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 Post subject: problem creating oceanS
PostPosted: Mon Aug 07, 2017 12:11 pm 
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Location: Universidade Federal do Maranhão, Brazil
Hi all,
When I ran build.bash for upwelling, I got the following error massages.

makefile:235: INCLUDING FILE Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
./ROMS/Bin/sfmakedepend --cpp --fext=f90 --file=- --objdir=Build -DROMS_HEADER="upwelling.h" -I ROMS/Include -I ROMS/Nonlinear -I ROMS/Nonlinear/Biology -I ROMS/Nonlinear/Sediment -I ROMS/Utility -I ROMS/Drivers -I ROMS/Functionals -I Master -I Compilers --silent --moddir Build ROMS/Nonlinear/ini_fields.F ROMS/Nonlinear/step3d_t.F ROMS/Nonlinear/interp_floats.F ROMS/Nonlinear/main2d.F ROMS/Nonlinear/gls_prestep.F ROMS/Nonlinear/set_avg.F ROMS/Nonlinear/bc_2d.F ROMS/Nonlinear/set_zeta.F ROMS/Nonlinear/lmd_bkpp.F ROMS/Nonlinear/nesting.F ROMS/Nonlinear/zetabc.F ROMS/Nonlinear/lmd_skpp.F ROMS/Nonlinear/uv3dmix.F ROMS/Nonlinear/set_tides.F ROMS/Nonlinear/bc_bry2d.F ROMS/Nonlinear/conv_2d.F ROMS/Nonlinear/exchange_3d.F ROMS/Nonlinear/bulk_flux.F ROMS/Nonlinear/u2dbc_im.F ROMS/Nonlinear/v2dbc_im.F ROMS/Nonlinear/lmd_vmix.F ROMS/Nonlinear/frc_adjust.F ROMS/Nonlinear/lmd_swfrac.F ROMS/Nonlinear/bbl.F ROMS/Nonlinear/gls_corstep.F ROMS/Nonlinear/set_depth.F ROMS/Nonlinear/tkebc_im.F ROMS/Nonlinear/hmixing.F ROMS/Nonlinear/my25_corstep.F ROMS/Nonlinear/conv_bry3d.F ROMS/Nonlinear/conv_bry2d.F ROMS/Nonlinear/main3d.F ROMS/Nonlinear/u3dbc_im.F ROMS/Nonlinear/step2d.F ROMS/Nonlinear/output.F ROMS/Nonlinear/t3dbc_im.F ROMS/Nonlinear/omega.F ROMS/Nonlinear/wetdry.F ROMS/Nonlinear/set_massflux.F ROMS/Nonlinear/exchange_2d.F ROMS/Nonlinear/step3d_uv.F ROMS/Nonlinear/step_floats.F ROMS/Nonlinear/initial.F ROMS/Nonlinear/get_data.F ROMS/Nonlinear/prsgrd.F ROMS/Nonlinear/obc_volcons.F ROMS/Nonlinear/rho_eos.F ROMS/Nonlinear/conv_3d.F ROMS/Nonlinear/wvelocity.F ROMS/Nonlinear/diag.F ROMS/Nonlinear/t3dmix.F ROMS/Nonlinear/radiation_stress.F ROMS/Nonlinear/mpdata_adiff.F ROMS/Nonlinear/forcing.F ROMS/Nonlinear/v3dbc_im.F ROMS/Nonlinear/rhs3d.F ROMS/Nonlinear/set_data.F ROMS/Nonlinear/get_idata.F ROMS/Nonlinear/obc_adjust.F ROMS/Nonlinear/bc_bry3d.F ROMS/Nonlinear/my25_prestep.F ROMS/Nonlinear/pre_step3d.F ROMS/Nonlinear/vwalk_floats.F ROMS/Nonlinear/bvf_mix.F ROMS/Nonlinear/bc_3d.F ROMS/Nonlinear/set_vbc.F ROMS/Nonlinear/Biology/biology.F ROMS/Nonlinear/Biology/biology_floats.F ROMS/Nonlinear/Sediment/sediment.F ROMS/Nonlinear/Sediment/sed_bedload.F ROMS/Nonlinear/Sediment/sed_settling.F ROMS/Nonlinear/Sediment/sed_surface.F ROMS/Nonlinear/Sediment/sed_fluxes.F ROMS/Nonlinear/Sediment/sed_bed.F ROMS/Functionals/analytical.F ROMS/Utility/obs_depth.F ROMS/Utility/checkerror.F ROMS/Utility/dotproduct.F ROMS/Utility/set_2dfldr.F ROMS/Utility/posterior.F ROMS/Utility/normalization.F ROMS/Utility/set_3dfld.F ROMS/Utility/nf_fwrite2d_bry.F ROMS/Utility/def_tides.F ROMS/Utility/get_gst.F ROMS/Utility/wpoints.F ROMS/Utility/congrad.F ROMS/Utility/wrt_hessian.F ROMS/Utility/get_bounds.F ROMS/Utility/read_sedpar.F ROMS/Utility/nf_fwrite3d_bry.F ROMS/Utility/time_corr.F ROMS/Utility/def_gst.F ROMS/Utility/packing.F ROMS/Utility/nf_fwrite3d.F ROMS/Utility/regrid.F ROMS/Utility/def_norm.F ROMS/Utility/def_lanczos.F ROMS/Utility/state_scale.F ROMS/Utility/wrt_info.F ROMS/Utility/read_asspar.F ROMS/Utility/obs_k2z.F ROMS/Utility/wrt_diags.F ROMS/Utility/obs_initial.F ROMS/Utility/read_fltpar.F ROMS/Utility/abort.F ROMS/Utility/get_cycle.F ROMS/Utility/stats_modobs.F ROMS/Utility/checkadj.F ROMS/Utility/back_cost.F ROMS/Utility/nf_fwrite2d.F ROMS/Utility/state_initialize.F ROMS/Utility/state_product.F ROMS/Utility/extract_sta.F ROMS/Utility/obs_read.F ROMS/Utility/def_ini.F ROMS/Utility/zeta_balance.F ROMS/Utility/ini_lanczos.F ROMS/Utility/def_mod.F ROMS/Utility/ludcmp.F ROMS/Utility/read_biopar.F ROMS/Utility/set_contact.F