Problem with the file makefile

Discussion on computers, ROMS installation and compiling

Moderators: arango, robertson

Post Reply
Message
Author
alexandrosmf
Posts: 5
Joined: Sun May 26, 2019 3:56 pm
Location: University of Aegean/ Greece

Problem with the file makefile

#1 Post by alexandrosmf » Tue Jun 25, 2019 10:47 pm

Hello guys,

I am quite new in the community. I am trying to compile ROMS. So, when I type make, it gives me the following error

Code: Select all

cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math mod_netcdf.f90
Fatal Error: While reading module 'netcdf' found module version 0, expected 9.
ROMS/Modules/Module.mk:15: recipe for target 'Build/mod_netcdf.o' failed
make: *** [Build/mod_netcdf.o] Error 1

Code: Select all

~/src$ make
cp -f /usr/include/netcdf.mod Build
cp -f /usr/include/typesizes.mod Build
cp -p /home/al/make_macros.mk Build
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Utility/obs_depth.F > Build/obs_depth.f90
ROMS/Bin/cpp_clean Build/obs_depth.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_fourdvar.F > Build/mod_fourdvar.f90
ROMS/Bin/cpp_clean Build/mod_fourdvar.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_iounits.F > Build/mod_iounits.f90
ROMS/Bin/cpp_clean Build/mod_iounits.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_param.F > Build/mod_param.f90
ROMS/Bin/cpp_clean Build/mod_param.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_kinds.F > Build/mod_kinds.f90
ROMS/Bin/cpp_clean Build/mod_kinds.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math mod_kinds.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math mod_param.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math mod_iounits.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_ncparam.F > Build/mod_ncparam.f90
ROMS/Modules/mod_ncparam.F:1165:0: warning: extra tokens at end of #ifdef directive
 #ifdef ECOSIM && defined DIAGNOSTICS_BIO
 
ROMS/Bin/cpp_clean Build/mod_ncparam.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_biology.F > Build/mod_biology.f90
ROMS/Bin/cpp_clean Build/mod_biology.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_scalars.F > Build/mod_scalars.f90
ROMS/Bin/cpp_clean Build/mod_scalars.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math -ffree-form -ffree-line-length-huge mod_scalars.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math -ffree-form -ffree-line-length-huge mod_biology.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_parallel.F > Build/mod_parallel.f90
ROMS/Bin/cpp_clean Build/mod_parallel.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"' -DMY_OS='"Linux"' -DMY_CPU='"x86_64"' -DMY_FORT='"g95"' -DMY_FC='"/usr/bin/g95"' -DMY_FFLAGS='"-fno-second-underscore -O3 -ffast-math -ffree-form -ffree-line-length-huge -ffree-form -ffree-line-length-huge"'  ROMS/Modules/mod_strings.F > Build/mod_strings.f90
ROMS/Bin/cpp_clean Build/mod_strings.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math -ffree-form -ffree-line-length-huge -ffree-form -ffree-line-length-huge mod_strings.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math -ffree-form -ffree-line-length-huge mod_parallel.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_sediment.F > Build/mod_sediment.f90
ROMS/Bin/cpp_clean Build/mod_sediment.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math -ffree-form -ffree-line-length-huge mod_sediment.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math -ffree-form -ffree-line-length-huge mod_ncparam.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Modules/mod_netcdf.F > Build/mod_netcdf.f90
ROMS/Bin/cpp_clean Build/mod_netcdf.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Utility/dateclock.F > Build/dateclock.f90
ROMS/Bin/cpp_clean Build/dateclock.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Utility/round.F > Build/round.f90
ROMS/Bin/cpp_clean Build/round.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math round.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math dateclock.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Utility/distribute.F > Build/distribute.f90
ROMS/Bin/cpp_clean Build/distribute.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math distribute.f90
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/src/ROMS/Functionals"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/al/src/ROMS/Include"'  ROMS/Utility/strings.F > Build/strings.f90
ROMS/Bin/cpp_clean Build/strings.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math strings.f90
cd Build; /usr/bin/g95 -c -fno-second-underscore -O3 -ffast-math mod_netcdf.f90
Fatal Error: While reading module 'netcdf' found module version 0, expected 9.
ROMS/Modules/Module.mk:15: recipe for target 'Build/mod_netcdf.o' failed
make: *** [Build/mod_netcdf.o] Error 1

I also tried to compile the upwelling project (As suggest it from the page https://www.myroms.org/wiki/ROMS_UNSW2008#Compile_ROMS) but still, I have the following problem:

