[Trilinos-Users] decomp tool Error

[Sai P Uppati]

Hi,

I installed Trilinos and Peridigm (official versions hosted on GitHub) on
my Mac OS X 10.11.3, including the dependencies boost, hdf5 and netcdf. I
followed the instructions on Sandia's Peridigm installation guide to the
dot.

The Peridigm unit tests all passed, which is good. However, when I try to
use the decomp tool from Trilinos, I get the following errors:


########################################################################
The "getopt" executable that is available on this system is an older
version that is not compatible with the needs of the "decomp" tool.
If possible, you should update your getopt to a newer version and make
sure that the new getopt is in your path.

Below are some options for getting the current getopt version:
* If on a Mac: "sudo port install getopt"
* Search the internet for "getopt-1.1.5" or "getopt-1.1.4"; download and
build

Enter "-h" for the modified options that this version supports.
Enter "-H" for the options that the standard version supports.
########################################################################



Executing:
   /usr/local/trilinos/bin/nem_slice -e -S  -l inertial -c -o
prism-precrack.g.nem -m mesh=8 prism-precrack.g
   ...see prism-precrack.g.decomp.out for nem_slice status

Beginning nem_slice execution.
Input Mesh File = 'prism-precrack.g'
Using 32-bit integer mode for decomposition...
Exodus Library Warning/Error: [ex_put_cmap_params_cc]
Error: unable to output variable in file ID 65536
NetCDF: Index exceeds dimension bound
================================messages================================
fatal: unable to output communication map parameters
fatal: could not output Nemesis file

ERROR:******************************************************************
ERROR:
ERROR     During nem_slice execution. Check error output above and rerun
ERROR:
ERROR:******************************************************************


There are multiple errors here.

1) I don't know how to update the getopt executable. It seems Mac OS X
already comes with a built in version (which I checked and found to be in
/usr/bin), but this version in not compatible with decomp. I checked
Homebrew, and there is a key only option to install gnu-getopt, but they
have a warning that installing different versions in parallel can cause
trouble. I'm not able to find any other working way to install get opt with
out causing errors.

2) NetCDF error about exceeding dimensions. I installed the latest version
of netcdf-c, 4.4.0. I changed the numbers in netcdf.h as instructed in the
Peridigm installation guide. I have a feeling that this may have something
to do with the error, but I'm not quite sure. All tests passed, however,
when I installed netcdf from source.

There may be other errors I'm not seeing. Please, I would appreciate if I
can get some guidance on how to address these errors.

Sai
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