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] <mailto:[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
<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
<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
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