Re: Buffer overflow error
Paul Wessel <[email protected]> Tue, 27 May 2014 07:53:54 -1000
| Newsgroups | gmane.comp.gis.gmt.user |
|---|---|
| Message-ID | <[email protected]> |
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 On May 27, 2014, at 4:58 AM, Denis Felikson <[email protected]> wrote: > 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 > > > > On Wed, May 21, 2014 at 2:28 PM, Denis Felikson <[email protected]> wrote: > 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 > > > On Mon, May 19, 2014 at 6:04 PM, Paul Wessel <[email protected]> wrote: > 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 >> >> 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. >> >> >> >> >> -- >> 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 >> 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. > > 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. 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.