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Error in porting CESM2

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fkc000@...
Error in porting CESM2

Hello there, I'm trying to build CESM2 in our server. But I couldn't even creat a new case. 

The result of create_newcase is like below:


./create_newcase --case test --compset FW2000 --res f09_g16 --machine silicon

Compset longname is 2000_CAM60%WCTS_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV

Compset specification file is /public/home/fkc/cesm2/cime/../components/cam//cime_config/config_compsets.xml

Compset forcing is 1972-2004

ATM component is CAM cam6 physics:WACCM with tropospheric, stratospheric, mesospheric, and lower thermospheric chemistry:

LND component is clm5.0:BGC (vert. resol. CN and methane) with prognostic crop:

ICE component is Sea ICE (cice) model version 5 :prescribed cice

OCN component is DOCN   prescribed ocean mode

ROF component is MOSART: MOdel for Scale Adaptive River Transport

GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):

WAV component is Stub wave component

ESP component is 

Pes     specification file is /public/home/fkc/cesm2/cime/../components/cam//cime_config/config_pes.xml

Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1x1_2000climo_c180511.nc

Traceback (most recent call last):

  File "./create_newcase", line 218, in <module>

    _main_func(__doc__)

  File "./create_newcase", line 213, in _main_func

    input_dir=input_dir, driver=driver)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 1431, in create

    input_dir=input_dir, driver=driver)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 808, in configure

    machobj = Machines(machine=machine_name)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/machines.py", line 36, in __init__

    GenericXML.__init__(self, infile, schema)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 57, in __init__

    self.read(infile, schema)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read

    self.read_fd(fd)

  File "/public/home/fkc/cesm2/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 112, in read_fd

    self.tree = ET.parse(fd)

  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/ElementTree.py", line 1182, in parse

    tree.parse(source, parser)

  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/ElementTree.py", line 656, in parse

    parser.feed(data)

  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/ElementTree.py", line 1642, in feed

    self._raiseerror(v)

  File "/public/biosoftware/python/2.7.9/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror

    raise err

xml.etree.ElementTree.ParseError: mismatched tag: line 2313, column 6

 

Besides, when I run query_config and other executables in /scripts, similar errors occured(also traced back to ElementTree.py). So I guess there might be something wrong with my python 2.7, but python seemed work well and I don't know how to fix it. Should I build python2.7 again or a new python3.7?

Thank you in advance!

jedwards

I think that there is a problem with something in your config_machines.xml file - do you have an xmllint program on your system?

CESM Software Engineer

fkc000@...

Thank you for your reply.

Yes, we do have xmllint installed and the version of xmllint is 20908.

And the odd thing is, I got the same error even running query_config. I'm a little confused because running query_config should have nothing to do with config_machine.xml.

jedwards

Query_config does parse the config_machines.xml file - please post that file and I'll try to spot the error.   You can add that file as an attachment here by adding a .txt to the filename.

CESM Software Engineer

fkc000@...

Here's my config_machines.xml, and my machine name is silicon.

Thank you for your reply!

Attachment: 
jedwards

You have an error in this file - you should have seen it with the command 

xmllint --noout --schema $CIMEROOT/config/xml_schemas/config_machines.xsd config_machines.xml

after the <cmd_path> entry you have two <modules> lines in a row, remove one of them.  Then run the xmllint command again to make sure everything is okay.

CESM Software Engineer

fkc000@...

It worked! Thank you very very much!

xueyanzhang520@...

Hi, I have the same error and I use your idea: xmllint --noout --schema $CIMEROOT/config/xml_schemas/config_machines.xsd config_machines.xml to see the error in my config_machines.xml, but I got Segmentation fault (core dumped).

Work hard

xueyanzhang520@...

Hi, I have the same error with you, but when I tried xmllint --noout --schema ../../../config/xml_schemas/config_machines.xsd config_machines.xml --debugent, I met an error: 

new input from file: ../../../config/xml_schemas/config_machines.xsd
Segmentation fault (core dumped)
 How to solve it?

Work hard

jedwards

I'm not sure what the --debugent flag is about.   But you should be able to run the xmllint tool on the unmodified config_machines.xml file.   

Then add a little at a time until you find the error.

CESM Software Engineer

xueyanzhang520@...

Sorry, I am not sure what you said the unmodified config_machines.xml file, you mean the original file in clm5?

Work hard

yelshorbany@...

