Problem with running TC.exe

Having problems running the WRF Preprocessing Sysmte (WPS)?

Problem with running TC.exe

Postby minhpt » Wed Mar 02, 2011 5:53 am

hi all,

I am running tc.exe then run real.exe successfully. But I dont run wrf.exe, error which sent when run wrf.exe:

-------- FATAL CALLED ---------------
input_wrf.F: SIZE MISMATCH: namelist ide,jde,kde= 161 161 28 ; input data ide,jde,kde= 161 161 27
-------------------------------------------
wrf_abort
Namelist dfi_control not found in namelist.input. Using registry defaults for variables in dfi_control
Namelist scm not found in namelist.input. Using registry defaults for variables in scm
Namelist fire not found in namelist.input. Using registry defaults for variables in fire
--- NOTE: sst_update is 0, setting io_form_auxinput4 = 0 and auxinput4_interval = 0 for all domains
--- NOTE: grid_fdda is 0 for domain 1, setting gfdda interval and ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 1, setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 1, setting obs nudging interval and ending time to 0 for that domain.
--- NOTE: num_soil_layers has been set to 4
WRF V3.2.1 MODEL
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 466438644 bytes allocated
med_initialdata_input: calling input_input
FATAL CALLED FROM FILE: <stdin> LINE: 666

would you help me?
minhpt
 
Posts: 2
Joined: Wed Feb 23, 2011 11:16 pm

Re: Problem with running TC.exe

Postby dcvz » Sat Mar 05, 2011 4:01 am

Your namelist expects 28 vertical levels. The input data has 27 vertical levels.
dcvz
 
Posts: 192
Joined: Tue Apr 15, 2008 12:02 am

Re: Problem with running TC.exe

Postby minhpt » Sun Mar 06, 2011 11:33 pm

Thank dcvz,

But my namelist use to run wrf model without TC.exe is normal. When I use output of TC.exe that is the same input of real.exe is ok, but I don't run wrf.exe and I was recieved a error messange: input_wrf.F: SIZE MISMATCH: namelist ide,jde,kde= 161 161 28 ; input data ide,jde,kde= 161 161 27.

have dcvz run TC.exe? Would you help me?
minhpt
 
Posts: 2
Joined: Wed Feb 23, 2011 11:16 pm

Re: Problem with running TC.exe

Postby Shepherd_NZ » Tue May 07, 2013 3:02 am

Did you manage to solve this problem? I am experiencing the same issue running tc.exe.

-------------- FATAL CALLED --------------------------------------------------------
FATAL CALLED FROM FILE: <stdin> LINE: 698
input_wrf.F: SIZE MISMATCH: namelist ide,jde,kde= 423 324
33; input data ide,jde,kde= 423 324 27
------------------------------------------------------------------------------------------

I have a feeling there is an issue with the tc.exe script and the way it writes attributes to the aux_* output file. I notice the global attributes in the aux file of bogus data carry the attribute 'BOTTOM_TOP_PATCH_END_STAG = 33' (33 is the number of vertical model levels I have requested). I assume tc.exe reads this from the namelist and then writes it to the global attributes, where the met_em file does not have this attribute.

To try get around this, I used ncks to extract the UU, VV and PMSL variables (without their global attributes) from the bogus data file and append them to the met_em file. This was not successful - the same error is present when running wrf.exe.

I have no other explanation for this, given the model works fine previously for the namelist settings below, so it has to be the bogussing scheme which is creating this problem. Any suggestions on how to solve this would be useful.

Regards,
Tristan

&domains
time_step = 30,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 3,
s_we = 1, 1, 1,
e_we = 423, 202, 241,
s_sn = 1, 1, 1,
e_sn = 324, 202, 241,
s_vert = 1, 1, 1,
e_vert = 33, 33, 33,
num_metgrid_levels = 27,
eta_levels = 1.000, 0.999,
0.998, 0.997,
0.995, 0.993,
0.991, 0.989,
0.987, 0.985,
0.982, 0.979,
0.976, 0.973,
0.970, 0.950,
0.900, 0.850,
0.800, 0.750,
0.700, 0.650,
0.600, 0.550,
0.500, 0.450,
0.400, 0.350,
0.300, 0.250,
0.200, 0.100,
0.000,
Shepherd_NZ
 
Posts: 22
Joined: Sun Apr 27, 2008 11:09 pm

Another Problem with running TC.exe

Postby T00 » Tue Sep 10, 2013 4:01 pm

Hi
I have successfully compiled and run wrf.exe, but when I tryed to run tc.exe and I've got the following:
Obs: I have compiled tc.exe in serial mode, with gfortran and gcc.

