[ncl-talk] Seg fault on draw() after a WRAPIT function call

[Alan Brammer]

Ok, it seems like it was my error.

I was calling an out of bound index in my fortran code. However, the
function returned values. I could print the values. It wasn't until I did
something completely separate that it decided to segfault.



On Tue, Jun 30, 2015 at 5:23 PM, Alan Brammer <abrammer at albany.edu> wrote:

> Nope, That was just for my terrible pseudo example of whats going on.
>
>  Thought it may have been something like that so have changed my
> variables, and function names.  Haven't managed to figure it out yet.
>
> On Tue, Jun 30, 2015 at 4:59 PM, Dennis Shea <shea at ucar.edu> wrote:
>
>> Wild guess. R u using 'data' as a variable? Try another name. NCL's
>> parser may be confused
>>
>> Sent from my iPhone
>>
>> On Jun 30, 2015, at 2:34 PM, Alan Brammer <abrammer at albany.edu> wrote:
>>
>> I have a bizarre error, where after I have processed data through a
>> fortran function. When I call the plotting routines I will then get a
>> seg-fault.
>>
>>
>> pseudo-code
>>
>> external ex01 "./somefunctions.so"
>>
>> plot = gsn_csm_map(wks, mpres)
>> draw(plot)
>> frame(wks)
>> ;; everything is fine.
>>
>>
>> ex01::somefunction(data,data2)
>> printVarSummary(data)
>> ;; everything is still fine.
>>
>> plot = gsn_csm_map(wks, mpres)
>>  printVarSummary(plot)
>> ;; everything still good.
>>
>>
>> draw(plot)  ;; and now we seg fault.
>>
>>
>> Below is the memory dump I got on one occasion.
>> I can send the code to one of the devs for further delving if needed.
>>
>> Thanks,
>> Alan.
>>
>>
>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
>>
>>
>> *** glibc detected *** ncl: free(): invalid next size (normal):
>> 0x000000001d0c7530 ***
>>
>> ======= Backtrace: =========
>>
>> /lib64/libc.so.6[0x3e89e714af]
>>
>> /lib64/libc.so.6(cfree+0x4b)[0x3e89e757ab]
>>
>> ncl(NhlFree+0xe)[0xacc6c5]
>>
>> ncl(_NhlSetLayerValues+0x659)[0xaa3d5b]
>>
>> ncl(NhlVASetValues+0xf2)[0xaa42be]
>>
>> ncl[0xb086f7]
>>
>> ncl[0xb08cae]
>>
>> ncl[0xa9761c]
>>
>> ncl(_NhlDraw+0x7f)[0xa97845]
>>
>> ncl[0xafd72b]
>>
>> ncl[0xa9761c]
>>
>> ncl(_NhlPlotManagerDraw+0xbd)[0xa97999]
>>
>> ncl(NhlDraw+0xd1)[0xa97af1]
>>
>> ncl(_NclIDraw+0xaa)[0x8610fb]
>>
>> ncl(CallINTRINSIC_PROC_CALL+0x43)[0x80e472]
>>
>> ncl(_NclExecute+0x3e8)[0x8160d5]
>>
>> ncl(yyparse+0x78f)[0x6d9a59]
>>
>> ncl(NclDriver+0xc23)[0x6d61b2]
>>
>> ncl(main+0x9)[0x6d27c1]
>>
>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x3e89e1d9f4]
>>
>> ncl(vfprintf+0x729)[0x6d2709]
>>
>> ======= Memory map: ========
>>
>> 00400000-0254a000 r-xp 00000000 00:13 85713900
>> /nfs/ct12/abrammer/ncl6.3.0/bin/ncl
>>
>> 02749000-0299a000 rw-p 02149000 00:13 85713900
>> /nfs/ct12/abrammer/ncl6.3.0/bin/ncl
>>
>> 0299a000-06bd9000 rw-p 0299a000 00:00 0
>>
>> 14210000-1d1ba000 rw-p 14210000 00:00 0
>> [heap]
>>
>> 3e89a00000-3e89a1c000 r-xp 00000000 08:01 5096834
>> /lib64/ld-2.5.so
