Hell community,
Following a recent merge in Dolfinx anable to use integration over vertices, I wanted to update my FEniCSx installation. Here is my spack.yaml file :
spack:
specs:
- petsc@main +mpi +complex +mumps+hypre+superlu-dist
- slepc@main
- py-fenics-dolfinx@main +petsc4py +slepc4py
- gmsh
view: true
config:
fetchers: [curl]
packages:
apple-clang:
externals:
- spec: apple-clang@16.0.0
prefix: /usr
extra_attributes:
compilers:
c: /usr/bin/clang
cxx: /usr/bin/clang++
gcc:
externals:
- spec: gcc@15.1.0 languages:='c,c++,fortran'
prefix: /opt/homebrew
extra_attributes:
compilers:
c: /opt/homebrew/bin/gcc-15
cxx: /opt/homebrew/bin/g++-15
fortran: /opt/homebrew/bin/gfortran
After running the following commands :
spack clean -a
spack concretize --force
spack install
I obtain the following error :
(base) pierremariotti@n148-p112 fenicsx-env % spack install
[+] /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk (external apple-gl-4.1.0-myqzsbgrwnxvq4kqs7g33mxgn4xl5gmo)
[+] /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk (external apple-glu-1.3.0-oj2gyysbo4whi5i2xsisgzdkikyrs73v)
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/gcc-runtime-15.1.0-ejupt3n4etxiyyarutkwiyo3lbxiuzxo
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libiconv-1.18-2gvlmi2a4l5nvvjwso2y6glc6nzt6mct
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/xz-5.6.3-2l3r3634ohrhmcrhjvrwvxeqv6tzhknv
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/zlib-ng-2.2.4-3rv7azhouyos6u3wm3b3rnvj7sjrbjdp
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/ncurses-6.5-20250705-cyluvgpmi3jm7hioyu4somawgjfjkrz2
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/bzip2-1.0.8-ixcy2hc6usssxlo6cgkpbz7365ypxopp
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/zstd-1.5.7-xw532jzejio4b7rxd3tvrepxviwttpma
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libxcrypt-4.4.38-tmqiwhihdoskcnhqtrmbmooahcoywuxv
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/pkgconf-2.5.1-bxg75pth7zwyqodlhz4cskposjbrst2m
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libpthread-stubs-0.5-zwfv6p624qmr3c2kuh24gx2zcshym2n5
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/gmp-6.3.0-bwlcfpedej5sqn3c5wpgvgibv3vawtx7
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libjpeg-turbo-3.0.4-43usyfl7csptommoqxqhxzr6vux6q5pp
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/metis-5.1.0-fvb75xri2ntibwvvukfs2bwzcko4vpdi
[+] /usr (external apple-clang-16.0.0-w4igtthjd3bxqu5vgzl53ajmfjsgmurq)
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/compiler-wrapper-1.0-43vtcvlyyjzwnwzbgijybruzdpqwe6iq
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/fenics-ufcx-main-5nzfmozz2dbegyqf7llliyj733tqdrij
[+] /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk (external apple-libuuid-1353.100.2-zx33nml62stmmsz2tbfdopy4zxy72gn4)
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/boost-1.88.0-omhiykd3eaduiemrsard6336edonf4s2
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/openssl-3.4.1-boxwwqg53welohjdi6mqcp2gvfezapks
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/xproto-7.0.31-qdxpzhwiqx3ybnya3ypjijjpe6uohn3e
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/openblas-0.3.30-yfxxgog5qrmjcjswcozqcwqeuzlvh57e
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libxml2-2.13.5-7syerdfweyberu46hx3i4vabwzzwge2j
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/xtrans-1.6.0-xcrhxa7ornhy453j22fctydcbdpa4x6m
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libffi-3.4.8-v5ggjlagtjh2xd3v3uenptnc2c2kk556
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/nghttp2-1.65.0-yd5gtwg2xmzq5htbp26a6mjpliy7ghzy
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/readline-8.3-isb63mm4jmkhpy6y53mh4ozshqtv4mmf
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/gmake-4.4.1-v3pbo3zjysvtdra56riweop4vvcmz7dr
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libevent-2.1.12-t7swxtea4ad2xcqkpzd4ddbc55bjtupo
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/hwloc-2.11.1-h76zzntu4dvdjdqsu4hdo5zocnt6sxhv
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libxdmcp-1.1.5-4eqcvz42knean2mddgacl23wycnpud3a
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/curl-8.15.0-n3u6rxf4n47t4hr3fxeg2z67fspr7w2f
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libedit-3.1-20240808-wzm77xdbo6i3tme6dsbweefexmkminrh
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/pugixml-1.14-cjtgcklgtu5nuhyebzz4qn5i2g2m653q
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/expat-2.7.1-v75tiwr3j32iql54irf4txs6r5tegqvt
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/pigz-2.8-7k4hi6cqvujsl6a2fuz7g3szliiq7aqf
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/gdbm-1.23-6itdgtlmcexg2iwkx3fxlqe2yuphiamq
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/sqlite-3.46.0-sowek457ph2ant5o4lmnsfacroc7ysih
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libxau-1.0.12-46qvycp7epspy7uszrvka4ty3df7qui5
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/kbproto-1.0.7-s6sead2tg263zwnzy4tni42t32rt2irx
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libpng-1.6.47-dn2h5q75ajcpfe762aqs7u5lf7mrh463
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/fenics-basix-main-jefwr3ht3ggz6tkoeirbprdjkneawn3s