I am trying also to port CESM2 to my machine and having an error test_createnewcase as following (attached are my *xml files)

./scripts_regression_tests.py 

 

Testing commit 3861ef9f890b0d169982014c0204faab091845c3

Using cime_model = cesm

Testing machine = circe

Test root: /work/e/elshorbany/CESM/scripts_regression_test.20190322_191327

 

pylint version 1.5 or newer not found, pylint tests skipped

test_CIMEXML_doctests (__main__.A_RunUnitTests) ... ok

test_CIME_doctests (__main__.A_RunUnitTests) ... ok

test_resolve_variable_name (__main__.A_RunUnitTests) ... ok

test_unittests (__main__.A_RunUnitTests) ... .........................

----------------------------------------------------------------------

Ran 25 tests in 0.073s

 

OK

ok

test_script_is_callable (__main__.G_TestMacrosBasic)

The test script can be called on valid output without dying. ... ok

test_script_rejects_bad_build_system (__main__.G_TestMacrosBasic)

The macro writer rejects a bad build system string. ... ok

test_script_rejects_bad_xml (__main__.G_TestMacrosBasic)

The macro writer rejects input that's not valid XML. ... ok

test_append_flags (__main__.H_TestMakeMacros)

Test appending flags to a list. ... ok

test_append_flags_without_base (__main__.H_TestMakeMacros)

Test appending flags to a value set before Macros is included. ... ok

test_base_flags (__main__.H_TestMakeMacros)

Test that we get "base" compiler flags. ... ok

test_build_time_append_flags (__main__.H_TestMakeMacros)

Test build_time selection of compiler flags. ... ok

test_build_time_attribute (__main__.H_TestMakeMacros)

The macro writer writes conditionals for build-time choices. ... ok

test_build_time_base_flags (__main__.H_TestMakeMacros)

Test selection of base flags based on build-time attributes. ... ok

test_build_time_base_flags_same_parent (__main__.H_TestMakeMacros)

Test selection of base flags in the same parent element. ... ok

test_compiler_changeable_at_build_time (__main__.H_TestMakeMacros)

The macro writer writes information for multiple compilers. ... ok

test_config_reject_cyclical_references (__main__.H_TestMakeMacros)

Test that cyclical <var> references are rejected. ... ok

test_config_reject_self_references (__main__.H_TestMakeMacros)

Test that <var> self-references are rejected. ... ok

test_config_variable_insertion (__main__.H_TestMakeMacros)

Test that <var> elements insert variables from config_build. ... ok

test_env_and_shell_command (__main__.H_TestMakeMacros)

Test that <env> elements work inside <shell> elements. ... ok

test_environment_variable_insertion (__main__.H_TestMakeMacros)

Test that <env> elements insert environment variables. ... ok

test_generic_item (__main__.H_TestMakeMacros)

The macro writer can write out a single generic item. ... ok

test_ignore_non_match (__main__.H_TestMakeMacros)

The macro writer ignores an entry with the wrong machine name. ... ok

test_mach_and_os_beats_mach (__main__.H_TestMakeMacros)

The macro writer chooses the most-specific match possible. ... ok

test_mach_beats_os (__main__.H_TestMakeMacros)

The macro writer chooses machine-specific over os-specific matches. ... ok

test_machine_specific_append_flags (__main__.H_TestMakeMacros)

Test appending flags that are either more or less machine-specific. ... ok

test_machine_specific_base_and_append_flags (__main__.H_TestMakeMacros)

Test that machine-specific base flags coexist with machine-specific append flags. ... ok

test_machine_specific_base_flags (__main__.H_TestMakeMacros)

Test selection among base compiler flag sets based on machine. ... ok

test_machine_specific_base_over_append_flags (__main__.H_TestMakeMacros)

Test that machine-specific base flags override default append flags. ... ok

test_machine_specific_item (__main__.H_TestMakeMacros)

The macro writer can pick out a machine-specific item. ... ok

test_multiple_shell_commands (__main__.H_TestMakeMacros)

Test that more than one <shell> element can be used. ... ok

test_os_specific_item (__main__.H_TestMakeMacros)

The macro writer can pick out an OS-specific item. ... ok

test_reject_ambiguous (__main__.H_TestMakeMacros)

The macro writer dies if given an ambiguous set of matches. ... ok

test_reject_duplicate_defaults (__main__.H_TestMakeMacros)

