[MITgcm-support] Segmentation fault trying to capture location in ptracers array.
Patrick Heimbach
heimbach at mit.edu
Tue Jun 9 21:44:43 EDT 2015
Try replacing PTRACERS_num by PTRACERS_numInUse
I.e. only loop over number of ptracers actually assigned.
-Patrick
On Jun 9, 2015, at 9:36 PM, Michael Schaferkotter <schaferk at bellsouth.net> wrote:
> 1) Print the counter
>
>
>>>>> DO nTrac=1,PTRACERS_num,1
> Print*,nTrac
>>>>> fldName=PTRACERS_names(nTrac)
>>>>> IF ( fldName(1:4) .EQ. 'apre' ) THEN
>>>>> itrc_apre=nTrac
>>>>> ELSEIF ( fldName(1:4) .EQ. 'ppre' ) THEN
>>>>> itrc_ppre=nTrac
>>>>> ELSEIF ( fldName(1:7) .EQ. 'atmpco2' ) THEN
>>>>> itrc_pco2=nTrac
>>>>> ENDIF
>>>>> ENDDO
>
> 2) Use a debugger, ie gdb to trap the segfault with backtrace
> And find exactly where the segfault occurs.
>
> Sent from Here3.
>
> On Jun 9, 2015, at 18:33, Jonathan Lauderdale <jml1 at mit.edu> wrote:
>
>> Hi Michael,
>>
>> Thanks for your reply, I am using gfortran (gcc49 on an iMac 10.10) with -g and -C and that is all the output I get, but I will check for specific version flags, etc….
>>
>> If I comment out the loop in my previous message and just leave in "[….reset preformed surface tracer concentration…]” which has the same set of logical calls to PTRACERS_names then there is no segfault. Also if I comment out just the itrc_xxxx=nTrac or itrc_xxxx=tmp lines then there is no problem, so it must be something to do with initializing or assigning these values.
>>
>> Here are some of the other things you asked about:
>>
>> In EEPARMS.h
>> PARAMETER ( MAX_LEN_FNAM = 512 )
>> In PTRACERS_SIZE.h
>> INTEGER PTRACERS_num
>> PARAMETER(PTRACERS_num = 12 )
>> In PTRACERS_PARAMS.h
>> CHARACTER*(MAX_LEN_FNAM) PTRACERS_names(PTRACERS_num)
>>
>> Thanks again,
>>
>> Jon
>>
>>> On 9 Jun 2015, at 18:59, Michael Schaferkotter <schaferk at bellsouth.net> wrote:
>>>
>>> Recompile with -g -C ( or with whatever the bounds check switch is with the compiler).
>>>
>>> Also set the switches to trap segfault at run time.
>>>
>>> You could add print statements for all counters, and extents values.
>>> What is the value of MAX_LEN_FNAM, PTRACERS_num?
>>> How is PTRACERS_names instantiated?
>>>
>>>
>>> Sent from Here3.
>>>
>>> On Jun 9, 2015, at 16:49, Jonathan Lauderdale <jml1 at mit.edu> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am trying to add a few passive/preformed tracers to the end of the pTracers array. In my code (gchem_forcing_sep.F to be precise), I cycle through the extra tracers in a “do” loop and use PTRACERS_names to decide how to reset the surface values (e.g. preformed phosphate, ppre, is reset to surface po4 values; cpre to surface dic values). This works great.
