[aspect-devel] Problem compiling Aspect on Tacc-Stampede2
John Naliboff
jbnaliboff at ucdavis.edu
Sat May 12 16:51:00 PDT 2018
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
> On May 12, 2018, at 12:00 AM, FELIPE ORELLANA ROVIROSA <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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