The macro writer dies if given many defaults. ... ok

test_reject_duplicates (__main__.H_TestMakeMacros)

The macro writer dies if given many matches for a given configuration. ... ok

test_shell_command_insertion (__main__.H_TestMakeMacros)

Test that <shell> elements insert shell command output. ... ok

test_variable_insertion_with_machine_specific_setting (__main__.H_TestMakeMacros)

Test that machine-specific <var> dependencies are correct. ... ok

test_append_flags (__main__.I_TestCMakeMacros)

Test appending flags to a list. ... ok

test_append_flags_without_base (__main__.I_TestCMakeMacros)

Test appending flags to a value set before Macros is included. ... ok

test_base_flags (__main__.I_TestCMakeMacros)

Test that we get "base" compiler flags. ... ok

test_build_time_append_flags (__main__.I_TestCMakeMacros)

Test build_time selection of compiler flags. ... ok

test_build_time_attribute (__main__.I_TestCMakeMacros)

The macro writer writes conditionals for build-time choices. ... ok

test_build_time_base_flags (__main__.I_TestCMakeMacros)

Test selection of base flags based on build-time attributes. ... ok

test_build_time_base_flags_same_parent (__main__.I_TestCMakeMacros)

Test selection of base flags in the same parent element. ... ok

test_compiler_changeable_at_build_time (__main__.I_TestCMakeMacros)

The macro writer writes information for multiple compilers. ... ok

test_config_reject_cyclical_references (__main__.I_TestCMakeMacros)

Test that cyclical <var> references are rejected. ... ok

test_config_reject_self_references (__main__.I_TestCMakeMacros)

Test that <var> self-references are rejected. ... ok

test_config_variable_insertion (__main__.I_TestCMakeMacros)

Test that <var> elements insert variables from config_build. ... ok

test_env_and_shell_command (__main__.I_TestCMakeMacros)

Test that <env> elements work inside <shell> elements. ... ok

test_environment_variable_insertion (__main__.I_TestCMakeMacros)

Test that <env> elements insert environment variables. ... ok

test_generic_item (__main__.I_TestCMakeMacros)

The macro writer can write out a single generic item. ... ok

test_ignore_non_match (__main__.I_TestCMakeMacros)

The macro writer ignores an entry with the wrong machine name. ... ok

test_mach_and_os_beats_mach (__main__.I_TestCMakeMacros)

The macro writer chooses the most-specific match possible. ... ok

test_mach_beats_os (__main__.I_TestCMakeMacros)

The macro writer chooses machine-specific over os-specific matches. ... ok

test_machine_specific_append_flags (__main__.I_TestCMakeMacros)

Test appending flags that are either more or less machine-specific. ... ok

test_machine_specific_base_and_append_flags (__main__.I_TestCMakeMacros)

Test that machine-specific base flags coexist with machine-specific append flags. ... ok

test_machine_specific_base_flags (__main__.I_TestCMakeMacros)

Test selection among base compiler flag sets based on machine. ... ok

test_machine_specific_base_over_append_flags (__main__.I_TestCMakeMacros)

Test that machine-specific base flags override default append flags. ... ok

test_machine_specific_item (__main__.I_TestCMakeMacros)

The macro writer can pick out a machine-specific item. ... ok

test_multiple_shell_commands (__main__.I_TestCMakeMacros)

Test that more than one <shell> element can be used. ... ok

test_os_specific_item (__main__.I_TestCMakeMacros)

The macro writer can pick out an OS-specific item. ... ok

test_reject_ambiguous (__main__.I_TestCMakeMacros)

The macro writer dies if given an ambiguous set of matches. ... ok

test_reject_duplicate_defaults (__main__.I_TestCMakeMacros)

The macro writer dies if given many defaults. ... ok

test_reject_duplicates (__main__.I_TestCMakeMacros)

The macro writer dies if given many matches for a given configuration. ... ok

test_shell_command_insertion (__main__.I_TestCMakeMacros)

Test that <shell> elements insert shell command output. ... ok

test_variable_insertion_with_machine_specific_setting (__main__.I_TestCMakeMacros)