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/fmt-11.2.0-lse674meamrsnrcy3g7lqk7h5masj3ej
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/pmix-6.0.0-ilkgznyrt3fd3ssscu5ybu33kfbtxelj
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/cmake-3.31.8-6imgoykuu6auupyrgbbrxx5xdus2wq2s
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/tar-1.35-fw73mvvygf3pczaamwmes2z7gcwhlghx
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libxcb-1.17.0-qfx4ier6togapnx6eph3oly6r3o6sdtw
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/freetype-2.13.2-hxwmwkixdpdaqsgg7q4avbgdzy353ikc
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/spdlog-1.15.2-2xkztklxdplelwtr4caoi4p6h5jyl6xh
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/prrte-4.0.0-2cupwwobrjfkc5senkepapg5gzrnftmd
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/gettext-0.23.1-jhpxbsfibiuea6iozzwiftpkcqojgxv6
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/libx11-1.8.12-nzyz5fiit54vdfdze5i4p3pfa67iqbya
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/python-3.12.9-nr6wo7dbkme5wrrc5tqwtvzglsy7x2ta
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/krb5-1.21.3-f4jg2o2xxdibmywqtofv7irrjkl4cab2
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/fltk-1.4.4-w7c5vmk2qvadp7hllgmbe2u7cfmdcdvq
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/python-venv-1.0-txdjfk2vpfwyvd2eaz3zebhu6cbndfjl
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/openssh-9.9p1-fjqabjepvuupijfvzzihnuxcag32decl
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-pathspec-0.12.1-m6wmw43x3n7dkcdi56facuaxuexlq7cb
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-wheel-0.45.1-ddtrefkyxkfwchogscfgvhq4cwkk6tsz
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-setuptools-80.9.0-sjhwncwucs6g4sgljkaow74xnzqks42p
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-pip-25.1.1-3ur25lgnyylo4u2xmntta3tnvnybae4t
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/openmpi-5.0.8-kjwlt3a7hlu72wwzw6omrg3gskbbuocz
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-numpy-2.3.2-nfbetdmgilhocqs5wf5pttxdbawenwc2
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-packaging-25.0-ynvibtlmcecucbv6gsfbrwpu7flhobqo
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-pycparser-2.21-jrkgflu3mwpe34kqawwxl3yrw2i73taf
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-nanobind-2.8.0-qpzpbycayut7b7wlb642houtn5a5f446
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/parmetis-4.0.3-vnglvcpnsrqoixyajve4mpoub3fkizwd
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-mpi4py-4.0.1-tckrhic2pxceojrzeakkeonkq7bxdwp6
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/scotch-7.0.8-uoznl2mo3sacsb42m2l2jjslnmdew63w
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/hypre-develop-khtgsyc3msfmufsdbwuokzbjlymahbk3
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/hdf5-1.12.3-22eorjdsji4ugckwsrasmyfrqr7q7isn
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/arpack-ng-3.9.1-i756zo2x2nkbn5vhf7mn6v7cw3nw43wi
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/netlib-scalapack-2.2.2-efo7qssccvy4bakfjd6t4hc4dhbn3anx
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-fenics-ufl-main-dpvvtg7aa2ryylecj57p4ljlfkuzyhbc
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-scikit-build-core-0.11.5-fw37pycy5aiqwavqzw3dqonuzfx5am3e
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-cffi-1.16.0-sovrsc4bhaajzayuw4pch4aydij6rzoy
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/superlu-dist-develop-pei5fi6i7s4ertdtwxv2eewzsuwvmpvx
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/mmg-5.8.0-pqwk7aak4oo5f3ulrvyvhu23bpxe7nzk
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/med-5.0.0-slc243qyqqmiuqg5k5qhfgijgrvasw4p
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/cgns-4.5.0-ynbeo2jhjqtkrryf2hksmlpcgvfxh44w
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/mumps-5.8.0-cqqt3ia2ixhv7d5lzq2cqkzh26wfkatf
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-fenics-basix-main-xj44ph7iorowlkhxrjkado6bnfdjhaet
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/gmsh-4.13.1-he7kqisykx72ax4m7oxir7qwxeyanojs
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/petsc-main-aidhbb7s3xcm4ue7fks534dyp4uu4fcz
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-fenics-ffcx-main-5i36ozqb5qxae2mt5gy3l4ovafzniqlc
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/slepc-main-hngxwrjvyr6avgeb2rkbmq7jfjoqlbot
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-petsc4py-main-m23y66tcdunnuodic4gcnmfhpgoyrh4n
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/fenics-dolfinx-main-powlqar4sn4ipt5ejoyk5yqs4fiz3nlk
[+] /Users/pierremariotti/spack/opt/spack/darwin-m1/py-slepc4py-main-7iya66dd6k6qxehlcuisgdkjcbizsxt5
==> No binary for py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r found: installing from source
==> Installing py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r [91/91]
==> No patches needed for py-fenics-dolfinx
==> py-fenics-dolfinx: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
'/Users/pierremariotti/spack/opt/spack/darwin-m1/python-venv-1.0-txdjfk2vpfwyvd2eaz3zebhu6cbndfjl/bin/python3' '-m' 'pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/Users/pierremariotti/spack/opt/spack/darwin-m1/py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r' '.'