>>
>> 3e89c1c000-3e89c1d000 r--p 0001c000 08:01 5096834
>> /lib64/ld-2.5.so
>>
>> 3e89c1d000-3e89c1e000 rw-p 0001d000 08:01 5096834
>> /lib64/ld-2.5.so
>>
>> 3e89e00000-3e89f4f000 r-xp 00000000 08:01 5096835
>> /lib64/libc-2.5.so
>>
>> 3e89f4f000-3e8a14f000 ---p 0014f000 08:01 5096835
>> /lib64/libc-2.5.so
>>
>> 3e8a14f000-3e8a153000 r--p 0014f000 08:01 5096835
>> /lib64/libc-2.5.so
>>
>> 3e8a153000-3e8a154000 rw-p 00153000 08:01 5096835
>> /lib64/libc-2.5.so
>>
>> 3e8a154000-3e8a159000 rw-p 3e8a154000 00:00 0
>>
>> 3e8a200000-3e8a282000 r-xp 00000000 08:01 5096849
>> /lib64/libm-2.5.so
>>
>> 3e8a282000-3e8a481000 ---p 00082000 08:01 5096849
>> /lib64/libm-2.5.so
>>
>> 3e8a481000-3e8a482000 r--p 00081000 08:01 5096849
>> /lib64/libm-2.5.so
>>
>> 3e8a482000-3e8a483000 rw-p 00082000 08:01 5096849
>> /lib64/libm-2.5.so
>>
>> 3e8a600000-3e8a602000 r-xp 00000000 08:01 5096852
>> /lib64/libdl-2.5.so
>>
>> 3e8a602000-3e8a802000 ---p 00002000 08:01 5096852
>> /lib64/libdl-2.5.so
>>
>> 3e8a802000-3e8a803000 r--p 00002000 08:01 5096852
>> /lib64/libdl-2.5.so
>>
>> 3e8a803000-3e8a804000 rw-p 00003000 08:01 5096852
>> /lib64/libdl-2.5.so
>>
>> 3e8aa00000-3e8aa14000 r-xp 00000000 08:01 5096841
>> /lib64/libz.so.1.2.3
>>
>> 3e8aa14000-3e8ac13000 ---p 00014000 08:01 5096841
>> /lib64/libz.so.1.2.3
>>
>> 3e8ac13000-3e8ac14000 rw-p 00013000 08:01 5096841
>> /lib64/libz.so.1.2.3
>>
>> 3e8ae00000-3e8ae16000 r-xp 00000000 08:01 5096903
>> /lib64/libpthread-2.5.so
>>
>> 3e8ae16000-3e8b016000 ---p 00016000 08:01 5096903
>> /lib64/libpthread-2.5.so
>>
>> 3e8b016000-3e8b017000 r--p 00016000 08:01 5096903
>> /lib64/libpthread-2.5.so
>>
>> 3e8b017000-3e8b018000 rw-p 00017000 08:01 5096903
>> /lib64/libpthread-2.5.so
>>
>> 3e8b018000-3e8b01c000 rw-p 3e8b018000 00:00 0
>>
>> 3e8b200000-3e8b305000 r-xp 00000000 08:01 661720
>> /usr/lib64/libX11.so.6.2.0
>>
>> 3e8b305000-3e8b505000 ---p 00105000 08:01 661720
>> /usr/lib64/libX11.so.6.2.0
>>
>> 3e8b505000-3e8b50c000 rw-p 00105000 08:01 661720
>> /usr/lib64/libX11.so.6.2.0
>>
>> 3e8b600000-3e8b60d000 r-xp 00000000 08:01 661728
>> /usr/lib64/libgomp.so.1.0.0
>>
>> 3e8b60d000-3e8b80d000 ---p 0000d000 08:01 661728
>> /usr/lib64/libgomp.so.1.0.0
>>
>> 3e8b80d000-3e8b80e000 rw-p 0000d000 08:01 661728
>> /usr/lib64/libgomp.so.1.0.0
>>
>> 3e8ba00000-3e8ba05000 r-xp 00000000 08:01 661604
>> /usr/lib64/libXdmcp.so.6.0.0
>>
>> 3e8ba05000-3e8bc04000 ---p 00005000 08:01 661604
>> /usr/lib64/libXdmcp.so.6.0.0
>>
>> 3e8bc04000-3e8bc05000 rw-p 00004000 08:01 661604
>> /usr/lib64/libXdmcp.so.6.0.0
>>
>> 3e8be00000-3e8be10000 r-xp 00000000 08:01 663683
>> /usr/lib64/libXext.so.6.4.0
>>
>> 3e8be10000-3e8c010000 ---p 00010000 08:01 663683
>> /usr/lib64/libXext.so.6.4.0
>>
>> 3e8c010000-3e8c011000 rw-p 00010000 08:01 663683
>> /usr/lib64/libXext.so.6.4.0
>>
>> 3e8c200000-3e8c27f000 r-xp 00000000 08:01 658528
>> /usr/lib64/libfreetype.so.6.3.10
>>
>> 3e8c27f000-3e8c47f000 ---p 0007f000 08:01 658528
