Hi Jean-Paul,
Thanks very much again. '-j 2' worked! And deal.ii 9.2 was successfully
installed. It just has remained hopefully a minor issue; as when I test my
installation against step-18 I receive the following message showing cmake
is looking a wrong place for configurations:
Error! This tutorial requires a deal.II library that was configured with
the following options:
DEAL_II_WITH_MPI = ON
DEAL_II_WITH_PETSC = ON
DEAL_II_PETSC_WITH_COMPLEX = OFF
However, the deal.II library found at /usr/local was configured with these
options
DEAL_II_WITH_MPI = OFF
DEAL_II_WITH_PETSC = OFF
DEAL_II_PETSC_WITH_COMPLEX =
This is while I use the
'cmake -DDEAL_II_DIR=/path/to/the/source .'
command to address the right configurations. Also when I check the cmake
configurations in installed folder they look OK and with correct
configurations.
Could you please advise me on this issue as well?
Thank you,
Behrooz
On Thursday, January 14, 2021 at 7:52:38 PM UTC+1 Jean-Paul Pelteret wrote:
> Hi Behrooz,
>
> It looks like you're getting some internal compiler errors:
>
> g++: internal compiler error: Killed (program cc1plus)
> Please submit a full bug report,
> with preprocessed source if appropriate.
> See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
> source/dofs/CMakeFiles/obj_dofs_debug.dir/build.make:169: recipe for
> target 'source/dofs/CMakeFiles/obj_dofs_debug.dir/dof_handler_policy.cc.o'
> failed
> make[2]: ***
> [source/dofs/CMakeFiles/obj_dofs_debug.dir/dof_handler_policy.cc.o] Error 4
> make[2]: *** Waiting for unfinished jobs....
>
> This could indicate that you're still running out of memory. I would
> suggest compiling with '-j 2' or even '-j 1', just to be sure.
>
> Let us know if you still have troubles after trying that. You're using GCC
> 7.3.0, which as far as I know shouldn't have any troubles building the
> library.
>
> Best,
> Jean-Paul
>
>
> On 14.01.21 10:45, Behrooz Karami wrote:
>
> Hi Jean-Paul,
>
> Please kindly find the 'spack-build.out' file as attached. This is what
> Spack mentioned as a build log for details. Hope to be the correct one.
>
> Thank you very much,
> Behrooz
>
> On Wed, Jan 13, 2021 at 8:14 PM Jean-Paul Pelteret <[email protected]>
> wrote:
>
>> Hi Behrooz,
>>
>> Great, I'm glad that you're at least one step closer to getting deal.II
>> installed. Unfortunately, the information that you've provided about the
>> build error is not enough to diagnose what the problem is. Can you attach
>> the build log so that we can take a look at them? When the build is not
>> successful, Spack normally tells you where the log files are located
>> (they're in a "staging" directory where deal.II gets built, so its some
>> temporary that Spack sets up and is specific to your system so I can't tell
>> you precisely where they'd be). For further reference, search for "build
>> log" on this page
>>
>> https://spack-tutorial.readthedocs.io/en/latest/tutorial_packaging.html#creating-the-package-file
>> to see what I mean -- they give an example of some output of a package
>> that has not built successfully.
>>
>> Best,
>> Jean-Paul
>>
>> On 13.01.21 11:50, Behrooz Karami wrote:
>>
>> Dear Jean-Paul,
>>
>> Thanks very much for your explanations. It helped me a lot to better
>> understanding of Spack environment and its functionality. You were also
>> right, my Spack version is a bit old.
>> Anyway, after some further manipulations I was a able to configure
>> Trilions.
>>
>> However thereafter, and when it comes to deal.ii installation I receive
>> the following error message:
>> Error: ProcessError: Command exited with status 2:
>> 'make' '-j8'
>>
>> Since the machine on which I am trying to install deal.ii is old and I
>> have already been facing memory limitations, I thought it might be a again
>> memory related issue. Thereby I reduced the number of jobs to 4 but it did
>> not help this time and conditions exist with the same message.