7 errors found in build log:
105 [ 48%] Linking CXX static library libnanobind-static.a
106 [ 48%] Built target nanobind-static
107 [ 52%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/dolfinx.cpp.o
108 [ 56%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/assemble.cpp.o
109 [ 60%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/common.cpp.o
110 [ 64%] Building CXX object CMakeFiles/cpp.dir/dolfinx/wrappers/fem.cpp.o
>> 111 /private/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-src/python/dolfinx/wrappers/fem.cpp:760:56: error: no member named 'num_integrals' in 'dolfin
x::fem::Form<float, float>'
112 760 | .def("num_integrals", &dolfinx::fem::Form<T, U>::num_integrals)
113 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^
114 /private/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-src/python/dolfinx/wrappers/fem.cpp:1163:3: note: in instantiation of function template spe
cialization '(anonymous namespace)::declare_form<float>' requested here
115 1163 | declare_form<float>(m, "float32");
116 | ^
>> 117 /private/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-src/python/dolfinx/wrappers/fem.cpp:760:56: error: no member named 'num_integrals' in 'dolf
inx::fem::Form<double, double>'
118 760 | .def("num_integrals", &dolfinx::fem::Form<T, U>::num_integrals)
119 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^
120 /private/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-src/python/dolfinx/wrappers/fem.cpp:1164:3: note: in instantiation of function template spe
cialization '(anonymous namespace)::declare_form<double>' requested here
121 1164 | declare_form<double>(m, "float64");
122 | ^
>> 123 /private/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-src/python/dolfinx/wrappers/fem.cpp:760:56: error: no member named 'num_integrals' in 'dolf
inx::fem::Form<std::complex<float>, float>'
124 760 | .def("num_integrals", &dolfinx::fem::Form<T, U>::num_integrals)
125 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^
126 /private/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-src/python/dolfinx/wrappers/fem.cpp:1165:3: note: in instantiation of function template spe
cialization '(anonymous namespace)::declare_form<std::complex<float>>' requested here
127 1165 | declare_form<std::complex<float>>(m, "complex64");
128 | ^
>> 129 /private/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-src/python/dolfinx/wrappers/fem.cpp:760:56: error: no member named 'num_integrals' in 'dolf
inx::fem::Form<std::complex<double>, double>'
130 760 | .def("num_integrals", &dolfinx::fem::Form<T, U>::num_integrals)
131 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^
132 /private/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-src/python/dolfinx/wrappers/fem.cpp:1166:3: note: in instantiation of function template spe
cialization '(anonymous namespace)::declare_form<std::complex<double>>' requested here
133 1166 | declare_form<std::complex<double>>(m, "complex128");
134 | ^
135 4 errors generated.
>> 136 gmake[2]: *** [CMakeFiles/cpp.dir/build.make:121: CMakeFiles/cpp.dir/dolfinx/wrappers/fem.cpp.o] Error 1
>> 137 gmake[1]: *** [CMakeFiles/Makefile2:88: CMakeFiles/cpp.dir/all] Error 2
>> 138 gmake: *** [Makefile:136: all] Error 2
139
140 *** CMake build failed
141 error: subprocess-exited-with-error
142
143 × Building wheel for fenics-dolfinx (pyproject.toml) did not run successfully.
144 │ exit code: 1
See build log for details:
/var/folders/mt/b4lxpy7943940yj_07x3c7h80000gn/T/pierremariotti/spack-stage/spack-stage-py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r/spack-build-out.txt
==> Error: py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r: ProcessError: Command exited with status 1:
'/Users/pierremariotti/spack/opt/spack/darwin-m1/python-venv-1.0-txdjfk2vpfwyvd2eaz3zebhu6cbndfjl/bin/python3' '-m' 'pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/Users/pierremariotti/spack/opt/spack/darwin-m1/py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r' '.'
==> Error: py-fenics-dolfinx-main-iqvj2zu4tzntqaicsg2qyaehn6q5jb4r: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).
Do you have any idea what is happening here ? I downloading the main branch of dolfinx last week using these commands, and it doesn’t work anymore. Did I make a mistake here ?
All the best,
Pierre.