[Trilinos-Users] decomp tool Error

[John T. Foster]

Sai,

I believe your using homebrew as a package manager so use:

brew install getopt

To install the getopt command line utility.

JTF

On Wednesday, February 17, 2016, Sai P Uppati <uppatis at utexas.edu> wrote:

> 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
>


-- 
Sent from iPhone
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