Issue in .case_build

abhisheklodh · Mar 28, 2023

Hi,

I created one CASE by running "./create_newcase --case /home/abhishekl/SOURCE/CESM/cases/b.e20.B1850.f19_g17.test --compset B1850 --res f19_g17".
And the CASE was successfully set up and built for our machine.

However, when I tried to download the required input data with the command "./check_input_data --protocol=svn --server=https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/ --download", the following errors are happening.
I repeatedly tried to download these input data, but all failed.

---------------------------------------------------------------------------------
Using protocol svn with user None and passwd None
Loading input file list: 'Buildconf/ww3.input_data_list'
Loading input file list: 'Buildconf/cism.input_data_list'
Loading input file list: 'Buildconf/mosart.input_data_list'
Loading input file list: 'Buildconf/refcase.input_data_list'
Loading input file list: 'Buildconf/pop.input_data_list'
Loading input file list: 'Buildconf/clm.input_data_list'
Model clm missing file stream_fldfilename_popdens = '/home/abhishekl/OUTPUT/CESM/cesm-inputdata/lnd/clm2/firedata/clmforc.Li_2017_HYDEv3.2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2016_c180202.nc'
Trying to download file: 'lnd/clm2/firedata/clmforc.Li_2017_HYDEv3.2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2016_c180202.nc' to path '/home/abhishekl/OUTPUT/CESM/cesm-inputdata/lnd/clm2/firedata/clmforc.Li_2017_HYDEv3.2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2016_c180202.nc' using SVN protocol.
SUCCESS

ERROR: Failed to find or download file /home/abhishekl/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/run/inputdata_checksum.dat

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

---------------------------------------------------------------------------------
Also if i run "./case.build" again...the following error comes:

Building gptl with output to file /home/abhishekl/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gptl.bldlog.230328-121932
Calling /home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/src/build_scripts/buildlib.gptl
ERROR: /home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/abhishekl/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gptl.bldlog.230328-121932

---------------------------------------------------------------------------------
How can I solve it ? and download all the data in one command.

jedwards · Mar 28, 2023

Did you look at file /home/abhishekl/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gptl.bldlog.230328-121932 to see what the error is?

For check_input_data you should only use the --download flag, I think specifying the server and protocol explicitly is what is causing the error.

abhisheklodh · Mar 28, 2023

Thanks for your reply, after incorporating the error in "gmake", I am getting a further error while building the cesm model:

osart built in 20.566774 seconds
ww built in 30.462054 seconds
Component ice build complete with 1 warnings
cice built in 39.576247 seconds
Component ocn build complete with 13 warnings
pop built in 51.090144 seconds
Component atm build complete with 14 warnings
cam built in 79.141163 seconds
Component glc build complete with 3 warnings
cism built in 97.365230 seconds
Building cesm with output to /home/abhishekl/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/cesm.bldlog.230328-172713
ERROR: BUILD FAIL: buildexe failed, cat /home/abhishekl/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/cesm.bldlog.230328-172713

The cesm error file is attached. Kindly suggest as gmake i have aliased with make.

jedwards · Mar 28, 2023

nothing attached

abhisheklodh · Mar 28, 2023

Pl find the file attached. The steps and the comset i am following are : Quick Start: CESM Model Workflow (CESM2.1) — CESM CESM2.1 documentation

jedwards · Mar 28, 2023

1. It looks like you are trying to link two different versions of netcdf.
ld: warning: libnetcdf.so.15, needed by /usr/local/intel/netcdf/lib/libnetcdf.so, may conflict with libnetcdf.so.13
2. This issue is due to the memory requirement for static data exceeding the available memory. There are a number of
reasons that this may happen.
/home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:2707:(.text+0x21aa): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_ice_layout_' defined in COMMON section in ../../intel/impi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib/libcsm_share.a(seq_comm_mct.o)

Sometimes this is triggered by a constant value that is too large such as NC_MAX_VARS. It could also be triggered if you are trying to compile a high resolution component on too few tasks. I don't have enough information to determine the cause. Have you tried some simple tests first? 8. Testing — CIME master documentation

abhisheklodh · Mar 28, 2023

Thanks for your prompt reply. Actually i changed to a different compset option to :

