first run upwelling problem

[okami_zxh]

When I tried to run upwelling and followed the tutorial, after i typed ./oceanG < ocean_upwelling.in > out.text, the out.text shows an error, how can i solved this problem?
^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@

ROMS/TOMS - Input error ............. exit_flag: 2


ERROR: Abnormal termination: NetCDF INPUT.
REASON: No error
~
"out.text" 69L, 11105C

[kate]

"out.text" 69L, 11105C

Did you try and fail to attach the full output? I can't tell what went wrong from what you provided so far. There's probably an error message above the "Input error ... exit_flag: 2" line.

[okami_zxh]

Hi kate,
I think there is something wrong in compiling.Wehn I used makefile to compile, there is warning.
makefile:234: INCLUDING FILE Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
/share/apps/bin/mpif90 -heap-arrays -fp-model precise -ip -O3 Build/esmf_roms.o Build/master.o Build/ocean_control.o Build/ocean_coupler.o Build/propagator.o Build/roms_export.o Build/roms_import.o -o oceanM Build/libUTIL.a Build/libNLM.a Build/libNLM_bio.a Build/libNLM_sed.a Build/libANA.a Build/libUTIL.a Build/libMODS.a -L/home/zhou/netcdf/lib -lnetcdf
/opt/intel/Compiler/11.1/064/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
rm -f -r /home/zhou/make_macros.mk

[kate]

When you get an error like this, you can always do a web search. You might even get something useful:

I had this problem in the past. The problem is the you are linking against the Intel math library only. The Intel math library (libimf) has optimized replacements for many of the routines in the system math library (libm). However, the Intel math library does not provide replacements for all functions.

The solution is simple. Always link against both math libraries: libimf libm

[okami_zxh]

Thanks Kate,
So where should I make the change of the linking according to your solution,makefile? Can u give me the exact sentence in makefile about the linking intel library.
Xiaohui

[kate]

Here's what I see when linking with intel:

Code: Select all

/opt/scyld/openmpi/1.10.4/intel/bin/mpif90 -heap-arrays -fp-model precise -ip -O3  /center/w/kate/Build_CGOA/roms_import.o /center/w/kate/Build_CGOA/propagator.o /center/w/kate/Build_CGOA/master.o /center/w/kate/Build_CGOA/roms_export.o /center/w/kate/Build_CGOA/ocean_coupler.o /center/w/kate/Build_CGOA/esmf_roms.o /center/w/kate/Build_CGOA/ocean_control.o -o oceanM /center/w/kate/Build_CGOA/libMODS.a /center/w/kate/Build_CGOA/libNLM.a /center/w/kate/Build_CGOA/libNLM_bio.a /center/w/kate/Build_CGOA/libNLM_sed.a /center/w/kate/Build_CGOA/libANA.a /center/w/kate/Build_CGOA/libUTIL.a /center/w/kate/Build_CGOA/libMODS.a -L/usr/local/pkg/data/netCDF-Fortran/4.4.4-pic-intel-2016b/lib -lnetcdff -L/usr/local/pkg/compiler/icc/2016.3.210-GCC-5.4.0-2.26/lib/intel64 -L/usr/local/pkg/numlib/imkl/11.3.3.210-pic-iompi-2016b/lib -L/usr/local/pkg/numlib/imkl/11.3.3.210-pic-iompi-2016b/mkl/lib/intel64 -L/usr/local/pkg/numlib/imkl/11.3.3.210-pic-iompi-2016b/lib -L/usr/local/pkg/data/netCDF/4.4.1-pic-intel-2016b/lib64 -lnetcdf -lnetcdf -liomp5 -lpthread
564.415u 39.328s 3:15.07 309.4%	0+0k 108608+217632io 8pf+0w

I don't get the warning you saw. Can you run with your executable? You got a warning, not an error, so all might be well.

[okami_zxh]

Hi Kate
I tried to execute. there is an error in out.text as :
Model Input Parameters: ROMS/TOMS version 3.7
Tuesday - February 14, 2017 - 7:45:47 PM
-----------------------------------------------------------------------------

MOD_NCPARAM - Unable to open variable information file:
ROMS/External/varinfo.dat
Default file is located in source directory.
~

Actually, there is the file varinfo.dat in ROMS\External .
here is my batch file for job sumission

work_dir=/home/zhou/Projects/upwelling
cd $work_dir
mpirun -np 32 oceanM ../../MyDir/ROMS/External/ocean_upwelling.in > out.text

I only changed the Mt_HEADER_DIR in makefile, my makefile is
ROMS_APPLICATION ?= UPWELLING

# If application header files is not located in "ROMS/Include",
# provide an alternate directory FULL PATH.

MY_HEADER_DIR ?= /home/zhou/MyDir/ROMS/Include



Can u tell me which part is wrong

[kate]

MOD_NCPARAM - Unable to open variable information file:
ROMS/External/varinfo.dat

You didn't tell it the correct path to this file in the ocean_upwelling.in file. If you didn't change the path, it is "ROMS/External/varinfo.dat" from the current directory.