Code: Select all

~/Projects/upwelling$ ./build_roms.bash 
rm -f -r core *.ipo /home/al/Projects/upwelling/Build_romsG /home/al/make_macros.mk
cp -f /usr/include/netcdf.mod /home/al/Projects/upwelling/Build_romsG
cp -f /usr/include/typesizes.mod /home/al/Projects/upwelling/Build_romsG
cp -p /home/al/make_macros.mk /home/al/Projects/upwelling/Build_romsG
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/al/Projects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/Projects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -I/home/al/Projects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/home/al/Projects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/home/al/Projects/upwelling"'  ROMS/Utility/obs_depth.F > /home/al/Projects/upwelling/Build_romsG/obs_depth.f90
ROMS/Bin/cpp_clean /home/al/Projects/upwelling/Build_romsG/obs_depth.f90
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/al/Projects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/Projects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -I/home/al/Projects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/home/al/Projects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/home/al/Projects/upwelling"'  ROMS/Modules/mod_fourdvar.F > /home/al/Projects/upwelling/Build_romsG/mod_fourdvar.f90
ROMS/Bin/cpp_clean /home/al/Projects/upwelling/Build_romsG/mod_fourdvar.f90
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/al/Projects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/Projects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -I/home/al/Projects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/home/al/Projects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/home/al/Projects/upwelling"'  ROMS/Modules/mod_iounits.F > /home/al/Projects/upwelling/Build_romsG/mod_iounits.f90
ROMS/Bin/cpp_clean /home/al/Projects/upwelling/Build_romsG/mod_iounits.f90
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/al/Projects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/Projects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -I/home/al/Projects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/home/al/Projects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/home/al/Projects/upwelling"'  ROMS/Modules/mod_param.F > /home/al/Projects/upwelling/Build_romsG/mod_param.f90
ROMS/Bin/cpp_clean /home/al/Projects/upwelling/Build_romsG/mod_param.f90
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/al/src"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/al/Projects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/al/Projects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_URL="https://www.myroms.org/svn/src/trunk"' -D'SVN_REV="969"' -IROMS/Include -I/home/al/Projects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/home/al/Projects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/home/al/Projects/upwelling"'  ROMS/Modules/mod_kinds.F > /home/al/Projects/upwelling/Build_romsG/mod_kinds.f90
ROMS/Bin/cpp_clean /home/al/Projects/upwelling/Build_romsG/mod_kinds.f90
cd /home/al/Projects/upwelling/Build_romsG;  -c -fno-second-underscore -g -fbounds-check -ftrace=full mod_kinds.f90
/bin/sh: 1: -c: not found
ROMS/Modules/Module.mk:15: recipe for target '/home/al/Projects/upwelling/Build_romsG/mod_kinds.o' failed
make: *** [/home/al/Projects/upwelling/Build_romsG/mod_kinds.o] Error 127
Thanks

User avatar
kate
Posts: 3717
Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: Problem with the file makefile

#2 Post by kate » Tue Jun 25, 2019 11:38 pm

cp -f /usr/include/netcdf.mod /home/al/Projects/upwelling/Build_romsG
cp -f /usr/include/typesizes.mod /home/al/Projects/upwelling/Build_romsG
It is looking for the netcdf.mod file which got copied into the Build directory. You know those files got copied, but what compiler was used to make them? I'm guessing a different compiler from the one you are using now. You have to have one from the same compiler - and same version - as your current compiler. Sometimes the easiest way to achieve that is to compile netCDF and netCDF-Fortran yourself, sticking it under your home directory or some other safe place.

alexandrosmf
Posts: 5
Joined: Sun May 26, 2019 3:56 pm
Location: University of Aegean/ Greece

Re: Problem with the file makefile

#3 Post by alexandrosmf » Wed Jun 26, 2019 8:50 pm

Thank you very much Kate!
I compiled with gfortran everything from the beginning and of course the netCDF and netCDF-Fortran as you indicate. Although I had progress with the compile, I stuck in the following:

Code: Select all

Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_dim':
mod_netcdf.f90:(.text+0x16fff): undefined reference to `__netcdf_MOD_nf90_inquire'
mod_netcdf.f90:(.text+0x171b6): undefined reference to `__netcdf_MOD_nf90_inquire_dimension'
collect2: error: ld returned 1 exit status
Master/Module.mk:22: recipe for target 'romsS' failed
make: *** [romsS] Error 1

Thank you!

User avatar
kate
Posts: 3717
Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: Problem with the file makefile

#4 Post by kate » Wed Jun 26, 2019 9:11 pm

Now you have to tell it where to find the netCDF libraries at link time, both via the makefile and also via LD_LIBRARY_PATH or whatever the equivalent is on your OS (I live in a Linux world now).

alexandrosmf
Posts: 5
Joined: Sun May 26, 2019 3:56 pm
Location: University of Aegean/ Greece

Re: Problem with the file makefile

#5 Post by alexandrosmf » Fri Jun 28, 2019 11:00 am

Thanks, Kate again!

Finally, it gave me the executable romsS. I tried to run the command:

Code: Select all

 ./romsG ocean_upwelling.in
Only the following has appeared:

Code: Select all

~/Projects/upwelling$ ./romsG ocean_upwelling.in
--------------------------------------------------------------------------------
 Model Input Parameters:  ROMS/TOMS version 3.7  
                          Friday - June 27, 2019 - 09:37:56 AM
--------------------------------------------------------------------------------
Is it normal? I run it within a normal computer with the Ubuntu 18.04, the processor is Intel® Core™ i5-4300U CPU @ 1.90GHz × 4 and the RAM is 3.8 GiB. I know that ROMS is meant for running in supercomputers.
The strange thing is that it does not consume a lot of resources like the CPU or the RAM memory.

