gmane.comp.gis.gmt.user

SOLVED gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-25T22:56:30

Fixed thanks to Florian.  These steps might help others in same predicament.
J.

Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

Begin forwarded message:

From: John Helly <hellyj< at >UCSD.EDU>
Date: May 25, 2012 12:54:07 PM HST
To: Florian Wobbe <Florian.Wobbe< at >awi.de>
Subject: Re: [GMT-HELP] gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

Hi Florian.

It's fixed thanks to your insight.  I deleted /opt and rebuild gmt5 with cmake and everything seems to be fine now.

NeptuneStonesteps.local:/Volumes/Geospatial001/IcebergIII/src/gmt>~/bin/gshhg_test.bash
+ otool -L /Users/hellyj/src/GMTdev/gmt5/build/src/gshhg_version
/Users/hellyj/src/GMTdev/gmt5/build/src/gshhg_version:
/usr/local/netcdf-4.1.2/lib/libnetcdf.7.dylib (compatibility version 8.0.0, current version 8.1.0)
/usr/local/hdf5-

Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-25T21:05:16

Hi Florian.
Here's the result (same):

NeptuneStonesteps.local:~/src/GMTdev/gmt5/build/src>make gshhg_version
Built target gshhg_version

NeptuneStonesteps.local:~/src/GMTdev/gmt5/build/src>./gshhg_version ~/src/GMTdev/gshhg-gmt-nc4-2.2.1/binned_river_c.nc
gshhg_version: cannot open file "/Users/hellyj/src/GMTdev/gshhg-gmt-nc4-2.2.1/binned_river_c.nc" (-101).

Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

On May 24, 2012, at 10:42 PM, Florian Wobbe wrote:


Hi John, this is a good sign. Then try to reproduce the error with:

 src/gshhg_version gshhg-gmt-nc4/binned_river_c.nc

You need to 'svn up' before and run 'make gshhg_version' again in the build directory. No need to install or run cmake again unless you removed the build tree. Note that src/gshhg_version is in the build directory - it will not be installed.

Flori

full resolution data error

MOFFAT, L.C. (MR. — 2012-05-25T14:41:32

Hi All,

I have just installed GMT4.5.8 under Ubuntu 12.04. Now the problem is when I try to run any script containing "pscoast" command I get the following error:
[16:00]mmaoletsekae:~$ okavangogrd.sh
pscoast: full resolution shoreline data base not installed
pscoast: full resolution political boundary data base not installed
pscoast: full resolution river data base not installed
pscoast: No databases available - aborts

This is despite the fact that I have the files required by "pscoast" in the folder "/home/lucky/GMT4.5.8/share/coast", i.e binned_border_*.cdf,  binned_GSHHS_*.cdf & binned_river_*.cdf (with * representing c,f,h,i,l). I installed GMT using Ubuntu's repositories.

Here is some info about my platform:

hostname = lucky-HP-Pavilion-g6-Notebook-PC
uname -m = i686
uname -r = 3.2.0-24-generic-pae
uname -s = Linux
uname -v = #37-Ubuntu SMP Wed Apr 25 10:47:59 UTC 2012

And the following is some of the first few lines from "config.log" file:

$ ./configure --prefix=/home/lucky/GMT4.5.8 --bindir=/ho

Re: -W$ with a variable

Gery . — 2012-05-25T08:50:11


Thank you very much Jim, Oliver, Zhenwei and p Valdéz, many thanks guys for your nice support and suggestions, I'll try your codes.

Cheers,

Gery
       
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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

Florian Wobbe — 2012-05-25T08:42:06

Hi John, this is a good sign. Then try to reproduce the error with:

  src/gshhg_version gshhg-gmt-nc4/binned_river_c.nc

You need to 'svn up' before and run 'make gshhg_version' again in the build directory. No need to install or run cmake again unless you removed the build tree. Note that src/gshhg_version is in the build directory - it will not be installed.

Florian


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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-25T08:38:31

Hi.
I think there is something wrong with how you are opening the file.
Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

On May 24, 2012, at 10:29 PM, John Helly wrote:

Hi Florian.
Both of these commands work with my build.  No problems.
J.
Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

On May 24, 2012, at 9:40 PM, Florian Wobbe wrote:


Btw, you did not include any optimization flag in CFLAGS. Is this intention? Since you are running on Snow Leopard gcc should default to -arch x86_64 (aka -m64).

Before you try anything else could you make sure these work:

ncdump -h gshhg-gmt-nc4/binned_river_c.nc
ncdump gshhg-gmt-nc4/binned_river_c

Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-25T08:29:33

Hi Florian.
Both of these commands work with my build.  No problems.
J.
Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

On May 24, 2012, at 9:40 PM, Florian Wobbe wrote:


Btw, you did not include any optimization flag in CFLAGS. Is this intention? Since you are running on Snow Leopard gcc should default to -arch x86_64 (aka -m64).

