Buffer overflow error

Discussion:

Denis Felikson

2014-05-19 17:14:01 UTC

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 (
***@x86-003.build.bos.redhat.com) (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. Suárez

2014-05-19 17:27:18 UTC

Permalink

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.-

Post by Denis Felikson
I'm experiencing a buffer overflow error when executing the following
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
Linux version 2.6.32-131.4.1.el6.x86_64 (
Hat 4.4.5-6) (GCC) ) #1 SMP Fri Jun 10 10:54:26 EDT 2011
*** 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
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
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Note: gmt-help will become obsolete on Sept 1, 2014 - please use
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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.
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 ***@lists.hawaii.edu
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.

Denis Felikson

2014-05-19 18:38:29 UTC

Permalink

Post by Eduardo A. SuÃ¡rez
Hi,
echo "$inputFile $outputFile"
before the surface call, just to check if $inputFile and $outputFile are
defined in your script.
Eduardo.-
I'm experiencing a buffer overflow error when executing the following

Post by Denis Felikson
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
Linux version 2.6.32-131.4.1.el6.x86_64 (
Hat 4.4.5-6) (GCC) ) #1 SMP Fri Jun 10 10:54:26 EDT 2011
*** 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
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
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum
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--
Eduardo A. Suarez
Facultad de Ciencias AstronÃ³micas y GeofÃsicas - 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.
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
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on
gmt.soest.hawaii.edu instead.

Paul Wessel

2014-05-19 23:04:51 UTC

Permalink

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

Yes, the variables are defined. Further, the $inputFile actually exists (checked by putting an ls $inputFile before the surface command).
Here are some more clues. I'm trying again to run the command manually. When I use the -Lld and -Lud options, I get the buffer overflow error. When I omit these options, the surface command executes properly and writes a grid file.
Denis
Hi,
echo "$inputFile $outputFile"
before the surface call, just to check if $inputFile and $outputFile are defined in your script.
Eduardo.-
I'm experiencing a buffer overflow error when executing the following
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
Linux version 2.6.32-131.4.1.el6.x86_64 (
Hat 4.4.5-6) (GCC) ) #1 SMP Fri Jun 10 10:54:26 EDT 2011
*** 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
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
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.
--
Eduardo A. Suarez
Facultad de Ciencias Astronómicas y Geofísicas - UNLP
FCAG: (0221)-4236593 int. 172/Cel: (0221)-15-4557542/Casa: (0221)-4526589
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
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
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.

Denis Felikson

2014-05-21 19:28:03 UTC

Permalink

Hi Paul,

I'm using 4.5.9. This is really strange - I tried re-running the same
command but couldn't reproduce the error.

Denis

Post by Paul Wessel
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
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. SuÃ¡rez <

Post by Denis Felikson
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
Linux version 2.6.32-131.4.1.el6.x86_64 (
Hat 4.4.5-6) (GCC) ) #1 SMP Fri Jun 10 10:54:26 EDT 2011
*** 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
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
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
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
2014 - please use forum on gmt.soest.hawaii.edu instead.

Denis Felikson

2014-05-27 14:58:51 UTC

Permalink

OK running into a similar error, this time using the grdmath command.
Here's the full command I'm running, with all filenames expanded:

*grdmath
/data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/icesat_trend_OFP_case11l_1k_no8dy_regridded_grounded.llhdot.grd
/data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/icesat_trend_OFP_case11l_1k_no8dy_regridded_grounded_basin1.1.llhdot.grd
AND =
/data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/temp.grd*

When I run this, I get a buffer overflow error. When I run this command
with the -V option (I'm using GMT4), I don't get the buffer overflow. So
what's going on? Is there an issue with the filenames being too long? And
why does the -V option alter the way grdmath executes?

Denis

Post by Denis Felikson
Hi Paul,
I'm using 4.5.9. This is really strange - I tried re-running the same
command but couldn't reproduce the error.
Denis

Post by Paul Wessel
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
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. SuÃ¡rez <

Post by Denis Felikson
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
Linux version 2.6.32-131.4.1.el6.x86_64 (
Hat 4.4.5-6) (GCC) ) #1 SMP Fri Jun 10 10:54:26 EDT 2011
*** 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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Paul Wessel

2014-05-27 17:53:54 UTC

Permalink

Hi Denis-

If you are not running the latest release of GMT4, which is GMT4.5.12, then you must first update to that and see if the problem goes away. I do seem to remember a problem with very long filenames causing a buffer overflow but that was fixed. We do not have resources to debug older versions. Please report back to us if GMT 4.5.12 gives the same behavior.

Paul

grdmath /data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/icesat_trend_OFP_case11l_1k_no8dy_regridded_grounded.llhdot.grd /data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/icesat_trend_OFP_case11l_1k_no8dy_regridded_grounded_basin1.1.llhdot.grd AND = /data2/science/dfelikson/VolumeChange/OFP/greenland/max12myr/blockmedian/t0.25/1k_10k/temp.grd
When I run this, I get a buffer overflow error. When I run this command with the -V option (I'm using GMT4), I don't get the buffer overflow. So what's going on? Is there an issue with the filenames being too long? And why does the -V option alter the way grdmath executes?
Denis
Hi Paul,
I'm using 4.5.9. This is really strange - I tried re-running the same command but couldn't reproduce the error.
Denis
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