build bash error

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Author
komet7
Posts: 11
Joined: Sun Aug 22, 2010 5:49 am
Location: university of florida

build bash error

#1 Unread post by komet7 »

Hi friends,

I am trying to build the bash to run upwelling example through Cygwin. I ended up having build folder but no executable file. I would be grateful if you could help. I followed every step in wiki page. I am having this error (sorry for the long paste):


rm -f -r core *.ipo /home/berk/roms/Projects/Upwelling/Build /home/berk/make_mac
ros.mk
makefile:238: INCLUDING FILE /home/berk/make_macros.mk WHICH CONTAINS APPLICATIO
N-DEPENDENT MAKE DEFINITIONS
which: no mpif90 in (/opt/gfortransoft/openmpi/bin:/usr/local/bin:/usr/bin:/cygd
rive/c/Program Files/Microsoft Visual Studio/Common/Tools:/cygdrive/c/Program Fi
les/Microsoft Visual Studio/Common/Msdev98/BIN:/cygdrive/c/Program Files/Microso
ft Visual Studio/DF98/BIN:/cygdrive/c/Program Files/Microsoft Visual Studio/VC98
/BIN:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System
32/Wbem:/cygdrive/c/Program Files/ATI Technologies/ATI Control Panel:/cygdrive/c
/Program Files/MATLAB/R2008a/bin:/cygdrive/c/Program Files/MATLAB/R2008a/bin/win
32)
/bin/sh: --: invalid option
Usage: /bin/sh [GNU long option] [option] ...
/bin/sh [GNU long option] [option] script-file ...
GNU long options:
--debug
--debugger
--dump-po-strings
--dump-strings
--help
--init-file
--login
--noediting
--noprofile
--norc
--posix
--protected
--rcfile
--restricted
--verbose
--version
Shell options:
-irsD or -c command or -O shopt_option (invocation only)
-abefhkmnptuvxBCHP or -o option
cp -f /usr/local/include/netcdf.mod /home/berk/roms/Projects/Upwelling/Build
cp -f /usr/local/include/typesizes.mod /home/berk/roms/Projects/Upwelling/Build
./ROMS/Bin/sfmakedepend --cpp --fext=f90 --file=- --objdir=/home/berk/roms/Proje
cts/Upwelling/Build -DROMS_HEADER="upwelling.h" -I ROMS/Include -I /home/berk/ro
ms/Projects/Upwelling -I ROMS/Nonlinear -I ROMS/Nonlinear/Biology -I ROMS/Nonlin
ear/Sediment -I ROMS/Utility -I ROMS/Drivers -I ROMS/Functionals -I /home/berk/r
oms/Projects/Upwelling -I Master -I Compilers --silent --moddir /home/berk/roms/
Projects/Upwelling/Build ROMS/Nonlinear/bbl.F ROMS/Nonlinear/bc_2d.F ROMS/Nonli
near/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/con
v_3d.F ROMS/Nonlinear/conv_bry2d.F ROMS/Nonlinear/conv_bry3d.F ROMS/Nonlinear/di
ag.F ROMS/Nonlinear/exchange_2d.F ROMS/Nonlinear/exchange_3d.F ROMS/Nonlinear/fo
rcing.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/Nonlinea
r/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/Nonline
ar/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/Nonli
near/my25_prestep.F ROMS/Nonlinear/obc_adjust.F ROMS/Nonlinear/obc_volcons.F ROM
S/Nonlinear/omega.F ROMS/Nonlinear/output.F ROMS/Nonlinear/pre_step3d.F ROMS/Non
linear/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/Nonlin
ear/set_depth.F ROMS/Nonlinear/set_massflux.F ROMS/Nonlinear/set_tides.F ROMS/No
nlinear/set_vbc.F ROMS/Nonlinear/set_zeta.F ROMS/Nonlinear/step2d.F ROMS/Nonline
ar/step3d_t.F ROMS/Nonlinear/step3d_uv.F ROMS/Nonlinear/step_floats.F ROMS/Nonli
near/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/v2
dbc_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/Biolo
gy/biology.F ROMS/Nonlinear/Sediment/sed_bed.F ROMS/Nonlinear/Sediment/sed_bedlo
ad.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/F
unctionals/analytical.F ROMS/Utility/abort.F ROMS/Utility/array_modes.F ROMS/Uti