From this:

mpirun -np 32 oceanM ../../MyDir/ROMS/External/ocean_upwelling.in > out.text

I assume that you are not in the parent ROMS directory. You should create a ROMS directory where you are now, create an External subdirectory, then copy the varinfo.dat to that directory.

[okami_zxh]

Hi Kate,
Thanks a lot.
But there is another error in out.text.

Compiler system : ifort
Compiler command : /share/apps/bin/mpif90
Compiler flags : -heap-arrays -fp-model precise -ip -O3 -free -free -free

Input Script :

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 825M

Local Root : /home/zhou/MyDir
Header Dir : /home/zhou/MyDir/ROMS/Include
Header file : upwelling.h
Analytical Dir: /home/zhou/MyDir/ROMS/Functionals

Resolution, Grid 01: 0041x0080x016, Parallel Nodes: 32, 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.

Elapsed CPU time (seconds):


ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Partition error ......... exit_flag: 6


ERROR: Illegal domain partition.
33,0-1 Bot

[okami_zxh]

Hi Kate
according to the out.text, I have changed the np in bash script. But the problem still occure.
here is my bash:

work_dir=/home/zhou/Projects/upwelling
cd $work_dir
mpirun -np 8 oceanM ocean_upwelling.in > out.text

#pbsnodes -a
##PBS -l nodes=compute-0-19:ppn=16+compute-0-18:ppn=16
#nodes=2:ppn=16


Here is the out.text
Using username "zhou".

Local Root : /home/zhou/MyDir
Header Dir : /home/zhou/MyDir/ROMS/Include
Header file : upwelling.h
Analytical Dir: /home/zhou/MyDir/ROMS/Functionals

Resolution, Grid 01: 0041x0080x016, Parallel Nodes: 8, 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.

Elapsed CPU time (seconds):


ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Partition error ......... exit_flag: 6


ERROR: Illegal domain partition.
39,1 Bot

Can u help me solve this problem?

[kate]

Parallel Nodes: 8, Tiling: 001x001

You have NtileI = 1 and NtileJ = 1 in the input file. You need to change one or both so that NtileI * NtileJ = 8. Or ask for 1 processor in your job script. UPWELLING is so small I usually don't even compile it with the parallel option.

[okami_zxh]

Hi Kate,
I think I got the output now. I really appreciate your help.
Thank you a lot.

[okami_zxh]

Hi Kate,
why my time step (parameter :ocean_time) in ocean_his.nc file is 0, according to the results, it should be 288 time steps, but i did not change any code in input file.
my result of temp in ocean_his.nc:

temp
Size: 43x82x16x1
Dimensions: xi_rho,eta_rho,s_rho,ocean_time
Datatype: single
Attributes:
long_name = 'potential temperature'
units = 'Celsius'
time = 'ocean_time'
grid = 'grid'
location = 'face'
coordinates = 'x_rho y_rho s_rho ocean_time'
field = 'temperature, scalar, series'
Can u help me solve the problem?

[kate]

The question is, how many steps did you run for and how often did you tell it to save history files? It would have written a history record at time zero, but you only have one in that file. Is it the only history file? Did ROMS crash before getting to step 288? I can't tell.

[okami_zxh]

Hi Kate
in the ocean_upwelling.in file, i set :
! Time-Stepping parameters.
!------------------------------------------------------------------------------
!
! NTIMES Total number time-steps in current run. If 3D configuration,
! NTIMES is the total of baroclinic time-steps. If only 2D
! configuration, NTIMES is the total of barotropic time-steps.

NTIMES == 1440
DT == 300.0d0
NDTFAST == 30


Output history, quicksave, average, and diagnostic files parameters.

LDEFOUT == T
utput history, quicksave, average, and diagnostic files parameters.

LDEFOUT == T
NHIS == 1
NDEFHIS == 0
NQCK == 0
NDEFQCK == 0
NTSAVG == 1
NAVG == 72
NDEFAVG == 0
NTSDIA == 1
NDIA == 72
NDEFDIA == 0
LDEFOUT == T;
Becasue NHIS is the Number of time-steps between writing fields into HISTORY file. If I set 1, so it should have 1440 time points. I did not change anything other in the original ocean_upwelling.in file. Bu the output file (ocean_his.nc) shows thatthe parameter
temp
Size: 43x82x16x2
What is the problem?

[kate]

Did ROMS run for 1440 steps? It should have printed to the output every time it called WRT_HIS. Did you look at the standard output file?

[okami_zxh]

Hi Kate
I don't know what happened. It should be run for 1440 times. I did not change anything. Is there any standard output files?

