dealii v 9.2.0 installation difficulty (also posted on spack group)

[Andrew Li]

Dear all,

I hope this is the right place to post this question. I am trying to install an older version of dealii on a centos7 cluster using spack, and am running into issues. I have no problem installing dea...@9.4.2, but am unable to install dea...@9.2.0.

If I run without specifying boost cxxstd

spack install dea...@9.2.0 %g...@12.2.0

 I get an error

==> boost: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
    './b2' 'install' 'threading=multi' '-j' '4' '--user-config=/tmp/al5/spack-stage/spack-stage-boost-1.76.0-2ykrczt6n7igaz645shnq2pscuosk3al/spack-src/user-config.jam' 'variant=release' '--disable-icu' '-s' 'BZIP2_INCLUDE=/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-12.2.0/bzip2-1.0.8-lhu2fvk3ssx5w66tth4tp6kjorlgfj2u/include' '-s' 'BZIP2_LIBPATH=/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-12.2.0/bzip2-1.0.8-lhu2fvk3ssx5w66tth4tp6kjorlgfj2u/lib' '-s' 'ZLIB_INCLUDE=/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-12.2.0/zlib-1.2.13-qemlwst2qu3yyrmrlgdnomlmzbjsgs34/include' '-s' 'ZLIB_LIBPATH=/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-12.2.0/zlib-1.2.13-qemlwst2qu3yyrmrlgdnomlmzbjsgs34/lib' '-s' 'LZMA_INCLUDE=/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-12.2.0/xz-5.4.1-lux543af2a73htjercpienfpkmx64zez/include' '-s' 'LZMA_LIBPATH=/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-12.2.0/xz-5.4.1-lux543af2a73htjercpienfpkmx64zez/lib' '-s' 'ZSTD_INCLUDE=/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-12.2.0/zstd-1.5.5-gfcgznqbaijyvpybcdyqkpjhzc3zylg2/include' '-s' 'ZSTD_LIBPATH=/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-12.2.0/zstd-1.5.5-gfcgznqbaijyvpybcdyqkpjhzc3zylg2/lib' 'link=static,shared' '--layout=system' 'toolset=gcc' 'cxxstd=17' 'visibility=hidden'

If I run with either setting boost cxxstd=11 or 98

spack install dea...@9.2.0 ^bo...@1.76.0 cxxstd=11 %g...@12.2.0,

I get the error

1 out of 1 hunk FAILED -- saving rejects to file cmake/modules/FindGINKGO.cmake.rej
1 out of 1 hunk FAILED -- saving rejects to file cmake/modules/FindGINKGO.cmake.rej
==> Using cached archive: /home/al5/.spack/var/spack/cache/_source-cache/archive/d0/d05a82fb40f1f1e24407451814b5a6004e39366a44c81208b1ae9d65f3efa43a.tar.gz
==> Using cached archive: /home/al5/.spack/var/spack/cache/_source-cache/archive/90/90ae9ddefe77fffd297bba6b070ab68d07306d4ef525ee994e8c49cef68f76f3
==> Using cached archive: /home/al5/.spack/var/spack/cache/_source-cache/archive/c9/c9884ebb0fe379c539012a225d8bcdcfe288edec8dc9d319fbfd64d8fbafba8e
==> Applied patch https://github.com/dealii/dealii/commit/3b815e21c4bfd82c792ba80e4d90314c8bb9edc9.patch?full_index=1
==> Patch https://github.com/dealii/dealii/commit/df6c5de8d6785fce701c10575982858f3aeb4cbd.patch?full_index=1 failed.
==> Error: ProcessError: Command exited with status 1:
    '/usr/bin/patch' '-s' '-p' '1' '-i' '/tmp/al5/spack-stage/spack-stage-s5pzaunz/df6c5de8d6785fce701c10575982858f3aeb4cbd.patch?full_index=1' '-d' '.'

Can anyone advise me on what to do?

Thank you,
Andrew

[Bruno Turcksin]

Andrew,

What's the error message that you get when using `spack install dea...@9.2.0 %g...@12.2.0` ? spack writes the exact error in an output file. I don't think changing the C++ standard is the right fix, instead I would change the version of boost.