>> So I was wondering if there might still be any way around?
>>
>> Thank you very much,
>> Behrooz
>>
>>
>>
>> On Friday, January 8, 2021 at 7:22:45 PM UTC+1 Jean-Paul Pelteret wrote:
>>
>>> Dear Behrooz,
>>>
>>> The problem here is that your Trilinos installation includes the
>>> SEACASChaco package. We'd discovered that there's a common global symbol
>>> that both ADOL-C and Trilinos-SEACASChaco emit, which causes some very
>>> strange issues when using ADOL-C. Naturally, we had to make sure that
>>> nobody runs into these troubles, because the symptoms of the issue are not
>>> indicative of the underlying problem and are incredibly difficult to debug.
>>> So although deal.II is picking up the ADOL-C library, deal.II also detects
>>> that Trilinos has the SEACASChaco module enabled and therefore is doing the
>>> safe thing by having the configuration process fail with an error.
>>>
>>> I'm betting that you have a slightly old version of Spack, because we
>>> have some conflicts in place to prevent this "illegal" combination of
>>> packages / package variants from being installed. You can see these
>>> restrictions here:
>>>
>>> https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/dealii/package.py#L273-L284
>>> The way to fix the problem is by recompiling Trilinos without this
>>> package (variant, in Spack parlance) enabled. You can do this in the
>>> following way:
>>> spack install [email protected]+adol-c+trilinos ^trilinos~chaco
>>>
>>> You'll note that it's also not possible to enable both ADOL-C and
>>> Netcdf, for the same reason, so you actually want to be even more
>>> restrictive:
>>> spack install [email protected]+adol-c+trilinos~netcdf
>>> ^trilinos~chaco~exodus~netcdf~pnetcdf
>>>
>>> I hope that this helps you getting deal.II installed through Spack.
>>>
>>> Best,
>>> Jean-Paul
>>>
>>>
>>>
>>> On 08.01.21 08:22, Behrooz Karami wrote:
>>>
>>> Dear Everyone,
>>>
>>> During installation of deal.ii 9.2 through SPACK I receive the following
>>> error on ADOL-C:
>>> 1 error found in build log:
>>> 549 -- Could not find a sufficient ADOL-C installation: Possible
>>> symbol
>>> clash between the ADOL-C library and Trilinos' SEACASChaco
>>> detecte
>>> d
>>> 550 -- Performing Test ADOLC_DOUBLE_CAST_CHECK
>>> 551 -- Performing Test ADOLC_DOUBLE_CAST_CHECK - Success
>>> 552 -- Performing Test ADOLC_ADOUBLE_OSTREAM_CHECK
>>> 553 -- Performing Test ADOLC_ADOUBLE_OSTREAM_CHECK - Success
>>> 554 -- DEAL_II_WITH_ADOLC has unmet external dependencies.
>>> >> 555 CMake Error at
>>> cmake/macros/macro_configure_feature.cmake:112 (MESS
>>> AGE):
>>>
>>> This is while 3 versions of ADOL-C are installed (separately and through
>>> SPACK as well) and even deal.ii is detecting one of them as:
>>> ==> adol-c is already installed in
>>> /home/behrooz/Spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/adol-c-develop-omjty56hedqyctgkyppbd5cgszby3fmv
>>>
>>> Any idea on what I should do about that?
>>> Thanks very much,
>>> Behrooz
>>>
>>>
>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see
>>> https://groups.google.com/d/forum/dealii?hl=en
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>>>
>>> <https://groups.google.com/d/msgid/dealii/CAPPKNqY0h0ZBUQ_D8tzPOuP_mz7L%3DwaPFUD%2B0dmHgqtCQMwmJA%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>>>
>>> --
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>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>>
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>>
>>
>> --
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>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>> .
>>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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>
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> .
>
>
>
--
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