Buffer Overflow if Compiling KPP

Posts related to the installation of WRF Chemistry

Buffer Overflow if Compiling KPP

Postby wintermute » Wed Nov 27, 2013 5:00 am

Hi all,

I've been recently trying to compile WRF Chem on Ubuntu 13.10 x64. If I set the compiler to compile also KPP I receive a buffer overflow error that completely disappears if I choose not to compile KPP...has anyone experienced the same problem?

Are there are any known workaround to this solution?
wintermute
 
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Re: Buffer Overflow if Compiling KPP

Postby Rocky_zp » Fri Apr 18, 2014 4:29 am

Hello,
I am a new user to WRF-CHEM.When I tried to compile it ,I met the same problem as you.Have you known how to solve it yet?
my compiler is gcc 4.4 and the OS is Ubuntu 10.10. By the way, I chose the serial mode.
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Re: Buffer Overflow if Compiling KPP

Postby wintermute » Wed Apr 23, 2014 7:25 am

Sorry, no. I do not have a clue to what is causing that buffer overflow: probably something related to YACC and FLEX, but I'm not expert enough with these packages to know what changes I could make to solve the issue.
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Re: Buffer Overflow if Compiling KPP

Postby humaid » Fri May 02, 2014 12:23 pm

I faced this problem too
I don't know exactly what cause it, but it disappeared when I compiled with FLEX 2.5.3
The compiler used was Gnu 4.6.4
If you want to keep higher version of FLEX try to fix it with this solution
http://ruc.noaa.gov/wrf/WG11/KPP_yacc_flex_problems.pdf
Reference to viewtopic.php?f=39&t=3302#p15513
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Re: Buffer Overflow if Compiling KPP

Postby Niteo » Tue Aug 16, 2016 10:50 am

Sorry for necroposting, just a more detailed instruction here. Most likely, this error occurs due to the wrong version of FLEX library. EXPORT FLEX='path_to_flex' turned out to be not enough on my system, cause still somewhere in the code system FLEX was called, so I needed to additionally add the directory with compiled FLEX 2.5.3 executable to PATH. Hope that helps.
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Buffer Overflow if Compiling KPP

Postby VBSEEN » Fri Dec 01, 2017 1:23 am

Hi I am installing WRF-CHEM with KPP, I am also getting the buffer overflow detected error message while compiling with KPP
export WRF_EM_CORE=1
export WRF_CHEM=1
export WRF_KPP=1
export FLEX_LIB_DIR=/usr/lib/x86_64-linux-gnu
export YACC='/usr/bin/yacc -d'

I am using GNU (gfortran/gcc)

The error message is shown here for your suggestions

vijay@vijay-desktop:~/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3$ ./compile em_real >& log
*** buffer overflow detected ***: /home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f31a225e7e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f31a230011c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117120)[0x7f31a22fe120]
/lib/x86_64-linux-gnu/libc.so.6(+0x116472)[0x7f31a22fd472]
/home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp[0x404a1f]
/home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp[0x401729]
/home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp[0x4026c7]
/home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp[0x40694f]
/home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp[0x408712]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f31a2207830]
/home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp[0x401239]
======= Memory map: ========
00400000-00429000 r-xp 00000000 08:02 6423340 /home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp
00628000-00629000 r--p 00028000 08:02 6423340 /home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp
00629000-0062b000 rw-p 00029000 08:02 6423340 /home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp
0062b000-006bb000 rw-p 00000000 00:00 0
01cb7000-023bb000 rw-p 00000000 00:00 0 [heap]
7f31a1fd0000-7f31a1fe6000 r-xp 00000000 08:02 58200329 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f31a1fe6000-7f31a21e5000 ---p 00016000 08:02 58200329 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f31a21e5000-7f31a21e6000 r--p 00015000 08:02 58200329 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f31a21e6000-7f31a21e7000 rw-p 00016000 08:02 58200329 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f31a21e7000-7f31a23a7000 r-xp 00000000 08:02 58200484 /lib/x86_64-linux-gnu/libc-2.23.so
7f31a23a7000-7f31a25a7000 ---p 001c0000 08:02 58200484 /lib/x86_64-linux-gnu/libc-2.23.so
7f31a25a7000-7f31a25ab000 r--p 001c0000 08:02 58200484 /lib/x86_64-linux-gnu/libc-2.23.so
7f31a25ab000-7f31a25ad000 rw-p 001c4000 08:02 58200484 /lib/x86_64-linux-gnu/libc-2.23.so
7f31a25ad000-7f31a25b1000 rw-p 00000000 00:00 0
7f31a25b1000-7f31a25d7000 r-xp 00000000 08:02 58195982 /lib/x86_64-linux-gnu/ld-2.23.so
7f31a27af000-7f31a27b2000 rw-p 00000000 00:00 0
7f31a27d3000-7f31a27d6000 rw-p 00000000 00:00 0
7f31a27d6000-7f31a27d7000 r--p 00025000 08:02 58195982 /lib/x86_64-linux-gnu/ld-2.23.so
7f31a27d7000-7f31a27d8000 rw-p 00026000 08:02 58195982 /lib/x86_64-linux-gnu/ld-2.23.so
7f31a27d8000-7f31a27d9000 rw-p 00000000 00:00 0
7ffd4b517000-7ffd4b539000 rw-p 00000000 00:00 0 [stack]
7ffd4b58d000-7ffd4b58f000 r--p 00000000 00:00 0 [vvar]
7ffd4b58f000-7ffd4b591000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
*** buffer overflow detected ***: /home/vijay/Desktop/WRF/Build_WRF/WRFCHEM/WRFV3/chem/KPP/kpp/kpp-2.1/bin/kpp terminated
======= Backtrace: =========
VBSEEN
 
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