[okami_zxh]

Hi Kate,
This is y out.text

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

1440 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.
288 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.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
72 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
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.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
72 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
72 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
5.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
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.

[kate]

Standard output is where all the print statements go. It writes to the screen if you run interactively. With NINFO=1 I get information every timestep, like this:

Code: Select all

   STEP   Day HH:MM:SS  KINETIC_ENRG   POTEN_ENRG    TOTAL_ENRG    NET_VOLUME
          C => (i,j,k)       Cu            Cv            Cw         Max Speed

       0 39446 00:00:00  1.889733E-03  1.959613E+04  1.959613E+04  4.096830E+15
          (097,191,50)  2.114777E-02  8.108576E-03  0.000000E+00  8.530640E-01
      DEF_HIS     - creating  history      file, Grid 01: nwgoa_his_00001.nc
      WRT_HIS     - wrote history     fields (Index=1,1) in record = 0000001
      DEF_STATION - creating  stations     file, Grid 01: nwgoa_sta.nc
       1 39446 00:02:00  1.883119E-03  1.960669E+04  1.960669E+04  4.094599E+15
          (300,101,01)  0.000000E+00  0.000000E+00  4.309511E+00  8.466840E-01
       2 39446 00:04:00  1.874179E-03  1.960664E+04  1.960664E+04  4.094586E+15
          (234,202,50)  3.103330E-03  6.650405E-03  7.207450E-01  8.402656E-01
       3 39446 00:06:00  1.867679E-03  1.960659E+04  1.960659E+04  4.094574E+15
          (234,202,50)  3.489571E-03  7.511304E-03  7.519809E-01  8.343320E-01
       4 39446 00:08:00  1.862443E-03  1.960654E+04  1.960654E+04  4.094562E+15
          (241,190,50)  1.114989E-05  1.756952E-05  8.244364E-01  8.280427E-01
       5 39446 00:10:00  1.858217E-03  1.960649E+04  1.960649E+04  4.094550E+15
          (234,202,50)  3.828630E-03  7.610422E-03  8.369061E-01  8.212624E-01
       6 39446 00:12:00  1.854687E-03  1.960645E+04  1.960645E+04  4.094538E+15
          (234,202,50)  3.678040E-03  6.916985E-03  8.404064E-01  8.152598E-01
       7 39446 00:14:00  1.851558E-03  1.960641E+04  1.960641E+04  4.094527E+15
          (300,101,50)  1.038696E-04  1.412139E-04  9.076163E-01  8.100066E-01
       8 39446 00:16:00  1.848700E-03  1.960637E+04  1.960637E+04  4.094516E+15
          (300,101,06)  4.073273E-08  4.073281E-08  6.778341E-01  8.051808E-01
       9 39446 00:18:00  1.846233E-03  1.960633E+04  1.960633E+04  4.094506E+15
          (298,025,50)  1.776752E-03  1.061148E-03  5.463311E-01  8.006113E-01
      10 39446 00:20:00  1.844143E-03  1.960629E+04  1.960630E+04  4.094496E+15
          (284,003,50)  3.917988E-04  4.038878E-03  5.455851E-01  7.961011E-01
      DEF_HIS     - creating  history      file, Grid 01: nwgoa_his_00002.nc
      WRT_HIS     - wrote history     fields (Index=1,1) in record = 0000001

Yes, I'm trying to debug something with frequent history files.

[okami_zxh]

This is the whole out.text, it seems same as the standard one, I don't know what's wrong

Model Input Parameters: ROMS/TOMS version 3.7
Friday - February 17, 2017 - 2:28:05 PM
-----------------------------------------------------------------------------

Wind-Driven Upwelling/Downwelling over a Periodic Channel

Operating system : Linux
CPU/hardware : x86_64
Compiler system : ifort
Compiler command : /share/apps/bin/mpif90
Compiler flags : -heap-arrays -fp-model precise -ip -O3 -free -free -free

Input Script :

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 825M

Local Root : /home/zhou/MyDir
Header Dir : /home/zhou/MyDir/ROMS/Include
Header file : upwelling.h
Analytical Dir: /home/zhou/MyDir/ROMS/Functionals

Resolution, Grid 01: 0041x0080x016, Parallel Nodes: 8, Tiling: 008x001


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

1440 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.
288 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.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
72 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
72 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
5.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
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).
0.0000E+00 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 Aout(idFsur) Write out averaged free-surface.
T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idVbar) Write out averaged 2D V-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idOvel) Write out averaged omega vertical velocity.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

T Dout(M2rate) Write out 2D momentum acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.

T Dout(M3rate) Write out 3D momentum acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.