Test that machine-specific <var> dependencies are correct. ... ok

test_a_createnewcase (__main__.J_TestCreateNewcase) ... FAIL

test_aa_no_flush_on_instantiate (__main__.J_TestCreateNewcase) ... FAIL

test_b_user_mods (__main__.J_TestCreateNewcase) ... FAIL

test_c_create_clone_keepexe (__main__.J_TestCreateNewcase) ... ok

test_d_create_clone_new_user (__main__.J_TestCreateNewcase) ... ERROR

test_e_xmlquery (__main__.J_TestCreateNewcase) ... FAIL

test_f_createnewcase_with_user_compset (__main__.J_TestCreateNewcase) ... FAIL

test_g_createnewcase_with_user_compset_and_env_mach_pes (__main__.J_TestCreateNewcase) ... FAIL

test_h_primary_component (__main__.J_TestCreateNewcase) ... FAIL

test_j_createnewcase_user_compset_vs_alias (__main__.J_TestCreateNewcase) ... FAIL

test_k_append_config (__main__.J_TestCreateNewcase) ... ok

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190322_191327/TestCreateNewcase/testcreatenewcase

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190322_191327/TestCreateNewcase/testusermods

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190322_191327/TestCreateNewcase/test_create_clone_new_user

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190322_191327/TestCreateNewcase/testcreatenewcase_with_user_compset

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190322_191327/TestCreateNewcase/testcreatenewcase_with_user_compset_and_env_mach_pes

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190322_191327/TestCreateNewcase/testprimarycomponent

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190322_191327/TestCreateNewcase/testcreatenewcase_user_compset

test_cime_case (__main__.K_TestCimeCase) ... FAIL

test_cime_case_allow_failed_prereq (__main__.K_TestCimeCase) ... ^CFAIL

 

======================================================================

ERROR: test_d_create_clone_new_user (__main__.J_TestCreateNewcase)

 

-------------------------------------------------------------------

 

jedwards

Please run

scripts_regression_tests.py J_TestCreateNewcase


and send the complete output.  

CESM Software Engineer

yelshorbany@...

./scripts_regression_tests.py J_TestCreateNewcase

 

Testing commit 3861ef9f890b0d169982014c0204faab091845c3

Using cime_model = cesm

Testing machine = circe

Test root: /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701

 

pylint version 1.5 or newer not found, pylint tests skipped

test_a_createnewcase (__main__.J_TestCreateNewcase) ... FAIL

test_aa_no_flush_on_instantiate (__main__.J_TestCreateNewcase) ... FAIL

test_b_user_mods (__main__.J_TestCreateNewcase) ... FAIL

test_c_create_clone_keepexe (__main__.J_TestCreateNewcase) ... ok

test_d_create_clone_new_user (__main__.J_TestCreateNewcase) ... ERROR

test_e_xmlquery (__main__.J_TestCreateNewcase) ... FAIL

test_f_createnewcase_with_user_compset (__main__.J_TestCreateNewcase) ... FAIL

test_g_createnewcase_with_user_compset_and_env_mach_pes (__main__.J_TestCreateNewcase) ... FAIL

test_h_primary_component (__main__.J_TestCreateNewcase) ... FAIL

test_j_createnewcase_user_compset_vs_alias (__main__.J_TestCreateNewcase) ... FAIL

test_k_append_config (__main__.J_TestCreateNewcase) ... ok

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testusermods

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/test_create_clone_new_user

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase_with_user_compset

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase_with_user_compset_and_env_mach_pes

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testprimarycomponent

Detected failed test or user request no teardown

Leaving case directory : /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase_user_compset

 

======================================================================

ERROR: test_d_create_clone_new_user (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 389, in test_d_create_clone_new_user

    from_dir=prevtestdir)

  File "./scripts_regression_tests.py", line 54, in run_cmd_assert_result

    stat, output, errput = run_cmd(cmd, from_dir=from_dir, env=env)

  File "/home/e/elshorbany/CESM/cesm2.1/cime/scripts/tests/../lib/CIME/utils.py", line 425, in run_cmd

    env=env)

  File "/apps/python/3.6.2/lib/python3.6/subprocess.py", line 707, in __init__

    restore_signals, start_new_session)

  File "/apps/python/3.6.2/lib/python3.6/subprocess.py", line 1333, in _execute_child

    raise child_exception_type(errno_num, err_msg)

FileNotFoundError: [Errno 2] No such file or directory: '/work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase'

 

======================================================================

FAIL: test_a_createnewcase (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 285, in test_a_createnewcase

    run_cmd_assert_result(self, "./create_newcase %s"%(args), from_dir=SCRIPT_DIR)

  File "./scripts_regression_tests.py", line 67, in run_cmd_assert_result

    test_obj.assertEqual(stat, expected_stat, msg=msg)