ROMS/Utility/read_phypar.F ROMS/Utility/def_quick.F ROMS/Utility/inner2state.F ROMS/Utility/def_hessian.F ROMS/Utility/def_dim.F ROMS/Utility/get_wetdry.F ROMS/Utility/wrt_floats.F ROMS/Utility/check_multifile.F ROMS/Utility/lubksb.F ROMS/Utility/nf_fread3d_bry.F ROMS/Utility/wrt_his.F ROMS/Utility/state_addition.F ROMS/Utility/nf_fread3d.F ROMS/Utility/def_info.F ROMS/Utility/set_2dfld.F ROMS/Utility/read_fltbiopar.F ROMS/Utility/def_diags.F ROMS/Utility/extract_obs.F ROMS/Utility/wrt_rst.F ROMS/Utility/metrics.F ROMS/Utility/rpcg_lanczos.F ROMS/Utility/inp_par.F ROMS/Utility/set_ngfld.F ROMS/Utility/def_station.F ROMS/Utility/stiffness.F ROMS/Utility/wrt_evolved.F ROMS/Utility/set_diags.F ROMS/Utility/wrt_impulse.F ROMS/Utility/set_3dfldr.F ROMS/Utility/read_couplepar.F ROMS/Utility/uv_rotate.F ROMS/Utility/nf_fwrite4d.F ROMS/Utility/wrt_quick.F ROMS/Utility/gasdev.F ROMS/Utility/grid_coords.F ROMS/Utility/sum_grad.F ROMS/Utility/nf_fread4d.F ROMS/Utility/get_2dfldr.F ROMS/Utility/strings.F ROMS/Utility/ran_state.F ROMS/Utility/get_3dfld.F ROMS/Utility/set_weights.F ROMS/Utility/erf.F ROMS/Utility/cgradient.F ROMS/Utility/state_copy.F ROMS/Utility/def_floats.F ROMS/Utility/random_ic.F ROMS/Utility/def_his.F ROMS/Utility/lbc.F ROMS/Utility/rep_matrix.F ROMS/Utility/def_avg.F ROMS/Utility/mp_routines.F ROMS/Utility/set_scoord.F ROMS/Utility/def_rst.F ROMS/Utility/posterior_var.F ROMS/Utility/wrt_avg.F ROMS/Utility/comp_Jb0.F ROMS/Utility/get_date.F ROMS/Utility/wrt_error.F ROMS/Utility/get_2dfld.F ROMS/Utility/inquire.F ROMS/Utility/def_var.F ROMS/Utility/read_stapar.F ROMS/Utility/def_impulse.F ROMS/Utility/get_varcoords.F ROMS/Utility/set_masks.F ROMS/Utility/checkvars.F ROMS/Utility/get_ngfldr.F ROMS/Utility/ini_adjust.F ROMS/Utility/wrt_gst.F ROMS/Utility/ini_hmixcoef.F ROMS/Utility/get_grid.F ROMS/Utility/obs_write.F ROMS/Utility/wrt_ini.F ROMS/Utility/close_io.F ROMS/Utility/get_nudgcoef.F ROMS/Utility/shapiro.F ROMS/Utility/ntimestep.F ROMS/Utility/obs_cost.F ROMS/Utility/get_state.F ROMS/Utility/nrutil.F ROMS/Utility/interpolate.F ROMS/Utility/sum_imp.F ROMS/Utility/checkdefs.F ROMS/Utility/ran1.F ROMS/Utility/timers.F ROMS/Utility/set_ngfldr.F ROMS/Utility/sqlq.F ROMS/Utility/mp_exchange.F ROMS/Utility/lanc_resid.F ROMS/Utility/def_dai.F ROMS/Utility/white_noise.F ROMS/Utility/wrt_tides.F ROMS/Utility/cost_grad.F ROMS/Utility/def_error.F ROMS/Utility/vorticity.F ROMS/Utility/frc_weak.F ROMS/Utility/wrt_aug_imp.F ROMS/Utility/get_ngfld.F ROMS/Utility/wrt_dai.F ROMS/Utility/state_dotprod.F ROMS/Utility/distribute.F ROMS/Utility/array_modes.F ROMS/Utility/get_3dfldr.F ROMS/Utility/wrt_station.F ROMS/Utility/nf_fread2d_bry.F ROMS/Utility/convolve.F ROMS/Utility/nf_fread2d.F ROMS/Modules/mod_mixing.F ROMS/Modules/mod_sedbed.F ROMS/Modules/mod_sources.F ROMS/Modules/mod_scalars.F ROMS/Modules/mod_fourdvar.F ROMS/Modules/mod_tides.F ROMS/Modules/mod_strings.F ROMS/Modules/mod_sediment.F ROMS/Modules/mod_grid.F ROMS/Modules/mod_boundary.F ROMS/Modules/mod_storage.F ROMS/Modules/mod_parallel.F ROMS/Modules/mod_arrays.F ROMS/Modules/mod_ocean.F ROMS/Modules/mod_ncparam.F ROMS/Modules/mod_nesting.F ROMS/Modules/mod_behavior.F ROMS/Modules/mod_average.F ROMS/Modules/mod_forces.F ROMS/Modules/mod_eoscoef.F ROMS/Modules/mod_eclight.F ROMS/Modules/mod_bbl.F ROMS/Modules/mod_kinds.F ROMS/Modules/mod_stepping.F ROMS/Modules/mod_biology.F ROMS/Modules/mod_diags.F ROMS/Modules/mod_iounits.F ROMS/Modules/mod_param.F ROMS/Modules/mod_coupler.F ROMS/Modules/mod_netcdf.F ROMS/Modules/mod_clima.F ROMS/Modules/mod_floats.F ROMS/Modules/mod_coupling.F Master/roms_import.F Master/propagator.F Master/master.F Master/roms_export.F Master/ocean_coupler.F Master/esmf_roms.F Master/ocean_control.F > Build/MakeDepend
cp -p /home/ppgoceano/make_macros.mk Build
makefile:235: INCLUDING FILE Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
rm -f -r /home/ppgoceano/make_macros.mk