Thanks

User avatar
kate
Posts: 3717
Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: Problem with the file makefile

#6 Post by kate » Fri Jun 28, 2019 2:50 pm

If you have a romsS, it is a serial executable. Run it with:

Code: Select all

romsS < roms_upwelling.in
The way you had it, it was waiting for you to type in the whole of roms_upwelling to standard-in (stdin).

alexandrosmf
Posts: 5
Joined: Sun May 26, 2019 3:56 pm
Location: University of Aegean/ Greece

Re: Problem with the file makefile

#7 Post by alexandrosmf » Sat Jun 29, 2019 6:31 pm

Do you know why it cannot create the netcdf file?

Code: Select all

~/Projects/upwelling$ ./romsS < ocean_upwelling.in
--------------------------------------------------------------------------------
 Model Input Parameters:  ROMS/TOMS version 3.7  
                          Saturday - June 29, 2019 -  7:19:06 PM
--------------------------------------------------------------------------------

 Wind-Driven Upwelling/Downwelling over a Periodic Channel

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : gfortran
 Compiler command : /usr/bin/gfortran
 Compiler flags   : -frepack-arrays -O3 -ffast-math -

 SVN Root URL     : https://www.myroms.org/svn/src/trunk
 SVN Revision     : 969

 Local Root       : /home/al/src
 Header Dir       : /home/al/src/ROMS/Include
 Header file      : upwelling.h
 Analytical Dir   : /home/al/src/ROMS/Functionals

 Resolution, Grid 01: 41x80x16,  Parallel Threads: 1,  Tiling: 2x1


 Physical Parameters, Grid: 01
 =============================

       1440  ntimes            Number of timesteps for 3-D equations.
    300.000  dt                Timestep size (s) for 3-D equations.
         30  ndtfast           Number of timesteps for 2-D equations between
                                 each 3D timestep.
          1  ERstr             Starting ensemble/perturbation run number.
          1  ERend             Ending ensemble/perturbation run number.
          0  nrrec             Number of restart records to read from disk.
          T  LcycleRST         Switch to recycle time-records in restart file.
        288  nRST              Number of timesteps between the writing of data
                                 into restart fields.
          1  ninfo             Number of timesteps between print of information
                                 to standard output.
          T  ldefout           Switch to create a new output NetCDF file(s).
         72  nHIS              Number of timesteps between the writing fields
                                 into history file.
 1904844672  nQCK              Number of timesteps between the writing fields
                                 into quicksave file.
 1904843264  ndefQCK           Number of timesteps between creation of new
                                 brief snpashots files.
          1  ntsAVG            Starting timestep for the accumulation of output
                                 time-averaged data.
         72  nAVG              Number of timesteps between the writing of
                                 time-averaged data into averages file.
          1  ntsDIA            Starting timestep for the accumulation of output
                                 time-averaged diagnostics data.
         72  nDIA              Number of timesteps between the writing of
                                 time-averaged data into diagnostics file.
 0.0000E+00  nl_tnu2(01)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 01: temp
 0.0000E+00  nl_tnu2(02)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 02: salt
 5.0000E+00  nl_visc2          NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for momentum.
          F  LuvSponge         Turning OFF sponge on horizontal momentum.
          F  LtracerSponge(01) Turning OFF sponge on tracer 01: temp
          F  LtracerSponge(02) Turning OFF sponge on tracer 02: salt
 1.0000E-06  Akt_bak(01)       Background vertical mixing coefficient (m2/s)
                                 for tracer 01: temp
 1.0000E-06  Akt_bak(02)       Background vertical mixing coefficient (m2/s)
                                 for tracer 02: salt
 1.0000E-05  Akv_bak           Background vertical mixing coefficient (m2/s)
                                 for momentum.
 3.0000E-04  rdrg              Linear bottom drag coefficient (m/s).
 3.0000E-03  rdrg2             Quadratic bottom drag coefficient.
 2.0000E-02  Zob               Bottom roughness (m).
          2  Vtransform        S-coordinate transformation equation.
          4  Vstretching       S-coordinate stretching function.
 3.0000E+00  theta_s           S-coordinate surface control parameter.
 0.0000E+00  theta_b           S-coordinate bottom  control parameter.
     25.000  Tcline            S-coordinate surface/bottom layer width (m) used
                                 in vertical coordinate stretching.
   1025.000  rho0              Mean density (kg/m3) for Boussinesq approximation.
      0.000  dstart            Time-stamp assigned to model initialization (days).
       0.00  time_ref          Reference time for units attribute (yyyymmdd.dd)
 0.0000E+00  Tnudg(01)         Nudging/relaxation time scale (days)
                                 for tracer 01: temp
 0.0000E+00  Tnudg(02)         Nudging/relaxation time scale (days)
                                 for tracer 02: salt
 0.0000E+00  Znudg             Nudging/relaxation time scale (days)
                                 for free-surface.
 0.0000E+00  M2nudg            Nudging/relaxation time scale (days)
                                 for 2D momentum.
 0.0000E+00  M3nudg            Nudging/relaxation time scale (days)
                                 for 3D momentum.
 0.0000E+00  obcfac            Factor between passive and active
                                 open boundary conditions.
          F  VolCons(1)        NLM western  edge boundary volume conservation.
          F  VolCons(2)        NLM southern edge boundary volume conservation.
          F  VolCons(3)        NLM eastern  edge boundary volume conservation.
          F  VolCons(4)        NLM northern edge boundary volume conservation.
     14.000  T0                Background potential temperature (C) constant.
     35.000  S0                Background salinity (PSU) constant.
   1027.000  R0                Background density (kg/m3) used in linear Equation
                                 of State.
 1.7000E-04  Tcoef             Thermal expansion coefficient (1/Celsius).
 0.0000E+00  Scoef             Saline contraction coefficient (1/PSU).
      1.000  gamma2            Slipperiness variable: free-slip (1.0) or 
                                                      no-slip (-1.0).
          F  LuvSrc            Turning OFF momentum point Sources/Sinks.
          F  LwSrc             Turning OFF volume influx point Sources/Sinks.
          F  LtracerSrc(01)    Turning OFF point Sources/Sinks on tracer 01: temp
          F  LtracerSrc(02)    Turning OFF point Sources/Sinks on tracer 02: salt
          F  LsshCLM           Turning OFF processing of SSH climatology.
          F  Lm2CLM            Turning OFF processing of 2D momentum climatology.
          F  Lm3CLM            Turning OFF processing of 3D momentum climatology.
          F  LtracerCLM(01)    Turning OFF processing of climatology tracer 01: temp
          F  LtracerCLM(02)    Turning OFF processing of climatology tracer 02: salt
          F  LnudgeM2CLM       Turning OFF nudging of 2D momentum climatology.
          F  LnudgeM3CLM       Turning OFF nudging of 3D momentum climatology.
          F  LnudgeTCLM(01)    Turning OFF nudging of climatology tracer 01: temp
          F  LnudgeTCLM(02)    Turning OFF nudging of climatology tracer 02: salt

