Re: grdmath problems

Branden,


 The workaround appears to be use "./1grd" instead of "1.grd":

/usr/src/gmt-4.5.11/bin/grdmath *./*1.grd DUP DUP 10 LE 0.65 MUL EXCH DUP
DUP DUP 10 GT EXCH 20 LE MUL EXCH 10 SUB 10 DIV -0.05 MUL 0.65 ADD MUL EXCH
DUP DUP DUP 20 GT EXCH 30 LE MUL EXCH 20 SUB 10 DIV -0.07 MUL 0.60 ADD MUL
EXCH DUP DUP DUP 30 GT EXCH 40 LE MUL EXCH 30 SUB 10 DIV -0.08 MUL 0.53 ADD
MUL EXCH 40 GT 0.45 MUL ADD ADD ADD ADD 686 2.grd DIV EXCH POW MUL = 3.grd


 I quite sure that anyone could reproduce this error doing:

mkdir strange_behavior

cd strange_behavior

ln -s ~/this_gmt/bin . # or whatever is your gmt4 path

bin/grdmath -R0/10/0/10 -I1 X = 1.grd

bin/grdmath -R0/10/0/10 -I1 X = 2.grd

bin/grdmath 1.grd DUP DUP 10 LE 0.65 MUL EXCH DUP DUP DUP 10 GT EXCH 20 LE
MUL EXCH 10 SUB 10 DIV -0.05 MUL 0.65 ADD MUL EXCH DUP DUP DUP 20 GT EXCH
30 LE MUL EXCH 20 SUB 10 DIV -0.07 MUL 0.60 ADD MUL EXCH DUP DUP DUP 30 GT
EXCH 40 LE MUL EXCH 30 SUB 10 DIV -0.08 MUL 0.53 ADD MUL EXCH 40 GT 0.45
MUL ADD ADD ADD ADD 686 2.grd DIV EXCH POW MUL = 3.grd


 Marcelo




On Thu, Jan 23, 2014 at 5:16 PM, Branden Christensen <
[email protected]> wrote:

