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This occurs when using Python 3 rather than Python 2. Module load python2.7.X and clean build.

(4) Build error - fail with 'isalnum'

During the model build the following error occurs:

error: call to undeclared library function 'isalnum' with type 'int (int)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]

To address this error went into: $CESM_ROOT/components/cism/source_cism/libglimmer/

Opened: writestats.c and added the line: 

#include <ctype.h>

to the include header section. The case was set up again and subsequently built and ran successfully.

This error was addressed in the discussion board comments:
https://bb.cgd.ucar.edu/cesm/threads/installing-cesm2-on-perlmutter.8488/
https://bb.cgd.ucar.edu/cesm/threads/cism-buildlib-failed-for-cesm2-1-4-on-derecho.8543/

(5) Submit error - files missing

Cloning and creating a branch is complete but the following error occurs:

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c) [Clone only] Make sure initialization files are not defined in the user_nl_cam or user_nl_clm files (i.e. remove those lines if they are there).

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6) Run error - model crash due to MPT error (not relevant anymore)

With a recent update to the MPT system on cheyenne during March 2019, the env_mach_specific.xml file needs to be updated. Otherwise you will be able to submit, but will find the simulation crashes with this error in the cesm.log.XXX file:

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>./case.setup --reset
>./case.build --clean
>./case.build

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7) Run error - model crash due to dry deposition

(seq_drydep_read) Read in drydep_inparm namelist from: drv_flds_in
 ERROR: (seq_drydep_read) ERROR: encountered end-of-file on namelist read

This error occurs when you add a gas species and make it to be dry deposited by adding the species name into ‘drydep_list’ in ‘&drydep_inparm’, but you don’t modify seq_drydep_mod.F90. See instructions on https://wiki.ucar.edu/display/camchem/Updating+Gas-Phase+Chemistry

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8) Run error - model crash past 2016

To run past 2016 you will need to make sure the correct sea ice specification is called. Edit in env_run.xml:

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Which repeats 2018 SSTs for 2019 and 2020.

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9) Run error - model crash due to rpointer.drv file check

(seq_infodata_Init) read rpointer file rpointer.drv
(seq_infodata_Init) restart file from rpointer= str_undefined
(seq_io_read_openfile) ERROR: file invalid str_undefined
ERROR: Unknown error submitted to shr_abort_abort.

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>./xmlchange CONTINUE_RUN=FALSE

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10) Run error - model crash due to meteorology defintion issues

The model freezes after or during reading in the LBC file. The atm.log.* file gives an error such as:

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Make sure your meteorology nudging style is consistent - i.e. you are calling Specified Dynamics everywhere or Physics-based nudging everywhere. The specific error above occurred when creating a new case with the FCnudged compset, but changing CAM_CONFIG_OPTS=‘-phys cam6 -chem trop_strat_mam4_vbs -age_of_air_trcs -offline_dyn -nlev 32’. Instead, it should be left at: CAM_CONFIG_OPTS: -phys cam6 -chem trop_strat_mam4_vbs -age_of_air_trcs.

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11) Run error - model crash in "shr_reprosum_calc"

The model crashed with an error in the atm.log.* such as:

Global flash freq (/s), lightning NOx (TgN/y) =   267.0744   13.8985

SHR_REPROSUM_CALC: Input contains  0.96000E+02 NaNs and  0.00000E+00 INFs on process       0

ERROR: shr_reprosum_calc ERROR: NaNs or INFs in input

Check which meteorology file the the model was most recently using, then perform an ncdump on the U, V and T variables to check whether there are missing values. The meteorology file will likely need to be reprocessed.

(12) NetCDF file version error (as of CESM2.2, may be solved in future versions)

If you provide emissions or any input files in NetCDF version 4 (either NetCDF4 or NetCDF4_classic), the model will crash.

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