          T  Hout(idFsur)      Write out free-surface.
          T  Hout(idUbar)      Write out 2D U-momentum component.
          T  Hout(idVbar)      Write out 2D V-momentum component.
          T  Hout(idUvel)      Write out 3D U-momentum component.
          T  Hout(idVvel)      Write out 3D V-momentum component.
          T  Hout(idWvel)      Write out W-momentum component.
          T  Hout(idOvel)      Write out omega vertical velocity.
          T  Hout(idTvar)      Write out tracer 01: temp
          T  Hout(idTvar)      Write out tracer 02: salt

          T  Aout(idFsur)      Write out averaged free-surface.
          T  Aout(idUbar)      Write out averaged 2D U-momentum component.
          T  Aout(idVbar)      Write out averaged 2D V-momentum component.
          T  Aout(idUvel)      Write out averaged 3D U-momentum component.
          T  Aout(idVvel)      Write out averaged 3D V-momentum component.
          T  Aout(idWvel)      Write out averaged W-momentum component.
          T  Aout(idOvel)      Write out averaged omega vertical velocity.
          T  Aout(idTvar)      Write out averaged tracer 01: temp
          T  Aout(idTvar)      Write out averaged tracer 02: salt

          T  Dout(M2rate)      Write out 2D momentum acceleration.
          T  Dout(M2pgrd)      Write out 2D momentum pressure gradient.
          T  Dout(M2fcor)      Write out 2D momentum Coriolis force.
          T  Dout(M2hadv)      Write out 2D momentum horizontal advection.
          T  Dout(M2xadv)      Write out 2D momentum horizontal X-advection.
          T  Dout(M2yadv)      Write out 2D momentum horizontal Y-advection.
          T  Dout(M2hvis)      Write out 2D momentum horizontal viscosity.
          T  Dout(M2xvis)      Write out 2D momentum horizontal X-viscosity.
          T  Dout(M2yvis)      Write out 2D momentum horizontal Y-viscosity.
          T  Dout(M2sstr)      Write out 2D momentum surface stress.
          T  Dout(M2bstr)      Write out 2D momentum bottom stress.

          T  Dout(M3rate)      Write out 3D momentum acceleration.
          T  Dout(M3pgrd)      Write out 3D momentum pressure gradient.
          T  Dout(M3fcor)      Write out 3D momentum Coriolis force.
          T  Dout(M3hadv)      Write out 3D momentum horizontal advection.
          T  Dout(M3xadv)      Write out 3D momentum horizontal X-advection.
          T  Dout(M3yadv)      Write out 3D momentum horizontal Y-advection.
          T  Dout(M3vadv)      Write out 3D momentum vertical advection.
          T  Dout(M3hvis)      Write out 3D momentum horizontal viscosity.
          T  Dout(M3xvis)      Write out 3D momentum horizontal X-viscosity.
          T  Dout(M3yvis)      Write out 3D momentum horizontal Y-viscosity.
          T  Dout(M3vvis)      Write out 3D momentum vertical viscosity.