Before you try anything else could you make sure these work:

 ncdump -h gshhg-gmt-nc4/binned_river_c.nc
 ncdump gshhg-gmt-nc4/binned_river_c.nc > /dev/null

If these fail and the same works with the file binned_border_c.nc (this file is classic netcdf) it is a HDF5 issue. I've been using compressed files starting with netcdf-4.1.1 and hdf5-1.8.2 and never saw your -101 error. Now I use netcdf-4.2.0 and hdf5-1.8.9 (macports). You might consider upgrading or using a package manager instead. The

Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

Florian Wobbe — 2012-05-25T07:40:59

Btw, you did not include any optimization flag in CFLAGS. Is this intention? Since you are running on Snow Leopard gcc should default to -arch x86_64 (aka -m64).

Before you try anything else could you make sure these work:

  ncdump -h gshhg-gmt-nc4/binned_river_c.nc
  ncdump gshhg-gmt-nc4/binned_river_c.nc > /dev/null

If these fail and the same works with the file binned_border_c.nc (this file is classic netcdf) it is a HDF5 issue. I've been using compressed files starting with netcdf-4.1.1 and hdf5-1.8.2 and never saw your -101 error. Now I use netcdf-4.2.0 and hdf5-1.8.9 (macports). You might consider upgrading or using a package manager instead. They are quite up to date these days. No use going into the trouble compiling everything yourself.

Good luck,
Florian

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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-25T03:51:29

Also, I ran 'make check' in the netcdf-4.1.2 directory and it passed all the tests.
J.

Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

On May 24, 2012, at 4:46 PM, John Helly wrote:

Hi.
Here's how my netcdf was built:

NeptuneStonesteps.local:~/bin>more makeNetCDF_OSX_64bit.bash
#!/bin/bash
make distclean
#
#./configure >configure.log 2>&1 \
#       CC="gcc -m64" \
#       CFLAGS="-g -O2" \
#       CXX="g++ -m64" \
#       CXXFLAGS="-g -O2" \
#       CPPFLAGS="-DNDEBUG -DgFortran" \
#       FC="gfortran -m64" \
#       FCFLAGS="-g -O2"

export CFLAGS=-m64
export FFLAGS=-m64
export FCFLAGS=-m64
export CXXFLAGS=-m64
export CPPFLAGS=-DgFortran

#export CC=/usr/bin/cc 
export F77=gfortran
export FC=gfortran
#export FCFLAGS=-qsuffix=cpp=f90
#
./configure --prefix=/usr/local/netcdf-4.1.2 --enable-netcdf-4 --enable-f90  --with

Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-25T02:46:16

Hi.
Here's how my netcdf was built:

NeptuneStonesteps.local:~/bin>more makeNetCDF_OSX_64bit.bash
#!/bin/bash
make distclean
#
#./configure >configure.log 2>&1 \
#       CC="gcc -m64" \
#       CFLAGS="-g -O2" \
#       CXX="g++ -m64" \
#       CXXFLAGS="-g -O2" \
#       CPPFLAGS="-DNDEBUG -DgFortran" \
#       FC="gfortran -m64" \
#       FCFLAGS="-g -O2"

export CFLAGS=-m64
export FFLAGS=-m64
export FCFLAGS=-m64
export CXXFLAGS=-m64
export CPPFLAGS=-DgFortran

#export CC=/usr/bin/cc 
export F77=gfortran
export FC=gfortran
#export FCFLAGS=-qsuffix=cpp=f90
#
./configure --prefix=/usr/local/netcdf-4.1.2 --enable-netcdf-4 --enable-f90  --with-hdf5=/usr/local/hdf5-1.8.6

**************** Here is what nc-config reports ****************************************

NeptuneStonesteps.local:/usr/local/netcdf-4.1.2/bin>nc-config --all

This netCDF 4.1.2 has been built with the following features: 

  --cc        -> cc
  --cflags    ->  -I/usr/local/netcdf-4.1.2/include  -I/usr/local/hdf5-1.8.6/include 
  --libs      ->

Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

J. Luis — 2012-05-25T02:42:50

Just google it. It's for those who "prefer not to use fink or macports"



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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-25T02:37:38

Hi J.
Don't know what you refer to as 'Homebrew'.  
Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

On May 24, 2012, at 2:18 PM, J. Luis wrote:

On 24-05-2012 22:50, Florian Wobbe wrote:

Or Homebrew. It works fine with the brew formula and the libs will land at /usr/local/lib as you (John) already have them.

Joaquim

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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-25T02:36:15

Hi.

Thanks for the explanation.  I'll check on my netcdf build and make sure it is netcdf4 with HDF5 first.  I prefer not to use fink or macports.

Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

On May 24, 2012, at 11:50 AM, Florian Wobbe wrote:


-101 indicates a HDF5 error. Could you try again with netcdf from fink or macports?
Florian

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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

J. Luis — 2012-05-25T00:18:35

Or Homebrew. It works fine with the brew formula and the libs will land 
at /usr/local/lib as you (John) already have them.

Joaquim

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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

Florian Wobbe — 2012-05-24T21:50:35

-101 indicates a HDF5 error. Could you try again with netcdf from fink or macports?
Florian

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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

Paul Wessel — 2012-05-25T00:00:53

Odd.  Until Florian/Remko pipes in, are you using netcdf4 with HDF5 support?  It seems the nc_open command fails immediately.  The error (-101) is Error at HDF5 layer. 