> Marcelo:
>
>
> Some more information:
>
> When I execute /usr/src/gmt-4.5.11/bin/grdmath 1.grd DUP DUP 10 LE 0.65
> MUL EXCH DUP DUP DUP 10 GT EXCH 20 LE MUL EXCH 10 SUB 10 DIV -0.05 MUL 0.65
> ADD MUL EXCH DUP DUP DUP 20 GT EXCH 30 LE MUL EXCH 20 SUB 10 DIV -0.07 MUL
> 0.60 ADD MUL EXCH DUP DUP DUP 30 GT EXCH 40 LE MUL EXCH 30 SUB 10 DIV -0.08
> MUL 0.53 ADD MUL EXCH 40 GT 0.45 MUL ADD ADD ADD ADD 686 2.grd DIV EXCH POW
> MUL = 3.grd
>
> It tries to find 1.grd at /usr/src/gmt-4.5.11/bin/ and when it doesn't it
> spits out the buffer overflow error.
>
> But when I change the command a little (see bold), no error!:
> /usr/src/gmt-4.5.11/bin/grdmath */home/osop/*1.grd DUP DUP 10 LE 0.65 MUL
> EXCH DUP DUP DUP 10 GT EXCH 20 LE MUL EXCH 10 SUB 10 DIV -0.05 MUL 0.65 ADD
> MUL EXCH DUP DUP DUP 20 GT EXCH 30 LE MUL EXCH 20 SUB 10 DIV -0.07 MUL 0.60
> ADD MUL EXCH DUP DUP DUP 30 GT EXCH 40 LE MUL EXCH 30 SUB 10 DIV -0.08 MUL
> 0.53 ADD MUL EXCH 40 GT 0.45 MUL ADD ADD ADD ADD 686 2.grd DIV EXCH POW MUL
> = 3.grd
>
> The strange thing is that it does not need the complete path for 2.grd...
>
> Thoughts?
>
>
>
> *Branden Christensen*
> The Seismo Guys Blog: http://www.osop.com.pa/blog/the-seismo-guys/
> Take a Virtual Tour: http://www.osop.com.pa/tour
> Sign up for the OSOP mailing list:
> http://www.osop.com.pa/about/osop-mailing-list/
>
>
> On Thu, Jan 23, 2014 at 7:04 PM, Branden Christensen <
> [email protected]> wrote:
>
>> Marcelo:
>>
>>
>> Excellent. We are making progress!
>>
>>
>> After running "export PATH=$PATH:/usr/src/gmt-4.5.11/bin" I get the same
>> as you:
>>
>> osop@osop-displays2:~$ grdmath 1.grd DUP DUP 10 LE 0.65 MUL EXCH DUP DUP
>> DUP 10 GT EXCH 20 LE MUL EXCH 10 SUB 10 DIV -0.05 MUL 0.65 ADD MUL EXCH DUP
>> DUP DUP 20 GT EXCH 30 LE MUL EXCH 20 SUB 10 DIV -0.07 MUL 0.60 ADD MUL EXCH
>> DUP DUP DUP 30 GT EXCH 40 LE MUL EXCH 30 SUB 10 DIV -0.08 MUL 0.53 ADD MUL
>> EXCH 40 GT 0.45 MUL ADD ADD ADD ADD 686 2.grd DIV EXCH POW MUL = 3.grd
>> osop@osop-displays2:~$ /usr/src/gmt-4.5.11/bin/grdmath 1.grd DUP DUP 10
>> LE 0.65 MUL EXCH DUP DUP DUP 10 GT EXCH 20 LE MUL EXCH 10 SUB 10 DIV -0.05
>> MUL 0.65 ADD MUL EXCH DUP DUP DUP 20 GT EXCH 30 LE MUL EXCH 20 SUB 10 DIV
>> -0.07 MUL 0.60 ADD MUL EXCH DUP DUP DUP 30 GT EXCH 40 LE MUL EXCH 30 SUB 10
>> DIV -0.08 MUL 0.53 ADD MUL EXCH 40 GT 0.45 MUL ADD ADD ADD ADD 686 2.grd
>> DIV EXCH POW MUL = 3.grd
>>  *** buffer overflow detected ***: /usr/src/gmt-4.5.11/bin/grdmath
>> terminated
>>
>> I am relying on another program that calls grdmath using an explicit
>> path. So is there a fix to make it work with the explicit path?
>>
>> Thanks again!
>>
>>
>> Kind Regards,
>>
>>
>> *Branden Christensen*
>> The Seismo Guys Blog: http://www.osop.com.pa/blog/the-seismo-guys/
>> Take a Virtual Tour: http://www.osop.com.pa/tour
>> Sign up for the OSOP mailing list:
>> http://www.osop.com.pa/about/osop-mailing-list/
>>
>>
>> On Thu, Jan 23, 2014 at 6:02 PM, Marcelo Banik <[email protected]>wrote:
>>
>>>  Hi Branden,
>>>
>>>
>>>  I didn't execute script siposg4511-1.sh because:
