Re: grdmath problems

Marcelo Banik <[email protected]>
Newsgroups gmane.comp.gis.gmt.user
Message-ID <CAN-U1_YtOZpUCP1hXadMrwVnp57sFfsdTe8CSD6hSfq1uYA8Ew@mail.gmail.com> 
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]
GMT4param.txt (text/plain, 2.5 KB) 
# This file contains parameters needed by the install script
# for GMT4 Version 4.5.1.  Give this parameter file
# as the argument to the install_gmt.sh script and the whole
# installation process can be placed in the background.
# Default answers will be selected where none is given.
# You can edit the values, but do not remove definitions!
#
# This script was created by install_gmt.sh on
#
#	2013. nov. 23., szombat, 16.17.17 CET
#
# Do NOT add any spaces around the = signs.  The
# file MUST conform to Bourne shell syntax
#---------------------------------------------
#       GMT4 VERSION TO INSTALL
#---------------------------------------------
VERSION=4.5.11
#---------------------------------------------
#       SYSTEM UTILITIES AND FTP SETTING
#---------------------------------------------
GMT_make=make
passive_ftp=y
#---------------------------------------------
#       NETCDF SECTION
#---------------------------------------------
netcdf_path=/usr
#---------------------------------------------
#       GSHHG SECTION
#---------------------------------------------
GSHHG_install=y
GSHHG_ftp=n
GSHHG_path=/usr/src
#---------------------------------------------
#       GDAL SECTION
#---------------------------------------------
use_gdal=y
gdal_path=/usr/bin/gdal-config
#---------------------------------------------
#       GMT4 & GSHHG FTP SECTION
#---------------------------------------------
GMT_ftp=n
GMT_inst_gmt=y
GMT_ftpsite=1
#---------------------------------------------
#       GMT4 SUPPLEMENTS SELECT SECTION
#---------------------------------------------
GMT_suppl_mex=d
GMT_suppl_xgrid=d
#---------------------------------------------
#       GMT4 ENVIRONMENT SECTION
#---------------------------------------------
GMT_si=y
GMT_ps=y
GMT_prefix=/usr/src/gmt-4.5.11
GMT_bin=/usr/src/gmt-4.5.11/bin
GMT_lib=/usr/src/gmt-4.5.11/lib
GMT_share=/usr/src/gmt-4.5.11/share
GMT_include=/usr/src/gmt-4.5.11/include
GMT_man=/usr/src/gmt-4.5.11/man
GMT_doc=/usr/src/gmt-4.5.11/share/doc/gmt
GMT_sharedir=/usr/src/gmt-4.5.11/share
#---------------------------------------------
#       COMPILING & LINKING SECTION
#---------------------------------------------
GMT_sharedlib=n
GMT_cc=
GMT_64=
GMT_triangle=n
GMT_flock=n
#---------------------------------------------
#       TEST & PRINT SECTION
#---------------------------------------------
GMT_run_examples=y
GMT_delete=n
#---------------------------------------------
#       MEX SECTION
#---------------------------------------------
MATDIR=/usr/local/matlab
mex_mdir=
mex_xdir=
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