Hi,
I'm new to the ROMS model, and I've encountered a problem with 'make'. I run 'make' like this, make -f makefile.gnu
& the output is
makefile.gnu:226: INCLUDING FILE Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
make: execvp: svnversion: Permission denied
cd Build; /share/apps/gnu/mpich2/bin/mpif90 -c -fno-second-underscore -O3 -ffast-math mod_kinds.f90
/share/apps/gnu/gcc/libexec/gcc/x86_64-unknown-linux-gnu/4.2.1/f951: symbol lookup error: /share/apps/gnu/mpf r/lib/libmpfr.so.1: undefined symbol: __gmp_get_memory_functions
make: *** [Build/mod_kinds.o] Error 1
[deepti@Godavari trunk]$ make clean
rm -f -r core *.ipo Build Compilers/make_macros.mk
[deepti@Godavari trunk]$ make -f makefile.gnu
makefile.gnu:230: INCLUDING FILE Compilers/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIO NS
make: execvp: svnversion: Permission denied
cp -f /home/deepti/gnu_netcdf_path/include/netcdf.mod Build
cp -f /home/deepti/gnu_netcdf_path/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/SeaIce -I ROMS/Utility -I ROMS/Drivers -I ROMS/Functionals -I Master -I Compilers - -silent --moddir Build ROMS/Nonlinear/bbl.F ROMS/Nonlinear/bc_2d.F ROMS/Nonlinear/bc_3d.F ROMS/Nonlinear/bio logy.F ROMS/Nonlinear/bulk_flux.F ROMS/Nonlinear/bvf_mix.F ROMS/Nonlinear/conv_2d.F ROMS/Nonlinear/conv_3d.F ROMS/Nonlinear/diag.F ROMS/Nonlinear/exchange_2d.F ROMS/Nonlinear/exchange_3d.F ROMS/Nonlinear/forcing.F ROMS /Nonlinear/get_data.F ROMS/Nonlinear/get_idata.F ROMS/Nonlinear/gls_corstep.F ROMS/Nonlinear/gls_prestep.F RO MS/Nonlinear/ini_fields.F ROMS/Nonlinear/initial.F ROMS/Nonlinear/interp_floats.F ROMS/Nonlinear/lmd_bkpp.F R OMS/Nonlinear/lmd_skpp.F ROMS/Nonlinear/lmd_swfrac.F ROMS/Nonlinear/lmd_vmix.F ROMS/Nonlinear/main2d.F ROMS/N onlinear/main3d.F ROMS/Nonlinear/mpdata_adiff.F ROMS/Nonlinear/my25_corstep.F ROMS/Nonlinear/my25_prestep.F R OMS/Nonlinear/obc_volcons.F ROMS/Nonlinear/omega.F ROMS/Nonlinear/output.F ROMS/Nonlinear/pre_step3d.F ROMS/N onlinear/prsgrd.F ROMS/Nonlinear/radiation_stress.F ROMS/Nonlinear/rho_eos.F ROMS/Nonlinear/rhs3d.F ROMS/Nonl inear/sediment.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/t3d bc_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/wvelocity.F ROMS /Nonlinear/zetabc.F ROMS/Functionals/analytical.F ROMS/SeaIce/seaice.F ROMS/Utility/abort.F ROMS/Utility/back_cost.F ROMS/Utility/back_cov.F ROMS/Utility/back_step.F ROMS/Utility/cgradient.F ROMS/Utility/checkdefs.F ROMS/Utility/checkerror.F ROMS/Utility/checkvars.F ROMS/Utility/close_io.F ROMS/Utility/congrad.F ROMS/Utility/cost_grad.F ROMS/Utility/cost_norm.F ROMS/Utility/def_avg.F ROMS/Utility/def_diags.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_mod.F ROMS/Utility/def_norm.F ROMS/Utility/def_rst.F ROMS/Utility/def_station.F ROMS/Utility/def_tides.F ROMS/Utility/def_var.F ROMS/Utility/descent.F ROMS/Utility/distribute.F ROMS/Utility/dotproduct.F ROMS/Utility/downhill.F ROMS/Utility/extract_obs.F ROMS/Utility/extract_sta.F ROMS/Utility/frc_adjust.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_state.F ROMS/Utility/get_varcoords.F ROMS/Utility/grid_coords.F ROMS/Utility/impulse.F ROMS/Utility/ini_adjust.F ROMS/Utility/inp_par.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_fread3d.F ROMS/Utility/nf_fread4d.F ROMS/Utility/nf_fwrite2d.F ROMS/Utility/nf_fwrite3d.F ROMS/Utility/nf_fwrite4d.F ROMS/Utility/normalization.F ROMS/Utility/nrutil.F ROMS/Utility/obs_cost.F ROM S/Utility/obs_depth.F ROMS/Utility/obs_initial.F ROMS/Utility/obs_read.F ROMS/Utility/obs_scale.F ROMS/Utilit y/obs_write.F ROMS/Utility/oi_update.F ROMS/Utility/opencdf.F ROMS/Utility/packing.F ROMS/Utility/ran1.F ROMS/Utility/ran_state.F ROMS/Utility/regrid.F ROMS/Utility/set_2dfld.F ROMS/Utility/set_2dfldr.F ROMS/Utility/set_3dfld.F ROMS/Utility/set_3dfldr.F ROMS/Utility/set_diags.