ROMS Runtime error.

Message

novice · #1 Unread post by **novice** » Sun Mar 13, 2016 3:16 pm

Hi forum,
I am getting a segmentation fault error while trying to use the ROMS source code version provided by the following link

https://github.com/kshedstrom
I successfully compiled the model using gfortran, but while trying to run with the following command,

mpirun -np 24 ./oceanM Apps/test_ocean/test_ocean.in

I am getting the error like this.

Model Input Parameters: ROMS/TOMS version 3.7
Sunday - March 13, 2016 - 8:30:22 PM
-----------------------------------------------------------------------------

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7F38CC593777
#1 0x7F38CC593D7E
#2 0x7F38CBEE5D3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?
#0 0x7F01D673E777
#1 0x7F01D673ED7E
#2 0x7F01D6090D3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#0 0x7F4DA5AFA777
#7 0x403363 in MAIN__ at master.f90:?
#1 0x7F4DA5AFAD7E
#2 0x7F4DA544CD3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?
#0 0x7F94BDFFC777
#1 0x7F94BDFFCD7E
#2 0x7F94BD94ED3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#7 0x403363 in MAIN__ at master.f90:?
#0 0x7F8AF30C8777
#1 0x7F8AF30C8D7E
#2 0x7F8AF2A1AD3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7F24F91E9777
#1 0x7F24F91E9D7E
#2 0x7F24F8B3BD3F
#3 0x5EB94E in load_s2d_

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7F9211C2E777
#1 0x7F9211C2ED7E
#2 0x7F9211580D3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7FF717611777
#1 0x7FF717611D7E
#0 0x7FA61F42B777
#1 0x7FA61F42BD7E
#2 0x7FA61ED7DD3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?
#0 0x7FD503551777
#1 0x7FD503551D7E
#2 0x7FD502EA3D3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?
#0 0x7F61E93CA777
#1 0x7F61E93CAD7E
#2 0x7F61E8D1CD3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7F02D51FA777
#1 0x7F02D51FAD7E

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7F9B90DA7777
#1 0x7F9B90DA7D7E
#2 0x7F9B906F9D3F
#0 0x7F1B1542D777
#1 0x7F1B1542DD7E
#2 0x7F1B14D7FD3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?
#2 0x7FF716F63D3F
#2 0x7F02D4B4CD3F
#3 0x5EB94E in load_s2d_
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#0 0x7F3549390777
#1 0x7F3549390D7E
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#2 0x7F3548CE2D3F
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?
#3 0x5EB94E in load_s2d_
#7 0x403363 in MAIN__ at master.f90:?
#7 0x403363 in MAIN__ at master.f90:?
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#0 0x7F011401E777
#1 0x7F011401ED7E
#2 0x7F0113970D3F
#7 0x403363 in MAIN__ at master.f90:?
#3 0x5EB94E in load_s2d_

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#4 0x629E06 in read_phypar_
#0 0x7F87F1AAC777
#1 0x7F87F1AACD7E
#2 0x7F87F13FED3F
#5 0x5E2B31 in inp_par_
#0 0x7FF1DB523777
#1 0x7FF1DB523D7E
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#2 0x7FF1DAE75D3F
#3 0x5EB94E in load_s2d_
#7 0x403363 in MAIN__ at master.f90:?
#4 0x629E06 in read_phypar_
#3 0x5EB94E in load_s2d_
#5 0x5E2B31 in inp_par_
#4 0x629E06 in read_phypar_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#5 0x5E2B31 in inp_par_
#7 0x403363 in MAIN__ at master.f90:?
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7F8BCC1C6777
#1 0x7F8BCC1C6D7E
#2 0x7F8BCBB18D3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7F7F892FD777
#1 0x7F7F892FDD7E
#2 0x7F7F88C4FD3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#0 0x7FE48CDE2777
#1 0x7FE48CDE2D7E
#7 0x403363 in MAIN__ at master.f90:?
#2 0x7FE48C734D3F
#3 0x5EB94E in load_s2d_
#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
#7 0x403363 in MAIN__ at master.f90:?
#0 0x7FC990690777
#1 0x7FC990690D7E
#2 0x7FC98FFE2D3F
#0 0x7F15E05DD777
#1 0x7F15E05DDD7E
#2 0x7F15DFF2FD3F
#3 #3 0x5EB94E in load_s2d_
0x#4 0x629E06 in read_phypar_
5EB94E#5 0x5E2B31 in inp_par_
in #6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
load_s2d_#7 0x403363 in MAIN__ at master.f90:?

#4 0x629E06 in read_phypar_
#5 0x5E2B31 in inp_par_
#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize#0 0x7FD8DA2AA777
#1 0x7FD8DA2AAD7E
#2 0x7FD8D9BFCD3F

#3 0x5EB94E in load_s2d_
#7 #4 0x629E06 in read_phypar_
0x#5 0x5E2B31 in inp_par_
403363#6 0x4039D4 in __ocean_control_mod_MOD_roms_initialize
in #7 0x403363 in MAIN__ at master.f90:?
MAIN__ at master.f90:?

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

I would be grateful, if anybody point can out the possible causes of the above error?

kate · #2 Unread post by **kate** » Mon Mar 14, 2016 6:39 am

#3 #3 0x5EB94E in load_s2d_
0x#4 0x629E06 in read_phypar_

We didn't need all 24 copies of the same thing...