./create_newcase --case /home/abhishekl/SOURCE/CESM/cases/f09_f09_mg17 --compset 2000_CAM%CAMM_CLM50%SP_CICE%PRES_DOCN%DOM_RTM_SGLC_SWAV --res f09_f09_mg17 --run-unsupported

With the CESM verison 2.1.3 built, while doing ./case.submit
I am getting the following error:

---------------------------------------------------------------------------------
Client protocol gftp not enabled
Using protocol wget with user anonymous and passwd user@example.edu
Could not connect to repo 'ftp://ftp.cgd.ucar.edu/cesm/inputdata'
This is most likely either a proxy, or network issue .
Trying to download file: '../inputdata_checksum.dat' to path '/home/abhishekl/OUTPUT/CESM/scratch/f09_f09_mg17/run/inputdata_checksum.dat.raw' using NoneType protocol.
Traceback (most recent call last):
File "/home/abhishekl/SOURCE/CESM/cases/f09_f09_mg17/./case.submit", line 107, in <module>
_main_func(__doc__)
File "/home/abhishekl/SOURCE/CESM/cases/f09_f09_mg17/./case.submit", line 102, in _main_func
case.submit(job=job, no_batch=no_batch, prereq=prereq, allow_fail=allow_fail,
File "/home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 156, in submit
run_and_log_case_status(functor, "case.submit", caseroot=caseroot,
File "/home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/utils.py", line 1683, in run_and_log_case_status
rv = func()
File "/home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 151, in <lambda>
functor = lambda: _submit(self, job=job, no_batch=no_batch, prereq=prereq,
File "/home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 85, in _submit
case.check_case()
File "/home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 171, in check_case
self.check_all_input_data()
File "/home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/check_input_data.py", line 163, in check_all_input_data
_download_checksum_file(self.get_value("RUNDIR"))
File "/home/abhishekl/SOURCE/CESM/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/check_input_data.py", line 54, in _download_checksum_file
success = server.getfile(rel_path, new_file)
AttributeError: 'NoneType' object has no attribute 'getfile'
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How can i change "NoneType protocol" to "wget or SVN" protocol?
Please suggest.

jedwards · Mar 28, 2023

I'm not sure where the NoneType protocol is coming from - has your config_inputdata.xml file been changed?

It looks like there is a problem with the ftp server on our end, I will get that addressed as soon as possible and let you know when it's resolved.

jedwards · Mar 28, 2023

The ftp issue should now be resolved, you can test it with:
wget ftp://ftp.cgd.ucar.edu/cesm/inputdata/
which should download a file index.html with the following contents:

Code:

<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html>
<head>
<title>Index of /cesm/inputdata on ftp.cgd.ucar.edu:21</title>
</head>
<body>
<h1>Index of /cesm/inputdata on ftp.cgd.ucar.edu:21</h1>
<hr>
<pre>
  2022 Nov 27 21:18  Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/.svn/">.svn/</a>
  2018 Mar 20        File        <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/MaxTSIInput">MaxTSIInput</a>  (242 bytes)
  2018 Mar 20        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/atm/">atm/</a>
  2019 Dec 31        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/ccsm4_init/">ccsm4_init/</a>
  2021 Oct 22        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/cesm2_init/">cesm2_init/</a>
  2021 Mar 12        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/cism/">cism/</a>
  2018 Apr 04        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/cpl/">cpl/</a>
  2018 Mar 20        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/dx7/">dx7/</a>
  2019 May 24        File        <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/filelist">filelist</a>  (4721 bytes)
  2018 Mar 20        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/glc/">glc/</a>
  2018 Mar 20        File        <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/hiresFiles">hiresFiles</a>  (124 bytes)
  2018 Mar 20        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/ice/">ice/</a>
  2018 Mar 20        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/import/">import/</a>
  2021 Nov 06        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/lnd/">lnd/</a>
  2018 Apr 04        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/ocn/">ocn/</a>
  2020 Jun 25        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/rof/">rof/</a>
  2021 Jun 30        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/share/">share/</a>
  2018 Mar 20        File        <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/template.readme">template.readme</a>  (1346 bytes)
  2019 Jun 12        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/validation/">validation/</a>
  2018 Mar 20        Directory   <a href="ftp://ftp.cgd.ucar.edu:21/cesm/inputdata/wav/">wav/</a>
</pre>
</body>
</html>

abhisheklodh · Apr 4, 2023

Thanks the error got resolved. But now while running the aquaplanet (both prescribed SST and Slab-Ocean Model, case)

case : ./create_newcase --case aqua_case --compset QPC6 --res f09_f09_mg17

./case.submit ...... i am getting this new error:

