Deal.ii installation failure

[Vasu Kolli]

Hello guys,

I'm a new user to spack and I tried to install deal.ii 9.3.0 with spack with the following command. 

spack install dea...@9.3.0 +optflags

The installation failed due to the installation failure of a depedency for 'gmsh' called 'mmg'.  Here is the terminal output.

==> Error: ProcessError: Command exited with status 1:
   'cmake' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:STRING=/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/mmg-5.5
.2-xgedxktnlpqhkokixz5sgleo22kd6yyv' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-DCMAKE_VE
RBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF' '-DCMAKE_INSTALL_RPATH:STRING=/home/kolli/spack/opt/spack/linux-manj
aro21-sandybridge/gcc-11.1.0/mmg-5.5.2-xgedxktnlpqhkokixz5sgleo22kd6yyv/lib;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.
1.0/mmg-5.5.2-xgedxktnlpqhkokixz5sgleo22kd6yyv/lib64;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/scotch-6.1.1-fijl6u
smrg67ovkdvuens4yjrmpeny4x/lib;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/openmpi-4.1.2-4tnlbvf6drgqmsu2tdkxj3rczah
joyxd/lib;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/hwloc-2.7.0-rj6hofnte6jtfzfv6sahpbwzskxfplx2/lib;/home/kolli/s
pack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/libpciaccess-0.16-ed7r2y2gv7wdi6zs66qcl7ai4oe56axh/lib;/home/kolli/spack/opt/spack/li
nux-manjaro21-sandybridge/gcc-11.1.0/libxml2-2.9.12-6vmaehqlboekudl4psyxsz6auy3vld4h/lib;/home/kolli/spack/opt/spack/linux-manjaro21-sandyb
ridge/gcc-11.1.0/libiconv-1.16-xw7e4azn7gbvg3kghsxkpwqmmxabxla7/lib;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/xz-5
.2.5-lev54rycwren3zkdc4md3va76vb3hc66/lib;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/zlib-1.2.11-gf5h7tg75hrhioama3
mbdz33paoxq3vm/lib;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/ncurses-6.2-hqgwojkxbdfgxnrfog52t7lw73reygvg/lib;/hom
e/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/libevent-2.1.12-xfy7oj7szz6zrx34pqejeidhw3nhxl4e/lib;/home/kolli/spack/opt/s
pack/linux-manjaro21-sandybridge/gcc-11.1.0/openssl-1.1.1m-gzecewh7y3miawsh2xqhxtz3kmuh4e37/lib;/home/kolli/spack/opt/spack/linux-manjaro21
-sandybridge/gcc-11.1.0/numactl-2.0.14-fmvs5wlzdxzy6x2slr3tdxyts3oiw2pv/lib' '-DCMAKE_PREFIX_PATH:STRING=/home/kolli/spack/opt/spack/linux-
manjaro21-sandybridge/gcc-11.1.0/scotch-6.1.1-fijl6usmrg67ovkdvuens4yjrmpeny4x;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-
11.1.0/openmpi-4.1.2-4tnlbvf6drgqmsu2tdkxj3rczahjoyxd;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/numactl-2.0.14-fmv
s5wlzdxzy6x2slr3tdxyts3oiw2pv;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/libevent-2.1.12-xfy7oj7szz6zrx34pqejeidhw3
nhxl4e;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/hwloc-2.7.0-rj6hofnte6jtfzfv6sahpbwzskxfplx2;/home/kolli/spack/op
t/spack/linux-manjaro21-sandybridge/gcc-11.1.0/libpciaccess-0.16-ed7r2y2gv7wdi6zs66qcl7ai4oe56axh;/home/kolli/spack/opt/spack/linux-manjaro
21-sandybridge/gcc-11.1.0/libxml2-2.9.12-6vmaehqlboekudl4psyxsz6auy3vld4h;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.
0/xz-5.2.5-lev54rycwren3zkdc4md3va76vb3hc66;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/cmake-3.22.1-kbituuq2zxohusd
2pzv7c6g6vb67gwxp;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/openssl-1.1.1m-gzecewh7y3miawsh2xqhxtz3kmuh4e37;/home/
kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/zlib-1.2.11-gf5h7tg75hrhioama3mbdz33paoxq3vm;/home/kolli/spack/opt/spack/linux
-manjaro21-sandybridge/gcc-11.1.0/libiconv-1.16-xw7e4azn7gbvg3kghsxkpwqmmxabxla7;/home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gc
c-11.1.0/ncurses-6.2-hqgwojkxbdfgxnrfog52t7lw73reygvg' '-DUSE_SCOTCH=ON' '-DLIBMMG3D_SHARED=ON' '-DLIBMMG2D_SHARED=ON' '-DLIBMMGS_SHARED=ON
' '-DLIBMMG_SHARED=ON' '/tmp/kolli/spack-stage/spack-stage-mmg-5.5.2-xgedxktnlpqhkokixz5sgleo22kd6yyv/spack-src'

