We hope you don’t run into these errors. But if you do, we hope they will be a useful reference.
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WRF-GC has several output files. Most GEOS-Chem output is in the root CPU output file,
rsl.out.0000. Look in this file for any GEOS-Chem related errors. HEMCO-related errors are in
HEMCO.log. WRF-related errors can be in any of the files numbered
rsl.out.*. You may want to use
tail -n 5 rsl.* | less to quickly look at all log files to identify errors.
THe HEMCO error log,
HEMCO.log, only writes errors/warnings from the root process. In order to see HEMCO errors for all processes, edit
HEMCO_Config.rc and set
*. Then you will be able to see HEMCO logs for all processes in the
error #7013: This module file was not generated by any release of this compiler.
Did you copy your WRF-GC directory from somewhere else? Some module files appear to be lingering over from a previous compile. Try running
./clean -a, reconfiguring WRF-GC (
./configure -hyb for WRFV3,
./configure for WRFV4), and rebuliding (
ld: cannot find -lGIGC -lHistory -lGeosCore -lHistory -lKpp -lGeosCore -lIsorropia -lHCOI -lHCOX -lHCO -lGeosUtil -lKpp -lHeaders -lNcUtils
A few things to check:
WRF/chem/gc/lib. Do you see all these files?
WRF/chem/gc/lib$ ls libGeosCore.a libGIGC.a libHCOI.a libHeaders.a libIsorropia.a libNcUtils.a libGeosUtil.a libHCO.a libHCOX.a libHistory.a libKpp.a libObsPack.a
If yes, proceed to 2. If no, GEOS-Chem was not compiled correctly. Go to
make compile_chem, then check if there are any errors.
WRF/main/Makefile. Search for something like
... -L/n/home04/hplin/wrfgc_dev_202110/WRF/chem/gc/lib -lHistory ....
Does this path, which points to
chem/gc/lib, exist and is correct? Is is the same path as 1?
If no, go to step 3. The error is because you (or someone) moved your WRF-GC directly after compiling it once. We can fix this.
WRF/main/Makefile. Make sure this replaced version does not have
-lGIGCanywhere within this file. If yes, download a fresh copy of WRF and move the
main/Makefilefrom there into
Now, go to
make compile_chem. Verify that
chem/gc/libpointing to the right path. Go back to the root WRF directory and compile again:
./compile em_real. No clean is necessary.
This happens in
mozbc. Check if you have netCDF-C and netCDF-Fortran in the same directory. Your
$NETCDF_DIR should include
include/libnetcdff.a - if not, you’re missing the netCDF-Fortran.
lib64: file not recognized: Is a directory; make: [geogrid.exe] Error 1 (ignored)`.
This may happen if you are on a cluster and are compiling WPS. Run
export MPI_LIB="" then recompile WPS.
Cannot find input.geos, HEMCO_Config.rc or other configuration files in the run directory after compile
Make sure that you have compiled with
export WRF_CHEM=1, which enables chemistry compilation. If this was not done, you must start over going to
./clean -a, then
./compile em_real again.
Error: Dummy argument ‘datasetname’ with INTENT(IN) in variable definition context (actual argument to INTENT = OUT/INOUT) at (1)
This happens if you are using GNU Fortran (gfortran) compilers version 10 and above to try to build WRF v3. You may have to apply these patches manually to your WRF installation to get gfortran to compile.
If you see anything on this list, this is not the root cause - this means that there’s an error somewhere else! Always check other log files (
rsl.*) and also further upstream in the error files first.
HEMCO ERROR: MaxNest too low, cannot enter GET_TIMEIDX (hco_read_std_mod.F90)
Any kind of error that says
HEMCO ERROR: MaxNest too low means that there is an error somewhere above, in
HEMCO.log. Check further! See GEOS-Chem ERROR: Error encountered in “HCO_Run”! -> at HCOI_GC_Run (in module GeosCore/hcoi_gc_main_mod.F90).
forrtl: severe (408): fort: (2): Subscript #1 of the array LOC has value 11 which is greater than the upper bound of 10
This means that there is an error in
HEMCO.log - check the HEMCO log instead! Maybe inventories are missing, etc. Also, see GEOS-Chem ERROR: Error encountered in “HCO_Run”! -> at HCOI_GC_Run (in module GeosCore/hcoi_gc_main_mod.F90).
forrtl: severe (408): fort: (2): Subscript #1 of the array ZPJ has value 1 which is greater than the upper bound of -1
Same! Check rsl.error. files for another error - it may be hundreds of lines above (searching for
GEOS-Chem ERROR: or
REQUIRED FILE NOT FOUND helps).
It may be helpful to first check this: FAST-JX (RD_XXX): REQUIRED FILE NOT FOUND to make sure your
input.geos paths are correct.
This error indicates that another error occurred somewhere upstream.
forrtl: error (78): process killed (SIGTERM)
Check if your system has enough memory. Also, check
rsl.out.0000 – this is usually an error within GEOS-Chem.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Check if your system has enough memory and try to run with
ulimit -c unlimited,
ulimit -s unlimited.
This may also mean there is an error somewhere else upstream. Look further below for a “stack trace”, e.g.,
forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source wrf.exe xxxxxxxxxxxxxxxx Unknown Unknown Unknown libpthread-2.17.s xxxxxxxxxxxxxxxx Unknown Unknown Unknown wrf.exe xxxxxxxxxxxxxxxx error_mod_mp_erro 437 error_mod.F90 wrf.exe xxxxxxxxxxxxxxxx flexchem_mod_mp_d 1057 flexchem_mod.F90 wrf.exe xxxxxxxxxxxxxxxx chemistry_mod_mp_ 299 chemistry_mod.F90 wrf.exe xxxxxxxxxxxxxxxx gigc_chunk_mod_mp 1277 gigc_chunk_mod.F90
Then look in this page for the error that corresponds to where the model has crashed.
Exit 152 mpirun -np ./wrf.exe
Check if your system / cluster job is allowing for enough memory. Also, check errors in other
forrtl: error (78): process killed (SIGTERM)
Check other files first - this CPU is not the root cause of the problem.
Not actually errors
Cannot find -lGCHPint
This is not an error, ignore. If you cannot successfully compile WRF-GC, there is an error above in the compile log.
cannot stat ‘geos’: No such file or directory
Also shows sometimes as
make: [exe] Error 1 (ignored). This is not an error, ignore. If you cannot successfully compile WRF-GC, there is an error above in the compile log.
Trapping levels are weird and they should not be equal
This doesn’t seem to be an issue. If your run was interrupted, there might be an error elsewhere.
47 more processes have sent help message help-mpi-btl-openib.txt / no device params found
This is usually not an issue. If your run stopped, check all the other run files.
tropopause_climate: Warning: Done finding tropopause
This is not an issue, but may be related to your model vertical level configuration. If your outputs look reasonable, it is safe to ignore.