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GNU compiler error

Yongzuo123

Yongzuo Li
New Member
When I try to run the test case
MOM6-examples/ocean_only/MESO_025_63L
I get the error:
FATAL from PE 13: fms_io(read_data_3d_new), field u in file INPUT/MESO_025_63L_IC.nc: field size mismatch 1
Could this be due to me using NetCDF 4?
We generally use netcdf 4, our netcdf 4 is compiled with the same GNU compiler I'm using. When I compile the FMS and MOM6 I use the option:
(cd build/gnu/shared/repro/; make NETCDF=4 REPRO=1 libfms.a -j)
I tried compiling FMS and MOM6 with netcdf3 but we only have netcdf 4 here at NRL. I get the same error.
Could this be the problem?
If I go back to an old version of netcdf 3, then I would have to use an old compiler, which I know will have problems.
Any ideas?
I am new MOM6 user. I also have error “FATAL from PE 140”. How did you solve this error?
Thank you
Yongzuo
 

Yongzuo123

Yongzuo Li
New Member
Hey, I just impressed myself, if nobody else. Based on Bob Hallberg's instructions, I went into MOM_horizontal_regridding.F90 and added the filename and variable name to the error message! Now I get more information about my error:

FATAL from PE 14: error in INPUT/hycom_type_ts_data_mimi_z100.nc inquiring dimensions for water_temp hinterp_extrap

FATAL from PE 15: error in INPUT/hycom_type_ts_data_mimi_z100.nc inquiring dimensions for water_temp hinterp_extrap

[wyman.code7300.nrlssc.navy.mil:16775] 18 more processes have sent help message help-mpi-api.txt / mpi-abort
[wyman.code7300.nrlssc.navy.mil:16775] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

Thanks for your help!
Hi Bob,
Did you solve “FATAL from PE” problem? I have the same problem.
Thanks
Yongzuo
 

helber

Bob Helber
New Member
I am new MOM6 user. I also have error “FATAL from PE 140”. How did you solve this error?
Thank you
Yongzuo
I have not solved my problem. It is perplexing. It keeps complaining about my netcdf files. I even tried the MESO_025_63L test case with the test data sets and still get the problem. I'm using GNU compilers. My best guess is that it is a compiler issue. I'm planning on using a different compiler and different machine. I'll post here when I figure out what the problem is.
 

helber

Bob Helber
New Member
Just tried to run MESO_025_63L on a different machine using intel compilers and get the same error:
FATAL from PE 0: fms_io(read_data_3d_new), field u in file INPUT/MESO_025_63L_IC.nc: field size mismatch 1
Actually, this is not a compiler error. The model compiles just fine. It fails when I try to run a test case with netcdf inputs.
 

helber

Bob Helber
New Member
Just tried to run MESO_025_63L on a different machine using intel compilers and get the same error:
FATAL from PE 0: fms_io(read_data_3d_new), field u in file INPUT/MESO_025_63L_IC.nc: field size mismatch 1
Actually, this is not a compiler error. The model compiles just fine. It fails when I try to run a test case with netcdf inputs.
Just ran test case MESO_025_23L and that runs fine. Neither of the input initial condition netcdf files have unit attributes.
One difference are MESO_025_63L has initial velocities:

float u(Layer, latitude, longitude_q) ;
float v(Layer, latitude_q, longitude) ;
In this case, both q and non-q dimensions in the IC are the same.
 
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