          T  Dout(iTrate)      Write out rate of change of tracer 01: temp
          T  Dout(iTrate)      Write out rate of change of tracer 02: salt
          T  Dout(iThadv)      Write out horizontal advection, tracer 01: temp
          T  Dout(iThadv)      Write out horizontal advection, tracer 02: salt
          T  Dout(iTxadv)      Write out horizontal X-advection, tracer 01: temp
          T  Dout(iTxadv)      Write out horizontal X-advection, tracer 02: salt
          T  Dout(iTyadv)      Write out horizontal Y-advection, tracer 01: temp
          T  Dout(iTyadv)      Write out horizontal Y-advection, tracer 02: salt
          T  Dout(iTvadv)      Write out vertical advection, tracer 01: temp
          T  Dout(iTvadv)      Write out vertical advection, tracer 02: salt
          T  Dout(iThdif)      Write out horizontal diffusion, tracer 01: temp
          T  Dout(iThdif)      Write out horizontal diffusion, tracer 02: salt
          T  Dout(iTxdif)      Write out horizontal X-diffusion, tracer 01: temp
          T  Dout(iTxdif)      Write out horizontal X-diffusion, tracer 02: salt
          T  Dout(iTydif)      Write out horizontal Y-diffusion , tracer 01: temp
          T  Dout(iTydif)      Write out horizontal Y-diffusion , tracer 02: salt
          T  Dout(iTvdif)      Write out vertical diffusion, tracer 01: temp
          T  Dout(iTvdif)      Write out vertical diffusion, tracer 02: salt

 Output/Input Files:

             Output Restart File:  ./out/ocean_rst.nc
             Output History File:  ./out/ocean_his.nc
            Output Averages File:  ./out/ocean_avg.nc
         Output Diagnostics File:  ./out/ocean_dia.nc

 Tile partition information for Grid 01:  41x80x16  tiling: 2x1

     tile     Istr     Iend     Jstr     Jend     Npts

        0        1       21        1       80    26880
        1       22       41        1       80    25600

 Tile minimum and maximum fractional coordinates for Grid 01:
   (interior points only)

     tile     Xmin     Xmax     Ymin     Ymax     grid

        0    -1.50    43.50     0.50    81.50  RHO-points
        1    -2.50    42.50     0.50    81.50  RHO-points

        0    -2.00    43.50     0.50    81.50    U-points
        1    -2.50    42.00     0.50    81.50    U-points

        0    -1.50    43.50     0.00    81.00    V-points
        1    -2.50    42.50     0.00    81.00    V-points

 Lateral Boundary Conditions: NLM
 ============================

 Variable               Grid  West Edge    South Edge   East Edge    North Edge
 ---------              ----  ----------   ----------   ----------   ----------

 zeta                     1   Periodic     Closed       Periodic     Closed

 ubar                     1   Periodic     Closed       Periodic     Closed

 vbar                     1   Periodic     Closed       Periodic     Closed

 u                        1   Periodic     Closed       Periodic     Closed

 v                        1   Periodic     Closed       Periodic     Closed

 temp                     1   Periodic     Closed       Periodic     Closed

 salt                     1   Periodic     Closed       Periodic     Closed

 Activated C-preprocessing Options:

 UPWELLING               Wind-Driven Upwelling/Downwelling over a Periodic Channel
 ANA_BSFLUX              Analytical kinematic bottom salinity flux
 ANA_BTFLUX              Analytical kinematic bottom temperature flux
 ANA_GRID                Analytical grid set-up
 ANA_INITIAL             Analytical initial conditions
 ANA_SMFLUX              Analytical kinematic surface momentum flux
 ANA_SSFLUX              Analytical kinematic surface salinity flux
 ANA_STFLUX              Analytical kinematic surface temperature flux
 ANA_VMIX                Analytical vertical mixing coefficients
 ASSUMED_SHAPE           Using assumed-shape arrays
 AVERAGES                Writing out time-averaged nonlinear model fields
 DIAGNOSTICS_TS          Computing and writing tracer diagnostic terms
 DIAGNOSTICS_UV          Computing and writing momentum diagnostic terms
 DJ_GRADPS               Parabolic Splines density Jacobian (Shchepetkin, 2002)
 DOUBLE_PRECISION        Double precision arithmetic numerical kernel.
 MIX_S_TS                Mixing of tracers along constant S-surfaces
 MIX_S_UV                Mixing of momentum along constant S-surfaces
 NONLINEAR               Nonlinear Model
 !NONLIN_EOS             Linear Equation of State for seawater
 POWER_LAW               Power-law shape time-averaging barotropic filter
 PROFILE                 Time profiling activated
 !RST_SINGLE             Double precision fields in restart NetCDF file
 SALINITY                Using salinity
 SOLVE3D                 Solving 3D Primitive Equations
 SPLINES_VDIFF           Parabolic Spline Reconstruction for Vertical Diffusion
 SPLINES_VVISC           Parabolic Spline Reconstruction for Vertical Viscosity
 TS_U3HADVECTION         Third-order upstream horizontal advection of tracers
 TS_C4VADVECTION         Fourth-order centered vertical advection of tracers
 TS_DIF2                 Harmonic mixing of tracers
 UV_ADV                  Advection of momentum
 UV_COR                  Coriolis term
 UV_U3HADVECTION         Third-order upstream horizontal advection of 3D momentum
 UV_C4VADVECTION         Fourth-order centered vertical advection of momentum
 UV_LDRAG                Linear bottom stress
 UV_VIS2                 Harmonic mixing of momentum
 VAR_RHO_2D              Variable density barotropic mode