How should I do to solve the errors ?
How should I rewrite my build.bash ?
I attached my build.bash here.

Thanks.


Attachments:
build.bash [16.81 KiB]
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PostPosted: Mon Aug 07, 2017 4:32 pm 
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I don't actually see any errors there. Then again, it should start compiling after what you show. I get:
Code:
...  ROMS/Modules/mod_sediment.F ROMS/Modules/mod_sources.F ROMS/Modules/mod_stepping.F ROMS/Modules/mod_storage.F ROMS/Modules/mod_strings.F ROMS/Modules/mod_tides.F ROMS/Modules/mod_trc_sources.F Master/coupler.F Master/esmf_roms.F Master/master.F Master/ocean_control.F Master/propagator.F Master/roms_export.F Master/roms_import.F > Build_up/MakeDepend
cp -p /Users/kate/make_macros.mk Build_up
makefile.UP:224: INCLUDING FILE Build_up/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
/usr/bin/cpp -P -traditional -DMPI -DDARWIN -DX86_64 -DGFORTRAN -D'ROOT_DIR="/Users/kate/ROMS/feedme"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -D'ANALYTICAL_DIR="/Users/kate/ROMS/feedme/ROMS/Functionals"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/Users/kate/ROMS/feedme/ROMS/Include"'  ROMS/Modules/mod_arrays.F > Build_up/mod_arrays.f90
ROMS/Bin/cpp_clean Build_up/mod_arrays.f90
/usr/bin/cpp -P -traditional -DMPI -DDARWIN -DX86_64 -DGFORTRAN -D'ROOT_DIR="/Users/kate/ROMS/feedme"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -D'ANALYTICAL_DIR="/Users/kate/ROMS/feedme/ROMS/Functionals"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/Users/kate/ROMS/feedme/ROMS/Include"'  ROMS/Modules/mod_average.F > Build_up/mod_average.f90
ROMS/Bin/cpp_clean Build_up/mod_average.f90
...


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PostPosted: Mon Aug 07, 2017 8:12 pm 
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Thank you very much kate,but my OceanS file is attached and I believe it was not compiled because it was very fast and it shows me the error: makefile: 235: INCLUDING FILE Build / make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS. Can you tell me about everything that is right with the file?