>>>
>>> # dirty link creation to find gdal.h
>>>
>>> rm -R /usr/local/include
>>>
>>> ln -s /usr/include/gdal /usr/local/include
>>>
>>>
>>>  Appears to be much aggressive to my system.
>>>
>>>
>>>  I decide to use the original install_gmt4.sh script, without your
>>> minor modification, and some minimal modification in your GMT4param.txt to
>>> fit my system configuration (see attached file). Then from a directory with
>>> files:
>>>
>>> $ ls
>>>
>>> gmt-4.5.11-src.tar.bz2 GMT4param.txt gshhg-gmt-nc4-2.2.4.tar.gz
>>> install_gmt4.sh
>>>
>>>
>>>  I run the command:
>>>
>>> $ sudo sh -c "sh install_gmt4.sh GMT4param.txt" > install.log 2>&1
>>>
>>>
>>>  And did the test:
>>>
>>> $ /usr/src/gmt-4.5.11/bin/grdmath -R0/10/0/10 -I1 X = 1.grd
>>>
>>> $ /usr/src/gmt-4.5.11/bin/grdmath -R0/10/0/10 -I1 X = 2.grd
>>>
>>> $ /usr/src/gmt-4.5.11/bin/grdmath 1.grd DUP DUP 10 LE 0.65 MUL EXCH DUP
>>> DUP DUP 10 GT EXCH 20 LE MUL EXCH 10 SUB 10 DIV -0.05 MUL 0.65 ADD MUL EXCH
>>> DUP DUP DUP 20 GT EXCH 30 LE MUL EXCH 20 SUB 10 DIV -0.07 MUL 0.60 ADD MUL
>>> EXCH DUP DUP DUP 30 GT EXCH 40 LE MUL EXCH 30 SUB 10 DIV -0.08 MUL 0.53 ADD
>>> MUL EXCH 40 GT 0.45 MUL ADD ADD ADD ADD 686 2.grd DIV EXCH POW MUL = 3.grd
>>>
>>> *** buffer overflow detected ***: /usr/src/gmt-4.5.11/bin/grdmath
>>> terminated
>>>
>>>
>>>  Finally I get your error!
>>>
>>>
>>>  Then I did:
>>>
>>> $ export PATH=$PATH:/usr/src/gmt-4.5.11/bin
>>>
>>> $ which grdmath
>>>
>>> /usr/src/gmt-4.5.11/bin/grdmath
>>>
>>>
>>>  $ grdmath 1.grd DUP DUP 10 LE 0.65 MUL EXCH DUP DUP DUP 10 GT EXCH 20
>>> LE MUL EXCH 10 SUB 10 DIV -0.05 MUL 0.65 ADD MUL EXCH DUP DUP DUP 20 GT
>>> EXCH 30 LE MUL EXCH 20 SUB 10 DIV -0.07 MUL 0.60 ADD MUL EXCH DUP DUP DUP
>>> 30 GT EXCH 40 LE MUL EXCH 30 SUB 10 DIV -0.08 MUL 0.53 ADD MUL EXCH 40 GT
>>> 0.45 MUL ADD ADD ADD ADD 686 2.grd DIV EXCH POW MUL = 3.grd
>>>
>>>
>>>  And now it works.
>>>
>>>
>>>  For some unknown reason, it fails if an explicit path is used. I don't
>>> have this problem with my gmt4.5.11 installation. I'm not sure if it have
>>> some relation with your choice to not use shared lib. I could test it
>>> later, but first, let us now if including /usr/src/gmt-4.5.11/bin to your
>>> PATH works.
>>>
>>>
>>>  Regards,
>>>
>>>
>>>  Marcelo
>>>
>>>
>>>
>>>
>>> On Thu, Jan 23, 2014 at 2:36 PM, Branden Christensen <
>>> [email protected]> wrote:
>>>
>>>> Marcelo:
>>>>
>>>>
>>>> I also get:
>>>>
>>>> e51a8827d9b0ce3f36cfe6be01f24931  gmt-4.5.11-src.tar.bz2
>>>>
>>>> Attached is the script I used to install GMT 4.5.11. Unpack this tgz
>>>> file, cd to usr/src and execute "siposg4511-1.sh".
>>>>
>>>>
>>>> Kind Regards,
>>>>
>>>>
>>>> *Branden Christensen*
>>>> The Seismo Guys Blog: http://www.osop.com.pa/blog/the-seismo-guys/
>>>> Take a Virtual Tour: http://www.osop.com.pa/tour
>>>> Sign up for the OSOP mailing list:
>>>> http://www.osop.com.pa/about/osop-mailing-list/
>>>>
>>>>
>>>> On Thu, Jan 23, 2014 at 4:07 PM, Marcelo Banik <[email protected]
>>>> > wrote:
>>>>
>>>>>  Hi Branden,
>>>>>
>>>>>
>>>>>  Here I have:
>>>>>