lity/back_cost.F ROMS/Utility/cgradient.F ROMS/Utility/checkadj.F ROMS/Utility/c
heckdefs.F ROMS/Utility/checkerror.F ROMS/Utility/checkvars.F ROMS/Utility/close
_io.F ROMS/Utility/congrad.F ROMS/Utility/convolve.F ROMS/Utility/cost_grad.F RO
MS/Utility/def_avg.F ROMS/Utility/def_diags.F ROMS/Utility/def_dim.F ROMS/Utilit
y/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_inf
o.F ROMS/Utility/def_ini.F ROMS/Utility/def_lanczos.F ROMS/Utility/def_mod.F ROM
S/Utility/def_norm.F ROMS/Utility/def_rst.F ROMS/Utility/def_station.F ROMS/Util
ity/def_tides.F ROMS/Utility/def_var.F ROMS/Utility/distribute.F ROMS/Utility/do
tproduct.F ROMS/Utility/extract_obs.F ROMS/Utility/extract_sta.F ROMS/Utility/fr
c_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 R
OMS/Utility/get_cycle.F ROMS/Utility/get_date.F ROMS/Utility/get_grid.F ROMS/Uti
lity/get_gst.F ROMS/Utility/get_ngfld.F ROMS/Utility/get_ngfldr.F ROMS/Utility/g
et_state.F ROMS/Utility/get_varcoords.F ROMS/Utility/grid_coords.F ROMS/Utility/
ini_adjust.F ROMS/Utility/ini_hmixcoef.F ROMS/Utility/ini_lanczos.F ROMS/Utility
/inp_par.F ROMS/Utility/inquire.F ROMS/Utility/interpolate.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 RO
MS/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_fwrite
3d.F ROMS/Utility/nf_fwrite3d_bry.F ROMS/Utility/nf_fwrite4d.F ROMS/Utility/norm
alization.F ROMS/Utility/nrutil.F ROMS/Utility/obs_cost.F ROMS/Utility/obs_depth
.F ROMS/Utility/obs_initial.F ROMS/Utility/obs_read.F ROMS/Utility/obs_write.F R
OMS/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/r
egrid.F ROMS/Utility/rep_matrix.F ROMS/Utility/set_2dfld.F ROMS/Utility/set_2dfl
dr.F ROMS/Utility/set_3dfld.F ROMS/Utility/set_3dfldr.F ROMS/Utility/set_diags.F
ROMS/Utility/set_masks.F ROMS/Utility/set_ngfld.F ROMS/Utility/set_ngfldr.F ROM
S/Utility/set_scoord.F ROMS/Utility/set_weights.F ROMS/Utility/shapiro.F ROMS/Ut
ility/sqlq.F ROMS/Utility/state_addition.F ROMS/Utility/state_copy.F ROMS/Utilit
y/state_dotprod.F ROMS/Utility/state_initialize.F ROMS/Utility/state_product.F R
OMS/Utility/state_scale.F ROMS/Utility/stats_modobs.F ROMS/Utility/stiffness.F R
OMS/Utility/strings.F ROMS/Utility/sum_grad.F ROMS/Utility/timers.F ROMS/Utility
/vorticity.F ROMS/Utility/white_noise.F ROMS/Utility/wpoints.F ROMS/Utility/wrt_
avg.F ROMS/Utility/wrt_diags.F ROMS/Utility/wrt_error.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/Utilit
y/wrt_rst.F ROMS/Utility/wrt_station.F ROMS/Utility/wrt_tides.F ROMS/Utility/zet
a_balance.F ROMS/Modules/mod_arrays.F ROMS/Modules/mod_average.F ROMS/Modules/mo
d_bbl.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_f
loats.F ROMS/Modules/mod_forces.F ROMS/Modules/mod_fourdvar.F ROMS/Modules/mod_g
rid.F ROMS/Modules/mod_iounits.F ROMS/Modules/mod_kinds.F ROMS/Modules/mod_mixin
g.F ROMS/Modules/mod_ncparam.F ROMS/Modules/mod_nesting.F ROMS/Modules/mod_netcd
f.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_stora
ge.F ROMS/Modules/mod_strings.F ROMS/Modules/mod_tides.F Master/esmf_roms.F Mast
er/master.F Master/ocean_control.F Master/ocean_coupler.F Master/propagator.F Ma
ster/roms_export.F Master/roms_import.F > /home/berk/roms/Projects/Upwelling/Bui
ld/MakeDepend
cp -p /home/berk/make_macros.mk /home/berk/roms/Projects/Upwelling/Build
makefile:234: INCLUDING FILE /home/berk/roms/Projects/Upwelling/Build/make_macro
s.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
which: no mpif90 in (/opt/gfortransoft/openmpi/bin:/usr/local/bin:/usr/bin:/cygd