Thank you very much for the reply!


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PostPosted: Mon Aug 07, 2017 8:51 pm 
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Quote:
makefile: 235: INCLUDING FILE Build / make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
This is not an error. My output has something very like it, before it starts compiling.

Can you show us a listing of your Build directory?


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PostPosted: Tue Aug 08, 2017 10:55 am 
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Hi, kate!
Thank you for attention!


Last edited by adilsonborges on Tue Aug 08, 2017 2:31 pm, edited 1 time in total.

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PostPosted: Tue Aug 08, 2017 10:56 am 
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The gfortran compiler is not being set correctly


Last edited by adilsonborges on Tue Aug 08, 2017 2:34 pm, edited 1 time in total.

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PostPosted: Tue Aug 08, 2017 12:18 pm 
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The error has changed!

/bin/sh: 1: ROMS/Bin/cpp_clean: Permission denied
makefile:239: INCLUDING FILE /home/ppgoceano/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
cd Build; /usr/bin/gfortran -c -frepack-arrays -O3 -ffast-math checkerror.f90
checkerror.f90:199:10:

USE mod_param
1
Fatal Error: Can't open module file ‘mod_param.mod’ for reading at (1): Arquivo ou diretório não encontrado
compilation terminated.
make: *** [ROMS/Utility/Module.mk:15: Build/checkerror.o] Error 1


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PostPosted: Tue Aug 08, 2017 1:15 pm 
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My Build:

checkerror.f90 MakeDepend netcdf.mod obs_depth.f90 obs_depth.o typesizes.mod

There has been a change


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PostPosted: Tue Aug 08, 2017 3:53 pm 
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Quote:
/bin/sh: 1: ROMS/Bin/cpp_clean: Permission denied
That's odd. What do you get doing a long listing on it?
Code:
chinook01 184% ls -l ROMS/Bin/cpp_clean
4 -rwxr-xr-x 1 kshedstrom akwaters 1512 Aug  7 15:52 ROMS/Bin/cpp_clean*
Actually, I see that it's a Perl program. What do you get from "which perl"?
Code:
chinook01 186% which perl
/usr/bin/perl
chinook01 187% perl --version

This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi
If your perl isn't working, that could explain why it didn't compile mod_param before checkerror. What is in the Build/MakeDepend file? Mine starts with these lines:
Code:
/center1/w/kshedstrom/Build_CGOAG/esmf_roms.o: cppdefs.h ngoa.h globaldefs.h
/center1/w/kshedstrom/Build_CGOAG/esmf_roms.f90: cppdefs.h ngoa.h globaldefs.h
/center1/w/kshedstrom/Build_CGOAG/esmf_roms.o: /center1/w/kshedstrom/Build_CGOAG/distribute.o
/center1/w/kshedstrom/Build_CGOAG/esmf_roms.o: /center1/w/kshedstrom/Build_CGOAG/mod_coupler.o
/center1/w/kshedstrom/Build_CGOAG/esmf_roms.o: /center1/w/kshedstrom/Build_CGOAG/mod_forces.o
It should have many lines in that format, a chunk for each ROMS source code.


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PostPosted: Tue Aug 08, 2017 4:05 pm 
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doing a long listing
LL (ll) at the Linux command terminal

ppgoceano@laclimadell:~$ which perl
/usr/bin/perl

ppgoceano@laclimadell:~$ perl --version

This is perl 5, version 22, subversion 2 (v5.22.2) built for x86_64-linux-gnu-thread-multi
(with 67 registered patches, see perl -V for more detail)

Copyright 1987-2015, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.

There is nothing written in my makeDepended file :(
When I change gfortran by g95 in FORT from the Makefile it gives a different error. Can the problem be the compiler?

Thanks!


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PostPosted: Tue Aug 08, 2017 6:30 pm 
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There's something wrong with the "make depend" phase. Can you delete the Build directory and try again? Your perl is newer than mine - I think I would have heard about it if the make depend failed at some perl version. It works on my Mac at 5.18.2.


