[ncl-talk] problem with ESFM mapping

Fri Jul 27 06:53:30 MDT 2018

Hi Kevin,

an important update.

I uninstalled Homebrew ncl and used conda to reinstall it.

Now it all works fine! So it was completely my fault - not installing ncl with one of suggestions in ncl webpage.

Maybe it’s good that other people are aware of this bug (?) when installing ncl with Homebrew..

thanks,
M

******************************************************************
Michele Petrini, PhD

Department of Geoscience and Remote Sensing, TUDelft
Delft, The Netherlands

M.Petrini at tudelft.nl<mailto:M.Petrini at tudelft.nl>
+39 3398367372
michele.petrins (Skype alias)

On 27 Jul 2018, at 14:26, Michele Petrini - CITG <M.Petrini at tudelft.nl<mailto:M.Petrini at tudelft.nl>> wrote:

Hi Kevin,

yes, it looks exactly like you say - but I checked previously, and everything seems to be at the right place.

Here are outputs that you asked

laptop-petrini:~ michele$ echo $PATH
/usr/local/opt/texinfo/bin:/usr/local/Cellar/gcc at 7/7.3.0/bin:/usr/local/ncl-6.5.0/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin
laptop-petrini:~ michele$ which ncl
/usr/local/ncl-6.5.0/bin/ncl
laptop-petrini:~ michele$ ls -l "$(dirname "$(which ncl)")/ESMF_RegridWeightGen"
-rwxr-xr-x  1 michele  admin  26373304 Jul 16 15:37 /usr/local/ncl-6.5.0/bin/ESMF_RegridWeightGen
laptop-petrini:~ michele$ find / -name ESMF_RegridWeightGen 2>/dev/null
/usr/local/ncl-6.5.0/bin/ESMF_RegridWeightGen

About ncl, I installed 6.5.0 version with Homebrew

==> Purging files for version 6.5.0 of Cask ncar-ncl
==> Installing Cask ncar-ncl
==> Moving Generic Artifact 'include' to '/usr/local/ncl-6.5.0/include'.
==> Moving Generic Artifact 'bin' to '/usr/local/ncl-6.5.0/bin'.
==> Moving Generic Artifact 'lib' to '/usr/local/ncl-6.5.0/lib'.
🍺  ncar-ncl was successfully installed!

and I confirm that it works normally for other scripts not including ESFM mapping..

thanks,
Michele

******************************************************************
Michele Petrini, PhD

Department of Geoscience and Remote Sensing, TUDelft
Delft, The Netherlands

M.Petrini at tudelft.nl<mailto:M.Petrini at tudelft.nl>
+39 3398367372
michele.petrins (Skype alias)

On 26 Jul 2018, at 23:53, Kevin Hallock <hallock at ucar.edu<mailto:hallock at ucar.edu>> wrote:

Hi Michele,

It looks like either ESMF_RegridWeightGen is not installed on your machine, or the directory containing it is not in your PATH environment variable.

Out of curiosity, which method of installing NCL did you use? ESMF_RegridWeightGen should be included by default with both of our two preferred installation methods (binary<https://www.ncl.ucar.edu/Download/install_from_binary.shtml> and conda<https://www.ncl.ucar.edu/Download/conda.shtml>).

Also, could you please try running the following commands in your shell (not in NCL) and reply with the output:

echo $PATH
which ncl
ls -l "$(dirname "$(which ncl)")/ESMF_RegridWeightGen"
find / -name ESMF_RegridWeightGen 2>/dev/null

Regarding the “libgfortran” error, this is a known issue and we have a note in our documentation<https://www.ncl.ucar.edu/Download/macosx.shtml#InstallCompilers> recommending the use of GNU 7.x with NCL 6.5.0 on Mac OS. Based on your email, it seems like NCL itself (just not the ESMF regridding) is at least running now that you’ve upgraded from gcc-6 to gcc-7?

Thanks,
Kevin

On Jul 26, 2018, at 8:00 AM, Michele Petrini - CITG <M.Petrini at tudelft.nl<mailto:M.Petrini at tudelft.nl>> wrote:

Dear Dennis,
thanks for the reply.

