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

[Sai P Uppati]

Andrew,

There is no change in the error it throws. Still uses a 32-bit integer mode
for decomposition.

Sai
ᐧ

On Thu, Feb 18, 2016 at 5:28 PM, Bradley, Andrew Michael <ambradl at sandia.gov
> wrote:

> Hi Sai,
>
>
> Just a guess, but what happens if you add the command-line flag -64 ?
>
>
> Andrew
>
>
> ------------------------------
> *From:* Trilinos-Users <trilinos-users-bounces at trilinos.org> on behalf of
> Sai P Uppati <uppatis at utexas.edu>
> *Sent:* Thursday, February 18, 2016 4:23 PM
> *To:* Sjaardema, Gregory D
> *Cc:* trilinos-users at trilinos.org
> *Subject:* Re: [Trilinos-Users] [EXTERNAL] Re: decomp tool Error
>
> UPDATE:
>
> I think all other tools may be working fine from my trilinos build. The
> tools I commonly use from trilinos include decomp, epu, exodiff and epu.
> All except decomp seem to working fine.
>
> Even after rebuilding trilinos several times (varying some options each
> time) and Peridigm passing all the tests each time, decomp throws errors
> like these:
>
> Executing:
>    /usr/local/trilinos/bin/nem_slice -e -S  -l inertial -c -o
> HEGF-res-cylin.g.nem -m mesh=4 HEGF-res-cylin.g
>    ...see HEGF-res-cylin.g.decomp.out for nem_slice status
>
> Beginning nem_slice execution.
> Input Mesh File = 'HEGF-res-cylin.g'
> Using 32-bit integer mode for decomposition...
> Exodus Library Warning/Error: [ex_put_cmap_params_cc]
> Error: failed to add dimension for "ncnt_cmap" of size 6313656973 in file
> ID 65536
> NetCDF: Invalid dimension size
> ================================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:******************************************************************
>
> Sai
> ᐧ
>
> On Thu, Feb 18, 2016 at 11:03 AM, Sai P Uppati <uppatis at utexas.edu> wrote:
>
>> 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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