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no input data in FHIST_BGC, Model cam missing file mode_defs for soa_a1

X

xiaxs

xiaxs
New Member
Hi,

I am trying to run a case using FHIST_BGC compset, ./create_newcase --compset FHIST_BGC --res f09_f09_mg17 --case ~/CESM2/scratch/FHIST_BGC. when check the input data, I found three soa_a1 files are missing that could not found in ftp://ftp.cgd.ucar.edu/cesm/inputdata/.

my CESM release is 2.1.3, and how can I fix the problem?

Thanks!


[sysu_syli_3@lon26%tianhe2-H FHIST_BGC]$ ./check_input_data
Loading input file list: 'Buildconf/cpl.input_data_list'
Loading input file list: 'Buildconf/mosart.input_data_list'
Loading input file list: 'Buildconf/cism.input_data_list'
Loading input file list: 'Buildconf/clm.input_data_list'
Loading input file list: 'Buildconf/cice.input_data_list'
Loading input file list: 'Buildconf/docn.input_data_list'
Loading input file list: 'Buildconf/refcase.input_data_list'
Loading input file list: 'Buildconf/cam.input_data_list'
Model cam missing file mode_defs for soa_a1 = '/BIGDATA1/sysu_syli_3/CESM2/inputdata/atm/cam/phncdata'
Model cam missing file mode_defs for soa_a1 = '/BIGDATA1/sysu_syli_3/CESM2/inputdata/atm/cam/phtropopause_climo_file'
Model cam missing file mode_defs for soa_a1 = '/BIGDATA1/sysu_syli_3/CESM2/inputdata/atm/cam/phprescribed_strataero_file'
Traceback (most recent call last):
File "./check_input_data", line 76, in <module>
_main_func(__doc__)
File "./check_input_data", line 71, in _main_func
chksum=chksum) else 1)
File "/BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/check_input_data.py", line 160, in check_all_input_data
input_data_root=input_data_root, data_list_dir=data_list_dir, chksum=chksum)
File "/BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/check_input_data.py", line 307, in check_input_data
description, full_path = tokens[0].strip(), tokens[1].strip()
IndexError: list index out of range
 
C

cacraig

Cheryl Craig
CSEG and Liaisons
Staff member
I believe something may have gotten accidentally changed in your checkout. I downloaded CESM2.1.3 and issued your ./create_newcase command. I did a
./case.setup
./preview_namelists
./check_input_data

and did not have any errors.

Please download a fresh copy and try again. If you still have problems, please give us the exact commands you use from the time you do the git clone until you get the error.
 
X

xiaxs

xiaxs
New Member
cacraig said:
I believe something may have gotten accidentally changed in your checkout. I downloaded CESM2.1.3 and issued your ./create_newcase command. I did a
./case.setup
./preview_namelists
./check_input_data

and did not have any errors.

Please download a fresh copy and try again. If you still have problems, please give us the exact commands you use from the time you do the git clone until you get the error.
Click to expand...
Hi, Cheryl.

Thank you for suggestion! pardon me for the delayed reply.
I have checked my downloaded CESM2.1.3 code, and find some error as folllows:

(base) [xiaxsh3@login my_cesm_sandbox_shaoyi]$ ./manage_externals/checkout_externals -S
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CAM.cfg
Processing externals description file : ../Externals_cime.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CLM.cfg
Processing externals description file : Externals_POP.cfg
Checking status of externals: cam, chem_proc, carma, clubb, cosp2, cice, cime, cmeps, fox, cism, source_cism, clm, fates, ptclm, fms, mom, mosart, pop, cvmix, marbl, rtm, ww3,
?M ./cime
e- ./cime/src/drivers/nuopc/
e- ./cime/src/externals/fox
?M ./components/cam
./components/cam/chem_proc
./components/cam/src/physics/carma/base
M ./components/cam/src/physics/clubb
./components/cam/src/physics/cosp2/src
sM ./components/cice
sM ./components/cism
M ./components/cism/source_cism
sM ./components/clm
M ./components/clm/src/fates
M ./components/clm/tools/PTCLM
e- ./components/mom
sM ./components/mosart
?M ./components/pop
M ./components/pop/externals/CVMix
M ./components/pop/externals/MARBL
sM ./components/rtm
sM ./components/ww3
e- ./libraries/FMS

