[aspect-devel] Problem compiling Aspect on Tacc-Stampede2

John Naliboff jbnaliboff at ucdavis.edu
Sat May 12 16:53:53 PDT 2018


Hello again,

I just saw that some of the formatting (tabs) in the instructions were mis-aligned. Nothing incorrect, but the attached copy should have everything neatly aligned.

Cheers,
John


> On May 12, 2018, at 4:51 PM, John Naliboff <jbnaliboff at ucdavis.edu> wrote:
> 
> Hi Felipe,
> 
> I went back and reinstalled everything from scratch on STAMPEDE2 for deal.II 8.5.1 and ASPECT version 2.0 
> 
> The attached instructions are designed to be nearly copy and paste and unless I copied something incorrectly, there should be no issues arising when you compile any of the packages.
> 
> Before installing, please have a look through and let me know if you have any questions.
> 
> Also, I’ve attached an example Stampede2 submission script and parameter file that you can try running. The model should take ~ 30 seconds (30.2 s be exact).
> 
> If the installation works for you, I’ll add the instructions to the Wiki. Thanks for being a tester ;)
> 
> Cheers,
> John
> 
> <ASPECT_STAMPEDE2_INSTALLATION_JBN_2018-05-12>
> <sses_192_3_1.prm>
> <run.sh>
> 
> 
> 
> 
>> On May 12, 2018, at 12:00 AM, FELIPE ORELLANA ROVIROSA <f_orellana at berkeley.edu <mailto:f_orellana at berkeley.edu>> wrote:
>> 
>> 
>>  Hi John Naliboff,
>> 
>>       Have you had the time to work on the Aspect build on Stampede2?
>> 
>>       If we ask the TACC administrators to install dealii as a special module for Aspect, shouldn't we ask for two versions, 8.5.1 and 9.0 ? If that's not a problem, or too much to ask.
>> 
>> cheers,
>> Felipe 
>> 
>> On Thu, May 10, 2018 at 12:02 PM, John Naliboff <jbnaliboff at ucdavis.edu <mailto:jbnaliboff at ucdavis.edu>> wrote:
>> Hi Felipe,
>> 
>>>    I guess it would be healthy to ask the TACC guys to build a dealii 8.5.1? for Aspect.
>> 
>> Yep, I think that is the best path forward. I’m currently working on a new build on a Stampede2 that uses very general instructions. Please ping me if you have not heard back by tomorrow afternoon.
>> 
>> Cheers,
>> John
>> 
>> 
>> 
>>> On May 10, 2018, at 11:32 AM, FELIPE ORELLANA ROVIROSA <f_orellana at berkeley.edu <mailto:f_orellana at berkeley.edu>> wrote:
>>> 
>>> 
>>>  Hello John,
>>> 
>>>          I have been trying to proceed with ASPECT installation on Stampede2. Unfortunately I have not succeeded.
>>> 
>>>         I have loaded all the modules on the list you suggested.
>>> 
>>>         There are a number of ways in which the compilation fails. I guess these are due to different ways to write the instructions you suggest (one single character change causes changes). The last error message I got is this:
>>> 
>>>     c506-011[skx](427)$ cmake \
>>> > >        -DDEAL_II_DIR=/work/01038/jboff/stampede2/software/gcc-7.1.0/dealii/v8.5.1/install/lib/cmake \
>>> > -DCMAKE_INSTALL_PREFIX=/home1/04020/unfelipe/aspect-1.5/ \
>>> > -DCMAKE_BUILD_TYPE=Release
>>> -bash: -DDEAL_II_DIR=/work/01038/jboff/stampede2/software/gcc-7.1.0/dealii/v8.5.1/install/lib/cmake: No such file or directory
>>> 
>>>   so, seemingly, it is not connecting properly.
>>> 
>>>    I have tried this installation, using slight modifications, more than 10 times.
>>> 
>>>    I installed different versions of ASPECT on Stampede1 long ago, using the 'aspect-setup-stampede.sh' script. It was definitely doable.
>>> 
>>>    I guess it would be healthy to ask the TACC guys to build a dealii 8.5.1? for Aspect.
>>> 
>>> cheers,
>>> Felipe
>>>   
>>> 
>>> 
>>> On Mon, May 7, 2018 at 3:01 PM, John Naliboff <jbnaliboff at ucdavis.edu <mailto:jbnaliboff at ucdavis.edu>> wrote:
>>> Hi Felipe,
>>> 