>> /usr/lib64/libfreetype.so.6.3.10
>>
>> 3e8c47f000-3e8c484000 rw-p 0007f000 08:01 658528
>> /usr/lib64/libfreetype.so.6.3.10
>>
>> 3e8c600000-3e8c621000 r-xp 00000000 08:01 5096843
>> /lib64/libexpat.so.0.5.0
>>
>> 3e8c621000-3e8c820000 ---p 00021000 08:01 5096843
>> /lib64/libexpat.so.0.5.0
>>
>> 3e8c820000-3e8c823000 rw-p 00020000 08:01 5096843
>> /lib64/libexpat.so.0.5.0
>>
>> 3e8ca00000-3e8ca07000 r-xp 00000000 08:01 5096905
>> /lib64/librt-2.5.so
>>
>> 3e8ca07000-3e8cc07000 ---p 00007000 08:01 5096905
>> /lib64/librt-2.5.so
>>
>> 3e8cc07000-3e8cc08000 r--p 00007000 08:01 5096905
>> /lib64/librt-2.5.so
>>
>> 3e8cc08000-3e8cc09000 rw-p 00008000 08:01 5096905
>> /lib64/librt-2.5.so
>>
>> 3e8d200000-3e8d229000 r-xp 00000000 08:01 659871
>> /usr/lib64/libfontconfig.so.1.1.0
>>
>> 3e8d229000-3e8d429000 ---p 00029000 08:01 659871
>> /usr/lib64/libfontconfig.so.1.1.0
>>
>> 3e8d429000-3e8d433000 rw-p 00029000 08:01 659871
>> /usr/lib64/libfontconfig.so.1.1.0
>>
>> 3e8d433000-3e8d434000 rw-p 3e8d433000 00:00 0
>>
>> 3e8d600000-3e8d609000 r-xp 00000000 08:01 661844
>> /usr/lib64/libXrender.so.1.3.0
>>
>> 3e8d609000-3e8d808000 ---p 00009000 08:01 661844
>> /usr/lib64/libXrender.so.1.3.0
>>
>> 3e8d808000-3e8d809000 rw-p 00008000 08:01 661844
>> /usr/lib64/libXrender.so.1.3.0
>>
>> 3e8fe00000-3e8fe0d000 r-xp 00000000 08:01 5096853
>> /lib64/libgcc_s-4.1.2-20080825.so.1
>>
>> 3e8fe0d000-3e9000d000 ---p 0000d000 08:01 5096853
>> /lib64/libgcc_s-4.1.2-20080825.so.1
>>
>> 3e9000d000-3e9000e000 rw-p 0000d000 08:01 5096853
>> /lib64/libgcc_s-4.1.2-20080825.so.1
>>
>> 3e90600000-3e906e6000 r-xp 00000000 08:01 664282
>> /usr/lib64/libstdc++.so.6.0.8
>>
>> 3e906e6000-3e908e5000 ---p 000e6000 08:01 664282
>> /usr/lib64/libstdc++.so.6.0.8
>>
>> 3e908e5000-3e908eb000 r--p 000e5000 08:01 664282
>> /usr/lib64/libstdc++.so.6.0.8
>>
>> 3e908eb000-3e908ee000 rw-p 000eb000 08:01 664282
>> /usr/lib64/libstdc++.so.6.0.8
>>
>> 3e908ee000-3e90900000 rw-p 3e908ee000 00:00 0
>>
>> 3e90e00000-3e90e15000 r-xp 00000000 08:01 5096863
>> /lib64/libselinux.so.1
>>
>> 3e90e15000-3e91015000 ---p 00015000 08:01 5096863
>> /lib64/libselinux.so.1
>>
>> 3e91015000-3e91017000 rw-p 00015000 08:01 5096863
>> /lib64/libselinux.so.1
>>
>> 3e91017000-3e91018000 rw-p 3e91017000 00:00 0
>>
>> 3e91200000-3e9123b000 r-xp 00000000 08:01 5096861
>> /lib64/libsepol.so.1
>>
>> 3e9123b000-3e9143b000 ---p 0003b000 08:01 5096861
>> /lib64/libsepol.so.1
>>
>> 3e9143b000-3e9143c000 rw-p 0003b000 08:01 5096861
>> /lib64/libsepol.so.1
>>
>> 3e9143c000-3e91446000 rw-p 3e9143c000 00:00 0
>>
>> 3e93c00000-3e93c15000 r-xp 00000000 08:01 5097142
>> /lib64/libnsl-2.5.so
>>
>> 3e93c15000-3e93e14000 ---p 00015000 08:01 5097142
>> /lib64/libnsl-2.5.so
>>
>> 3e93e14000-3e93e15000 r--p 00014000 08:01 5097142
>> /lib64/libnsl-2.5.so
>>
>> 3e93e15000-3e93e16000 rw-p 0001Abort
>>
>>
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