T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Diagnostics File: ocean_dia.nc

Tile partition information for Grid 01: 0041x0080x0016 tiling: 008x001

tile Istr Iend Jstr Jend Npts

0 1 3 1 80 3840
1 4 9 1 80 7680
2 10 15 1 80 7680
3 16 21 1 80 7680
4 22 27 1 80 7680
5 28 33 1 80 7680
6 34 39 1 80 7680
7 40 41 1 80 2560

Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 3.50 0.50 80.50 RHO-points
1 3.50 9.50 0.50 80.50 RHO-points
2 9.50 15.50 0.50 80.50 RHO-points
3 15.50 21.50 0.50 80.50 RHO-points
4 21.50 27.50 0.50 80.50 RHO-points
5 27.50 33.50 0.50 80.50 RHO-points
6 33.50 39.50 0.50 80.50 RHO-points
7 39.50 41.50 0.50 80.50 RHO-points

0 1.00 3.50 0.50 80.50 U-points
1 3.50 9.50 0.50 80.50 U-points
2 9.50 15.50 0.50 80.50 U-points
3 15.50 21.50 0.50 80.50 U-points
4 21.50 27.50 0.50 80.50 U-points
5 27.50 33.50 0.50 80.50 U-points
6 33.50 39.50 0.50 80.50 U-points
7 39.50 41.00 0.50 80.50 U-points

0 0.50 3.50 1.00 80.00 V-points
1 3.50 9.50 1.00 80.00 V-points
2 9.50 15.50 1.00 80.00 V-points
3 15.50 21.50 1.00 80.00 V-points
4 21.50 27.50 1.00 80.00 V-points
5 27.50 33.50 1.00 80.00 V-points
6 33.50 39.50 1.00 80.00 V-points
7 39.50 41.50 1.00 80.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 54
HaloSizeJ(1) = 273
TileSide(1) = 85
TileSize(1) = 1020


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.
AVERAGES Writing out time-averaged nonlinear model 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.
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_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion.
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity.
TS_U3HADVECTION Third-order upstream 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 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.

Process Information:

Node # 0 (pid= 32601) is active.
Node # 4 (pid= 32605) is active.
Node # 7 (pid= 32608) is active.
Node # 6 (pid= 32607) is active.
Node # 2 (pid= 32603) is active.
Node # 3 (pid= 32604) is active.
Node # 5 (pid= 32606) is active.
Node # 1 (pid= 32602) is active.

INITIAL: Configuring and initializing forward nonlinear model ...
*******

Vertical S-coordinate System, Grid 01:

level S-coord Cs-curve Z at hmin at hc half way at hmax

16 0.0000000 0.0000000 0.000 0.000 0.000 0.000
15 -0.0625000 -0.0019442 -0.809 -0.806 -1.348 -1.589
14 -0.1250000 -0.0078455 -1.668 -1.661 -2.966 -3.687
13 -0.1875000 -0.0179119 -2.580 -2.568 -4.867 -6.321
12 -0.2500000 -0.0324983 -3.549 -3.531 -7.077 -9.535
11 -0.3125000 -0.0521190 -4.581 -4.558 -9.630 -13.397
10 -0.3750000 -0.0774659 -5.686 -5.656 -12.573 -17.996
9 -0.4375000 -0.1094327 -6.875 -6.837 -15.967 -23.445
8 -0.5000000 -0.1491465 -8.162 -8.114 -19.889 -29.890
7 -0.5625000 -0.1980075 -9.564 -9.506 -24.435 -37.512
6 -0.6250000 -0.2577387 -11.104 -11.034 -29.721 -46.531
5 -0.6875000 -0.3304460 -12.808 -12.724 -35.892 -57.218
4 -0.7500000 -0.4186931 -14.709 -14.609 -43.121 -69.903
3 -0.8125000 -0.5255915 -16.846 -16.726 -51.622 -84.987
2 -0.8750000 -0.6549105 -19.266 -19.124 -61.651 -102.953
1 -0.9375000 -0.8112096 -22.028 -21.859 -73.518 -124.388
0 -1.0000000 -1.0000000 -25.200 -25.000 -87.600 -150.000

Time Splitting Weights for Grid 01: ndtfast = 30 nfast = 42
==================================

Primary Secondary Accumulated to Current Step

1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257356 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001213 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565097 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716643 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402368 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399432 0.6603333185976138
21 0.0256737146312911 0.0297153720153352 0.1342125541712342 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524359 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729578 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236653 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893981 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886213 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451924 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772280 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880565 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442384 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256415 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325521 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348098 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479478 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213239 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232269 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079423 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497611 0.9930692679747334
39 0.0376397765791564 0.0033640675316746 0.9367177506289175 0.9964333355064080
40 0.0305543017255206 0.0021094083123694 0.9672720523544381 0.9985427438187774
41 0.0217382098544504 0.0010909315881854 0.9890102622088885 0.9996336754069628
42 0.0109897377911118 0.0003663245930371 1.0000000000000004 0.9999999999999999

ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000

Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.18933

Metrics information for Grid 01:
===============================

Minimum X-grid spacing, DXmin = 1.00000000E+00 km
Maximum X-grid spacing, DXmax = 1.00000000E+00 km
Minimum Y-grid spacing, DYmin = 1.00000000E+00 km
Maximum Y-grid spacing, DYmax = 1.00000000E+00 km
Minimum Z-grid spacing, DZmin = 8.08965824E-01 m
Maximum Z-grid spacing, DZmax = 2.56123321E+01 m

Minimum barotropic Courant Number = 2.22358627E-01
Maximum barotropic Courant Number = 5.42494240E-01
Maximum Coriolis Courant Number = 2.47800000E-02


Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 6.931666E-02 (Beckmann and Haidvogel)
rx1 = 8.661243E-01 (Haney)

Initial basin volumes: TotVolume = 3.8843755884E+11 m3
MinVolume = 8.4521383562E+05 m3
MaxVolume = 2.5612332106E+07 m3
Max/Min = 3.0302783777E+01

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00001440)


STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0 00:00:00 0.000000E+00 6.585677E+02 6.585677E+02 3.884376E+11
(00,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: ocean_his.nc
WRT_HIS - wrote history fields (Index=1,1) in record = 0000001
DEF_AVG - creating average file, Grid 01: ocean_avg.nc
DEF_DIAGS - creating diagnostics file, Grid 01: ocean_dia.nc
1 0 00:05:00 6.479408E-13 6.585677E+02 6.585677E+02 3.884376E+11
(01,01,01) 1.069435E-09 1.950204E-06 0.000000E+00 9.216783E-06
2 0 00:10:00 9.293195E-12 6.585677E+02 6.585677E+02 3.884376E+11
(01,02,08) 6.735167E-08 1.785829E-06 1.433648E-05 3.660353E-05

[kate]

It just ended like that? There should be more. When ROMS dies or finishes cleanly it lets you know:

36 39446 01:12:00 1.812177E-03 1.960581E+04 1.960581E+04 4.094320E+15
(245,180,50) 5.393447E-04 2.809401E-03 1.611229E+00 8.123321E-01
DIAG temperature trouble -53.2869692686739 1

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=1,1) in record = 0000001

Elapsed CPU time (seconds):

Node # 0 CPU: 305.040
Node # 9 CPU: 684.506
Node # 12 CPU: 686.090
:
Node # 2 CPU: 685.977
Total: 32545.970

Nonlinear ocean model elapsed time profile, Grid: 01

Allocation and array initialization .............. 31.997 ( 0.0983 %)
Ocean state initialization ....................... 8.595 ( 0.0264 %)
Reading of input data ............................ 19989.176 (61.4183 %)
Processing of input data ......................... 256.178 ( 0.7871 %)
Processing of output time averaged data .......... 22.410 ( 0.0689 %)
Computation of vertical boundary conditions ...... 0.273 ( 0.0008 %)
Computation of global information integrals ...... 27.175 ( 0.0835 %)
Writing of output data ........................... 3911.487 (12.0183 %)
Model 2D kernel .................................. 121.796 ( 0.3742 %)
Tidal forcing .................................... 18.102 ( 0.0556 %)
2D/3D coupling, vertical metrics ................. 17.178 ( 0.0528 %)
Omega vertical velocity .......................... 9.799 ( 0.0301 %)
Equation of state for seawater ................... 25.302 ( 0.0777 %)
Biological module, source/sink terms ............. 1064.812 ( 3.2717 %)
Atmosphere-Ocean bulk flux parameterization ...... 2.326 ( 0.0071 %)
KPP vertical mixing parameterization ............. 40.724 ( 0.1251 %)
3D equations right-side terms .................... 15.291 ( 0.0470 %)
3D equations predictor step ...................... 301.170 ( 0.9254 %)
Pressure gradient ................................ 8.416 ( 0.0259 %)
Harmonic stress tensor, S-surfaces ............... 8.002 ( 0.0246 %)
Corrector time-step for 3D momentum .............. 23.092 ( 0.0710 %)
Corrector time-step for tracers .................. 323.810 ( 0.9949 %)
Total: 26227.112 80.5848

[okami_zxh]

yes, my out.text just look like this, it lost something

[okami_zxh]