Opened existing file
[1] /home/abhishekl/OUTPUT/CESM/cesm-inputdata/atm/cam/chem/trop_mozart/dvel/regrid
[1] _vegetation_all_zero_aquaplanet_1deg_regularGrid_c20170421.nc 262144
[14] forrtl: severe (174): SIGSEGV, segmentation fault occurred
[14] Image PC Routine Line Source
[14] cesm.exe 0000000001AED67A Unknown Unknown Unknown
[14] libpthread-2.31.s 00007F1E1E5A1420 Unknown Unknown Unknown
[14] cesm.exe 0000000001278B30 mo_drydep_mp_inte 2320 mo_drydep.F90
[14] cesm.exe 0000000001275F2C mo_drydep_mp_dvel 1927 mo_drydep.F90
[14] cesm.exe 0000000001258EC0 mo_chemini_mp_che 188 mo_chemini.F90
[14] cesm.exe 00000000010C7076 chemistry_mp_chem 882 chemistry.F90
[14] cesm.exe 00000000006E1092 physpkg_mp_phys_i 822 physpkg.F90
[14] cesm.exe 0000000000502106 cam_comp_mp_cam_i 201 cam_comp.F90
[14] cesm.exe 00000000004F9917 atm_comp_mct_mp_a 209 atm_comp_mct.F90
[14] cesm.exe 0000000000438E53 component_mod_mp_ 267 component_mod.F90
[14] cesm.exe 00000000004275DB cime_comp_mod_mp_ 1231 cime_comp_mod.F90
[14] cesm.exe 0000000000435E69 MAIN__ 114 cime_driver.F90
[14] cesm.exe 0000000000418462 Unknown Unknown Unknown
[14] libc-2.31.so 00007F1E1E270083 __libc_start_main Unknown Unknown
[14] cesm.exe 000000000041836E Unknown Unknown Unknown
[15] forrtl: severe (174): SIGSEGV, segmentation fault occurred
[15] Image PC Routine Line Source
[15] cesm.exe 0000000001AED67A Unknown Unknown Unknown
[15] libpthread-2.31.s 00007F5870F58420 Unknown Unknown Unknown
[15] cesm.exe 0000000001278B30 mo_drydep_mp_inte 2320 mo_drydep.F90
[15] cesm.exe 0000000001275F2C mo_drydep_mp_dvel 1927 mo_drydep.F90
[15] cesm.exe 0000000001258EC0 mo_chemini_mp_che 188 mo_chemini.F90
[15] cesm.exe 00000000010C7076 chemistry_mp_chem 882 chemistry.F90

jedwards · Apr 4, 2023

Perhaps you should follow the porting guide. 6. Porting and validating CIME on a new platform — CIME master documentation
Start with some simple cases and move slowly toward your goal.

abhisheklodh · Apr 5, 2023

Hi,
I could install and run the CESMv2.2 model. The cpmset option i choosed is : 2000_CAM%SPCAMM_CLM50%SP_CICE%PRES_DOCN%DOM_RTM_SGLC_SWAV
The status is as follows :

------------------------------------------------------------------------
- Prestage required restarts into /home/abhishekl/OUTPUT/CESM/scratch/f19_f19_spcam_slnd/run
- Case input data directory (DIN_LOC_ROOT) is /home/abhishekl/OUTPUT/CESM/cesm-inputdata
- Checking for required input datasets in DIN_LOC_ROOT
run command is mpirun -np 8 --prepend-rank /home/abhishekl/OUTPUT/CESM/scratch/f19_f19_spcam_slnd/bld/cesm.exe >> cesm.log.$LID 2>&1
-------------------------------------------------------------------------
Also the one moment microphysics case is running.

It will be a real help to know the steps to run a 3D version of the SP (super parameterization)-CAM model over the global domain ???
Thanks in advance.

Issue in .case_build

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