rive/c/Program Files/Microsoft Visual Studio/Common/Tools:/cygdrive/c/Program Fi
les/Microsoft Visual Studio/Common/Msdev98/BIN:/cygdrive/c/Program Files/Microso
ft Visual Studio/DF98/BIN:/cygdrive/c/Program Files/Microsoft Visual Studio/VC98
/BIN:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System
32/Wbem:/cygdrive/c/Program Files/ATI Technologies/ATI Control Panel:/cygdrive/c
/Program Files/MATLAB/R2008a/bin:/cygdrive/c/Program Files/MATLAB/R2008a/bin/win
32)
/bin/sh: --: invalid option
Usage: /bin/sh [GNU long option] [option] ...
/bin/sh [GNU long option] [option] script-file ...
GNU long options:
--debug
--debugger
--dump-po-strings
--dump-strings
--help
--init-file
--login
--noediting
--noprofile
--norc
--posix
--protected
--rcfile
--restricted
--verbose
--version
Shell options:
-irsD or -c command or -O shopt_option (invocation only)
-abefhkmnptuvxBCHP or -o option
/usr/bin/cpp -P -traditional -DMPI -DCYGWIN -DI686 -DGFORTRAN -D'ROOT_DIR="/home
/berk/roms/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/be
rk/roms/Projects/Upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home
/berk/roms/Projects/Upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="566M"' -IROMS
/Include -I/home/berk/roms/Projects/Upwelling -IROMS/Nonlinear -IROMS/Nonlinear/
Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functiona
ls -I/home/berk/roms/Projects/Upwelling -IMaster -ICompilers -D'HEADER_DIR="/hom
e/berk/roms/Projects/Upwelling"' ROMS/Utility/abort.F > /home/berk/roms/Project
s/Upwelling/Build/abort.f90
ROMS/Bin/cpp_clean /home/berk/roms/Projects/Upwelling/Build/abort.f90
/usr/bin/cpp -P -traditional -DMPI -DCYGWIN -DI686 -DGFORTRAN -D'ROOT_DIR="/home
/berk/roms/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/be
rk/roms/Projects/Upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home
/berk/roms/Projects/Upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="566M"' -IROMS
/Include -I/home/berk/roms/Projects/Upwelling -IROMS/Nonlinear -IROMS/Nonlinear/
Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functiona
ls -I/home/berk/roms/Projects/Upwelling -IMaster -ICompilers -D'HEADER_DIR="/hom
e/berk/roms/Projects/Upwelling"' Master/ocean_control.F > /home/berk/roms/Proje
cts/Upwelling/Build/ocean_control.f90
ROMS/Bin/cpp_clean /home/berk/roms/Projects/Upwelling/Build/ocean_control.f90
/usr/bin/cpp -P -traditional -DMPI -DCYGWIN -DI686 -DGFORTRAN -D'ROOT_DIR="/home
/berk/roms/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/be
rk/roms/Projects/Upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home
/berk/roms/Projects/Upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="566M"' -IROMS
/Include -I/home/berk/roms/Projects/Upwelling -IROMS/Nonlinear -IROMS/Nonlinear/
Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functiona
ls -I/home/berk/roms/Projects/Upwelling -IMaster -ICompilers -D'HEADER_DIR="/hom
e/berk/roms/Projects/Upwelling"' ROMS/Functionals/analytical.F > /home/berk/rom
s/Projects/Upwelling/Build/analytical.f90
ROMS/Bin/cpp_clean /home/berk/roms/Projects/Upwelling/Build/analytical.f90
/usr/bin/cpp -P -traditional -DMPI -DCYGWIN -DI686 -DGFORTRAN -D'ROOT_DIR="/home
/berk/roms/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/be
rk/roms/Projects/Upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home
/berk/roms/Projects/Upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="566M"' -IROMS
/Include -I/home/berk/roms/Projects/Upwelling -IROMS/Nonlinear -IROMS/Nonlinear/
Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functiona
ls -I/home/berk/roms/Projects/Upwelling -IMaster -ICompilers -D'HEADER_DIR="/hom
e/berk/roms/Projects/Upwelling"' ROMS/Utility/distribute.F > /home/berk/roms/Pr
ojects/Upwelling/Build/distribute.f90
ROMS/Bin/cpp_clean /home/berk/roms/Projects/Upwelling/Build/distribute.f90
/usr/bin/cpp -P -traditional -DMPI -DCYGWIN -DI686 -DGFORTRAN -D'ROOT_DIR="/home
/berk/roms/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/be
rk/roms/Projects/Upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home
/berk/roms/Projects/Upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="566M"' -IROMS
/Include -I/home/berk/roms/Projects/Upwelling -IROMS/Nonlinear -IROMS/Nonlinear/
Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functiona
ls -I/home/berk/roms/Projects/Upwelling -IMaster -ICompilers -D'HEADER_DIR="/hom
e/berk/roms/Projects/Upwelling"' ROMS/Modules/mod_iounits.F > /home/berk/roms/P
rojects/Upwelling/Build/mod_iounits.f90
ROMS/Bin/cpp_clean /home/berk/roms/Projects/Upwelling/Build/mod_iounits.f90
/usr/bin/cpp -P -traditional -DMPI -DCYGWIN -DI686 -DGFORTRAN -D'ROOT_DIR="/home
/berk/roms/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/be
rk/roms/Projects/Upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home
/berk/roms/Projects/Upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="566M"' -IROMS
/Include -I/home/berk/roms/Projects/Upwelling -IROMS/Nonlinear -IROMS/Nonlinear/
Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functiona
ls -I/home/berk/roms/Projects/Upwelling -IMaster -ICompilers -D'HEADER_DIR="/hom
e/berk/roms/Projects/Upwelling"' ROMS/Modules/mod_param.F > /home/berk/roms/Pro
jects/Upwelling/Build/mod_param.f90
ROMS/Bin/cpp_clean /home/berk/roms/Projects/Upwelling/Build/mod_param.f90
/usr/bin/cpp -P -traditional -DMPI -DCYGWIN -DI686 -DGFORTRAN -D'ROOT_DIR="/home
/berk/roms/trunk"' -DUPWELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="/home/be
rk/roms/Projects/Upwelling/upwelling.h"' -DNestedGrids= -D'ANALYTICAL_DIR="/home
/berk/roms/Projects/Upwelling"' -D'MY_ANALYTICAL="on"' -D'SVN_REV="566M"' -IROMS
/Include -I/home/berk/roms/Projects/Upwelling -IROMS/Nonlinear -IROMS/Nonlinear/
Biology -IROMS/Nonlinear/Sediment -IROMS/Utility -IROMS/Drivers -IROMS/Functiona
ls -I/home/berk/roms/Projects/Upwelling -IMaster -ICompilers -D'HEADER_DIR="/hom
e/berk/roms/Projects/Upwelling"' ROMS/Modules/mod_kinds.F > /home/berk/roms/Pro
jects/Upwelling/Build/mod_kinds.f90
ROMS/Bin/cpp_clean /home/berk/roms/Projects/Upwelling/Build/mod_kinds.f90
cd /home/berk/roms/Projects/Upwelling/Build; -c -frepack-arrays -O3 -ffast-math
-ffree-form -ffree-line-length-none mod_kinds.f90
/bin/sh: -c: command not found
make: *** [/home/berk/roms/Projects/Upwelling/Build/mod_kinds.o] Error 127


$ ls
Build build.bash ocean_upwelling.in upwelling.h


Thank you
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komet7
Posts: 11
Joined: Sun Aug 22, 2010 5:49 am
Location: university of florida

Re: build bash error

#2 Unread post by komet7 »

no worries, i fixed my problem by changing the build.bash (btw im running it on windows xp) to:

#export USE_LARGE=on (commented)

and
changing:

export USE_MPI=on # distributed-memory parallelism
export USE_MPIF90=on # compile with mpif90 script

to

export USE_MPI= # distributed-memory parallelism
export USE_MPIF90= # compile with mpif90 script
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