(base) [xiaxsh3@login my_cesm_sandbox_shaoyi]$ ./describe_version
fatal: No names found, cannot describe anything.
Traceback (most recent call last):
File "./describe_version", line 71, in <module>
main()
File "./describe_version", line 52, in main
git_describe = subprocess.check_output(['git', 'describe', '--long'],
File "/wind1/home/xiaxsh3/anaconda3/lib/python3.8/subprocess.py", line 411, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/wind1/home/xiaxsh3/anaconda3/lib/python3.8/subprocess.py", line 512, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['git', 'describe', '--long']' returned non-zero exit status 128.

So, I download the CESM2.1.3 code again, here is new check:
(base) [xiaxsh3@login my_cesm_sandbox_zhuxf]$ ./manage_externals/checkout_externals -S
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CAM.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CLM.cfg
Processing externals description file : Externals_POP.cfg
Checking status of externals: cam, chem_proc, carma, clubb, cosp2, cice, cime, cism, source_cism, clm, fates, ptclm, mosart, pop, cvmix, marbl, rtm, ww3,
M ./cime
./components/cam
./components/cam/chem_proc
./components/cam/src/physics/carma/base
./components/cam/src/physics/clubb
./components/cam/src/physics/cosp2/src
./components/cice
./components/cism
./components/cism/source_cism
./components/clm
./components/clm/src/fates
./components/clm/tools/PTCLM
./components/mosart
./components/pop
./components/pop/externals/CVMix
./components/pop/externals/MARBL
./components/rtm
./components/ww3

(base) [xiaxsh3@login my_cesm_sandbox_zhuxf]$ ./describe_version
------------------------------------------------------------------------
git describe:
cesm2.1.3-rc.01-0-g0596a97
------------------------------------------------------------------------

Refresh index: 100% (213/213), done.
------------------------------------------------------------------------
git status:
Not currently on any branch.
nothing to commit, working tree clean
------------------------------------------------------------------------

------------------------------------------------------------------------
manage_externals status:
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CAM.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CLM.cfg
Processing externals description file : Externals_POP.cfg
Checking status of externals: cam, chem_proc, carma, clubb, cosp2, cice, cime, cism, source_cism, clm, fates, ptclm, mosart, pop, cvmix, marbl, rtm, ww3,
M ./cime
modified sandbox, on cime5.6.32
HEAD detached at cime5.6.32
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git restore <file>..." to discard changes in working directory)
modified: config/cesm/machines/config_batch.xml
modified: config/cesm/machines/config_compilers.xml

no changes added to commit (use "git add" and/or "git commit -a")

./components/cam
clean sandbox, on cam_cesm2_1_rel_41
HEAD detached at cam_cesm2_1_rel_41
Untracked files:
(use "git add <file>..." to include in what will be committed)
cime_config/__pycache__/

nothing added to commit but untracked files present (use "git add" to track)

./components/cam/chem_proc
clean sandbox, on tools/proc_atm/chem_proc/release_tags/chem_proc5_0_03_rel

./components/cam/src/physics/carma/base
clean sandbox, on carma/release_tags/carma3_49_rel

./components/cam/src/physics/clubb
clean sandbox, on vendor_clubb_r8099_n03
HEAD detached at vendor_clubb_r8099_n03
nothing to commit, working tree clean

./components/cam/src/physics/cosp2/src
clean sandbox, on CFMIP/COSPv2.0/tags/v2.1.4cesm/src

./components/cice
clean sandbox, on cice5_cesm2_1_1_20190321
HEAD detached at cice5_cesm2_1_1_20190321
nothing to commit, working tree clean

./components/cism
clean sandbox, on cism-release-cesm2.1.2_02
HEAD detached at cism-release-cesm2.1.2_02
nothing to commit, working tree clean

./components/cism/source_cism
clean sandbox, on release-cism2.1.03
HEAD detached at release-cism2.1.03
nothing to commit, working tree clean

./components/clm
clean sandbox, on release-clm5.0.30
HEAD detached at release-clm5.0.30
nothing to commit, working tree clean