Hi Kate,
there is some fault happened.
Image PC Routine Line Source
oceanM 00000000004EF245 Unknown Unknown Unknown
oceanM 00000000004E3E53 Unknown Unknown Unknown
oceanM 00000000004C4A92 Unknown Unknown Unknown
oceanM 00000000004249EC Unknown Unknown Unknown
oceanM 000000000042480B Unknown Unknown Unknown
oceanM 000000000042465C Unknown Unknown Unknown
libc.so.6 0000003083A1D994 Unknown Unknown Unknown
oceanM 0000000000424569 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
oceanM 00000000004EF245 Unknown Unknown Unknown
oceanM 00000000004E3E53 Unknown Unknown Unknown
oceanM 00000000004C4A92 Unknown Unknown Unknown
oceanM 00000000004249EC Unknown Unknown Unknown
oceanM 000000000042480B Unknown Unknown Unknown
oceanM 000000000042465C Unknown Unknown Unknown
libc.so.6 0000003083A1D994 Unknown Unknown Unknown
oceanM 0000000000424569 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
oceanM 00000000004EF245 Unknown Unknown Unknown
oceanM 00000000004E3E53 Unknown Unknown Unknown
oceanM 00000000004C4A92 Unknown Unknown Unknown
oceanM 00000000004249EC Unknown Unknown Unknown
oceanM 000000000042480B Unknown Unknown Unknown
oceanM 000000000042465C Unknown Unknown Unknown
libc.so.6 0000003083A1D994 Unknown Unknown Unknown
oceanM 0000000000424569 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
oceanM 00000000004EF245 Unknown Unknown Unknown
oceanM 00000000004E3E53 Unknown Unknown Unknown
oceanM 00000000004C4A92 Unknown Unknown Unknown
oceanM 00000000004249EC Unknown Unknown Unknown
What is that?

[kate]

Try again with just one or four processors? Remember to change NtileI.

I left off the end of the ROMS report before:

Code: Select all

 ROMS/TOMS - Output NetCDF summary for Grid 01:
             number of time records written in HISTORY file = 00000001
             number of time records written in RESTART file = 00000001
             number of time records written in STATION file = 00000002

 Analytical header files used:

     Apps_master/NGOA/ana_drag.h
     ROMS/Functionals/ana_btflux.h
     Apps_master/NGOA/ana_nudgcoef.h
     ROMS/Functionals/ana_stflux.h

 ROMS/TOMS: DONE... Thursday - February 16, 2017 - 10:22:11 PM

[kate]

As for the seg fault, recompile with USE_DEBUG=on and see if it gives more information.

[okami_zxh]

Hi Kate
I think maybe it is because of this warning,
makefile:234: INCLUDING FILE Build/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
/share/apps/bin/mpif90 -heap-arrays -fp-model precise -g -check bounds -traceback -check uninit -warn interfaces,nouncalled -gen-interfaces Build/esmf_roms.o Build/master.o Build/ocean_control.o Build/ocean_coupler.o Build/propagator.o Build/roms_export.o Build/roms_import.o -o oceanG Build/libUTIL.a Build/libNLM.a Build/libNLM_bio.a Build/libNLM_sed.a Build/libANA.a Build/libUTIL.a Build/libMODS.a -L/home/zhou/netcdf/lib -lnetcdf
/opt/intel/Compiler/11.1/064/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
rm -f -r /home/zhou/make_macros.mk
Even u told me what is this problem, but I don't know which file and where should i change it

[kate]

Well, maybe, maybe not. You still need to recompile with USE_DEBUG=on and rerun it.

[okami_zxh]

Kate
I still got the same output and out.text after i recompiled makefile and USE_DEBUG=on.

[kate]

You need to run oceanG, not oceanM. It's this output which should change:

Code: Select all

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
oceanM 00000000004EF245 Unknown Unknown Unknown
oceanM 00000000004E3E53 Unknown Unknown Unknown
oceanM 00000000004C4A92 Unknown Unknown Unknown
oceanM 00000000004249EC Unknown Unknown Unknown
oceanM 000000000042480B Unknown Unknown Unknown
oceanM 000000000042465C Unknown Unknown Unknown
libc.so.6 0000003083A1D994 Unknown Unknown Unknown
oceanM 0000000000424569 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred

[okami_zxh]

hi Kate
I used oceanG to run it.
work_dir=/home/zhou/Projects/upwelling
cd $work_dir
mpirun -np 8 oceanG ocean_upwelling.in > out.text

Then the out.text is

Model Input Parameters: ROMS/TOMS version 3.7
Friday - February 17, 2017 - 3:38:23 PM
-----------------------------------------------------------------------------

Wind-Driven Upwelling/Downwelling over a Periodic Channel

Operating system : Linux
CPU/hardware : x86_64
Compiler system : ifort
Compiler command : /share/apps/bin/mpif90
Compiler flags : -heap-arrays -fp-model precise -ip -O3 -free -free -free

Input Script :

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 825M

Local Root : /home/zhou/MyDir
Header Dir : /home/zhou/MyDir/ROMS/Include
Header file : upwelling.h
Analytical Dir: /home/zhou/MyDir/ROMS/Functionals

Resolution, Grid 01: 0041x0080x016, Parallel Nodes: 8, Tiling: 008x001


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

1440 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.
288 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).
1 nHIS Number of timesteps between the writing fields
into history file.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
72 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
72 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
5.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
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).
0.0000E+00 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 Aout(idFsur) Write out averaged free-surface.
T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idVbar) Write out averaged 2D V-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idOvel) Write out averaged omega vertical velocity.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

T Dout(M2rate) Write out 2D momentum acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.