Paul Wessel, Professor
Dept. of Geology & Geophysics
SOEST, University of Hawaii at Manoa
1680 East-West Rd, Honolulu, HI 96822 USA
1-808-956-4778(phone)/5154(fax)

On May 24, 2012, at 1:01 PM, John Helly wrote:



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Re: gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-24T23:01:37

I figured out how to get the shoreline files copied to the ./share/coast directory but they still cannot be opened for some reason.

*********************
+ grdinfo /Volumes/Geospatial001/IcebergIII/data/level1/PALSAR/ALPSRS166885900-W1.5/ALPSRS166885900-W1.5_UA.GC.grd
gshhg_version: cannot open file "/Users/hellyj/src/GMTdev/gmt5/build/gmt5/share/coast/binned_river_c.nc" (-101).
gshhg_version: cannot open file "/usr/local/gmt/share/coast/binned_river_c.nc" (-101).
grdinfo, GMT_begin, <unknown>: GSHHG version 2.2.0 or newer is needed to use coastlines with GMT.
Get and install GSHHG from ftp://ftp.soest.hawaii.edu/pwessel/gshhs/.
gshhg_version: cannot open file "/usr/local/gmt/share/coast/binned_GSHHS_l.nc" (-101).
gshhg_version: cannot open file "/usr/local/gmt/share/coast/binned_GSHHS_l.nc" (-101).
gshhg_version: cannot open file "/usr/local/gmt/share/coast/binned_river_l.nc" (-101).
gshhg_version: cannot open file "/usr/local/gmt/share/coast/binned_GSHHS_i.nc" (-101).
gshhg_version: cannot open file "/us

gmt5: cmake found GSHHG and built but execution of GMT script fails to find shorelines

John Helly — 2012-05-24T21:41:52

Hi.
Clearly found and build gmt5 with shorelines but (see below).  Also, don't understand why gmtset should throw this error.
J.

***************** tail of output from Cmake ********************************
*  Options:
*  Found GSHHG database : /Users/hellyj/src/GMTdev/gshhg-gmt-nc4-2.2.1 (2.2.1)
*  NetCDF library       : /usr/local/netcdf-4.1.2/lib/libnetcdf.dylib
*  NetCDF include dir   : /usr/local/netcdf-4.1.2/include
*  GDAL library         : /usr/local/lib/libgdal.dylib
*  GDAL include dir     : /Library/Frameworks/GDAL.framework/Versions/1.9/Headers
*  Regex support        : PCRE (/usr/local/pcre-8.12/lib/libpcre.dylib)
*  File locking         : off
*  Compatibility mode   : yes
*  Build Matlab API     : no
*  License restriction  : no
*  Triangulation method : Shewchuk
*
*  Locations:
*  Installing GMT in    : /Users/hellyj/src/GMTdev/gmt5/build/gmt5
*  GMT_SHARE_PATH       : /Users/hellyj/src/GMTdev/gmt5/build/gmt5/share
*  GMT_DOC_PATH         : /Users/hellyj/src/GMTdev/gmt5/build/gmt5/share/doc
*

Re: Problem installing of gmt5.0 using cmake

Paul Wessel — 2012-05-24T21:17:12

Sorry, ftp://ftp/soest/hawaii.edu/pwessel/gshhs/gshhg-gmt-nc4-2.2.1.tar.gz
It is a draft which will change before release.

Paul Wessel, Professor
Dept. of Geology & Geophysics
SOEST, University of Hawaii at Manoa
1680 East-West Rd, Honolulu, HI 96822 USA
1-808-956-4778(phone)/5154(fax)

On May 24, 2012, at 11:12 AM, John Helly wrote:



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Re: Problem installing of gmt5.0 using cmake

John Helly — 2012-05-24T21:12:00

Great. Worked fine.  I was following the README instead of the README.Cmake.  Amazingly fast build.

However, I cannot locate gshhg-gmt-nc4-2.2.1.tar.bz2 anywhere.  Is it really out there?

Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / stonesteps (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj

On May 24, 2012, at 10:51 AM, Paul Wessel wrote:

John, just STRICTLY follow the README.Cmake and you should be OK.  I.e., you need to be IN the build dir and issue the correct cmake command first.

-p

Paul Wessel, Professor
Dept. of Geology & Geophysics
SOEST, University of Hawaii at Manoa
1680 East-West Rd, Honolulu, HI 96822 USA
1-808-956-4778(phone)/5154(fax)

On May 24, 2012, at 10:24 AM, John Helly wrote:


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Re: Problem installing of gmt5.0 using cmake

Florian Wobbe — 2012-05-24T20:57:08

Hi,


this looks ok but below you are running cmake from ~/GMTdev/gmt5/src/cmake instead with the wrong target dir.


Assuming you have netcdf installed via fink or macports [1], nc-config should be in the PATH and hence the configuration of NETCDF_ROOT not necessary.

[1] http://gmtrac.soest.hawaii.edu/projects/gmt/wiki/BuildingGMT#MacOSX

I believe this is your mistake:


Should be:

cd ~/src/GMTdev/gmt5/build
cmake ..

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