./components/clm/src/fates
clean sandbox, on sci.1.30.0_api.8.0.0
HEAD detached at sci.1.30.0_api.8.0.0
nothing to commit, working tree clean

./components/clm/tools/PTCLM
clean sandbox, on PTCLM2_20200121
HEAD detached at PTCLM2_20200121
nothing to commit, working tree clean

./components/mosart
clean sandbox, on release-cesm2.0.04
HEAD detached at release-cesm2.0.04
nothing to commit, working tree clean

./components/pop
clean sandbox, on pop2_cesm2_1_rel_n09
HEAD detached at pop2_cesm2_1_rel_n09
Untracked files:
(use "git add <file>..." to include in what will be committed)
externals/CVMix/
externals/MARBL/

nothing added to commit but untracked files present (use "git add" to track)

./components/pop/externals/CVMix
clean sandbox, on v0.93-beta
HEAD detached at v0.93-beta
nothing to commit, working tree clean

./components/pop/externals/MARBL
clean sandbox, on cesm2.1-n00
HEAD detached at cesm2.1-n00
nothing to commit, working tree clean

./components/rtm
clean sandbox, on release-cesm2.0.04
HEAD detached at release-cesm2.0.04
nothing to commit, working tree clean

./components/ww3
clean sandbox, on ww3_181001
HEAD detached at ww3_cesm2_1_rel_01
nothing to commit, working tree clean

I do not know if I download the CESM2.1.3 code completely. it seems have some trouble in cime (M ./cime). But I do not meet the input data error.
I have got some else error after ./case.submit, here is my code and log files.

./create_newcase --compset FHIST_BGC --res f09_f09_mg17 --case ~/CESM2/scratch/FHIST_BGCtest &> FHIST_BGCtest.log
./case.setup
./case.preview_namelist
./check_input_data
./case.build
./case.submit

Thank you again.
 

Attachments

  • FHIST_BGCtest.build.log.txt
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  • FHIST_BGCtest_CaseStatus.txt
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  • FHIST_BGCtest_cesm.log.txt
    185.5 KB · Views: 2
C

cacraig

Cheryl Craig
CSEG and Liaisons
Staff member
This is behaving like you are running out of storage room during your download. An easy way to make sure you are not running out of room is to completely remove your current checkout (assuming that you have not made any mods to anything yourself). Then do your git clone and manage_externals/checkout_externals from scratch. This will download everything once again. Please immediately run manage_externals/checkout_externals a second time before doing anything else. If you see any "M" directories, then your checkout did not complete successfully as the "M" says there are modified files in that directory.

If you are not running out of room an alternate explanation could be that something happened during the download process. If on your second run of manage_externals/checkout_externals you see an "M" for dirXX and know that you have enough local space, you can "rm -rf dirXX" and run manage_externals/checkout_externals again. That will skip the directories which were successfully downloaded and redownload the dirXX.

Only after you run a manage_externals/checkout_externals that doesn't download anything new and does not give you an "M" would I suggest that you proceed with the create_newcase and successive commands.
 
X

xiaxs

xiaxs
New Member
cacraig said:
This is behaving like you are running out of storage room during your download. An easy way to make sure you are not running out of room is to completely remove your current checkout (assuming that you have not made any mods to anything yourself). Then do your git clone and manage_externals/checkout_externals from scratch. This will download everything once again. Please immediately run manage_externals/checkout_externals a second time before doing anything else. If you see any "M" directories, then your checkout did not complete successfully as the "M" says there are modified files in that directory.

If you are not running out of room an alternate explanation could be that something happened during the download process. If on your second run of manage_externals/checkout_externals you see an "M" for dirXX and know that you have enough local space, you can "rm -rf dirXX" and run manage_externals/checkout_externals again. That will skip the directories which were successfully downloaded and redownload the dirXX.

Only after you run a manage_externals/checkout_externals that doesn't download anything new and does not give you an "M" would I suggest that you proceed with the create_newcase and successive commands.
Click to expand...
Dear Cheryl,

Thank you very much. I will try to download CESM2.1.3 code again, and make sure no "M" for dirXX.

Best wishes
 
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