>>>>
>>>> For a few calculations later, I want to capture the order of these extra tracers (if they exist) and pass them as arguments to a subroutine, similar to how dic_biotic_forcing is done. Sounds simple...My minimal working example loop is as follows:
>>>>
>>>>> INTEGER nTrac
>>>>> INTEGER itrc_apre,itrc_ppre,itrc_pco2
>>>>> CHARACTER*(MAX_LEN_FNAM) fldName
>>>>>
>>>>> [….reset preformed surface tracer concentration…]
>>>>>
>>>>> DO nTrac=1,PTRACERS_num,1
>>>>> fldName=PTRACERS_names(nTrac)
>>>>> IF ( fldName(1:4) .EQ. 'apre' ) THEN
>>>>> itrc_apre=nTrac
>>>>> ELSEIF ( fldName(1:4) .EQ. 'ppre' ) THEN
>>>>> itrc_ppre=nTrac
>>>>> ELSEIF ( fldName(1:7) .EQ. 'atmpco2' ) THEN
>>>>> itrc_pco2=nTrac
>>>>> ENDIF
>>>>> ENDDO
>>>>
>>>> I keep getting the following error and I am having a nightmare trying to figure out what is wrong:
>>>>
>>>>> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
>>>>>
>>>>> Backtrace for this error:
>>>>> #0 0x160a7fa52
>>>>> #1 0x160a8021e
>>>>> #2 0x7fff92dc9f19
>>>>> #3 0x10f784c68
>>>>> #4 0x10f739973
>>>>> #5 0x10f74ae31
>>>>> #6 0x10f972c95
>>>>> #7 0x10f9b2818
>>>>> #8 0x10f9b2910
>>>>> #9 0x10f92a61d
>>>>> #10 0x10f9bbdb8
>>>>> Segmentation fault: 11
>>>>
>>>> I did think it might have something to do with interfering with the do-loop index, nTrac, but I tried it with a dumb counter with no success:
>>>>
>>>>> INTEGER nTrac,tmp1,tmp2,tmp3
>>>>> INTEGER itrc_apre,itrc_ppre,itrc_pco2
>>>>> CHARACTER*(MAX_LEN_FNAM) fldName
>>>>>
>>>>> [….reset preformed surface tracer concentration…]
>>>>> tmp1=0
>>>>> DO nTrac=1,PTRACERS_numInUse
>>>>> fldName=PTRACERS_names(nTrac)
>>>>> tmp1=tmp1+1
>>>>> IF ( fldName(1:4) .EQ. 'apre' ) THEN
>>>>> itrc_apre=tmp1
>>>>> ENDIF
>>>>> ENDDO
>>>>>
>>>>> tmp2=0
>>>>> DO nTrac=1,PTRACERS_numInUse
>>>>> fldName=PTRACERS_names(nTrac)
>>>>> tmp2=tmp2+1
>>>>> IF ( fldName(1:4) .EQ. 'ppre' ) THEN
>>>>> itrc_ppre=tmp2
>>>>> ENDIF
>>>>> ENDDO
>>>>>
>>>>> tmp3=0
>>>>> DO nTrac=1,PTRACERS_numInUse
>>>>> fldName=PTRACERS_names(nTrac)
>>>>> tmp3=tmp3+1
>>>>> IF ( fldName(1:7) .EQ. 'atmpco2' ) THEN
>>>>> itrc_pco2=tmp3
>>>>> ENDIF
>>>>> ENDDO
>>>>
>>>> I guess I will just have to hard code these locations in if not, but it would be nice to get this working! Thanks in advance!
>>>>
>>>> Jon
>>>>
>>>> ___________________________________________________________________________
>>>> Dr. Jonathan M. Lauderdale
>>>> Postdoctoral Research Associate
>>>> Department of Earth, Atmosphere and Planetary Sciences
>>>> Massachusetts Institute of Technology
>>>> 77 Massachusetts Avenue
>>>> Cambridge, MA 02139, USA
>>>> Office: +1 617 324 3401
>>>> Cell : +1 617 304 5661
>>>> Email: <mailto:jml1 at mit.edu>
>>>> Web: <http://eaps-www.mit.edu/paoc/people/jonathan-lauderdale>
>>>> Association of Polar Early Career Scientists <http://www.apecs.is/>
>>>> ___________________________________________________________________________
>>>>
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--------------------------------------------------------
Patrick Heimbach, Ph.D. | http://heimbach.wordpress.com
* The University of Texas at Austin *
The Institute for Computational Engineering and Sciences
Institute for Geophysics | Jackson School of Geosciences
201 East 24th Street, POB 4.232 | Austin, TX 78712 | USA
FON: +1-512-232-7694 | Email: heimbach at utexas.edu
* Massachusetts Institute of Technology *
Department of Earth, Atmospheric, and Planetary Sciences
77 Massachusetts Ave, 54-1420 | Cambridge MA 02139 | USA
FON: +1-617-253-5259 | Email: heimbach at mit.edu
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