 Process Information:

 Thread #    0 (pid=    8218) is active.

 INITIAL: Configuring and initializing forward nonlinear model ...
 *******

    ANA_GRID    - x-location of PSI-points: x_psi
                   (Grid = 01, Min =  0.00000000E+00 Max =  4.00000000E+04)
    ANA_GRID    - y-location of PSI-points: y_psi
                   (Grid = 01, Min =  0.00000000E+00 Max =  8.00000000E+04)
    ANA_GRID    - x-location of RHO-points: x_rho
                   (Grid = 01, Min =  5.00000000E+02 Max =  4.05000000E+04)
    ANA_GRID    - y-location of RHO-points: y_rho
                   (Grid = 01, Min = -5.00000000E+02 Max =  8.05000000E+04)
    ANA_GRID    - x-location of U-points: x_u
                   (Grid = 01, Min =  0.00000000E+00 Max =  4.00000000E+04)
    ANA_GRID    - y-location of U-points: y_u
                   (Grid = 01, Min = -5.00000000E+02 Max =  8.05000000E+04)
    ANA_GRID    - x-location of V-points: x_v
                   (Grid = 01, Min =  5.00000000E+02 Max =  4.05000000E+04)
    ANA_GRID    - y-location of V-points: y_v
                   (Grid = 01, Min =  0.00000000E+00 Max =  8.00000000E+04)
    ANA_GRID    - reciprocal XI-grid spacing: pm
                   (Grid = 01, Min =  1.00000000E-03 Max =  1.00000000E-03)
    ANA_GRID    - reciprocal ETA-grid spacing: pn
                   (Grid = 01, Min =  1.00000000E-03 Max =  1.00000000E-03)
    ANA_GRID    - angle between XI-axis and EAST: angler
                   (Grid = 01, Min =  0.00000000E+00 Max =  0.00000000E+00)
    ANA_GRID    - Coriolis parameter at RHO-points: f
                   (Grid = 01, Min = -8.26000000E-05 Max = -8.26000000E-05)
    ANA_GRID    - bathymetry at RHO-points: h
                   (Grid = 01, Min =  2.52004887E+01 Max =  1.50000000E+02)

 Vertical S-coordinate System, Grid 01:

 level   S-coord     Cs-curve   Z   at hmin       at hc    half way     at hmax

    16   0.0000000   0.0000000        0.000       0.000       0.000       0.000
    15  -0.0625000  -0.0019442       -0.809      -0.806      -1.348      -1.589
    14  -0.1250000  -0.0078455       -1.668      -1.661      -2.966      -3.687
    13  -0.1875000  -0.0179119       -2.580      -2.568      -4.867      -6.321
    12  -0.2500000  -0.0324983       -3.549      -3.531      -7.077      -9.535
    11  -0.3125000  -0.0521190       -4.581      -4.558      -9.630     -13.397
    10  -0.3750000  -0.0774659       -5.686      -5.656     -12.573     -17.996
     9  -0.4375000  -0.1094327       -6.875      -6.837     -15.967     -23.445
     8  -0.5000000  -0.1491465       -8.162      -8.114     -19.889     -29.890
     7  -0.5625000  -0.1980075       -9.564      -9.506     -24.435     -37.512
     6  -0.6250000  -0.2577387      -11.104     -11.034     -29.721     -46.531
     5  -0.6875000  -0.3304460      -12.808     -12.724     -35.892     -57.218
     4  -0.7500000  -0.4186931      -14.709     -14.609     -43.121     -69.903
     3  -0.8125000  -0.5255915      -16.846     -16.726     -51.622     -84.987
     2  -0.8750000  -0.6549105      -19.266     -19.124     -61.651    -102.953
     1  -0.9375000  -0.8112096      -22.028     -21.859     -73.518    -124.388
     0  -1.0000000  -1.0000000      -25.200     -25.000     -87.600    -150.000

 Time Splitting Weights for Grid 01:    ndtfast =  30    nfast =  42
 ==================================