>>>>> $ uname -a
>>>>>
>>>>> Linux acer 3.2.0-41-generic #66-Ubuntu SMP Thu Apr 25 03:27:11 UTC
>>>>> 2013 x86_64 x86_64 x86_64 GNU/Linux
>>>>>
>>>>>
>>>>>  $ cat /etc/issue
>>>>>
>>>>> Ubuntu 12.04.4 LTS \n \l
>>>>>
>>>>>
>>>>>  It isn't identical, but I didn't expect that these minor differences
>>>>> could be an issue.
>>>>>
>>>>>
>>>>>  From source files, I get:
>>>>>
>>>>> $ md5sum *.bz2
>>>>>
>>>>> fd4abdbbc5cb48087a12a4c762b87123 gmt-4.5.11-non-gpl-src.tar.bz2
>>>>>
>>>>> e51a8827d9b0ce3f36cfe6be01f24931 gmt-4.5.11-src.tar.bz2
>>>>>
>>>>>
>>>>>  Did you get the same values?
>>>>>
>>>>>
>>>>>  Could you send your GMT4param.txt file? I could try to install here
>>>>> using it, just to try to reproduce your results. I don't expect that it
>>>>> could change any thing, but I don't know what to do.
>>>>>
>>>>>
>>>>>  I only get a “buffer overflow detected” when I accidentally included
>>>>> option -Vd, but it don't appear to be your case.
>>>>>
>>>>>
>>>>>  Regards,
>>>>>
>>>>>
>>>>>  Marcelo
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Jan 23, 2014 at 1:08 PM, Branden Christensen <
>>>>> [email protected]> wrote:
>>>>>
>>>>>> Hi all:
>>>>>>
>>>>>>
>>>>>> Marcelo, thank you for taking the time to try that.
>>>>>>
>>>>>> I just created a new, virgin virtual machine with 12.04:
>>>>>>
>>>>>> osop@shakemap:~$ uname -a
>>>>>> Linux shakemap 3.5.0-23-generic #35~precise1-Ubuntu SMP Fri Jan 25
>>>>>> 17:13:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
>>>>>> osop@shakemap:~$ cat /etc/issue
>>>>>> Ubuntu 12.04.2 LTS \n \l
>>>>>>
>>>>>> I then installed GMT 4.5.11 from source.
>>>>>>
>>>>>> And then I attempted:
>>>>>>
>>>>>> osop@shakemap:~$ /usr/src/gmt-4.5.11/bin/grdmath -R0/10/0/10 -I1 X =
>>>>>> 1.grd
>>>>>> osop@shakemap:~$ /usr/src/gmt-4.5.11/bin/grdmath -R0/10/0/10 -I1 X =
>>>>>> 2.grd
>>>>>> osop@shakemap:~$  /usr/src/gmt-4.5.11/bin/grdmath 1.grd DUP DUP 10
>>>>>> LE 0.65 MUL EXCH DUP DUP DUP 10 GT EXCH 20 LE MUL EXCH 10 SUB 10 DIV -0.05
>>>>>> MUL 0.65 ADD MUL EXCH DUP DUP DUP 20 GT EXCH 30 LE MUL EXCH 20 SUB 10 DIV
>>>>>> -0.07 MUL 0.60 ADD MUL EXCH DUP DUP DUP 30 GT EXCH 40 LE MUL EXCH 30 SUB 10
>>>>>> DIV -0.08 MUL 0.53 ADD MUL EXCH 40 GT 0.45 MUL ADD ADD ADD ADD 686 2.grd
>>>>>> DIV EXCH POW MUL = 3.grd
>>>>>>  *** buffer overflow detected ***: /usr/src/gmt-4.5.11/bin/grdmath
>>>>>> terminated
>>>>>>
>>>>>> So I am getting the same results....
>>>>>>
>>>>>>
>>>>>> Kind Regards,
>>>>>>
>>>>>>
>>>>>>
>>>>>> *Branden Christensen*
>>>>>> The Seismo Guys Blog: http://www.osop.com.pa/blog/the-seismo-guys/
>>>>>> Take a Virtual Tour: http://www.osop.com.pa/tour
>>>>>> Sign up for the OSOP mailing list:
>>>>>> http://www.osop.com.pa/about/osop-mailing-list/
>>>>>>
>>>>>>
>>>>>> On Wed, Jan 22, 2014 at 7:59 PM, Marcelo Banik <
>>>>>> [email protected]> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> It works fine at my ubuntu 12.04 LTS 64bits GMT 4.5.11 installed
>>>>>>> from source code.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Marcelo