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/state_addition.F ROMS/Utility/state_copy.F ROMS/Utility/state_dotprod.F ROMS/Utility/state_initialize.F ROMS/Utility/state_scale.F ROMS/Utility/stats_modobs.F ROMS/Utility/stiffness.F ROMS/Utility/timers.F ROMS/Utility/utility.F ROMS/Utility/white_noise.F ROMS/Utility/wpoints.F ROMS/Utility/wrt_avg.F ROMS/Utility/wrt_diags.F ROMS/Utility/wrt_ floats.F ROMS/Utility/wrt_gst.F ROMS/Utility/wrt_hessian.F ROMS/Utility/wrt_his.F ROMS/Utility/wrt_info.F ROMS/Utility/wrt_ini.F ROMS/Utility/wrt_rst.F ROMS/Utility/wrt_station.F ROMS/Utility/wrt_tides.F ROMS/Modules/mod_arrays.F ROMS/Modules/mod_average.F ROMS/Modules/mod_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_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_obs.F ROMS/Modules/mod_ocean.F ROMS/Modules/mod_parallel.F ROMS/Modules/mod_param.F ROMS/Modules/mod_scalars.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 > Build/Ma keDepend
cp -p /home/deepti/rom-parallel/trunk/Compilers/make_macros.mk Build
makefile.gnu:226: INCLUDING FILE Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
make: execvp: svnversion: Permission denied
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/deepti/rom-parallel/trunk"' -DUP WELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids=1 -D'ANALYTICAL_DIR="/home/deept i/rom-parallel/trunk/ROMS/Functionals"' -D'SVN_REV=""' -IROMS/Include -IROMS/Nonlinear -IROMS/SeaIce -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="./ROMS/Include"' ROMS/Nonlinear/bbl.F > Build/bbl.f90
ROMS/Bin/cpp_clean Build/bbl.f90
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/deepti/rom-parallel/trunk"' -DUP WELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids=1 -D'ANALYTICAL_DIR="/home/deept i/rom-parallel/trunk/ROMS/Functionals"' -D'SVN_REV=""' -IROMS/Include -IROMS/Nonlinear -IROMS/SeaIce -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="./ROMS/Include"' ROMS/Nonlinear/bc_2d.F > Build/bc_2d.f90
ROMS/Bin/cpp_clean Build/bc_2d.f90
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/deepti/rom-parallel/trunk"' -DUP WELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids=1 -D'ANALYTICAL_DIR="/home/deept i/rom-parallel/trunk/ROMS/Functionals"' -D'SVN_REV=""' -IROMS/Include -IROMS/Nonlinear -IROMS/SeaIce -IROMS/U tility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="./ROMS/Include"' ROMS/Nonlinear/exchange_2d.F > Build/exchange_2d.f90
ROMS/Bin/cpp_clean Build/exchange_2d.f90
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/deepti/rom-parallel/trunk"' -DUP WELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids=1 -D'ANALYTICAL_DIR="/home/deept i/rom-parallel/trunk/ROMS/Functionals"' -D'SVN_REV=""' -IROMS/Include -IROMS/Nonlinear -IROMS/SeaIce -IROMS/U tility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="./ROMS/Include"' ROMS/Modules/mod_param.F > Build/mod_param.f90
ROMS/Bin/cpp_clean Build/mod_param.f90
/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/deepti/rom-parallel/trunk"' -DUP WELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids=1 -D'ANALYTICAL_DIR="/home/deept i/rom-parallel/trunk/ROMS/Functionals"' -D'SVN_REV=""' -IROMS/Include -IROMS/Nonlinear -IROMS/SeaIce -IROMS/U tility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="./ROMS/Include"' ROMS/Modules/mod_kinds.F > Build/mod_kinds.f90
ROMS/Bin/cpp_clean Build/mod_kinds.f90
cd Build; /share/apps/gnu/mpich2/bin/mpif90 -c -fno-second-underscore -O3 -ffast-math mod_kinds.f90
/share/apps/gnu/gcc/libexec/gcc/x86_64-unknown-linux-gnu/4.2.1/f951: symbol lookup error: /share/apps/gnu/mpfr/lib/libmpfr.so.1: undefined symbol: __gmp_get_memory_functions
make: *** [Build/mod_kinds.o] Error 1
problem during make
Have you tried compiling the model in serial (unset USE_MPI and USE_MPIF90 in your makefile) to make sure your Fortran compiler works?
