase.set_value("BUILD_COMPLETE","FALSE")

# set machdir
if mach_dir is not None:
newcase.set_value("MACHDIR", mach_dir)

# Set project id
# Note: we do not just copy this from the clone because it seems likely that
# users will want to change this sometimes, especially when cloning another
# user's case. However, note that, if a project is not given, the fallback will
# be to copy it from the clone, just like other xml variables are copied.
if project is None:
project = self.get_value("PROJECT", subgroup="case.run")
if project is not None:
newcase.set_value("PROJECT", project)

# create caseroot
newcase.create_caseroot(clone=True)
newcase.flush(flushall=True)

# copy user_ files
cloneroot = self._caseroot
files = glob.glob(cloneroot + '/user_*')

for item in files:
shutil.copy(item, newcaseroot)

# copy SourceMod and Buildconf files
# if symlinks exist, copy rather than follow links
for casesub in ("SourceMods", "Buildconf"):
shutil.copytree(os.path.join(cloneroot, casesub),
os.path.join(newcaseroot, casesub),
symlinks=True)

# lock env_case.xml in new case
lock_file("env_case.xml", newcaseroot)

# apply user_mods if appropriate
newcase_root = newcase.get_value("CASEROOT")
if user_mods_dir is not None:
if keepexe:
# If keepexe CANNOT change any env_build.xml variables - so make a temporary copy of
# env_build.xml and verify that it has not been modified
shutil.copy(os.path.join(newcaseroot, "env_build.xml"),
os.path.join(newcaseroot, "LockedFiles", "env_build.xml"))

# Now apply contents of user_mods directory
apply_user_mods(newcase_root, user_mods_dir, keepexe=keepexe)

# Determine if env_build.xml has changed
if keepexe:
success, comment = compare_files(os.path.join(newcaseroot, "env_build.xml"),
os.path.join(newcaseroot, "LockedFiles", "env_build.xml"))
if not success:
logger.warn(comment)
shutil.rmtree(newcase_root)
expect(False, "env_build.xml cannot be changed via usermods if keepexe is an option: \n "
"Failed to clone case, removed {}\n".format(newcase_root))

# if keep executable, then remove the new case SourceMods directory and link SourceMods to
# the clone directory
if keepexe:
shutil.rmtree(os.path.join(newcase_root, "SourceMods"))
os.symlink(os.path.join(cloneroot, "SourceMods"),
os.path.join(newcase_root, "SourceMods"))

# Update README.case
fclone = open(cloneroot + "/README.case", "r")
fnewcase = open(newcaseroot + "/README.case", "a")
fnewcase.write("\n *** original clone README follows ****")
fnewcase.write("\n " + fclone.read())

clonename = self.get_value("CASE")
logger.info(" Successfully created new case {} from clone case {} ".format(newcasename, clonename))

case_setup(newcase)

return newcase

def submit_jobs(self, no_batch=False, job=None, skip_pnl=False,
mail_user=None, mail_type='never', batch_args=None,
dry_run=False):
Expand Down
146 changes: 146 additions & 0 deletions scripts/lib/CIME/case_clone.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,146 @@
import os, glob, shutil, string
from CIME.XML.standard_module_setup import *
from CIME.utils import expect
from CIME.user_mod_support import apply_user_mods
from CIME.check_lockedfiles import lock_file
from CIME.case_setup import case_setup
from CIME.simple_compare import compare_files

logger = logging.getLogger(__name__)


def create_clone(case, newcase, keepexe=False, mach_dir=None, project=None, cime_output_root=None,
user_mods_dir=None):
"""
Create a case clone
"""
if cime_output_root is None:
cime_output_root = case.get_value("CIME_OUTPUT_ROOT")

newcaseroot = os.path.abspath(newcase)
expect(not os.path.isdir(newcaseroot),
"New caseroot directory {} already exists".format(newcaseroot))
newcasename = os.path.basename(newcaseroot)
newcase_cimeroot = os.path.abspath(get_cime_root())

# create clone from case to case
clone_cimeroot = case.get_value("CIMEROOT")
if newcase_cimeroot != clone_cimeroot:
logger.warning(" case CIMEROOT is {} ".format(newcase_cimeroot))
logger.warning(" clone CIMEROOT is {} ".format(clone_cimeroot))
logger.warning(" It is NOT recommended to clone cases from different versions of CIME.")