>>> I just installed ASPECT v1.5 with the one of the versions of deal.II (8.5.1) I built a while back. For now, perhaps try building ASPECT by linking to the version of deal.II on my account? Instructions to do this are at the bottom of the email. 
>>> 
>>> However, a number of things may change in the final Stampede2 installation instructions. For example, I get a number of warnings related to the version of BOOST (Stampede2 module). Linking to my version of deal.II may also not work (during installation or running a model) and please let me know if this is the case.
>>> 
>>> I'll have the instructions go through a round of review through an existing issue (https://github.com/geodynamics/aspect/issues/1838 <https://github.com/geodynamics/aspect/issues/1838>), and once everyone is happy I'll add the instructions to the ASPECT wiki: https://github.com/geodynamics/aspect/wiki <https://github.com/geodynamics/aspect/wiki>. From there, we can also have the TACC folks build a deal.II 8.5.1 module for ASPECT.
>>> 
>>> Cheers,
>>> John
>>> 
>>> ASPECT Installations Instructions for Stampede2 using pre-built deal.II 8.5.1 (***not guaranteed to work****)
>>> 1. Start idev session
>>>      idev -p skx-dev -N 1 -n 48 -m 60
>>> 
>>> 2. Make sure following modules are loaded
>>>      gcc/7.1.0 impi/17.0.3 mkl/17.0.4 python/2.7.13 boost/1.64 swig/3.0.12 cmake/3.8.2
>>>      phdf5/1.8.16 parallel-netcdf/4.3.3.1 <http://4.3.3.1/>
>>> 
>>> 3. Set cc and cxx compiler enivornment variables
>>>      export CC="${TACC_IMPI_BIN}"/mpicc; export CXX="${TACC_IMPI_BIN}"/mpicxx
>>> 
>>> 4. Configure (be sure to add in the correct path to your ASPECT installation folder)
>>>      cmake \
>>>        -DDEAL_II_DIR=/work/01038/jboff/stampede2/software/gcc-7.1.0/dealii/v8.5.1/install/lib/cmake \
>>>        -DCMAKE_INSTALL_PREFIX=""PATH_TO_YOUR_ASPECT_FOLDER" \
>>>        -DCMAKE_BUILD_TYPE=Release .
>>> 
>>> 5. Build
>>>      make -j32
>>> 
>>> 
>>> 
>>> On 05/03/2018 12:05 PM, FELIPE ORELLANA ROVIROSA wrote:
>>>> 
>>>>  Hi Timo and John,
>>>> 
>>>>      Thanks a loooooot for your support.
>>>> 
>>>>      I understand. There is a problem with dealii in Stampede2. 
>>>> 
>>>>      I installed dealii in my account on Stampede1 long ago, and it was kind of a big task for me.
>>>> 
>>>>      OK, I will wait for you John. In that way we will all be on the same track.
>>>> 
>>>> When you proceed, let me know if I can help with anything.
>>>> 
>>>> cheers,
>>>> thank you very much,
>>>> 
>>>> Felipe
>>>> 
>>>> 
>>>> 
>>>>      
>>>> 
>>>> On Thu, May 3, 2018 at 9:40 AM, John Naliboff <jbnaliboff at ucdavis.edu <mailto:jbnaliboff at ucdavis.edu>> wrote:
>>>> Hi all,
>>>> 
>>>> I'll coordinate with one of the TACC folks early next week and have a general deal.II module (8.5.1) built using gcc. I installed both the development and 8.5.0 on Stampede2 recently, so I'm not sure what the issue. I'll also put up general instructions for the installation on the ASPECT github page.
>>>> 
>>>> Felipe - As soon as I rebuild deal.II on my account, you can build ASPECT using that version until the general module is installed.
>>>> 
>>>> Cheers,
>>>> John
>>>> On 05/03/2018 09:34 AM, Timo Heister wrote:
>>>>>> login4.stampede2(364)$ find . -name trilinos_block*
>>>>>> ./include/deal.II/lac/trilinos_block_sparse_matrix.h
>>>>>> 
>>>>>> so, the file 'trilinos_block_vector.h' does not exists in this library
>>>>>> collection  :(
>>>>>> 
>>>>>> what should I do?
>>>>> This means the deal.II installation you are trying to use is broken.
>>>>> Your options:
>>>>> - install deal.II yourself
>>>>> - ask the admins to fix the installation
>>>>> - ask somebody else to install deal.II and use that installation (I am
>>>>> planning to do that at some point this summer)
>>>>> 
>>>>> 
>>>> 
>>>> 
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>>>> 
>>>> 
>>>> 
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