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PostPosted: Tue Aug 08, 2017 6:46 pm 
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kate wrote:
There's something wrong with the "make depend" phase. Can you delete the Build directory and try again? Your perl is newer than mine - I think I would have heard about it if the make depend failed at some perl version. It works on my Mac at 5.18.2.
ppgoceano@laclimadell:~/adilson_ppgoceano/roms_adilson$ make
/bin/sh: 1: ROMS/Bin/cpp_clean: Permission denied
makefile:239: INCLUDING FILE /home/ppgoceano/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
cp -f /usr/local/include/netcdf.mod Build
cp -f /usr/local/include/typesizes.mod Build
./ROMS/Bin/sfmakedepend --cpp --fext=f90 --file=- --objdir=Build -DROMS_HEADER="upwelling.h" -I ROMS/Include -I ROMS/Nonlinear -I ROMS/Nonlinear/Biology -I ROMS/Nonlinear/Sediment -I ROMS/Utility -I ROMS/Drivers -I ROMS/Functionals -I Master -I Compilers --silent --moddir Build ROMS/Nonlinear/ini_fields.F ROMS/Nonlinear/step3d_t.F ROMS/Nonlinear/interp_floats.F ROMS/Nonlinear/main2d.F ROMS/Nonlinear/gls_prestep.F ROMS/Nonlinear/set_avg.F ROMS/Nonlinear/bc_2d.F ROMS/Nonlinear/set_zeta.F ROMS/Nonlinear/lmd_bkpp.F ROMS/Nonlinear/nesting.F ROMS/Nonlinear/zetabc.F ROMS/Nonlinear/lmd_skpp.F ROMS/Nonlinear/uv3dmix.F ROMS/Nonlinear/set_tides.F ROMS/Nonlinear/bc_bry2d.F ROMS/Nonlinear/conv_2d.F ROMS/Nonlinear/exchange_3d.F ROMS/Nonlinear/bulk_flux.F ROMS/Nonlinear/u2dbc_im.F ROMS/Nonlinear/v2dbc_im.F ROMS/Nonlinear/lmd_vmix.F ROMS/Nonlinear/frc_adjust.F ROMS/Nonlinear/lmd_swfrac.F ROMS/Nonlinear/bbl.F ROMS/Nonlinear/gls_corstep.F ROMS/Nonlinear/set_depth.F ROMS/Nonlinear/tkebc_im.F ROMS/Nonlinear/hmixing.F ROMS/Nonlinear/my25_corstep.F ROMS/Nonlinear/conv_bry3d.F ROMS/Nonlinear/conv_bry2d.F ROMS/Nonlinear/main3d.F ROMS/Nonlinear/u3dbc_im.F ROMS/Nonlinear/step2d.F ROMS/Nonlinear/output.F ROMS/Nonlinear/t3dbc_im.F ROMS/Nonlinear/omega.F ROMS/Nonlinear/wetdry.F ROMS/Nonlinear/set_massflux.F ROMS/Nonlinear/exchange_2d.F ROMS/Nonlinear/step3d_uv.F ROMS/Nonlinear/step_floats.F ROMS/Nonlinear/initial.F ROMS/Nonlinear/get_data.F ROMS/Nonlinear/prsgrd.F ROMS/Nonlinear/obc_volcons.F ROMS/Nonlinear/rho_eos.F ROMS/Nonlinear/conv_3d.F ROMS/Nonlinear/wvelocity.F ROMS/Nonlinear/diag.F ROMS/Nonlinear/t3dmix.F ROMS/Nonlinear/radiation_stress.F ROMS/Nonlinear/mpdata_adiff.F ROMS/Nonlinear/forcing.F ROMS/Nonlinear/v3dbc_im.F ROMS/Nonlinear/rhs3d.F ROMS/Nonlinear/set_data.F ROMS/Nonlinear/get_idata.F ROMS/Nonlinear/obc_adjust.F ROMS/Nonlinear/bc_bry3d.F ROMS/Nonlinear/my25_prestep.F ROMS/Nonlinear/pre_step3d.F ROMS/Nonlinear/vwalk_floats.F ROMS/Nonlinear/bvf_mix.F ROMS/Nonlinear/bc_3d.F ROMS/Nonlinear/set_vbc.F ROMS/Nonlinear/Biology/biology.F ROMS/Nonlinear/Biology/biology_floats.F ROMS/Nonlinear/Sediment/sediment.F ROMS/Nonlinear/Sediment/sed_bedload.F ROMS/Nonlinear/Sediment/sed_settling.F ROMS/Nonlinear/Sediment/sed_surface.F ROMS/Nonlinear/Sediment/sed_fluxes.F ROMS/Nonlinear/Sediment/sed_bed.F ROMS/Functionals/analytical.F ROMS/Utility/obs_depth.F ROMS/Utility/checkerror.F ROMS/Utility/dotproduct.F ROMS/Utility/set_2dfldr.F ROMS/Utility/posterior.F ROMS/Utility/normalization.F ROMS/Utility/set_3dfld.F ROMS/Utility/nf_fwrite2d_bry.F ROMS/Utility/def_tides.F ROMS/Utility/wpoints.F ROMS/Utility/congrad.F ROMS/Utility/wrt_hessian.F ROMS/Utility/get_bounds.F ROMS/Utility/read_sedpar.F ROMS/Utility/nf_fwrite3d_bry.F ROMS/Utility/time_corr.F ROMS/Utility/def_gst.F ROMS/Utility/packing.F ROMS/Utility/nf_fwrite3d.F ROMS/Utility/regrid.F ROMS/Utility/def_norm.F ROMS/Utility/def_lanczos.F ROMS/Utility/state_scale.F ROMS/Utility/wrt_info.F ROMS/Utility/read_asspar.F ROMS/Utility/obs_k2z.F ROMS/Utility/wrt_diags.F ROMS/Utility/obs_initial.F ROMS/Utility/read_fltpar.F ROMS/Utility/abort.F ROMS/Utility/get_cycle.F ROMS/Utility/stats_modobs.F ROMS/Utility/checkadj.F ROMS/Utility/back_cost.F ROMS/Utility/nf_fwrite2d.F ROMS/Utility/state_initialize.F ROMS/Utility/state_product.F ROMS/Utility/extract_sta.F ROMS/Utility/obs_read.F ROMS/Utility/def_ini.F