[aspect-devel] Problem compiling Aspect on Tacc-Stampede2
FELIPE ORELLANA ROVIROSA
f_orellana at berkeley.edu
Sun May 13 23:46:29 PDT 2018
Hi John,
Thanks for all this help.
I am proceeding. Following your directions, I am building p4est,
trilinos, dealii,..
This is what I did when I installed aspect on Stampede1: to build
everything on my account, as a standalone set of softwares.
However, this is not what I was trying to do here: I was trying to use
the modules already built on Stampede2 (following the suggestions of the
TACC tech guys), as all this software is already installed on the cluster.
But right at the beginning I foresaw that using them, just by linking,
could be harder than installing them from scratch on the account.
whatever, I am progressing.
i will keep you updated.
thanks,
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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