[Trilinos-Users] [EXTERNAL] Re: decomp tool Error

[Sai P Uppati]

Hi Greg,

An example mesh I'm trying to decompose contains 178320 elements, 189405
nodes and 1 block. I tried decomposing for 4, 6 and 8 processors. I haven't
had problems with previous Trilinos versions I was using before. I think it
was only since I rebased to the official version hosted on the GitHub page.

Anyways, getopt I was able to fix with John Foster's help. I just installed
a gnu-getopt version from Homebrew and modified the PATH variable to look
for it first before looking in /usr/bin.

Coming to Netcdf, I followed the instructions exactly as they stated in the
following page: https://peridigm.sandia.gov/content/netcdf. So, I disabled
netcdf-4 and dap, and installed it using the changed numbers in netcdf.h
file as well. All the tests passed when I did 'make check'. So I didn't
think there were any issues with the netcdf installation. Doing it this
way, however, there was no referencing the HDF5 build I did in the previous
step. Even the in summary of netcdf configuation, the HDF5 support seems to
off. I left HDF5 installed though because I saw that it maybe needed for
the SEACAS package in Trilinos.

But as I mentioned before, I didn't have issues like this with previous
Trilinos versions (I also didn't follow the netcdf instructions given at
the webpage before, I just installed whatever was default from unidata).
Perhaps, the instructions on the page are not completely correct?

Sorry for the long email, but those are all the details.

Sai

On Thu, Feb 18, 2016 at 7:38 AM, Sjaardema, Gregory D <gdsjaar at sandia.gov>
wrote:

> What size mesh are you decomposing (#elem, #block, #node) and how many
> processors are you decompsing it for?
>
> Did you also install hdf5 and reference it in the netcdf build for
> netcdf-4 support, or is it a netcdf build only?
>
> The current getopt that you have will work, but will give reduced
> functionality in regards to long options which you can see by entering -H
> and -h and seeing the difference.  I’m not sure if installing the
> gnu-getopt in parallel with the system getopt would cause issues or not,
> but on my and many other macs we have both installed and have not noticed
> any issues (However, I use port instead of brew).
>
> ..Greg
> --
> "A supercomputer is a device for turning compute-bound problems into
> I/O-bound problems”
>
> From: Trilinos-Users <trilinos-users-bounces at trilinos.org> on behalf of
> "John T. Foster" <jfoster at austin.utexas.edu>
> Date: Wednesday, February 17, 2016 at 6:00 PM
> To: Sai P Uppati <uppatis at utexas.edu>
> Cc: "trilinos-users at trilinos.org" <trilinos-users at trilinos.org>
> Subject: [EXTERNAL] Re: [Trilinos-Users] decomp tool Error
>
> 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
>

ᐧ
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