I am trying to install it on cluster by spack， but I met this error after spack install. This is the output of gcc -v:http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --with-default-libstdcxx-abi=gcc4-compatible --enable-plugin --enable-initfini-array --with-isl=/builddir/build/BUILD/gcc-10.2.1-20210130/obj-x86_64-redhat-linux/isl-install --disable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
What should I do to install it.
dokken
December 26, 2022, 10:03am
2
Could you post the full error message/output from spack as well, using 3x` encapsulation
this is the full output
[root@localhost jzz]# spack install
==> Error: fenics-dolfinx requires GCC-9 or newer for improved C++17 support
dokken
December 26, 2022, 10:22am
4
Could you show all commands that you have executed (i.e. Spack install etc.)
Also, what is the output of spack concretize?
I follow the guide on github step by step,here are the commands:
git clone https://github.com/spack/spack.git
. ./spack/share/spack/setup-env.sh
spack env create fenicsx-env
spack env activate fenicsx-env
spack add py-fenics-dolfinx cflags="-O3" fflags="-O3"
spack install
And the output of spack concretize is the same error:
[root@localhost jzz]# spack concretize
==> Error: fenics-dolfinx requires GCC-9 or newer for improved C++17 support
dokken
December 26, 2022, 11:19am
6
Could you call spack compiler findspack add py-fenics-dolfinx%gcc cflags="-O3" fflags="-O3"
You could also checkspack compiler list
nate
December 26, 2022, 4:01pm
7
Additional to @dokken ’s comment here, if your system does not have a sufficient C/C++ compiler you can request spack to install the latest. Something along the lines of
spack install gcc
spack compiler find
then you can specify the compiler you want to use.
thank you for your help , but I meet another problem while installing：
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-petsc4py-3.18.2-mq3mkwgd2kl6u6nw32q7kyiqgmojekbj
==> Error: py-fenics-dolfinx-0.5.1-a3h3ikqpizu6fafkg7qaxhe4rxjckthe: Package was not installed
==> Error: py-fenics-dolfinx-0.5.1-a3h3ikqpizu6fafkg7qaxhe4rxjckthe: Package was not installed
==> Updating view at /home/jzz/spack/var/spack/environments/fenicsx-env/.spack-env/view
==> Error: Installation request failed. Refer to reported errors for failing package(s).
what should I do
dokken
December 27, 2022, 7:40am
9
It is unclear what instructions you have followed(both me and nate gave some suggestions) and if you made a new spack environment before executing any of the commands above.
I use spack compiler find and spack add py-fenics-dolfinx%gcc cflags="-O3" fflags="-O3" in the previous spack environment.
dokken
December 27, 2022, 8:46am
11
Try making a new spack env, and add all the instructions + all of the output in a reply.
These are all the commands:
spack env create fenicsx
spack env activate fenicsx
spack add py-fenics-dolfinx cflags="-O3" fflags="-O3"
spack install
And these are the full error information：
==> Installing intel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz
==> intel-tbb exists in binary cache but with different hash
==> No binary for intel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz found: installing from source
==> Using cached archive: /home/jzz/spack/var/spack/cache/_source-cache/archive/2c/2cae2a80cda7d45dc7c072e4295c675fff5ad8316691f26f40539f7e7e54c0cc.tar.gz
==> No patches needed for intel-tbb
==> intel-tbb: Executing phase: 'cmake'
==> intel-tbb: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j1'
4 errors found in build log:
257 from /tmp/root/spack-stage/jzz/spack-stage-i
ntel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz/spack-src/
src/tbb/../../include/tbb/../oneapi/tbb/concurrent_unordered_
map.h:21,
258 from /tmp/root/spack-stage/jzz/spack-stage-i
ntel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz/spack-src/
src/tbb/../../include/tbb/concurrent_unordered_map.h:17,
259 from /tmp/root/spack-stage/jzz/spack-stage-i
ntel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz/spack-src/
test/tbb/test_concurrent_unordered_map.cpp:22:
260 /opt/rh/devtoolset-10/root/usr/include/c++/10/bits/basic_stri
ng.h: In instantiation of 'class std::basic_string<char, std:
:char_traits<char>, tbb::detail::d1::tbb_allocator<char> >':
261 /tmp/root/spack-stage/jzz/spack-stage-intel-tbb-2021.7.0-na7f
hxqgmydjud6qn3uxpm2mzk6pp4kz/spack-src/test/common/concurrent
_associative_common.h:964:29: required from 'void test_map_
specific_types() [with Checker = UnorderedMapTypesTester]'
262 /tmp/root/spack-stage/jzz/spack-stage-intel-tbb-2021.7.0-na7f
hxqgmydjud6qn3uxpm2mzk6pp4kz/spack-src/test/tbb/test_concurre
nt_unordered_map.cpp:97:54: required from here
>> 263 /opt/rh/devtoolset-10/root/usr/include/c++/10/bits/basic_stri
ng.h:3150:57: error: no type named 'size_type' in 'std::basic
_string<char, std::char_traits<char>, tbb::detail::d1::tbb_al
locator<char> >::_CharT_alloc_type' {aka 'std::allocator_trai
ts<tbb::detail::d1::tbb_allocator<char> >::rebind_alloc<char>
'}
264 3150 | typedef typename _CharT_alloc_type::size_type
size_type;
265 |
^~~~~~~~~
266 compilation terminated due to -Wfatal-errors.