AssertionError: 1 != 0 : 

COMMAND: ./create_newcase  --case /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase --compset X --res f19_g16 --output-root /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase --handle-preexisting-dirs=r

FROM_DIR: /home/e/elshorbany/CESM/cesm2.1/cime/scripts

SHOULD HAVE WORKED, INSTEAD GOT STAT 1

OUTPUT: Compset longname is 2000_XATM_XLND_XICE_XOCN_XROF_XGLC_XWAV

Compset specification file is /home/e/elshorbany/CESM/cesm2.1/cime/src/drivers/mct/cime_config/config_compsets.xml

Compset forcing is 1972-2004

ATM component is Dead atm component

LND component is Dead land component

ICE component is Dead ice component

OCN component is Dead ocean component

ROF component is Dead river component

GLC component is Dead land-ice component

WAV component is Dead wave component

ESP component is 

Pes     specification file is /home/e/elshorbany/CESM/cesm2.1/cime/src/drivers/mct/cime_config/config_pes.xml

Machine is circe

ERRPUT: ERROR: Expected one child

 

 

======================================================================

FAIL: test_aa_no_flush_on_instantiate (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 314, in test_aa_no_flush_on_instantiate

    self.assertFalse(env_file.needsrewrite, msg="Instantiating a case should not trigger a flush call")

AssertionError: True is not false : Instantiating a case should not trigger a flush call

 

======================================================================

FAIL: test_b_user_mods (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 356, in test_b_user_mods

    % (SCRIPT_DIR, args),from_dir=SCRIPT_DIR)

  File "./scripts_regression_tests.py", line 67, in run_cmd_assert_result

    test_obj.assertEqual(stat, expected_stat, msg=msg)

AssertionError: 1 != 0 : 

COMMAND: /home/e/elshorbany/CESM/cesm2.1/cime/scripts/create_newcase  --case /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testusermods --compset X --res f19_g16 --user-mods-dir /home/e/elshorbany/CESM/cesm2.1/cime/scripts/lib/../tests/user_mods_test1 --output-root /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase --handle-preexisting-dirs=r 

FROM_DIR: /home/e/elshorbany/CESM/cesm2.1/cime/scripts

SHOULD HAVE WORKED, INSTEAD GOT STAT 1

OUTPUT: Compset longname is 2000_XATM_XLND_XICE_XOCN_XROF_XGLC_XWAV

Compset specification file is /home/e/elshorbany/CESM/cesm2.1/cime/src/drivers/mct/cime_config/config_compsets.xml

Compset forcing is 1972-2004

ATM component is Dead atm component

LND component is Dead land component

ICE component is Dead ice component

OCN component is Dead ocean component

ROF component is Dead river component

GLC component is Dead land-ice component

WAV component is Dead wave component

ESP component is 

Pes     specification file is /home/e/elshorbany/CESM/cesm2.1/cime/src/drivers/mct/cime_config/config_pes.xml

Machine is circe

ERRPUT: ERROR: Expected one child

 

 

======================================================================

FAIL: test_e_xmlquery (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 415, in test_e_xmlquery

    self.assertTrue(os.path.isfile(os.path.join(casedir,xmlquery)))

AssertionError: False is not true

 

======================================================================

FAIL: test_f_createnewcase_with_user_compset (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 473, in test_f_createnewcase_with_user_compset

    run_cmd_assert_result(self, "%s/create_newcase %s"%(SCRIPT_DIR, args), from_dir=SCRIPT_DIR)

  File "./scripts_regression_tests.py", line 67, in run_cmd_assert_result

    test_obj.assertEqual(stat, expected_stat, msg=msg)

AssertionError: 1 != 0 : 

COMMAND: /home/e/elshorbany/CESM/cesm2.1/cime/scripts/create_newcase --case /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase_with_user_compset --compset 2000_SATM_XLND_SICE_SOCN_XROF_XGLC_SWAV  --pesfile ../src/drivers/mct/cime_config/config_pes.xml --res f19_g16 --output-root /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase --handle-preexisting-dirs=r --run-unsupported

FROM_DIR: /home/e/elshorbany/CESM/cesm2.1/cime/scripts

SHOULD HAVE WORKED, INSTEAD GOT STAT 1

OUTPUT: Did not find an alias or longname compset match for 2000_SATM_XLND_SICE_SOCN_XROF_XGLC_SWAV 