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Jan 22, 2014 at 5:54 PM, J.J. Green <
>>>>>>> [email protected]> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> Sounds like a flakey GMT in Ubuntu, see earlier messages
>>>>>>>> on this list.  On
>>>>>>>>
>>>>>>>>   jjg@flounder ~ $ cat /etc/issue
>>>>>>>>   Linux Mint 16 Petra \n \l
>>>>>>>>
>>>>>>>> with
>>>>>>>>
>>>>>>>>   jjg@flounder ~ $ apt-cache policy gmt
>>>>>>>>   gmt:
>>>>>>>>     Installed: 4.5.7-2ubuntu1
>>>>>>>>     Candidate: 4.5.7-2ubuntu1
>>>>>>>>     Package pin: 4.5.7-2ubuntu1
>>>>>>>>     Version table:
>>>>>>>>        4.5.9-1 1001
>>>>>>>>         500 http://archive.ubuntu.com/ubuntu/ saucy/universe amd64
>>>>>>>>   Packages
>>>>>>>>    *** 4.5.7-2ubuntu1 1001
>>>>>>>>         500 http://archive.ubuntu.com/ubuntu/ raring/universe amd64
>>>>>>>>   Packages
>>>>>>>>         100 /var/lib/dpkg/status
>>>>>>>>
>>>>>>>> This achieved with
>>>>>>>>
>>>>>>>>   jjg@flounder ~ $ cat /etc/apt/preferences.d/pin-gmt4
>>>>>>>>   Package: gmt
>>>>>>>>   Pin: release n=raring*
>>>>>>>>   Pin-Priority: 1001
>>>>>>>>
>>>>>>>>   Package: gmt-doc
>>>>>>>>   Pin: release v=13.04, l=Ubuntu
>>>>>>>>   Pin-Priority: 1001
>>>>>>>>
>>>>>>>>   Package: libgmt4
>>>>>>>>   Pin: release v=13.04, l=Ubuntu
>>>>>>>>   Pin-Priority: 1001
>>>>>>>>
>>>>>>>>   Package: *
>>>>>>>>   Pin: release v=13.04, l=Ubuntu
>>>>>>>>   Pin-Priority: -1
>>>>>>>>
>>>>>>>> I get no error for
>>>>>>>>
>>>>>>>>   jjg@flounder ~ $ GMT grdmath -R0/10/0/10 -I1 X = 1.grd
>>>>>>>>   jjg@flounder ~ $ GMT grdmath -R0/10/0/10 -I1 X = 2.grd
>>>>>>>>   jjg@flounder ~ $ GMT grdmath 1.grd DUP DUP 10 LE 0.65 MUL EXCH
>>>>>>>> DUP DUP DUP 10 GT EXCH 20 LE MUL EXCH 10 SUB 10 DIV -0.05 MUL 0.65 ADD MUL
>>>>>>>> EXCH DUP DUP DUP 20 GT EXCH 30 LE MUL EXCH 20 SUB 10 DIV -0.07 MUL 0.60 ADD
>>>>>>>> MUL EXCH DUP DUP DUP 30 GT EXCH 40 LE MUL EXCH 30 SUB 10 DIV -0.08 MUL 0.53
>>>>>>>> ADD MUL EXCH 40 GT 0.45 MUL ADD ADD ADD ADD 686 2.grd DIV EXCH POW MUL =
>>>>>>>> 3.grd
>>>>>>>>
>>>>>>>> and
>>>>>>>>
>>>>>>>>   jjg@flounder ~ $ ls -l *.grd
>>>>>>>>   -rw-r--r-- 1 jjg jjg 1240 Jan 22 19:41 1.grd
>>>>>>>>   -rw-r--r-- 1 jjg jjg 1240 Jan 22 19:41 2.grd
>>>>>>>>   -rw-r--r-- 1 jjg jjg 1508 Jan 22 19:42 3.grd
>>>>>>>>
>>>>>>>> perhaps you could revert to 4.5.7 too
>>>>>>>>
>>>>>>>> Cheers
>>>>>>>>
>>>>>>>> Jim
>>>>>>>> --
>>>>>>>> J.J. Green,  Seaview Sensing Ltd.,
>>>>>>>> http://seaviewsensing.com
>>>>>>>>
>>>>>>>>
>>>>>>>> To unsubscribe, send the message "signoff gmt-help" to
>>>>>>>> [email protected]
>>>>>>>>
>>>>>>>
>>>>>>> To unsubscribe, send the message "signoff gmt-help" to
>>>>>>> [email protected]
>>>>>>>
>>>>>>
>>>>>> To unsubscribe, send the message "signoff gmt-help" to
>>>>>> [email protected]
>>>>>>
>>>>>
>>>>> To unsubscribe, send the message "signoff gmt-help" to
>>>>> [email protected]
>>>>>
>>>>
>>>> To unsubscribe, send the message "signoff gmt-help" to
>>>> [email protected]
>>>>
>>>
>>> To unsubscribe, send the message "signoff gmt-help" to
>>> [email protected]
>>>
>>
>>
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