[aspect-devel] Problem compiling Aspect on Tacc-Stampede2
FELIPE ORELLANA ROVIROSA
f_orellana at berkeley.edu
Mon May 14 00:32:59 PDT 2018
Hi John,
Here I am. I got stuck on Trilinos installation.
I downloaded the package, wget..
I changed the lines in
trilinos-12.10.1-Source/packages/epetra/src/Epetra_LAPACK_wrappers.h
then I created the build directory (as it is customary)
cd trilinos-12.10.1-Source/;
mkdir build;
cd build
then I copied the long list of commands, it failed, I guess trivially
cause I had not modified the directory path line (second to last executing
instruction), so
from
-DCMAKE_INSTALL_PREFIX:PATH="${WORK}"/software/trilinos/trilinos-12.10.1/install
\
I modified accordingly to:
-DCMAKE_INSTALL_PREFIX:PATH=/home1/04020/unfelipe/trilinos/trilinos-12.10.1/install
\
../
(just a note: I did not create the software directory, as these packages
are the only thing I have on my account, I hope this is not a problem as I
am not using any instruction containing the word software)
it didnt work, so I guessed the trilinos 12.10.1 was missing the full name
of the directory, so I appended the word 'Source'
-DCMAKE_INSTALL_PREFIX:PATH=/home1/04020/unfelipe/trilinos/trilinos-12.10.1-Source/install
\
../
it kept crashing with the message:
-bash:
-DCMAKE_INSTALL_PREFIX:PATH=/home1/04020/unfelipe/trilinos/trilinos-12.10.1-Source/install:
No such file or directory
It does not find the directory.
So, I created the 'install' directory: I did mkdir install
I run it again, from the build directory,
it crashes in the same way, it can't find such directory
-bash:
-DCMAKE_INSTALL_PREFIX:PATH=/home1/04020/unfelipe/trilinos/trilinos-12.10.1-Source/install:
No such file or directory
even though such directory actually exists !
dunno what to do :(
cheers,
Felipe
On Sat, May 12, 2018 at 4:53 PM, John Naliboff <jbnaliboff at ucdavis.edu>
wrote:
> 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> 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>
> 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> 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>
>> 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), and
>>> once everyone is happy I'll add the instructions to the 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
>>>
>>> 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>
>>> 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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>>>> Aspect-devel at geodynamics.org
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>>>
>>>
>>>
>>>
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