Error in compiling bio_toy

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mariefrahman
Posts: 8
Joined: Wed Jun 14, 2023 2:54 am
Location: Meteorological agency of Indonesia (BMKG)

Error in compiling bio_toy

#1 Unread post by mariefrahman »

Hi all,

I found this error when compiling build_roms.sh on the bio_toy test case, I didn't find this error when trying the upwelling test case. does anyone know how to solve this error?

Thank you.
Arief

Code: Select all

biology.f90:1:1:

    1 | /
      | 1
Error: Invalid character in name at (1)
biology.f90:2:1:

    2 | *
      | 1
Error: Invalid character in name at (1)
biology.f90:3:2:

    3 | ** git $Id$
      |  1
Error: Invalid character in name at (1)
biology.f90:4:2:

    4 | ************************************************************************
      |  1
Error: Invalid character in name at (1)
biology.f90:5:2:

    5 | **                                                                    **
      |  1
Error: Invalid character in name at (1)
biology.f90:6:2:

    6 | ** The current design allows the user to have a lot of latitude for   **
      |  1
Error: Invalid character in name at (1)
biology.f90:7:2:

    7 | ** customizing or adding any particular ecosystem model.              **
.
.
.
Error: Invalid character in name at (1)
biology.f90:98:2:

   98 | */
      |  1
Error: Invalid character in name at (1)
cd /home/roms/Project/roms_test/bio_toy/Build_romsM; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -O3 -ffast-math ADfromTL.f90
cd /home/roms/Project/roms_test/bio_toy/Build_romsM; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -O3 -ffast-math state_dotprod.f90
cd /home/roms/Project/roms_test/bio_toy/Build_romsM; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -O3 -ffast-math state_initialize.f90
make: *** [ROMS/Nonlinear/Biology/Module.mk:14: /home/roms/Project/roms_test/bio_toy/Build_romsM/biology.o] Error 1
make: *** Waiting for unfinished jobs....
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mariefrahman
Posts: 8
Joined: Wed Jun 14, 2023 2:54 am
Location: Meteorological agency of Indonesia (BMKG)

Re: Error in compiling bio_toy

#2 Unread post by mariefrahman »

Hi all,

I think i find a way to solve this. I change something in /ROMS/Nonlinear/Biology/biology.F

from this

Code: Select all

#include "cppdefs.h"
#if defined NONLINEAR && defined BIOLOGY
/
*
** git $Id$
to this

Code: Select all

#include "cppdefs.h"
#if defined NONLINEAR && defined BIOLOGY

/*
** git $Id$
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mariefrahman
Posts: 8
Joined: Wed Jun 14, 2023 2:54 am
Location: Meteorological agency of Indonesia (BMKG)

Re: Error in compiling bio_toy

#3 Unread post by mariefrahman »

Hi all,

another thing, Does anyone know why the input data cannot be used when running the model?

Code: Select all

 Process Information:

 Node #    0 (pid=   21169) is active.

 INITIAL: Configuring and initializing forward nonlinear model ...
 *******
 Found Error: -51  Line: 9402     Source: ROMS/Modules/mod_netcdf.F, netcdf_open

 NETCDF_OPEN - unable to open existing NetCDF file:
               /home/coawst/roms/Project/roms_test/bio_toy/Data/bio_toy_grd.nc
               call from:  ROMS/Utility/get_grid.F, get_grid_nf90
               NetCDF: Unknown file format
 Found Error: 3    Line: 154      Source: ROMS/Utility/get_grid.F, get_grid_nf90

 GET_GRID_NF90 - unable to open grid NetCDF file: /home/coawst/roms/Project/roms_test/bio_toy/Data/bio_toy_grd.nc
 Found Error: 3    Line: 91       Source: ROMS/Utility/get_grid.F
 Found Error: 3    Line: 88       Source: ROMS/Utility/set_grid.F
 Found Error: -51  Line: 9402     Source: ROMS/Modules/mod_netcdf.F, netcdf_open

 NETCDF_OPEN - unable to open existing NetCDF file:
               /home/coawst/roms/Project/roms_test/bio_toy/Data/bio_toy_ini_fennel.nc
               call from:  ROMS/Utility/get_state.F, get_state_nf90
               NetCDF: Unknown file format
 Found Error: 3    Line: 308      Source: ROMS/Utility/get_state.F, get_state_nf90

  GET_STATE_NF90 - NLM: unable to open input NetCDF file: /home/coawst/roms/Project/roms_test/bio_toy/Data/bio_toy_ini_fennel.nc
 Found Error: 3    Line: 151      Source: ROMS/Utility/get_state.F
 Found Error: 3    Line: 420      Source: ROMS/Nonlinear/initial.F
 Found Error: 3    Line: 211      Source: ROMS/Drivers/nl_roms.h, ROMS_initialize

Elapsed wall CPU time for each process (seconds):

 Node   #    0 CPU:       0.000
 Total:                   0.000

  Unique kernel(s) regions profiled ................         0.000       NaN %
  Residual, non-profiled code ......................         0.000       NaN %


 All percentages are with respect to total time =            0.000


>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

 Dynamic and Automatic memory (MB) usage for Grid 01:  4x4x30  tiling: 1x1

     tile          Dynamic        Automatic            USAGE      MPI-Buffers

        0             6.73             0.45             7.18             0.00

    TOTAL             6.73             0.45             7.18             0.00

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 Found Error: 3    Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 3    Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 3    Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 3    Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90
 Found Error: 3    Line: 85       Source: ROMS/Utility/close_io.F, close_file_nf90

 ROMS/TOMS - Output NetCDF summary for Grid 01:
 Found Error: 3    Line: 413      Source: ROMS/Utility/close_io.F, close_out

 ROMS/TOMS - Output error ............ exit_flag: 3


 ERROR: Abnormal termination: NetCDF OUTPUT.
 REASON: NetCDF: Unknown file format
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DIVIDE_BY_ZERO
ERROR STOP

Error termination. Backtrace:
#0  0x7fa9c5a83960 in ???
#1  0x7fa9c5a844d9 in ???
#2  0x7fa9c5a85b47 in ???
#3  0x7fa9c5e4cf64 in ???
#4  0x7fa9c5e4cb8e in ???
#5  0x7fa9c55c9d8f in __libc_start_call_main
        at ../sysdeps/nptl/libc_start_call_main.h:58
#6  0x7fa9c55c9e3f in __libc_start_main_impl
        at ../csu/libc-start.c:392
#7  0x7fa9c5e4cbe4 in ???
#8  0xffffffffffffffff in ???
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[36777,1],0]
  Exit code:    1
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jcwarner
Posts: 1197
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: Error in compiling bio_toy

#4 Unread post by jcwarner »

i think the path needs to be
Data/ROMS/grid/bio_toy.nc
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