# *** create case object as deepcopy of clone object ***
srcroot = os.path.join(newcase_cimeroot,"..")
newcase = case.copy(newcasename, newcaseroot, newsrcroot=srcroot)
newcase.set_value("CIMEROOT", newcase_cimeroot)

# if we are cloning to a different user modify the output directory
olduser = case.get_value("USER")
newuser = os.environ.get("USER")
if olduser != newuser:
cime_output_root = string.replace(cime_output_root, olduser, newuser)
newcase.set_value("USER", newuser)
newcase.set_value("CIME_OUTPUT_ROOT", cime_output_root)

# try to make the new output directory and raise an exception
# on any error other than directory already exists.
if os.path.isdir(cime_output_root):
expect(os.access(cime_output_root, os.W_OK), "Directory {} is not writable"
"by this user. Use the --cime-output-root flag to provide a writable "
"scratch directory".format(cime_output_root))
else:
try:
os.makedirs(cime_output_root)
except:
if not os.path.isdir(cime_output_root):
raise

# determine if will use clone executable or not
if keepexe:
orig_exeroot = case.get_value("EXEROOT")
newcase.set_value("EXEROOT", orig_exeroot)
newcase.set_value("BUILD_COMPLETE","TRUE")
orig_bld_complete = case.get_value("BUILD_COMPLETE")
if not orig_bld_complete:
logger.warn("\nWARNING: Creating a clone with --keepexe before building the original case may cause PIO_TYPENAME to be invalid in the clone")
logger.warn("Avoid this message by building case one before you clone.\n")
else:
newcase.set_value("BUILD_COMPLETE","FALSE")

# set machdir
if mach_dir is not None:
newcase.set_value("MACHDIR", mach_dir)

# Set project id
# Note: we do not just copy this from the clone because it seems likely that
# users will want to change this sometimes, especially when cloning another
# user's case. However, note that, if a project is not given, the fallback will
# be to copy it from the clone, just like other xml variables are copied.
if project is None:
project = case.get_value("PROJECT", subgroup="case.run")
if project is not None:
newcase.set_value("PROJECT", project)

# create caseroot
newcase.create_caseroot(clone=True)
newcase.flush(flushall=True)

# copy user_ files
cloneroot = case.get_case_root()
files = glob.glob(cloneroot + '/user_*')

for item in files:
shutil.copy(item, newcaseroot)

# copy SourceMod and Buildconf files
# if symlinks exist, copy rather than follow links
for casesub in ("SourceMods", "Buildconf"):
shutil.copytree(os.path.join(cloneroot, casesub),
os.path.join(newcaseroot, casesub),
symlinks=True)

# lock env_case.xml in new case
lock_file("env_case.xml", newcaseroot)

# apply user_mods if appropriate
newcase_root = newcase.get_value("CASEROOT")
if user_mods_dir is not None:
if keepexe:
# If keepexe CANNOT change any env_build.xml variables - so make a temporary copy of
# env_build.xml and verify that it has not been modified
shutil.copy(os.path.join(newcaseroot, "env_build.xml"),
os.path.join(newcaseroot, "LockedFiles", "env_build.xml"))

# Now apply contents of user_mods directory
apply_user_mods(newcase_root, user_mods_dir, keepexe=keepexe)

# Determine if env_build.xml has changed
if keepexe:
success, comment = compare_files(os.path.join(newcaseroot, "env_build.xml"),
os.path.join(newcaseroot, "LockedFiles", "env_build.xml"))
if not success:
logger.warn(comment)
shutil.rmtree(newcase_root)
expect(False, "env_build.xml cannot be changed via usermods if keepexe is an option: \n "
"Failed to clone case, removed {}\n".format(newcase_root))

# if keep executable, then remove the new case SourceMods directory and link SourceMods to
# the clone directory
if keepexe:
shutil.rmtree(os.path.join(newcase_root, "SourceMods"))
os.symlink(os.path.join(cloneroot, "SourceMods"),
os.path.join(newcase_root, "SourceMods"))

# Update README.case
fclone = open(cloneroot + "/README.case", "r")
fnewcase = open(newcaseroot + "/README.case", "a")
fnewcase.write("\n *** original clone README follows ****")
fnewcase.write("\n " + fclone.read())

clonename = case.get_value("CASE")
logger.info(" Successfully created new case {} from clone case {} ".format(newcasename, clonename))

case_setup(newcase)

return newcase