    Primary            Secondary            Accumulated to Current Step

  1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
  2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
  3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
  4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
  5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
  6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
  7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
  8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
  9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
 10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
 11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
 12 0.0043042707117221 0.0335513677379153-0.0022367614257357 0.4026337758325831
 13 0.0060106451121704 0.0334078920475245 0.0037738836864347 0.4360416678801076
 14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
 15 0.0099910761708920 0.0329439123123590 0.0216737068001212 0.5021931174029188
 16 0.0122483446563884 0.0326108764399960 0.0339220514565096 0.5348039938429148
 17 0.0146692120341107 0.0322025982847830 0.0485912634906203 0.5670065921276978
 18 0.0172400033810439 0.0317136245503127 0.0658312668716642 0.5987202166780105
 19 0.0199444086685725 0.0311389577709445 0.0857756755402367 0.6298591744489550
 20 0.0227631639997064 0.0304741441486588 0.1085388395399431 0.6603333185976138
 21 0.0256737146312910 0.0297153720153352 0.1342125541712341 0.6900486906129490
 22 0.0286498597812016 0.0288595815276255 0.1628624139524357 0.7189082721405746
 23 0.0316613792205220 0.0279045862015855 0.1945237931729577 0.7468128583421600
 24 0.0346736416507075 0.0268492068942347 0.2291974348236651 0.7736620652363948
 25 0.0376471948657328 0.0256934188392112 0.2668446296893979 0.7993554840756060
 26 0.0405373376992232 0.0244385123436867 0.3073819673886211 0.8237939964192927
 27 0.0432936737565711 0.0230872677537126 0.3506756411451922 0.8468812641730054
 28 0.0458596469320356 0.0216441452951603 0.3965352880772278 0.8685254094681656
 29 0.0481720587108284 0.0201154903974257 0.4447073467880562 0.8886408998655914
 30 0.0501605672561820 0.0185097551070648 0.4948679140442381 0.9071506549726561
 31 0.0517471682814030 0.0168377361985254 0.5466150823256412 0.9239883911711815
 32 0.0528456577069106 0.0151128305891453 0.5994607400325517 0.9391012217603267
 33 0.0533610761022577 0.0133513086655816 0.6528218161348094 0.9524525304259084
 34 0.0531891349131379 0.0115726061288397 0.7060109510479473 0.9640251365547481
 35 0.0522156244733761 0.0097996349650684 0.7582265755213234 0.9738247715198165
 36 0.0503158038019031 0.0080591141492892 0.8085423793232265 0.9818838856691057
 37 0.0473537721847153 0.0063819206892258 0.8558961515079418 0.9882658063583315
 38 0.0431818225418188 0.0048034616164019 0.8990779740497606 0.9930692679747335
 39 0.0376397765791564 0.0033640675316746 0.9367177506289170 0.9964333355064081
 40 0.0305543017255206 0.0021094083123694 0.9672720523544377 0.9985427438187775
 41 0.0217382098544505 0.0010909315881854 0.9890102622088881 0.9996336754069629
 42 0.0109897377911119 0.0003663245930371 1.0000000000000000 1.0000000000000000

 ndtfast, nfast =   30  42   nfast/ndtfast =  1.40000

 Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

    1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

 Power filter parameters, Fgamma, gamma =  0.28400   0.18933

 Metrics information for Grid 01:
 ===============================

 Minimum X-grid spacing, DXmin =  1.00000000E+00 km
 Maximum X-grid spacing, DXmax =  1.00000000E+00 km
 Minimum Y-grid spacing, DYmin =  1.00000000E+00 km
 Maximum Y-grid spacing, DYmax =  1.00000000E+00 km
 Minimum Z-grid spacing, DZmin =  8.08965824E-01 m
 Maximum Z-grid spacing, DZmax =  2.56123321E+01 m

 Minimum barotropic Courant Number =  2.22358627E-01
 Maximum barotropic Courant Number =  5.42494240E-01
 Maximum Coriolis   Courant Number =  2.47800000E-02

    ANA_INITIAL - vertically integrated u-momentum component: ubar
                   (Grid = 01, Min =  0.00000000E+00 Max =  0.00000000E+00)
    ANA_INITIAL - vertically integrated v-momentum component: vbar
                   (Grid = 01, Min =  0.00000000E+00 Max =  0.00000000E+00)
    ANA_INITIAL - free-surface: zeta
                   (Grid = 01, Min =  0.00000000E+00 Max =  0.00000000E+00)
    ANA_INITIAL - u-momentum component: u
                   (Grid = 01, Min =  0.00000000E+00 Max =  0.00000000E+00)
    ANA_INITIAL - v-momentum component: v
                   (Grid = 01, Min =  0.00000000E+00 Max =  0.00000000E+00)
    ANA_INITIAL - potential temperature: temp
                   (Grid = 01, Min =  1.45204834E+01 Max =  2.19365219E+01)
    ANA_INITIAL - salinity: salt
                   (Grid = 01, Min =  3.50000000E+01 Max =  3.50000000E+01)

 Basin information for Grid 01:

 Maximum grid stiffness ratios:  rx0 =   6.931666E-02 (Beckmann and Haidvogel)
                                 rx1 =   8.661243E-01 (Haney)