ROMS/Utility/zeta_balance.F ROMS/Utility/ini_lanczos.F ROMS/Utility/def_mod.F ROMS/Utility/ludcmp.F ROMS/Utility/read_biopar.F ROMS/Utility/set_contact.F ROMS/Utility/read_phypar.F ROMS/Utility/def_quick.F ROMS/Utility/inner2state.F ROMS/Utility/def_hessian.F ROMS/Utility/def_dim.F ROMS/Utility/round.F ROMS/Utility/get_wetdry.F ROMS/Utility/wrt_floats.F ROMS/Utility/check_multifile.F ROMS/Utility/lubksb.F ROMS/Utility/nf_fread3d_bry.F ROMS/Utility/wrt_his.F ROMS/Utility/state_addition.F ROMS/Utility/nf_fread3d.F ROMS/Utility/def_info.F ROMS/Utility/set_2dfld.F ROMS/Utility/read_fltbiopar.F ROMS/Utility/def_diags.F ROMS/Utility/extract_obs.F ROMS/Utility/wrt_rst.F ROMS/Utility/metrics.F ROMS/Utility/rpcg_lanczos.F ROMS/Utility/inp_par.F ROMS/Utility/set_ngfld.F ROMS/Utility/def_station.F ROMS/Utility/stiffness.F ROMS/Utility/wrt_evolved.F ROMS/Utility/set_diags.F ROMS/Utility/wrt_impulse.F ROMS/Utility/set_3dfldr.F ROMS/Utility/read_couplepar.F ROMS/Utility/uv_rotate.F ROMS/Utility/nf_fwrite4d.F ROMS/Utility/wrt_quick.F ROMS/Utility/gasdev.F ROMS/Utility/grid_coords.F ROMS/Utility/sum_grad.F ROMS/Utility/nf_fread4d.F ROMS/Utility/get_2dfldr.F ROMS/Utility/strings.F ROMS/Utility/ran_state.F ROMS/Utility/get_3dfld.F ROMS/Utility/set_weights.F ROMS/Utility/erf.F ROMS/Utility/cgradient.F ROMS/Utility/state_copy.F ROMS/Utility/def_floats.F ROMS/Utility/random_ic.F ROMS/Utility/inquiry.F ROMS/Utility/def_his.F ROMS/Utility/lbc.F ROMS/Utility/rep_matrix.F ROMS/Utility/def_avg.F ROMS/Utility/mp_routines.F ROMS/Utility/set_scoord.F ROMS/Utility/white_noise.F ROMS/Utility/wrt_ini.F ROMS/Utility/posterior_var.F ROMS/Utility/wrt_avg.F ROMS/Utility/dateclock.F ROMS/Utility/comp_Jb0.F ROMS/Utility/wrt_error.F ROMS/Utility/get_2dfld.F ROMS/Utility/def_var.F ROMS/Utility/read_stapar.F ROMS/Utility/def_impulse.F ROMS/Utility/get_varcoords.F ROMS/Utility/set_masks.F ROMS/Utility/checkvars.F ROMS/Utility/get_ngfldr.F ROMS/Utility/ini_adjust.F ROMS/Utility/wrt_gst.F ROMS/Utility/ini_hmixcoef.F ROMS/Utility/get_grid.F ROMS/Utility/obs_write.F ROMS/Utility/close_io.F ROMS/Utility/get_nudgcoef.F ROMS/Utility/shapiro.F ROMS/Utility/ntimestep.F ROMS/Utility/obs_cost.F ROMS/Utility/get_state.F ROMS/Utility/nrutil.F ROMS/Utility/interpolate.F ROMS/Utility/sum_imp.F ROMS/Utility/checkdefs.F ROMS/Utility/ran1.F ROMS/Utility/timers.F ROMS/Utility/set_ngfldr.F ROMS/Utility/def_rst.F ROMS/Utility/sqlq.F ROMS/Utility/mp_exchange.F ROMS/Utility/lanc_resid.F ROMS/Utility/def_dai.F ROMS/Utility/cost_grad.F ROMS/Utility/wrt_tides.F ROMS/Utility/def_error.F ROMS/Utility/get_gst.F ROMS/Utility/vorticity.F ROMS/Utility/frc_weak.F ROMS/Utility/wrt_aug_imp.F ROMS/Utility/get_ngfld.F ROMS/Utility/wrt_dai.F ROMS/Utility/state_dotprod.F ROMS/Utility/distribute.F ROMS/Utility/array_modes.F ROMS/Utility/get_3dfldr.F ROMS/Utility/wrt_station.F ROMS/Utility/nf_fread2d_bry.F ROMS/Utility/convolve.F ROMS/Utility/nf_fread2d.F ROMS/Modules/mod_mixing.F ROMS/Modules/mod_sedbed.F ROMS/Modules/mod_sources.F ROMS/Modules/mod_scalars.F ROMS/Modules/mod_fourdvar.F ROMS/Modules/mod_tides.F ROMS/Modules/mod_strings.F ROMS/Modules/mod_sediment.F ROMS/Modules/mod_grid.F ROMS/Modules/mod_boundary.F ROMS/Modules/mod_storage.F ROMS/Modules/mod_parallel.F ROMS/Modules/mod_arrays.F ROMS/Modules/mod_ocean.F ROMS/Modules/mod_ncparam.F ROMS/Modules/mod_nesting.F ROMS/Modules/mod_behavior.F ROMS/Modules/mod_average.F ROMS/Modules/mod_forces.F ROMS/Modules/mod_eoscoef.F ROMS/Modules/mod_eclight.F ROMS/Modules/mod_bbl.F ROMS/Modules/mod_kinds.F ROMS/Modules/mod_stepping.F ROMS/Modules/mod_biology.F ROMS/Modules/mod_diags.F ROMS/Modules/mod_iounits.F ROMS/Modules/mod_param.F ROMS/Modules/mod_coupler.F ROMS/Modules/mod_netcdf.F ROMS/Modules/mod_clima.F ROMS/Modules/mod_floats.F ROMS/Modules/mod_coupling.F Master/roms_import.F Master/propagator.F Master/master.F Master/roms_export.F Master/coupler.F Master/esmf_roms.F Master/ocean_control.F > Build/MakeDepend
/bin/sh: 1: ./ROMS/Bin/sfmakedepend: Permission denied
make: *** No rule to make target 'Build/MakeDepend', needed by 'all'. Pare.