If you recompile with USE_DEBUG turned on, it should give you line numbers. You can then see if it is happening while reading forcing filenames, boundary filenames, or climatology filenames. You should then inspect that part of your ocean.in file very carefully to be sure it is (a) consistent with the version of ROMS you are using and (b) lists 12 forcing files if you told it you had 12 forcing files. In particular, my ocean.in files need to say how many BRY/CLM files, much like the number of forcing files. Did you start with an example that has:

Code: Select all

NCLMFILES == 1                         ! number of climate files
NBCFILES == 4                          ! number of boundary files

novice · #3 Unread post by **novice** » Mon Mar 14, 2016 10:41 am

Hi Kate,
Thanks for your comments, as you suggested, I started with the an input file having these following lines
NCLMFILES == 1 ! number of climate files
NBCFILES == 4 ! number of boundary files
and also the USE DEBUG switched on, but now I am getting the following error.

-------------------------------------------------------------------------------------------------------
Model Input Parameters: ROMS/TOMS version 3.7
Monday - March 14, 2016 - 4:04:51 PM
-----------------------------------------------------------------------------
READ_PHYPAR - variable info not yet loaded, idUairE

Elapsed CPU time (seconds):
ROMS/TOMS - Output NetCDF summary for Grid 01:
ROMS/TOMS - Configuration error ..... exit_flag: 5
ERROR: Illegal model configuration.

---------------------------------------------------------------------------------------------------------
Can you give some suggestions to solve this... Thanks ...

kate · #4 Unread post by **kate** » Mon Mar 14, 2016 5:17 pm

Your varinfo.dat file also needs to be consistent. I use the one under the Apps directory - unless I need to change it up for COSINE or some such.

novice · #5 Unread post by **novice** » Tue Mar 15, 2016 4:37 am

Hi Kate,

Thanks for your kind reply. My model is running now,

I have one more doubt that if I want to switch on the "RUNOFF" option, what should be the structure of the forcing file that I have to provide?. I couldn't find any example cdl file for the runoff forcing file. Is the runoff forcing file has the same structure of point source forcing?

. I would be grateful for any comments.

kate · #6 Unread post by **kate** » Tue Mar 15, 2016 5:34 am

Nope, runoff is much more like rain than like the point sources. Here's an example CDL for it:

Code: Select all

dimensions:
	runoff_time = UNLIMITED ; // (360 currently)
	eta_rho = 1090 ;
	xi_rho = 690 ;
variables:
	double Runoff(runoff_time, eta_rho, xi_rho) ;
		Runoff:long_name = "Dai_Trenberth River Runoff" ;
		Runoff:missing_value = -1.e+30 ;
		Runoff:units = "kg/s/m^2" ;
	double Runoff_raw(runoff_time, eta_rho, xi_rho) ;
		Runoff_raw:long_name = "Dai_Trenberth River Runoff raw" ;
		Runoff_raw:missing_value = -1.e+30 ;
		Runoff_raw:units = "kg/s/m^2" ;
	double lat_rho(eta_rho, xi_rho) ;
		lat_rho:long_name = "latitude of RHO-points" ;
		lat_rho:units = "degree_north" ;
		lat_rho:field = "lat_rho, scalar" ;
	double lon_rho(eta_rho, xi_rho) ;
		lon_rho:long_name = "longitude of RHO-points" ;
		lon_rho:units = "degree_east" ;
		lon_rho:field = "lon_rho, scalar" ;
	double runoff_time(runoff_time) ;
		runoff_time:long_name = "time" ;
		runoff_time:units = "days since 1900-01-01 00:00:00" ;

// global attributes:
		:Description = "Dai & Trenberth Interannual monthly river discharge, 1948-2007" ;
		:Author = "make_ARCTIC2_runoff.py" ;
		:Created = "2014-04-29 14:37:34" ;
		:title = "Dai & Trenberth river discharge" ;
		:history = "Tue Mar 31 14:13:53 2015: ncks -d runoff_time,360, runoff_ARCTIC2_daitren_inter_annual_1948-2007.nc runoff_ARCTIC2_daitren_southern_1978-2007.nc" ;
		:NCO = "4.3.1" ;

You can ignore the Runoff_raw - it's a transitional step from one thing to another, not used by ROMS.

Note that unlike the rain file, this one has been mapped to the ROMS grid. We move the runoff to the ROMS coastal points, then spreading a few points offshore. Our coastline isn't exactly where the Dai and Trenberth coastline happens to be in most cases.

novice · #7 Unread post by **novice** » Tue Mar 15, 2016 6:34 am

Hi Kate,
Thanks for your help. I am trying to replicate your template cdl file. But is there any preprocessing script to create this forcing file?.

kate · #8 Unread post by **kate** » Tue Mar 15, 2016 7:41 pm

Yes, there's a script: 'Author = "make_ARCTIC2_runoff.py"'. I can add it to the pyroms examples, but you'll have to download the global Dai and Trenberth file, which I got from Rutgers. Actually, there are two, one with the interannual variability, one just a 12-month climatology.

At least for some domains, our group is moving away from RUNOFF and back to rivers files for ease in affecting tracers other than salinity.

novice · #9 Unread post by **novice** » Fri Apr 29, 2016 5:06 am

Hi Kate,
I was trying to use the pyroms tool make_runoff_file.py. But I am not able to figure out some things like how to decide the proper values for the variables "width" and "rspread" in the script. And also in the conservative horizontal mapping, is the runoff volume is conserved ?

kate · #10 Unread post by **kate** » Fri Apr 29, 2016 4:12 pm

I believe the runoff is conserved in the remapping.

I haven't fussed with width or rspread. In modeling, one often has to just try it and see what happens, adjust later.

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