 Initial domain volumes:  TotVolume =  3.8843755884E+11 m3
                         MinCellVol =  8.4521383562E+05 m3
                         MaxCellVol =  2.5612332106E+07 m3
                            Max/Min =  3.0302783777E+01

 NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000001440)


 TIME-STEP YYYY-MM-DD hh:mm:ss.ss  KINETIC_ENRG   POTEN_ENRG    TOTAL_ENRG    NET_VOLUME
                     C => (i,j,k)       Cu            Cv            Cw         Max Speed

         0 0001-01-01 00:00:00.00  0.000000E+00  6.585677E+02  6.585677E+02  3.884376E+11
                       (00,00,00)  0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00
      DEF_HIS     - creating  history      file, Grid 01: ./out/ocean_his.nc
 Found Error: 02   Line: 8152     Source: ROMS/Modules/mod_netcdf.F, netcdf_create

 NETCDF_CREATE - unable to create output NetCDF file:
                 ./out/ocean_his.nc
                 call from:  ROMS/Utility/def_his.F
 Found Error: 03   Line: 103      Source: ROMS/Utility/def_his.F

 DEF_HIS - unable to create history NetCDF file: ./out/ocean_his.nc
 Found Error: 03   Line: 134      Source: ROMS/Nonlinear/output.F
 Found Error: 03   Line: 502      Source: ROMS/Nonlinear/main3d.F
 Found Error: 03   Line: 298      Source: ROMS/Drivers/nl_ocean.h

 Elapsed CPU time (seconds):

 Thread #    0 CPU:       0.079
 Total:                   0.079

 Nonlinear model elapsed CPU time profile, Grid: 01

  Allocation and array initialization ..............         0.057  (71.8018 %)
  Ocean state initialization .......................         0.012  (15.0700 %)
  Reading of input data ............................         0.000  ( 0.0076 %)
  Processing of input data .........................         0.000  ( 0.0737 %)
  Processing of output time averaged data ..........         0.000  ( 0.0724 %)
  Computation of vertical boundary conditions ......         0.000  ( 0.0521 %)
  Computation of global information integrals ......         0.002  ( 1.9228 %)
  2D/3D coupling, vertical metrics .................         0.003  ( 4.1034 %)
  Omega vertical velocity ..........................         0.001  ( 1.8250 %)
  Equation of state for seawater ...................         0.003  ( 3.5319 %)
                                              Total:         0.078   98.4607

  Unique code regions profiled .....................         0.078   98.4607 %
  Residual, non-profiled code ......................         0.001    1.5393 %


 All percentages are with respect to total time =            0.079


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

 Dynamic and Automatic memory (MB) usage for Grid 01:  41x80x16  tiling: 2x1

     tile          Dynamic        Automatic            USAGE

        0            77.14             2.23            79.37
        1             0.00             2.14             2.14

    TOTAL            77.14             4.37            81.51

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

 ROMS/TOMS - Output NetCDF summary for Grid 01:

 Analytical header files used:

     ROMS/Functionals/ana_btflux.h
     ROMS/Functionals/ana_grid.h
     ROMS/Functionals/ana_initial.h
     ROMS/Functionals/ana_smflux.h
     ROMS/Functionals/ana_stflux.h
     ROMS/Functionals/ana_vmix.h
 Found Error: 03   Line: 350      Source: ROMS/Utility/close_io.F

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


 ERROR: Abnormal termination: NetCDF OUTPUT.
 REASON: No such file or directory 

Thanks again!

User avatar
kate
Posts: 3717
Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: Problem with the file makefile

#8 Post by kate » Sun Jun 30, 2019 12:25 am

Did you create the out directory for it?

alexandrosmf
Posts: 5
Joined: Sun May 26, 2019 3:56 pm
Location: University of Aegean/ Greece

Re: Problem with the file makefile

#9 Post by alexandrosmf » Sun Jun 30, 2019 12:37 pm

Finally, I ran it successfully. I had to create the folder out.

Thank you very much Kate! :D

alesss42
Posts: 2
Joined: Thu Oct 18, 2012 3:25 pm
Location: Oregon State University

Re: Problem with the file makefile

#10 Post by alesss42 » Mon Jul 08, 2019 10:19 am

Hi! sorry to be bothering with this question, but I couldn't find any information online. I'm also new to ROMS,

I was wondering if the executable file "romsS" is the same as "oceanS"? Is it a change in newer releases? or is there a different step to create the oceanS file?

Thank you!

User avatar
kate
Posts: 3717
Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: Problem with the file makefile

#11 Post by kate » Mon Jul 08, 2019 4:56 pm

There was a recent update from Hernan in which the makefile was changed. It used to make "oceanM" and so forth, now it makes "romsM" and family. The final letter is "S" for serial, "M" for parallel, and "G" for debug mode (serial or parallel).

alesss42
Posts: 2
Joined: Thu Oct 18, 2012 3:25 pm
Location: Oregon State University

Re: Problem with the file makefile

#12 Post by alesss42 » Thu Jul 11, 2019 2:45 am

thank you!

Post Reply