Re: grdmath problems

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
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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
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>>>
>>
>> To unsubscribe, send the message "signoff gmt-help" to
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>>
>
>

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