Compset forcing is 1972-2004

ATM component is Stub atm component

LND component is Dead land component

ICE component is Stub ice component

OCN component is Stub ocn component

ROF component is Dead river component

GLC component is Dead land-ice component

WAV component is Stub wave component

ESP component is 

Machine is circe

ERRPUT: ERROR: Expected one child

 

 

======================================================================

FAIL: test_g_createnewcase_with_user_compset_and_env_mach_pes (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 497, in test_g_createnewcase_with_user_compset_and_env_mach_pes

    run_cmd_assert_result(self, "%s/create_newcase %s"%(SCRIPT_DIR, args), from_dir=SCRIPT_DIR)

  File "./scripts_regression_tests.py", line 67, in run_cmd_assert_result

    test_obj.assertEqual(stat, expected_stat, msg=msg)

AssertionError: 1 != 0 : 

COMMAND: /home/e/elshorbany/CESM/cesm2.1/cime/scripts/create_newcase --case /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase_with_user_compset_and_env_mach_pes --compset 2000_SATM_XLND_SICE_SOCN_XROF_XGLC_SWAV --pesfile /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase_with_user_compset/env_mach_pes.xml --res f19_g16 --output-root /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase --handle-preexisting-dirs=r --run-unsupported

FROM_DIR: /home/e/elshorbany/CESM/cesm2.1/cime/scripts

SHOULD HAVE WORKED, INSTEAD GOT STAT 1

OUTPUT: 

ERRPUT: ERROR: Pes specification file /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase_with_user_compset/env_mach_pes.xml cannot be found

 

 

======================================================================

FAIL: test_h_primary_component (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 520, in test_h_primary_component

    run_cmd_assert_result(self, "%s/create_newcase %s" % (SCRIPT_DIR, args), from_dir=SCRIPT_DIR)

  File "./scripts_regression_tests.py", line 67, in run_cmd_assert_result

    test_obj.assertEqual(stat, expected_stat, msg=msg)

AssertionError: 1 != 0 : 

COMMAND: /home/e/elshorbany/CESM/cesm2.1/cime/scripts/create_newcase  --case CreateNewcaseTest --script-root /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testprimarycomponent --compset X --res f19_g16 --output-root /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase --handle-preexisting-dirs u

FROM_DIR: /home/e/elshorbany/CESM/cesm2.1/cime/scripts

SHOULD HAVE WORKED, INSTEAD GOT STAT 1

OUTPUT: Compset longname is 2000_XATM_XLND_XICE_XOCN_XROF_XGLC_XWAV

Compset specification file is /home/e/elshorbany/CESM/cesm2.1/cime/src/drivers/mct/cime_config/config_compsets.xml

Compset forcing is 1972-2004

ATM component is Dead atm component

LND component is Dead land component

ICE component is Dead ice component

OCN component is Dead ocean component

ROF component is Dead river component

GLC component is Dead land-ice component

WAV component is Dead wave component

ESP component is 

Pes     specification file is /home/e/elshorbany/CESM/cesm2.1/cime/src/drivers/mct/cime_config/config_pes.xml

Machine is circe

ERRPUT: ERROR: Expected one child

 

 

======================================================================

FAIL: test_j_createnewcase_user_compset_vs_alias (__main__.J_TestCreateNewcase)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./scripts_regression_tests.py", line 590, in test_j_createnewcase_user_compset_vs_alias

    run_cmd_assert_result(self, "{}/create_newcase {}" .format (SCRIPT_DIR, args), from_dir=SCRIPT_DIR)

  File "./scripts_regression_tests.py", line 67, in run_cmd_assert_result

    test_obj.assertEqual(stat, expected_stat, msg=msg)

AssertionError: 1 != 0 : 

COMMAND: /home/e/elshorbany/CESM/cesm2.1/cime/scripts/create_newcase  --case CreateNewcaseTest --script-root /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase/testcreatenewcase_user_compset --compset 2000_DATM%NYF_SLND_SICE_DOCN%SOMAQP_SROF_SGLC_SWAV --res f19_g16 --output-root /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701/TestCreateNewcase --handle-preexisting-dirs u --run-unsupported

