Error while loading shared libraries

[ryansmith]

I am new to ROMS and am trying to get it up and running on my linux box.
I downloaded and installed all the libraries; zlib, hdf5 and netCDF4.
I am using the gfortran compiler.
Running "make" in the ROMS home directory seems to work fine and produces the oceanS application. However, when I try to execute oceanS I get the following error

ryan@Gnomeputer:/media/sdb1/ROMS3$ sudo ./oceanS < /media/sdb1/ROMS3/ROMS/External/ocean_upwelling.in > test1.log
./oceanS: error while loading shared libraries: libhdf5_hl.so.0: cannot open shared object file: No such file or directory

The file "libhdf5_hl.so.0" exists and is in the lib folder of hdf5. I tried changing LD_LIBRARY path but get the same error.

Any suggestions???

Thanks,
Ryan

[feroda]

I am using the gfortran compiler.
./oceanS: error while loading shared libraries: libhdf5_hl.so.0: cannot open shared object file: No such file or directory

The file "libhdf5_hl.so.0" exists and is in the lib folder of hdf5. I tried changing LD_LIBRARY path but get the same error.
Ryan

I think you are quite near from the right way.
Firstly, $ vim /home/ryan/.bashrc
add
LD_LIBRARY_PATH=/usr/local/hdf5/lib
export LD_LIBRARY_PATH
at the end of the file.
:wq
$source .bashrc
$./oceanS < /media/sdb1/ROMS3/ROMS/External/ocean_upwelling.in > test1.log
It should work.
If not, please
try to use the ifort compiler to reset the NETCDF-4 and run makefile.

I have met the same problem, and I fixed it by using the first method.
Please let me know if it works for you.

[ryansmith]

Thank you very much for your comment. I ended up just copying the library to /usr/lib and it worked just fine.
I will also try your solution for a more robust fix.
Ryan

[soeyanto]

hello,
I am new in ROMS, just trying to compile for upwelling case. Compiling for ./OceanG is succsess but why when i run some error come, i.e:

Code: Select all

-----
[endros@pop4 roms]$ ./oceanG < ROMS/External/ocean_upwelling.in 
./oceanG: error while loading shared libraries: libhdf5_hl.so.6: cannot open shared object file: No such file or directory
-----

I have modify .bashrc file following as suggesting by feroda.
Anyone can help me?

Soeyanto

[machaielder]

hello Soeyanto ..did you manage to solve the problem...I am having the same problem now

[kate]

I think you are quite near from the right way.
Firstly, $ vim /home/ryan/.bashrc
add
export LD_LIBRARY_PATH=/usr/local/hdf5/lib
at the end of the file.

Yes, it's something like this, unless you are on a Mac in which case you want:

Code: Select all

export DYLD_LIBRARY_PATH=someValue

[machaielder]

hello Kate I am using ubuntu. whe do I type that command

[machaielder]

I tried the option you gave but the error persists...thanks Kate

[kate]

You type this:

Code: Select all

export LD_LIBRARY_PATH=/usr/local/hdf5/lib

but with the path to your hdf libraries. You can type it in your shell window and/or in your .bashrc, assuming you are using bash. Are you using bash? You put it in the shell window for this session, in your .bashrc for all your future session.

[machaielder]

I Kate it seams to work..here is a new problem
root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling# ./oceanS <ocean_upwelling.in

Model Input Parameters: ROMS/TOMS version 3.7
Saturday - April 18, 2015 - 7:46:19 AM
-----------------------------------------------------------------------------

MOD_NCPARAM - Unable to open variable information file:
../External/varinfo.dat
Default file is located in source directory.
root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling#

[machaielder]

solved using viewtopic.php?f=31&t=1

now I get the following error
root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling# ./oceanS <ocean_upwelling.in

Model Input Parameters: ROMS/TOMS version 3.7
Saturday - April 18, 2015 - 8:05:48 AM
-----------------------------------------------------------------------------

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 -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

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

Local Root : /home/dell/Roms/trunk
Header Dir : /home/dell/Roms/projects/upwelling
Header file : upwelling.h
Analytical Dir: /home/dell/Roms/projects/upwelling

Resolution, Grid 01: 0041x0080x016, Parallel Threads: 1, Tiling: 003x003


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

288 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.
72 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.
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).
7.6000E-04 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 Hout(idDano) Write out density anomaly.

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc

Tile partition information for Grid 01: 0041x0080x0016 tiling: 003x003

tile Istr Iend Jstr Jend Npts

0 1 14 1 27 6048
1 15 28 1 27 6048
2 29 41 1 27 5616
3 1 14 28 54 6048
4 15 28 28 54 6048
5 29 41 28 54 5616
6 1 14 55 80 5824
7 15 28 55 80 5824
8 29 41 55 80 5408

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 82.50 RHO-points
1 -2.50 43.50 0.50 82.50 RHO-points
2 -2.50 42.50 0.50 82.50 RHO-points
3 -1.50 43.50 -0.50 82.50 RHO-points
4 -2.50 43.50 -0.50 82.50 RHO-points
5 -2.50 42.50 -0.50 82.50 RHO-points
6 -1.50 43.50 -0.50 81.50 RHO-points
7 -2.50 43.50 -0.50 81.50 RHO-points
8 -2.50 42.50 -0.50 81.50 RHO-points

0 -2.00 43.50 0.50 82.50 U-points
1 -2.50 43.50 0.50 82.50 U-points
2 -2.50 42.00 0.50 82.50 U-points
3 -2.00 43.50 -0.50 82.50 U-points
4 -2.50 43.50 -0.50 82.50 U-points
5 -2.50 42.00 -0.50 82.50 U-points
6 -2.00 43.50 -0.50 81.50 U-points
7 -2.50 43.50 -0.50 81.50 U-points
8 -2.50 42.00 -0.50 81.50 U-points

0 -1.50 43.50 0.00 82.50 V-points
1 -2.50 43.50 0.00 82.50 V-points
2 -2.50 42.50 0.00 82.50 V-points
3 -1.50 43.50 -0.50 82.50 V-points
4 -2.50 43.50 -0.50 82.50 V-points
5 -2.50 42.50 -0.50 82.50 V-points
6 -1.50 43.50 -0.50 81.00 V-points
7 -2.50 43.50 -0.50 81.00 V-points
8 -2.50 42.50 -0.50 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.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
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_C4HADVECTION Fourth-order centered horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection 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.
VAR_RHO_2D Variable density barotropic mode.

CHECKDEFS - no bottom stress formulation is selected.

Elapsed CPU time (seconds):


ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Configuration error ..... exit_flag: 5


ERROR: Illegal model configuration.
root@dell-Inspiron-N5110:/home/dell/Roms/projects/upwelling#

[kate]

You don't need to post things twice...