Re: Buffer overflow error

Hi Denis-

I tried a surface job with -Lud -Lld and could not reproduce it.  What GMT version are we talking about? Could you please rerun your example with -V (GMT4) or -Vd (GMT 5) and send us the output?  Please expand what $inputFile and $outputFile are. E.g., are they excessively long path names?


-p

On May 19, 2014, at 8:38 AM, Denis Felikson <[email protected]> wrote:

> Yes, the variables are defined. Further, the $inputFile actually exists (checked by putting an ls $inputFile before the surface command).
> 
> Here are some more clues. I'm trying again to run the command manually. When I use the -Lld and -Lud options, I get the buffer overflow error. When I omit these options, the surface command executes properly and writes a grid file.
> 
> 
> Denis
> 
> 
> 
> On Mon, May 19, 2014 at 12:27 PM, Eduardo A. Suárez <[email protected]> wrote:
> Hi,
> 
> put a line with:
> 
> echo "$inputFile $outputFile"
> 
> before the surface call, just to check if $inputFile and $outputFile are defined in your script.
> 
> Eduardo.-
> 
> 
> Quoting Denis Felikson <[email protected]>:
> 
> I'm experiencing a buffer overflow error when executing the following
> surface command:
> 
> surface $inputFile -G$outputFile -I100k -R0/360/-90/-60 -T0.25 -Lld -Lud
> 
> What's odd is that I see the error when I run this command in my shell
> script. If I run it manually from the command line, everything works.
> 
> Here's some system info. Let me know if there's any other information
> needed:
> 
> Linux version 2.6.32-131.4.1.el6.x86_64 (
> [email protected]) (gcc version 4.4.5 20110214 (Red
> Hat 4.4.5-6) (GCC) ) #1 SMP Fri Jun 10 10:54:26 EDT 2011
> 
> And here's the error itself:
> 
> *** buffer overflow detected ***: surface terminated
> ======= Backtrace: =========
> /lib64/libc.so.6(__fortify_fail+0x37)[0x3f45701307]
> /lib64/libc.so.6[0x3f456ff1f0]
> /lib64/libc.so.6[0x3f456fe0a7]
> /usr/lib64/libgmt.so.4(GMT_grd_init+0xd6)[0x3608e2bd96]
> surface[0x4066d5]
> /lib64/libc.so.6(__libc_start_main+0xfd)[0x3f4561ecdd]
> surface[0x401439]
> ======= Memory map: ========
> 00400000-0040a000 r-xp 00000000 fd:05 9700262
>  /usr/bin/surface
> 00609000-00613000 rw-p 00009000 fd:05 9700262
>  /usr/bin/surface
> 01de0000-01e22000 rw-p 00000000 00:00 0
>  [heap]
> 3056400000-305641d000 r-xp 00000000 fd:01 2621513
>  /lib64/libselinux.so.1
> 305641d000-305661c000 ---p 0001d000 fd:01 2621513
>  /lib64/libselinux.so.1
> 305661c000-305661d000 r--p 0001c000 fd:01 2621513
>  /lib64/libselinux.so.1
> 305661d000-305661e000 rw-p 0001d000 fd:01 2621513
>  /lib64/libselinux.so.1
> 305661e000-305661f000 rw-p 00000000 00:00 0
> 305c000000-305c02a000 r-xp 00000000 fd:01 2621915
>  /lib64/libk5crypto.so.3.1
> 305c02a000-305c22a000 ---p 0002a000 fd:01 2621915
>  /lib64/libk5crypto.so.3.1
> 305c22a000-305c22c000 rw-p 0002a000 fd:01 2621915
>  /lib64/libk5crypto.so.3.1
> 305c400000-305c4d4000 r-xp 00000000 fd:01 2621916
>  /lib64/libkrb5.so.3.3
> 305c4d4000-305c6d4000 ---p 000d4000 fd:01 2621916
>  /lib64/libkrb5.so.3.3
> 305c6d4000-305c6df000 rw-p 000d4000 fd:01 2621916
>  /lib64/libkrb5.so.3.3
> 305c800000-305c802000 r-xp 00000000 fd:01 2621486
>  /lib64/libkeyutils.so.1.3
> 305c802000-305ca01000 ---p 00002000 fd:01 2621486
>  /lib64/libkeyutils.so.1.3
> 305ca01000-305ca02000 rw-p 00001000 fd:01 2621486
>  /lib64/libkeyutils.so.1.3
> 305cc00000-305cc0a000 r-xp 00000000 fd:01 2621914
>  /lib64/libkrb5support.so.0.1
> 305cc0a000-305ce09000 ---p 0000a000 fd:01 2621914
>  /lib64/libkrb5support.so.0.1
> 305ce09000-305ce0a000 rw-p 00009000 fd:01 2621914
>  /lib64/libkrb5support.so.0.1
> 305d000000-305d03f000 r-xp 00000000 fd:01 2621920
>  /lib64/libgssapi_krb5.so.2.2
> 305d03f000-305d23e000 ---p 0003f000 fd:01 2621920
>  /lib64/libgssapi_krb5.so.2.2
> 305d23e000-305d241000 rw-p 0003e000 fd:01 2621920
>  /lib64/libgssapi_krb5.so.2.2
> 305d400000-305d407000 r-xp 00000000 fd:01 2621918
>  /lib64/libcrypt-2.12.so
