unable to successfully compile ROMS with test case

[jhjanicki]

Hello,

I am trying to run the upwelling test case in ROMS. I am using a mac and have installed the dependencies as follows:
brew install gcc
brew install netcdf --with-fortran
brew install subversion
brew install openmpi
and I already had gnu make and perl installed.

I am following the tutorial "Installing and Running ROMS for First Time Users", and when I get to the step to compile ROMS with the command ./build.bash I am getting the following error message:

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

cp -p /Users/arilab/make_macros.mk /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build

makefile:235: INCLUDING FILE /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS

/usr/bin/cpp -P -traditional-cpp -DDARWIN -DX86_64 -DIFORT -D'ROOT_DIR="/Users/arilab/Desktop/ROMS/src/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/Users/arilab/Desktop/ROMS//MyProjects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' ROMS/Utility/abort.F > /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/abort.f90

ROMS/Bin/cpp_clean /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/abort.f90

/usr/bin/cpp -P -traditional-cpp -DDARWIN -DX86_64 -DIFORT -D'ROOT_DIR="/Users/arilab/Desktop/ROMS/src/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/Users/arilab/Desktop/ROMS//MyProjects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' Master/ocean_control.F > /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/ocean_control.f90

ROMS/Bin/cpp_clean /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/ocean_control.f90

/usr/bin/cpp -P -traditional-cpp -DDARWIN -DX86_64 -DIFORT -D'ROOT_DIR="/Users/arilab/Desktop/ROMS/src/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/Users/arilab/Desktop/ROMS//MyProjects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' ROMS/Functionals/analytical.F > /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/analytical.f90

ROMS/Bin/cpp_clean /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/analytical.f90

/usr/bin/cpp -P -traditional-cpp -DDARWIN -DX86_64 -DIFORT -D'ROOT_DIR="/Users/arilab/Desktop/ROMS/src/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/Users/arilab/Desktop/ROMS//MyProjects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' ROMS/Utility/distribute.F > /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/distribute.f90

ROMS/Bin/cpp_clean /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/distribute.f90

/usr/bin/cpp -P -traditional-cpp -DDARWIN -DX86_64 -DIFORT -D'ROOT_DIR="/Users/arilab/Desktop/ROMS/src/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/Users/arilab/Desktop/ROMS//MyProjects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' ROMS/Modules/mod_iounits.F > /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/mod_iounits.f90

ROMS/Bin/cpp_clean /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/mod_iounits.f90

/usr/bin/cpp -P -traditional-cpp -DDARWIN -DX86_64 -DIFORT -D'ROOT_DIR="/Users/arilab/Desktop/ROMS/src/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/Users/arilab/Desktop/ROMS//MyProjects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' ROMS/Modules/mod_param.F > /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/mod_param.f90

ROMS/Bin/cpp_clean /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/mod_param.f90

/usr/bin/cpp -P -traditional-cpp -DDARWIN -DX86_64 -DIFORT -D'ROOT_DIR="/Users/arilab/Desktop/ROMS/src/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/Users/arilab/Desktop/ROMS//MyProjects/upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="Unversioned directory"' -IROMS/Include -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IROMS/Nonlinear -IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -I/Users/arilab/Desktop/ROMS//MyProjects/upwelling -IMaster -ICompilers -D'HEADER_DIR="/Users/arilab/Desktop/ROMS//MyProjects/upwelling"' ROMS/Modules/mod_kinds.F > /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/mod_kinds.f90

ROMS/Bin/cpp_clean /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/mod_kinds.f90

cd /Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build; -c -heap-arrays -fp-model source -ip -O3 -free mod_kinds.f90

/bin/sh: -c: command not found

make: *** [/Users/arilab/Desktop/ROMS//MyProjects/upwelling/Build/mod_kinds.o] Error 127

Could someone point me in the right direction?
Thank you

Julia

[kate]

There are some hints here: FAQ (third bullet). Are you going for a serial or parallel run? UPWELLING is so fast you can go serial.

[jhjanicki]

Thank you, I was able to successfully compile it by following the link you provided and finding some hints.
I changed the following and it worked:
export USE_NETCDF4=on
export USE_MPIF90=on
export FORT=gfortran

By the way, do you by chance have any idea why when I try to visualize my output with ncview on a Mac I get "Error: Can't open display: "?

[kate]

ncview is an X11 application. Do you by chance have XQuartz installed?