What Fortran compiler are you using? Based on your /usr/bin/cpp lines it looks like you're using g95:
A preliminary google search suggests that your f951 (probably gfortran) may be linking to the wrong version of the MPFR
library. I have never used this library so I don't know anything about it.
Suggestions:
I could not find any explanation as to why svnversion is giving you permission denied. Perhaps you are not the owner of the files in that directory? This is error will not affect your ability to build ROMS so you should figure out all your other problems first.
What Fortran compiler are you using? Based on your /usr/bin/cpp lines it looks like you're using g95:
However, it appears from your path to f951 that mpif90 is trying to use gfortran:/usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D'ROOT_DIR="/home/deepti/rom-parallel/trunk"' -DUP WELLING -D'HEADER="upwelling.h"' -D'ROMS_HEADER="upwelling.h"' -DNestedGrids=1 -D'ANALYTICAL_DIR="/home/deept i/rom-parallel/trunk/ROMS/Functionals"' -D'SVN_REV=""' -IROMS/Include -IROMS/Nonlinear -IROMS/SeaIce -IROMS/Utility -IROMS/Drivers -IROMS/Functionals -IMaster -ICompilers -D'HEADER_DIR="./ROMS/Include"' ROMS/Nonlinear/bbl.F > Build/bbl.f90
The gcc/libexec/gcc/x86_64-unknown-linux-gnu/4.x.x is the usual path to gcc4 and gfortran software. I'm not sure that is your whole problem though./share/apps/gnu/gcc/libexec/gcc/x86_64-unknown-linux-gnu/4.2.1/f951: symbol lookup error:
A preliminary google search suggests that your f951 (probably gfortran) may be linking to the wrong version of the MPFR
library. I have never used this library so I don't know anything about it.Suggestions:
- Read about the ROMS Build Script to learn how to avoid modifying the makefile and creating extra makefiles
- Try to compile/run the model in serial first to make sure your Fortran compiler works.
- Find out if the mpif90 you are using was built with g95 or gfortran. You might just try switching FORT to gfortran and see if you get different results. If you want to use g95 in your mpif90 you may need to rebuild mpich2.
I could not find any explanation as to why svnversion is giving you permission denied. Perhaps you are not the owner of the files in that directory? This is error will not affect your ability to build ROMS so you should figure out all your other problems first.
Thank you sir.I have compiled/run the model in serial fashion also and it works.My problem for make is solved when i again built the netcdf with gfortran. I got the executable oceanM.
Then i submitted the job like this:-
mpirun -machinefile /home/deepti/rom-parallel/mcfile -np 4 oceanM ROMS/External/ocean_upwelling.in >&op
entry of my machinefile is
compute-0-0
compute-0-0
compute-0-1
compute-0-2
I got this output:-
Node # 2 (pid= 25987) is active.
Process Information:
Node # 0 (pid= 18704) is active.
Node # 1 (pid= 18703) is active.
Node # 3 (pid= 1490) is active.