---> TC: Processing storm number= 1
Storm center lat= -27.0 lon= -40.70.
Storm center grid position (x,y)= 118.08 44.93.
Storm max wind (m/s) and max radius (m)= -0.09 42.00.
Estimated central press dev (mb)= 40.00.
nstrm 42.000000 118.07767 44.928131
Bogus storm number 1 completed.
*** glibc detected *** ./tc.exe: free(): invalid pointer: 0x000000000a4b11b0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f421cf6eb96]
./tc.exe[0x40d5cc]
./tc.exe[0x405b83]
./tc.exe[0x40537f]
./tc.exe[0x4042f3]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f421cf1176d]
./tc.exe[0x403cb9]
======= Memory map: ========
00400000-01262000 r-xp 00000000 08:16 10230475 /home/ieapm-111/TC/WRFV3/main/tc.exe
01461000-01462000 r--p 00e61000 08:16 10230475 /home/ieapm-111/TC/WRFV3/main/tc.exe
01462000-01473000 rw-p 00e62000 08:16 10230475 /home/ieapm-111/TC/WRFV3/main/tc.exe
01473000-042f6000 rw-p 00000000 00:00 0
04e0f000-0a8b4000 rw-p 00000000 00:00 0 [heap]
7f4201cce000-7f421c9d3000 rw-p 00000000 00:00 0
7f421c9d3000-7f421ca08000 r-xp 00000000 08:16 19801034 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f421ca08000-7f421cc07000 ---p 00035000 08:16 19801034 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f421cc07000-7f421cc08000 r--p 00034000 08:16 19801034 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f421cc08000-7f421cc09000 rw-p 00035000 08:16 19801034 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f421cc09000-7f421cc9b000 r-xp 00000000 08:16 20186872 /usr/local/netcdf/lib/libnetcdf.so.7.2.0
7f421cc9b000-7f421ce9b000 ---p 00092000 08:16 20186872 /usr/local/netcdf/lib/libnetcdf.so.7.2.0
7f421ce9b000-7f421cee8000 r--p 00092000 08:16 20186872 /usr/local/netcdf/lib/libnetcdf.so.7.2.0
7f421cee8000-7f421ceea000 rw-p 000df000 08:16 20186872 /usr/local/netcdf/lib/libnetcdf.so.7.2.0
7f421ceea000-7f421cef0000 rw-p 00000000 00:00 0
7f421cef0000-7f421d0a5000 r-xp 00000000 08:16 262264 /lib/x86_64-linux-gnu/libc-2.15.so
7f421d0a5000-7f421d2a4000 ---p 001b5000 08:16 262264 /lib/x86_64-linux-gnu/libc-2.15.so
7f421d2a4000-7f421d2a8000 r--p 001b4000 08:16 262264 /lib/x86_64-linux-gnu/libc-2.15.so
7f421d2a8000-7f421d2aa000 rw-p 001b8000 08:16 262264 /lib/x86_64-linux-gnu/libc-2.15.so
7f421d2aa000-7f421d2af000 rw-p 00000000 00:00 0
7f421d2af000-7f421d2c4000 r-xp 00000000 08:16 265772 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f421d2c4000-7f421d4c3000 ---p 00015000 08:16 265772 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f421d4c3000-7f421d4c4000 r--p 00014000 08:16 265772 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f421d4c4000-7f421d4c5000 rw-p 00015000 08:16 265772 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f421d4c5000-7f421d5c0000 r-xp 00000000 08:16 262272 /lib/x86_64-linux-gnu/libm-2.15.so
7f421d5c0000-7f421d7bf000 ---p 000fb000 08:16 262272 /lib/x86_64-linux-gnu/libm-2.15.so
7f421d7bf000-7f421d7c0000 r--p 000fa000 08:16 262272 /lib/x86_64-linux-gnu/libm-2.15.so
7f421d7c0000-7f421d7c1000 rw-p 000fb000 08:16 262272 /lib/x86_64-linux-gnu/libm-2.15.so
7f421d7c1000-7f421d8d5000 r-xp 00000000 08:16 19800772 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f421d8d5000-7f421dad5000 ---p 00114000 08:16 19800772 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f421dad5000-7f421dad6000 r--p 00114000 08:16 19800772 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f421dad6000-7f421dad8000 rw-p 00115000 08:16 19800772 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f421dad8000-7f421db30000 r-xp 00000000 08:16 20191245 /usr/local/netcdf/lib/libnetcdff.so.5.3.1
7f421db30000-7f421dd2f000 ---p 00058000 08:16 20191245 /usr/local/netcdf/lib/libnetcdff.so.5.3.1
7f421dd2f000-7f421dd30000 r--p 00057000 08:16 20191245 /usr/local/netcdf/lib/libnetcdff.so.5.3.1
7f421dd30000-7f421dd31000 rw-p 00058000 08:16 20191245 /usr/local/netcdf/lib/libnetcdff.so.5.3.1
7f421dd31000-7f421dd53000 r-xp 00000000 08:16 262278 /lib/x86_64-linux-gnu/ld-2.15.so
7f421dd91000-7f421df3c000 rw-p 00000000 00:00 0
7f421df51000-7f421df53000 rw-p 00000000 00:00 0
7f421df53000-7f421df54000 r--p 00022000 08:16 262278 /lib/x86_64-linux-gnu/ld-2.15.so
7f421df54000-7f421df56000 rw-p 00023000 08:16 262278 /lib/x86_64-linux-gnu/ld-2.15.so
7fffd69c1000-7fffd69e2000 rw-p 00000000 00:00 0 [stack]
7fffd69ff000-7fffd6a00000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted

Could anybody help me?
T00
 
Posts: 2
Joined: Tue Sep 10, 2013 3:53 pm

Re: Problem with running TC.exe

Postby Shepherd_NZ » Wed Sep 11, 2013 10:00 pm

Hi,

this looks like a very similar error to the one reported here (albeit for WPS):
http://forum.wrfforum.com/viewtopic.php?f=21&t=3877

I believe your error is a compiler issue. A glance over the above forum link indicated an issue with pointers not being nullified. I experienced this error with WPS some time ago, for an intel compiler, but have now switched to a different HPC system, which is better configured for WRF.

In your case, I would advise trying a different compiler and see if you still get this problem. I have tc.exe working for intel-cc v.11. I have also successfully compiled for v13 too.

Can you try using a different compiler and then get back to me?

Cheers
Shepherd_NZ
 
Posts: 22
Joined: Sun Apr 27, 2008 11:09 pm

Re: Problem with running TC.exe

Postby T00 » Thu Sep 12, 2013 9:07 am

Well, I have tryed with ifort/icc serial mode, and again it compiled successfully, but running tc.exe results in:


Namelist logging not found in namelist.input. Using registry defaults for varia
bles in logging.
Namelist logging not found in namelist.input. Using registry defaults for varia
bles in logging.
Namelist dfi_control not found in namelist.input. Using registry defaults for v
ariables in dfi_control
Namelist noah_mp not found in namelist.input. Using registry defaults for varia
bles in noah_mp
Namelist fdda not found in namelist.input. Using registry defaults for variable
s in fdda
Namelist scm not found in namelist.input. Using registry defaults for variables
in scm
Namelist dynamics not found in namelist.input. Using registry defaults for vari
ables in dynamics
Namelist grib2 not found in namelist.input. Using registry defaults for variabl
es in grib2
Namelist fire not found in namelist.input. Using registry defaults for variable
s in fire
Namelist diags not found in namelist.input. Using registry defaults for variabl
es in diags
TC_EM V3.5 PREPROCESSOR
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1, 421634264 bytes allocat
ed
the start date char 2004-03-25_00:00:00
the end date char 2004-03-25_00:00:00

-----------------------------------------------------------------------------

Domain 1: Current date being processed: 2004-03-25_00:00:00.0000, which is loop # 1 out of 1
configflags%julyr, %julday, %gmt: 2004 85 0.0000000E+00
metgrid input_wrf.F first_date_input = 2004-03-25_00:00:00
metgrid input_wrf.F first_date_nml = 2004-03-25_00:00:00
d01 2004-03-25_00:00:00 Timing for input -2 s.
d01 2004-03-25_00:00:00 flag_soil_layers read from met_em file is 1
number of storms 1
Segmentation fault (imagem do núcleo gravada)

Thanks.
T00
 
Posts: 2
Joined: Tue Sep 10, 2013 3:53 pm

Re: Problem with running TC.exe

Postby Shepherd_NZ » Fri Sep 13, 2013 5:10 am

There could be any number of reasons for a segmentation fault. What a pain.

Did you recompile WPS with ifort/icc and use the met files from that compile? Or are you using previously generated met files from a different compile?

It might be worth putting some print statements into the tc bogus code to see where it is falling over. That might give you a clue as to the issue.
Shepherd_NZ
 
Posts: 22
Joined: Sun Apr 27, 2008 11:09 pm

Re: Problem with running TC.exe

Postby packard » Mon Feb 23, 2015 6:38 am

Thank you all for your discussions on runtime problems of tc.exe. I have met similar problems when I am using gfortran/gcc 4.4.6:
Code: Select all
Segmentation fault (core dumped)

Or something like:
Code: Select all
*** glibc detected *** ./tc.exe: munmap_chunk(): invalid pointer: 0x000000000fd19040 ***

And I have eventually solved the problem by employing another machine using ifort/icc (version 11).


In the following URL, I have posted a summary of my experience on running tc.exe.
http://forum.wrfforum.com/viewtopic.php?f=6&t=8716
I have included in that post, a link to this topic, as others may also find it useful as well.
packard
 
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Joined: Fri Apr 25, 2014 10:33 pm

Re: Problem with running TC.exe

Postby Jipson Johnson » Sun Mar 22, 2015 1:21 pm

I also have a problem like this which is shown below:

DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 178338656 bytes allocated
med_initialdata_input: calling input_input
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: <stdin> LINE: 852
input_wrf.F: SIZE MISMATCH: namelist ide,jde,kde= 81 75 28 ; input data ide,jde,kde= 40 49 59
-------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Please help anyone to solve this problem.
Thank you
Jipson Johnson
 
Posts: 24
Joined: Thu Jan 08, 2015 2:15 pm


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