First, this error


Second error:
/bin/sh: 1: ROMS/Bin/cpp_clean: Permission denied
makefile:239: INCLUDING FILE /home/ppgoceano/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
/usr/bin/cpp -P -traditional -DLINUX -DX86_64 -DGFORTRAN -D'ROOT_DIR="/home/ppgoceano/adilson_ppgoceano/roms_adilson"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home/ppgoceano/adilson_ppgoceano/roms_adilson/ROMS/Functionals"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="/home/ppgoceano/adilson_ppgoceano/roms_adilson/ROMS/Include"' ROMS/Utility/obs_depth.F > Build/obs_depth.f90
ROMS/Bin/cpp_clean Build/obs_depth.f90
make: execvp: ROMS/Bin/cpp_clean: Permissão negada
make: *** [ROMS/Utility/Module.mk:16: Build/obs_depth.f90] Error 127

And now:
/bin/sh: 1: ROMS/Bin/cpp_clean: Permission denied
makefile:239: INCLUDING FILE /home/ppgoceano/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
cd Build; /usr/bin/gfortran -c -frepack-arrays -O3 -ffast-math checkerror.f90
checkerror.f90:199:10:

USE mod_param
1
Fatal Error: Can't open module file ‘mod_param.mod’ for reading at (1): Arquivo ou diretório não encontrado
compilation terminated.
make: *** [ROMS/Utility/Module.mk:15: Build/checkerror.o] Error 1

I think it's the compiler, the error changes when I put g95 instead of gfortran.


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PostPosted: Tue Aug 08, 2017 6:52 pm 
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Quote:
/bin/sh: 1: ./ROMS/Bin/sfmakedepend: Permission denied
You need to find out why this is happening. This is the root of it all. The first attempt creates the empty MakeDepend file while the second attempt thinks it is up to date and doesn't retry making it. If you fix this, you will also fix the cpp_clean problem and the mod_param.mod problem.

You didn't show us the long listing of your ROMS/Bin files:
Code:
chinook01 192% ls -l ROMS/Bin/cpp_clean
4 -rwxr-xr-x 1 kshedstrom akwaters 1512 Aug  7 15:52 ROMS/Bin/cpp_clean*
chinook01 193% ls -l ROMS/Bin/sfmakedepend
24 -rwxr-xr-x 1 kshedstrom akwaters 22224 Jul 31 15:06 ROMS/Bin/sfmakedepend*
In the first "rwx" trio, that x is the execute bit and failing to have it would give you the permission denied error.