Model Input Parameters: ROMS/TOMS version 3.0
Monday - April 21, 2008 - 10:41:34 AM
-----------------------------------------------------------------------------
Wind-Driven Upwelling/Downwelling over a Periodic Channel
Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /share/apps/gnu/mpich2/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none
Input Script : ROMS/External/ocean_upwelling.in
SVN Root URL :
SVN Revision : exported
Local Root : /home/deepti/rom-parallel/trunk
Header Dir : /home/deepti/rom-parallel/trunk/ROMS/Include
Header file : upwelling.h
Analytical Dir: /home/deepti/rom-parallel/trunk/ROMS/Functionals
Resolution, Grid 01: 0041x0080x016, Parallel Nodes: 4, Tiling: 001x001
ROMS/TOMS: Wrong choice of domain 01 partition or number of parallel threads.
NtileI * NtileJ must be equal to the number of parallel nodes.
Change -np value to mpirun or
change domain partition in input script.
Tile partition information for Grid 01: 0041x0080x0016 tiling: 001x001
tile Istr Iend Jstr Jend Npts
0 1 41 1 80 52480
Maximum halo size in XI and ETA directions:
HaloSizeI(1) = 162
HaloSizeJ(1) = 273
TileSide(1) = 85
TileSize(1) = 4080
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 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.
EW_PERIODIC East-West periodic boundaries.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
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 Conservative parabolic spline reconstruction.
TS_U3HADVECTION Third-order upstream bias 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 bias 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.
rank 2 in job 20 Godavari.acms.cdac.in_41670 caused collective abort of all ranks
exit status of rank 2: killed by signal 9
Can you please suggest me where the problem is? or i had choosen the wrong number of threads.
Then i submitted the job like this:-
mpirun -machinefile /home/deepti/rom-parallel/mcfile -np 4 oceanM ROMS/External/ocean_upwelling.in >&op
entry of my machinefile is
compute-0-0
compute-0-0
compute-0-1
compute-0-2
I got this output:-
Node # 2 (pid= 25987) is active.
Process Information:
Node # 0 (pid= 18704) is active.
Node # 1 (pid= 18703) is active.
Node # 3 (pid= 1490) is active.
Model Input Parameters: ROMS/TOMS version 3.0
Monday - April 21, 2008 - 10:41:34 AM
-----------------------------------------------------------------------------
Wind-Driven Upwelling/Downwelling over a Periodic Channel
Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /share/apps/gnu/mpich2/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none
Input Script : ROMS/External/ocean_upwelling.in
SVN Root URL :
SVN Revision : exported
Local Root : /home/deepti/rom-parallel/trunk
Header Dir : /home/deepti/rom-parallel/trunk/ROMS/Include
Header file : upwelling.h
Analytical Dir: /home/deepti/rom-parallel/trunk/ROMS/Functionals
Resolution, Grid 01: 0041x0080x016, Parallel Nodes: 4, Tiling: 001x001
ROMS/TOMS: Wrong choice of domain 01 partition or number of parallel threads.
NtileI * NtileJ must be equal to the number of parallel nodes.
Change -np value to mpirun or
change domain partition in input script.
Tile partition information for Grid 01: 0041x0080x0016 tiling: 001x001
tile Istr Iend Jstr Jend Npts
0 1 41 1 80 52480
Maximum halo size in XI and ETA directions:
HaloSizeI(1) = 162
HaloSizeJ(1) = 273
TileSide(1) = 85
TileSize(1) = 4080
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 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.
EW_PERIODIC East-West periodic boundaries.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
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 Conservative parabolic spline reconstruction.
TS_U3HADVECTION Third-order upstream bias 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 bias 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.
rank 2 in job 20 Godavari.acms.cdac.in_41670 caused collective abort of all ranks
exit status of rank 2: killed by signal 9
Can you please suggest me where the problem is? or i had choosen the wrong number of threads.
You're on the right trac about the wrong number of threads. I believe you need to edit the ROMS/External/ocean_upwelling.in. You chose to run on 4 processors (-np 4) but the bold part of this line:
You need to set NtileI and NtileJ so their product (NtileI X NtileJ) equals the number of processors you want to run ROMS on; in your case, 4. I suggest setting both NtileI and NtileJ to 2 but you could use 4 and 1 if you like.
tells me that NtileI and NtileJ are set to 1.Tile partition information for Grid 01: 0041x0080x0016 tiling: 001x001
You need to set NtileI and NtileJ so their product (NtileI X NtileJ) equals the number of processors you want to run ROMS on; in your case, 4. I suggest setting both NtileI and NtileJ to 2 but you could use 4 and 1 if you like.