1 error found in build log:
    44      installed Elas and want to use it, please set the CMake variable or
    45      environment variable ELAS_DIR to your Elas directory.
    46     
    47     
    48    -- Could NOT find MPI_C (missing: MPI_C_WORKS)
    49    -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
 >> 50    CMake Error at /home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/cmake-3.22.1-kbituuq2zxohusd2pzv7c6g6vb67gwxp
          /share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
    51      Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
    52    Call Stack (most recent call first):
    53      /home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/cmake-3.22.1-kbituuq2zxohusd2pzv7c6g6vb67gwxp/share/cmake-
          3.22/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
    54      /home/kolli/spack/opt/spack/linux-manjaro21-sandybridge/gcc-11.1.0/cmake-3.22.1-kbituuq2zxohusd2pzv7c6g6vb67gwxp/share/cmake-
          3.22/Modules/FindMPI.cmake:1830 (find_package_handle_standard_args)
    55      /usr/lib/cmake/vtk/vtkm/cmake/VTKmWrappers.cmake:18 (find_package)
    56      /usr/lib64/cmake/vtk/vtkm/VTKmConfig.cmake:173 (include)

See build log for details:
 /tmp/kolli/spack-stage/spack-stage-mmg-5.5.2-xgedxktnlpqhkokixz5sgleo22kd6yyv/spack-build-out.txt

==> Warning: Skipping build of gmsh-4.8.4-s4pil4auwm7qnj3763qp6mw3s3wgnmbt since mmg-5.5.2-xgedxktnlpqhkokixz5sgleo22kd6yyv failed
==> Warning: Skipping build of dealii-9.3.0-gb4jjrb3ikupg5bkhw77d4lgbuk3ctaf since gmsh-4.8.4-s4pil4auwm7qnj3763qp6mw3s3wgnmbt failed
==> Error: dealii-9.3.0-gb4jjrb3ikupg5bkhw77d4lgbuk3ctaf: Package was not installed
==> Error: Installation request failed.  Refer to reported errors for failing package(s).

The spack build out file is in the attachments.  

Could somebody help me solve the issue ?

Regards,
Vasu Kolli.

[Groner, Rob]

When I have a spack install failing deep down in the dependencies, I usually get the list of dependencies from spack and try to install those with spack individually so I can see what is failing.

So, try "spack spec dea...@9.3.0" and that will give you the list of dependencies Spack thinks are needed (or it will fail doing that and tell you what it can't find).  So in that list somewhere, you should see your dependency for gmsh.  If that is what is failing, then I would try to "spack install" that particular piece by itself (so, spack install gmsh@<version>) and see what happens.  It simplifies the error messages you're dealing with so you only have to deal with one issue at a time.

I also try to use system-provided packages whenever I can.  So, for instance, if a package I want to install with spack has a zlib dependency, I'm SURE that there's a zlib implementation I can install on the system without it having to be built with spack.  I then tell spack about it in the packages.yaml file so it knows it's there and doesn't try to build it.  It's one less thing to worry about at that point.  Note this isn't always the best solution, but for very common packages, I prefer it.

Good luck!  

---

From: sp...@googlegroups.com <sp...@googlegroups.com> on behalf of Vasu Kolli <vasuk...@gmail.com>
Sent: Tuesday, January 18, 2022 10:44 AM
To: Spack <sp...@googlegroups.com>
Subject: [spack] Deal.ii installation failure

 

--
You received this message because you are subscribed to the Google Groups "Spack" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spack+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spack/1475d89c-9bd1-47e8-a78e-8dfc48256be9n%40googlegroups.com.