> 305d407000-305d607000 ---p 00007000 fd:01 2621918
>  /lib64/libcrypt-2.12.so
> 305d607000-305d608000 r--p 00007000 fd:01 2621918
>  /lib64/libcrypt-2.12.so
> 305d608000-305d609000 rw-p 00008000 fd:01 2621918
>  /lib64/libcrypt-2.12.so
> 305d609000-305d637000 rw-p 00000000 00:00 0
> 305d800000-305d85d000 r-xp 00000000 fd:01 2621870
>  /lib64/libfreebl3.so
> 305d85d000-305da5c000 ---p 0005d000 fd:01 2621870
>  /lib64/libfreebl3.so
> 305da5c000-305da5e000 rw-p 0005c000 fd:01 2621870
>  /lib64/libfreebl3.so
> 305da5e000-305da62000 rw-p 00000000 00:00 0
> 305dc00000-305dc38000 r-xp 00000000 fd:01 2621921
>  /lib64/libnspr4.so
> 305dc38000-305de38000 ---p 00038000 fd:01 2621921
>  /lib64/libnspr4.so
> 305de38000-305de3a000 rw-p 00038000 fd:01 2621921
>  /lib64/libnspr4.so
> 305de3a000-305de3d000 rw-p 00000000 00:00 0
> 305e400000-305e533000 r-xp 00000000 fd:05 9446798
>  /usr/lib64/libnss3.so
> 305e533000-305e733000 ---p 00133000 fd:05 9446798
>  /usr/lib64/libnss3.so
> 305e733000-305e73a000 rw-p 00133000 fd:05 9446798
>  /usr/lib64/libnss3.so
> 305e73a000-305e73b000 rw-p 00000000 00:00 0
> 305e800000-305e81a000 r-xp 00000000 fd:05 9437512
>  /usr/lib64/libnssutil3.so
> 305e81a000-305ea19000 ---p 0001a000 fd:05 9437512
>  /usr/lib64/libnssutil3.so
> 305ea19000-305ea1f000 rw-p 00019000 fd:05 9437512
>  /usr/lib64/libnssutil3.so
> 305ec00000-305ec04000 r-xp 00000000 fd:01 2621922
>  /lib64/libplc4.so
> 305ec04000-305ee03000 ---p 00004000 fd:01 2621922
>  /lib64/libplc4.so
> 305ee03000-305ee04000 rw-p 00003000 fd:01 2621922
>  /lib64/libplc4.so
> 305f000000-305f003000 r-xp 00000000 fd:01 2621923
>  /lib64/libplds4.so
> 305f003000-305f202000 ---p 00003000 fd:01 2621923
>  /lib64/libplds4.so
> 305f202000-305f203000 rw-p 00002000 fd:01 2621923
>  /lib64/libplds4.so
> 305f400000-305f428000 r-xp 00000000 fd:05 9446800
>  /usr/lib64/libsmime3.so
> 305f428000-305f628000 ---p 00028000 fd:05 9446800
>  /usr/lib64/libsmime3.so
> 305f628000-305f62c000 rw-p 00028000 fd:05 9446800
>  /usr/lib64/libsmime3.so
> 3060400000-3060419000 r-xp 00000000 fd:05 9446801
>  /usr/lib64/libsasl2.so.2.0.23
> 3060419000-3060619000 ---p 00019000 fd:05 9446801
>  /usr/lib64/libsasl2.so.2.0.23
> 3060619000-306061a000 rw-p 00019000 fd:05 9446801
>  /usr/lib64/libsasl2.so.2.0.23
> 3061c00000-3061c8c000 r-xp 00000000 fd:05 9437461
>  /usr/lib64/libsqlite3.so.0.8.6
> 3061c8c000-3061e8b000 ---p 0008c000 fd:05 9437461
>  /usr/lib64/libsqlite3.so.0.8.6
> 3061e8b000-3061e8f000 rw-p 0008b000 fd:05 9437461
>  /usr/lib64/libsqlite3.so.0.8.6
> 32dde00000-32dde41000 r-xp 00000000 fd:05 9446895
>  /usr/lib64/libproj.so.0.6.6
> 32dde41000-32de040000 ---p 00041000 fd:05 9446895
>  /usr/lib64/libproj.so.0.6.6
> 32de040000-32de043000 rw-p 00040000 fd:05 9446895
>  /usr/lib64/libproj.so.0.6.6
> 32de600000-32de610000 r-xp 00000000 fd:05 9446846
>  /usr/lib64/libodbcinst.so.2.0.0
> 32de610000-32de810000 ---p 00010000 fd:05 9446846
>  /usr/lib64/libodbcinst.so.2.0.0
> 
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> 
> 
> 
> 
> -- 
> Eduardo A. Suarez
> Facultad de Ciencias Astronómicas y Geofísicas - UNLP
> FCAG: (0221)-4236593 int. 172/Cel: (0221)-15-4557542/Casa: (0221)-4526589
> 
> 
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> Mailing list for GMT discussions of all kinds.  If you are not sure you have found a bug, discuss it here first.
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> 
> Mailing list for GMT discussions of all kinds. If you are not sure you have found a bug, discuss it here first. To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu To unsubscribe, send the message "signoff gmt-help" to [email protected] Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.


Mailing list for GMT discussions of all kinds.  If you are not sure you have found a bug, discuss it here first.
To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu
To unsubscribe, send the message "signoff gmt-help" to [email protected]
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.