FROM_DIR: /home/e/elshorbany/CESM/cesm2.1/cime/scripts

SHOULD HAVE WORKED, INSTEAD GOT STAT 1

OUTPUT: Compset longname is 2000_DATM%NYF_SLND_SICE_DOCN%SOMAQP_SROF_SGLC_SWAV

Compset specification file is /home/e/elshorbany/CESM/cesm2.1/cime/src/drivers/mct/cime_config/config_compsets.xml

Compset forcing is 1972-2004

ATM component is  Data driven ATM COREv2 normal year forcing

LND component is Stub land component

ICE component is Stub ice component

OCN component is DOCN   aquaplanet slab ocean mode

ROF component is Stub river component

GLC component is Stub glacier (land ice) component

WAV component is Stub wave component

ESP component is 

Pes     specification file is /home/e/elshorbany/CESM/cesm2.1/cime/src/drivers/mct/cime_config/config_pes.xml

Machine is circe

ERRPUT: ERROR: Expected one child

 

 

----------------------------------------------------------------------

Ran 11 tests in 3.176s

 

FAILED (failures=8, errors=1)

Detected failures, leaving directory: /work/e/elshorbany/CESM/scripts_regression_test.20190327_164701


jedwards

Machine is circe

ERRPUT: ERROR: Expected one child

 Do you have machine circe defined twice?  Maybe once in $HOME/.cime/config_machines/.xml and once in cesm2_1/cime/config/cesm/machines/config_machines.xml ?   

CESM Software Engineer

botto@...

The machine is only defined once, in $HOME/.cime/config_machines.xml

jedwards

Okay - it should be the only machine defined in that file?  and the file shoud start with 

<?xml version="1.0"?>

<machine MACH="circe">

and end with

</machine>

CESM Software Engineer

botto@...

I edited the ~/.cime/config_machines.xml to your suggestion, and it still produced the 8 failures when running "./scripts_regression_tests.py J_TestCreateNewcase":


Attached are the current config_machines.xml, config_batch.xml, and config_compilers.xml files we're using in ~/.cime.

jedwards

same issue with config_compilers.xml and config_batch.xml - they should only contain the sections that specifically call out your machine

CESM Software Engineer

botto@...

Ok: I made the changes you specified, and re-running scripts_regression_tests.py now gives 5 errors instead of the previous 8. I have uploaded the modified files, as well as the output from the scripts_regression_tests.py script.

jedwards

In the module paths you need to have init_path and cmd_path entries for lang="python"

CESM Software Engineer

jedwards

In the module paths you need to have init_path and cmd_path entries for lang="python" . I think that they would be:

      <init_path lang="python">/usr/share/Modules/init/python.py</init_path>

 <cmd_path lang="python">/usr/bin/modulecmd python </cmd_path>

CESM Software Engineer

botto@...

I added the lines in that you specified into config_machines.xml, and re-ran: it's still failing with 5 errors, as show in the output attached.

 

Thank you for all of your help so far!

jedwards

You config_compilers.xml has a typo in it.  

CESM Software Engineer

jedwards

Looking at the content of the file - lets just work with a single compiler for now and remove the other one - you also only need to add changes to the default settings from cime/config/cesm/machines/config_compilers.xml  don't repeat settings that are already there. 

CESM Software Engineer

botto@...

Thanks for the info! I now have J_TestCreateNewcase running correctly with no errors. Unfortunately, now L_TestSaveTimings is throwing errors. Attached are the outputs and config files used in ~/.cime.

jedwards

Your config batch file seems to be empty - you need at least the following: 

  <batch_system MACH="silicon" type="slurm" >

    <batch_submit>sbatch</batch_submit>

    <submit_args>

      <arg flag="--time" name="$JOB_WALLCLOCK_TIME"/>

      <arg flag="-q" name="$JOB_QUEUE"/>

    </submit_args>

    <queues>

      <queue walltimemax="36:00:00" nodemin="1" nodemax="2712" >regular</queue>

    </queues>

  </batch_system>

 

Modified appropriately for your queueing system

 

CESM Software Engineer

botto@...

I apologize: there was a leading character in the config_batch_04-01-19.xml file that caused web browsers to not render it. I have fixed it, so it now displays correctly.


The only difference between mine and the one you posted is the "<batch_submit>" statement: I will add then and then try.

botto@...

The initial errors reported are now cleared. Now, I am encountering a list of other errors. We'll start with "B_CheckCode":

 

 

jedwards

Botto - this is the expected result for B_Checkcode in your version of the model - that is there is one file (archive_metadat.py) . which does not conform.   

CESM Software Engineer

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