T Dout(M3rate) Write out 3D momentum acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.

T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Diagnostics File: ocean_dia.nc

Tile partition information for Grid 01: 0041x0080x0016 tiling: 008x001

tile Istr Iend Jstr Jend Npts

0 1 3 1 80 3840
1 4 9 1 80 7680
2 10 15 1 80 7680
3 16 21 1 80 7680
4 22 27 1 80 7680
5 28 33 1 80 7680
6 34 39 1 80 7680
7 40 41 1 80 2560

Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 3.50 0.50 80.50 RHO-points
1 3.50 9.50 0.50 80.50 RHO-points
2 9.50 15.50 0.50 80.50 RHO-points
3 15.50 21.50 0.50 80.50 RHO-points
4 21.50 27.50 0.50 80.50 RHO-points
5 27.50 33.50 0.50 80.50 RHO-points
6 33.50 39.50 0.50 80.50 RHO-points
7 39.50 41.50 0.50 80.50 RHO-points

0 1.00 3.50 0.50 80.50 U-points
1 3.50 9.50 0.50 80.50 U-points
2 9.50 15.50 0.50 80.50 U-points
3 15.50 21.50 0.50 80.50 U-points
4 21.50 27.50 0.50 80.50 U-points
5 27.50 33.50 0.50 80.50 U-points
6 33.50 39.50 0.50 80.50 U-points
7 39.50 41.00 0.50 80.50 U-points

0 0.50 3.50 1.00 80.00 V-points
1 3.50 9.50 1.00 80.00 V-points
2 9.50 15.50 1.00 80.00 V-points
3 15.50 21.50 1.00 80.00 V-points
4 21.50 27.50 1.00 80.00 V-points
5 27.50 33.50 1.00 80.00 V-points
6 33.50 39.50 1.00 80.00 V-points
7 39.50 41.50 1.00 80.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 54
HaloSizeJ(1) = 273
TileSide(1) = 85
TileSize(1) = 1020


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.
AVERAGES Writing out time-averaged nonlinear model 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.
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_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion.
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity.
TS_U3HADVECTION Third-order upstream 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 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.

Process Information:

Node # 0 (pid= 2681) is active.
Node # 7 (pid= 2688) is active.
Node # 3 (pid= 2684) is active.
Node # 4 (pid= 2685) is active.
Node # 6 (pid= 2687) is active.
Node # 1 (pid= 2682) is active.
Node # 2 (pid= 2683) is active.
Node # 5 (pid= 2686) is active.

INITIAL: Configuring and initializing forward nonlinear model ...
*******

Vertical S-coordinate System, Grid 01:

level S-coord Cs-curve Z at hmin at hc half way at hmax

16 0.0000000 0.0000000 0.000 0.000 0.000 0.000
15 -0.0625000 -0.0019442 -0.809 -0.806 -1.348 -1.589
14 -0.1250000 -0.0078455 -1.668 -1.661 -2.966 -3.687
13 -0.1875000 -0.0179119 -2.580 -2.568 -4.867 -6.321
12 -0.2500000 -0.0324983 -3.549 -3.531 -7.077 -9.535
11 -0.3125000 -0.0521190 -4.581 -4.558 -9.630 -13.397
10 -0.3750000 -0.0774659 -5.686 -5.656 -12.573 -17.996
9 -0.4375000 -0.1094327 -6.875 -6.837 -15.967 -23.445
8 -0.5000000 -0.1491465 -8.162 -8.114 -19.889 -29.890
7 -0.5625000 -0.1980075 -9.564 -9.506 -24.435 -37.512
6 -0.6250000 -0.2577387 -11.104 -11.034 -29.721 -46.531
5 -0.6875000 -0.3304460 -12.808 -12.724 -35.892 -57.218
4 -0.7500000 -0.4186931 -14.709 -14.609 -43.121 -69.903
3 -0.8125000 -0.5255915 -16.846 -16.726 -51.622 -84.987
2 -0.8750000 -0.6549105 -19.266 -19.124 -61.651 -102.953
1 -0.9375000 -0.8112096 -22.028 -21.859 -73.518 -124.388
0 -1.0000000 -1.0000000 -25.200 -25.000 -87.600 -150.000

Time Splitting Weights for Grid 01: ndtfast = 30 nfast = 42
==================================

Primary Secondary Accumulated to Current Step

1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257356 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001213 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565097 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716643 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402368 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399432 0.6603333185976138
21 0.0256737146312911 0.0297153720153352 0.1342125541712342 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524359 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729578 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236653 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893981 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886213 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451924 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772280 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880565 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442384 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256415 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325521 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348098 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479478 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213239 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232269 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079423 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497611 0.9930692679747334
39 0.0376397765791564 0.0033640675316746 0.9367177506289175 0.9964333355064080
40 0.0305543017255206 0.0021094083123694 0.9672720523544381 0.9985427438187774
41 0.0217382098544504 0.0010909315881854 0.9890102622088885 0.9996336754069628
42 0.0109897377911118 0.0003663245930371 1.0000000000000004 0.9999999999999999

ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000

Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.18933

Metrics information for Grid 01:
===============================

Minimum X-grid spacing, DXmin = 1.00000000E+00 km
Maximum X-grid spacing, DXmax = 1.00000000E+00 km
Minimum Y-grid spacing, DYmin = 1.00000000E+00 km
Maximum Y-grid spacing, DYmax = 1.00000000E+00 km
Minimum Z-grid spacing, DZmin = 8.08965824E-01 m
Maximum Z-grid spacing, DZmax = 2.56123321E+01 m

Minimum barotropic Courant Number = 2.22358627E-01
Maximum barotropic Courant Number = 5.42494240E-01
Maximum Coriolis Courant Number = 2.47800000E-02


Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 6.931666E-02 (Beckmann and Haidvogel)
rx1 = 8.661243E-01 (Haney)

Initial basin volumes: TotVolume = 3.8843755884E+11 m3
MinVolume = 8.4521383562E+05 m3
MaxVolume = 2.5612332106E+07 m3
Max/Min = 3.0302783777E+01

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00001440)


STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0 00:00:00 0.000000E+00 6.585677E+02 6.585677E+02 3.884376E+11
(00,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: ocean_his.nc
WRT_HIS - wrote history fields (Index=1,1) in record = 0000001
DEF_AVG - creating average file, Grid 01: ocean_avg.nc
DEF_DIAGS - creating diagnostics file, Grid 01: ocean_dia.nc
1 0 00:05:00 6.479408E-13 6.585677E+02 6.585677E+02 3.884376E+11
(01,01,01) 1.069435E-09 1.950204E-06 0.000000E+00 9.216783E-06
WRT_HIS - wrote history fields (Index=1,2) in record = 0000002
2 0 00:10:00 9.293195E-12 6.585677E+02 6.585677E+02 3.884376E+11
(01,02,08) 6.735167E-08 1.785829E-06 1.433648E-05 3.660353E-05

[okami_zxh]

This is the fault information

oceanG 00000000004C4A92 Unknown Unknown Unknown
oceanG 00000000004249EC Unknown Unknown Unknown
oceanG 000000000042480B Unknown Unknown Unknown
oceanG 000000000042465C Unknown Unknown Unknown
libc.so.6 00000033A1E1D994 Unknown Unknown Unknown
oceanG 0000000000424569 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
oceanG 00000000004EF245 Unknown Unknown Unknown
oceanG 00000000004E3E53 Unknown Unknown Unknown
oceanG 00000000004C4A92 Unknown Unknown Unknown
oceanG 00000000004249EC Unknown Unknown Unknown
oceanG 000000000042480B Unknown Unknown Unknown
oceanG 000000000042465C Unknown Unknown Unknown
libc.so.6 00000033A1E1D994 Unknown Unknown Unknown
oceanG 0000000000424569 Unknown Unknown Unknown
--------------------------------------------------------------------------
mpirun has exited due to process rank 7 with PID 2688 on
node compute-0-4.local exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

[kate]

That should be giving you line number information. I would try turning off USE_MPI and running in serial mode.

[kate]

You didn't delete the build directory, did you?

I managed to produce the sort of output you get with USE_DEBUG=on:

Code: Select all

forrtl: severe (408): fort: (3): Subscript #1 of the array TINTRP has value 0 which is less than the lower bound of 1

Image              PC                Routine            Line        Source             
oceanG             0000000002C36CD6  Unknown               Unknown  Unknown
oceanG             00000000021F4A4C  set_2dfld_mod_mp_         132  set_2dfld.f90
oceanG             0000000000BC0539  set_data_tile_            186  set_data.f90
oceanG             0000000000BADEFF  set_data_                  48  set_data.f90
oceanG             0000000000930071  main3d_                   128  main3d.f90
oceanG             000000000040CD11  ocean_control_mod         173  ocean_control.f90
oceanG             000000000040BB05  MAIN__                    108  master.f90
oceanG             000000000040B50E  Unknown               Unknown  Unknown
libc.so.6          00007F15D7037D1D  Unknown               Unknown  Unknown
oceanG             000000000040B3E9  Unknown               Unknown  Unknown

The next thing to do is go to the build directory and look at say line 186 of set_data.f90 there. Oops, problem with the #ifdefs back in set_data.F in the source tree.

[okami_zxh]

Hi Kate
I didn't remove the Build Directory. I found the set_data.f90 So what should I do to correct it?

[kate]

No, no, that was an example of what went wrong for me on some private code that isn't working yet. Your problem is something else again entirely. We need your line numbers and file names to know what your problem is.