[MITgcm-support] Segmentation fault trying to capture location in ptracers array.

Tue Jun 9 19:33:12 EDT 2015

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 <mailto: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 <mailto:jml1 at mit.edu>>
>> Web: <http://eaps-www.mit.edu/paoc/people/jonathan-lauderdale <http://eaps-www.mit.edu/paoc/people/jonathan-lauderdale>>
>> Association of Polar Early Career Scientists <http://www.apecs.is/ <http://www.apecs.is/>>
>> ___________________________________________________________________________
>> 
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