>> 267 make[2]: *** [test/CMakeFiles/test_concurrent_unordered_map.d
ir/build.make:79: test/CMakeFiles/test_concurrent_unordered_m
ap.dir/tbb/test_concurrent_unordered_map.cpp.o] Error 1
268 make[2]: Leaving directory '/tmp/root/spack-stage/jzz/spack-s
tage-intel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz/spac
k-build-na7fhxq'
>> 269 make[1]: *** [CMakeFiles/Makefile2:761: test/CMakeFiles/test_
concurrent_unordered_map.dir/all] Error 2
270 make[1]: Leaving directory '/tmp/root/spack-stage/jzz/spack-s
tage-intel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz/spac
k-build-na7fhxq'
>> 271 make: *** [Makefile:169: all] Error 2
See build log for details:
/tmp/root/spack-stage/jzz/spack-stage-intel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz/spack-build-out.txt
==> Warning: Skipping build of xtensor-0.24.1-4kyqnb5psxilxmgxaxch3sbbte2x2dqw since intel-tbb-2021.7.0-na7fhxqgmydjud6qn3uxpm2mzk6pp4kz failed
==> Warning: Skipping build of py-fenics-dolfinx-0.5.1-a3h3ikqpizu6fafkg7qaxhe4rxjckthe since xtensor-0.24.1-4kyqnb5psxilxmgxaxch3sbbte2x2dqw failed
==> Warning: Skipping build of fenics-dolfinx-0.5.1-mcvoeggdrotril2r5xierzh2324gy6hu since xtensor-0.24.1-4kyqnb5psxilxmgxaxch3sbbte2x2dqw failed
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/fenics-basix-0.5.1-wewd5p55fmtcrry3onj7soqrvvb55ezp
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/pmix-4.1.2-7evfnj7bupkwpv2n5nwqe4jpqvqfdakg
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/ninja-1.11.1-bd62itogvfhpduvrw6wx5zb4uj77odbi
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-pip-22.2.2-wlmej2nlc6thdrpnkeo33hkum4ma526b
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/openssh-9.1p1-et7vcymi45czd5vyizlul6h6ajnip6c3
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-wheel-0.37.1-2rzwy7vmhvk3urokvqqzw3gdkrh4hpg4
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-setuptools-63.0.0-ngyw2yvvp42kp5aasu5niqxjmbj3y4pb
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/openmpi-4.1.4-beeap2njsxu4ljokqauismz3jtnj2lkg
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-cython-0.29.32-yl76rjizk23wh6wt4ntj4q42raeus4an
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-pycparser-2.21-xj5d6jgkxtzi2npn55k5gzhelpstyrdw
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-pybind11-2.10.1-b7ovu6n25bfq7qivoaj4ho3fife3gxe6
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/parmetis-4.0.3-7jkb3njroebv37lcig7x74zuc6ovtjxz
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-mpi4py-3.1.4-wp4jupxzqlao7ihifecrtgqgwp4xiqbe
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/hypre-2.27.0-xe2si7ljbny5mynk6cnn4vodko3h46en
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/hdf5-1.12.2-pvegraf7za7v5eim2ojtzy66a34vzo5s
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-numpy-1.24.0-upor5yuoif63lm3xqqevwcsotqjx5rny
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-cffi-1.15.1-h7nim5nyzfdknggbcd46vvp6hffkaf2h
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/superlu-dist-8.1.2-32xbqn2qdwdg47lwy5qrnvnnjiu54rch
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-fenics-ufl-2022.2.0-t6hvihpmxrhv73cmdkjqwumpnpprfw76
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-fenics-basix-0.5.1-77ii2xpm7u66lpzfrm4xqwkxytrwouz4
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/petsc-3.18.2-3q62uhdszxk5nmbukxndktgbusgctvn7
==> Waiting for py-fenics-ffcx-0.5.0.post0-k2ei5erjkpb5wr3hbkkl2hhuc3uqaz6[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-fenics-ffcx-0.5.0.post0-k2ei5erjkpb5wr3hbkkl2hhuc3uqaz6e
[+] /home/jzz/spack/opt/spack/linux-centos7-skylake/gcc-10.2.1/py-petsc4py-3.18.2-mq3mkwgd2kl6u6nw32q7kyiqgmojekbj
==> Error: py-fenics-dolfinx-0.5.1-a3h3ikqpizu6fafkg7qaxhe4rxjckthe: Package was not installed
==> Error: py-fenics-dolfinx-0.5.1-a3h3ikqpizu6fafkg7qaxhe4rxjckthe: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).