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PostPosted: Tue Aug 08, 2017 7:07 pm 
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Location: Universidade Federal do Maranhão, Brazil
ppgoceano@laclimadell:~/adilson_ppgoceano/roms_adilson/ROMS/Bin$
drwxr-xr-x 2 ppgoceano ppgoceano 4096 ago 8 10:27 ./
drwxr-xr-x 16 ppgoceano ppgoceano 4096 ago 8 08:00 ../
-rw-r--r-- 1 ppgoceano ppgoceano 17180 ago 8 09:26 build.bash
-rw-r--r-- 1 ppgoceano ppgoceano 17569 ago 8 10:27 build.sh
-rw-r--r-- 1 ppgoceano ppgoceano 2032 ago 8 07:41 check_nc.sh
-rw-r--r-- 1 ppgoceano ppgoceano 4631 ago 8 07:41 copyright.bash
-rw-r--r-- 1 ppgoceano ppgoceano 4811 ago 8 07:41 copyright.sh
-rw-r--r-- 1 ppgoceano ppgoceano 1556 ago 8 07:41 cpp_clean
-rw-r--r-- 1 ppgoceano ppgoceano 1600 ago 8 07:41 job_afte.sh
-rw-r--r-- 1 ppgoceano ppgoceano 4323 ago 8 07:41 job_array_modes.sh
-rw-r--r-- 1 ppgoceano ppgoceano 1583 ago 8 07:41 job_fsv.sh
-rw-r--r-- 1 ppgoceano ppgoceano 1583 ago 8 07:41 job_fte.sh
-rw-r--r-- 1 ppgoceano ppgoceano 3963 ago 8 07:41 job_i4dvar_sen.sh
-rw-r--r-- 1 ppgoceano ppgoceano 3460 ago 8 07:41 job_i4dvar.sh
-rw-r--r-- 1 ppgoceano ppgoceano 3319 ago 8 07:41 job_normalization.sh
-rw-r--r-- 1 ppgoceano ppgoceano 1582 ago 8 07:41 job_op.sh
-rw-r--r-- 1 ppgoceano ppgoceano 4275 ago 8 07:41 job_psas_sen.sh
-rw-r--r-- 1 ppgoceano ppgoceano 3680 ago 8 07:41 job_psas.sh
-rw-r--r-- 1 ppgoceano ppgoceano 4620 ago 8 07:41 job_r4dvar_sen.sh
-rw-r--r-- 1 ppgoceano ppgoceano 4023 ago 8 07:41 job_r4dvar.sh
-rw-r--r-- 1 ppgoceano ppgoceano 1582 ago 8 07:41 job_so_semi.sh
-rw-r--r-- 1 ppgoceano ppgoceano 22271 ago 8 07:41 sfmakedepend
-rw-r--r-- 1 ppgoceano ppgoceano 11539 ago 8 07:41 submit_i4dvar.sh
-rw-r--r-- 1 ppgoceano ppgoceano 11346 ago 8 07:41 submit_is4dvar.bash
-rw-r--r-- 1 ppgoceano ppgoceano 1770 ago 8 07:41 substitute
-rw-r--r-- 1 ppgoceano ppgoceano 30550 ago 8 07:41 verify.bash
-rw-r--r-- 1 ppgoceano ppgoceano 7986 ago 8 07:41 ws_remove.bash
-rw-r--r-- 1 ppgoceano ppgoceano 8328 ago 8 07:41 ws_remove.sh
My list

I did not download the roms code on this machine, I downloaded it on my personal machine and brought it to this one. Could it be this problem?
I had several problems with svn. So I could not extract the code using the command svn checkout https://www.myroms.org/svn/src/trunk MyDir


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PostPosted: Tue Aug 08, 2017 7:12 pm 
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All of these need the execute bit turned on. I would go into ROMS/Bin and type:
Code:
chmod 755 *
Then remove the Build directory and try again.


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PostPosted: Tue Aug 08, 2017 7:19 pm 
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Location: Universidade Federal do Maranhão, Brazil
Kate, thank you very much! You're amazing!
You have no idea how much you helped me.

It worked, I was able to generate the oceanS. Do I need to do something to confirm that it was compiled?


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PostPosted: Tue Aug 08, 2017 7:26 pm 
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Run it?


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PostPosted: Tue Aug 08, 2017 8:16 pm 
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./oceanS?

Forgive me for asking..
But, thank you very much.


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PostPosted: Tue Aug 08, 2017 8:55 pm 
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./oceanS < ocean_whatever.in

Maybe it's
Code:
./oceanS < ROMS/External/ocean_upwelling.in
if you compiled the UPWELLING case.


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PostPosted: Tue Aug 08, 2017 10:02 pm 
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Thanks for the help, Kate. I wish you well! Thank you!


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