Best,

Bruno

[Andrew Li]

Hi Bruno, 

Thanks for your quick response! The error message I get when i run

[al5@coe ~]$ srun --mem-per-cpu=16G spack install dea...@9.2.0 %g...@12.2.0

is 

==> Installing dealii-9.2.0-27ysq7kvk7cdu7t2a6jjqmls4qd5fsbc
==> No binary for dealii-9.2.0-27ysq7kvk7cdu7t2a6jjqmls4qd5fsbc found: installing from source

1 out of 1 hunk FAILED -- saving rejects to file cmake/modules/FindGINKGO.cmake.rej
1 out of 1 hunk FAILED -- saving rejects to file cmake/modules/FindGINKGO.cmake.rej
==> Using cached archive: /home/al5/.spack/var/spack/cache/_source-cache/archive/d0/d05a82fb40f1f1e24407451814b5a6004e39366a44c81208b1ae9d65f3efa43a.tar.gz

==> Using cached archive: /home/al5/.spack/var/spack/cache/_source-cache/archive/c9/c9884ebb0fe379c539012a225d8bcdcfe288edec8dc9d319fbfd64d8fbafba8e

==> Patch https://github.com/dealii/dealii/commit/df6c5de8d6785fce701c10575982858f3aeb4cbd.patch?full_index=1 failed.
==> Error: ProcessError: Command exited with status 1:

    '/usr/bin/patch' '-s' '-p' '1' '-i' '/tmp/al5/spack-stage/spack-stage-fd9czbgb/df6c5de8d6785fce701c10575982858f3aeb4cbd.patch?full_index=1' '-d' '.'
srun: error: e001: task 0: Exited with exit code 1

I have also tried specifying boost to bo...@1.72 and bo...@1.68. the error is the same as the one above. 

Best, 

Andrew

[Andrew Li]

I assume the error has changed because spack automatically found the new boost package which has been installed using cxxstd=11. In fact, specifying the boost installation to cxxstd=17 again reproduces the original error message. I'm rerunning that installation to get the build-log file now

[Andrew Li]

Hi Bruno, 

I've attached the output file spack generated with the original error message. I changed the c++ standard originally because I saw a similar problem on this link (https://github.com/spack/spack/issues/15869). Currently I'm trying various boost versions with dea...@9.2.0, as well as versions down to dea...@9.0.0. So far nothing has worked yet.

Best, 

Andrew

[Bruno Turcksin]

The error is from here

In file included from ./boost/math/tools/mp.hpp:341,
                 from ./boost/math/policies/policy.hpp:11,
                 from ./boost/math/special_functions/math_fwd.hpp:31,
                 from ./boost/math/special_functions/airy.hpp:11,
                 from ./boost/math/special_functions.hpp:15,
                 from libs/math/build/../src/tr1/pch.hpp:9:
/home/al5/.spack/opt/spack/linux-centos7-broadwell/gcc-11.2.0/gcc-12.2.0-lwc56owtziygs5xlu3yqpulfp6fvaulb/lib/gcc/x86_64-pc-linux-gnu/12.2.0/../../../../include/c++/12.2.0/utility:94:14: error: '__and_' was not declared in this scope; did you mean 'std::__and_'?
   94 |     noexcept(__and_<is_nothrow_move_constructible<_Tp>,
      |              ^~~~~~
      |              std::__and_

I don't see ./boost/math/tools/mp.hpp in version 1.82 of boost. Does that one work?

Bruno

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[Andrew Li]

Unfortunately dea...@9.2.0 seems to be incompatible with boost versions greater than v1.77 according to spack

==> Error: concretization failed for the following reasons:

   1. Cannot select a single "version" for package "boost"
   2. Cannot satisfy 'boost@:1.77.0'
   3. Cannot satisfy 'boost@:1.76'
   4. Cannot satisfy 'bo...@1.82'
   5. Cannot satisfy 'bo...@1.59.0:1.63,1.65.1,1.67.0:1.79'

Best, 

Andrew

[Bruno Turcksin]

It looks like the error you get when using cxx=11 is from ginkgo so if you don't need ginkgo, you could try something like

spack install dea...@9.2.0 ~ginkgo ^bo...@1.76.0 cxxstd=11 %g...@12.2.0

Bruno

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/03fa41be-b0bc-49b6-866a-a17d4b5281ebn%40googlegroups.com.

[Andrew Li]

Hi Bruno, 

Thanks for your help! After removing ginkgo and testing several additional dependency combinations, the following spack install worked for me and I'm leaving it here in case someone else runs into a similar issue. 

spack install dea...@9.2.0 +p4est ~ginkgo ^mupa...@2.2.6.1  ^bo...@1.76.0 cxxstd=11 ^tril...@13.0.1 %g...@12.2.0

There are probably alternative combinations which would work with ginkgo, but the builds take a while so I have not tried most of them.

Best, 

Andrew