A fist immediate difference I saw was the output of gcc —version. By combining alias and export path, I managed to obtain

laptop-petrini:ESFM_regrid michele$ gcc --version
gcc-7 (Homebrew GCC 7.3.0) 7.3.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

laptop-petrini:ESFM_regrid michele$ uname -a
Darwin laptop-petrini.grs.vrlab.tudelft.nl<http://laptop-petrini.grs.vrlab.tudelft.nl/> 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

But I still get the same error - I really don’t understand why.

Right now, the only differences between my output and your output is the Kernel version (I have 17.5, you have 17.7) and the gcc version (I have 7.3.0, you have 6.2.0).

Please note that I installed gcc-7 because with ncl 6.5.0 I was getting an error re the fortran library libgfortran.4.dylib, which is not included in gcc-6 - that’s another difference.

any thoughts on that?

thanks,
Michele

******************************************************************
Michele Petrini, PhD

Department of Geoscience and Remote Sensing, TUDelft
Delft, The Netherlands

M.Petrini at tudelft.nl<mailto:M.Petrini at tudelft.nl>
+39 3398367372
michele.petrins (Skype alias)

On 26 Jul 2018, at 03:19, Dennis Shea <shea at ucar.edu<mailto:shea at ucar.edu>> wrote:

Hi Michele,

I just ran the example on my MAC with no problems using 6.5.0 and had no problem.

THX for including the output from your mchine (appended at the end of this email.)
Perhaps there is a setup issue. Unfortunately, I am not knowledgeable enough about
these types of thing. Hopefully, someone will chime in.

%> ncl ESMF_regrid_1.ncl

-rw-r--r--  1 shea  2200     6840 Jul 25 20:56 ESMF_regrid_1.ncl<http://www.ncl.ucar.edu/Applications/Scripts/ESMF_regrid_1.ncl>
-rw-r--r--  1 shea  2200    50104 Jul 25 20:58 sst.nc<http://sst.nc/>
-rw-r--r--  1 shea  2200   973768 Jul 25 21:00 source_grid_file.nc<http://source_grid_file.nc/>
-rw-r--r--  1 shea  2200   151908 Jul 25 21:00 destination_grid_file.nc<http://destination_grid_file.nc/>
-rw-r--r--  1 shea  2200      231 Jul 25 21:00 PET0.RegridWeightGen.Log
-rw-r--r--  1 shea  2200  1644652 Jul 25 21:00 NCEP_2_Rect.nc
-rw-r--r--  1 shea  2200     9424 Jul 25 21:00 sst_regrid.nc<http://sst_regrid.nc/>
-rw-r--r--  1 shea  2200   215451 Jul 25 21:00 ESMF_regrid.png

I am attaching to output from

%> ncdump -h sst.nc<http://sst.nc/>  >! out.ncdump_sst.txt

and the ESMF_regrid..png   file

Your MAC:

laptop-petrini:Downloads michele$ uname -a
Darwin Micheles-MacBook-Pro.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.10.25.5)
Target: x86_64-apple-darwin17.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

My MAC:

%> uname -a
Darwin sherkin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

%> gcc --version
gcc (GCC) 6.2.0

On Wed, Jul 25, 2018 at 7:45 AM, Michele Petrini - CITG <M.Petrini at tudelft.nl<mailto:M.Petrini at tudelft.nl>> wrote:
Dear ncl helpdesk,

I am trying to remap ocean data from a global rectlinear grid to the CISM Greenland grid using ncl.

As a fist step, I am trying to run ESMF_regrid_1.ncl<https://www.ncl.ucar.edu/Applications/Scripts/ESMF_regrid_1.ncl> from https://www.ncl.ucar.edu/Applications/ESMF.shtml.

I get the following error

sh: line 1: 33907 Abort trap: 6           ESMF_RegridWeightGen --help > /dev/null 2>&1
(0) ESMF_regrid_gen_weights: could not find ESMF_RegridWeightGen executable.

and I don’t understand why.

I am trying to run the script using ncl version 6.5.0 (installed gcc-8) - but I had same problem with older ncl version (for which I had to load di ESFM_regrid module).

What I am doing wrong?

thanks,
M

******************************************************************
Michele Petrini, PhD

Department of Geoscience and Remote Sensing, TUDelft
Delft, The Netherlands

M.Petrini at tudelft.nl<mailto:M.Petrini at tudelft.nl>
+39 3398367372
michele.petrins (Skype alias)

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<out.ncdump_sst.txt><ESMF_regrid.png>

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