This modified PKGBUILD is working from my side.
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Package Details: python-dolfin 2019.1.0.post0-2
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| Git Clone URL: | https://aur.archlinux.org/python-dolfin.git (read-only, click to copy) |
|---|---|
| Package Base: | python-dolfin |
| Description: | The Python interface of FEniCS |
| Upstream URL: | https://bitbucket.org/fenics-project/dolfin |
| Licenses: | LGPL3 |
| Submitter: | sigvald |
| Maintainer: | carlosal1015 |
| Last Packager: | carlosal1015 |
| Votes: | 6 |
| Popularity: | 0.090522 |
| First Submitted: | 2018-06-23 09:12 (UTC) |
| Last Updated: | 2023-06-17 23:11 (UTC) |
Dependencies (11)
- dolfin (dolfin-hpc)
- python-mpi4py (python-mpi4py-intel)
- python-pkgconfig (python-pkgconfig-1.1.0)
- python-ply
- cmake (cmake-git) (make)
- openssh (openssh-hpn-git, openssh-git, openssh-xdg-git, openssh-xdg, openssh-selinux, openssh-dotconfig-bin, openssh-dotconfig, openssh-gssapi, openssh-hpn-shim) (check)
- python-decorator (check)
- python-pytest (check)
- petsc (petsc-git, petsc-git-release, petsc-complex) (optional) – interface with PETSc from python
- python-matplotlib (python-matplotlib-git) (optional) – plotting support
- slepc (slepc-git) (optional) – interface with SLEPc from python
Required by (3)
Sources (1)
carlosal1015 commented on 2022-06-30 03:19 (UTC)
carlosal1015 commented on 2022-06-22 14:16 (UTC) (edited on 2022-06-22 14:27 (UTC) by carlosal1015)
I will try the advice, I was suspecting that the issue is more related with petsc4py and cmake stuff than with python. I am reading both FindPetsc.cmake for have a better understanding and try a patch. It is ok, it takes some time to fix.
I also should mentioned that before petsc includes petsc4py by default, like 3 month agos, python-dolfin was working fine, always that user install cmake before to compile for avoid errors, but recently broke with openmpi 4.1.4 upgrade.
entshuld commented on 2022-06-20 17:58 (UTC)
@carlosal1015 To be honest, I don't think that I will have much time to add all the dependencies into the PKGBUILD for now (may be in a couple of weeks). For the moment, I would recommend you to install all the packages which are listed in the following post manually (note that it's 2 columns): https://aur.archlinux.org/packages/python-dolfin#comment-829010 . If you want, you can try with:
depends=('dolfin=2019.1.0.post0' 'mpfr'
librsvg=2:2.50.7-1 libsasl=2.1.27-3 libseccomp=2.5.2-1 libsecret=0.20.4-1 libsm=1.2.3-2 libsoup=2.74.0-1 libssh2=1.9.0-3 libtasn1=4.17.0-1 libthai=0.1.28-2 libtiff=4.3.0-1 libtirpc=1.3.2-1 libtool=2.4.6+42+gb88cebd5-16 libunistring=0.9.10-3 libunwind=1.5.0-1 libuv=1.42.0-1 libx11=1.7.2-1 libxau=1.0.9-3 libxaw=1.0.14-1 libxcb=1.14-1 libxcomposite=0.4.5-3 libxcrypt=4.4.25-1 libxcursor=1.2.0-2 libxdamage=1.1.5-3 libxdmcp=1.1.3-3 libxext=1.3.4-3 libxfixes=6.0.0-1 libxfont2=2.0.5-1 libxft=2.3.4-1 libxi=1.7.10-3 libxinerama=1.1.4-3 libxkbcommon=1.3.1-1 libxkbfile=1.1.0-2 libxml2=2.9.12-2 libxmu=1.1.3-2 libxpm=3.5.13-2 libxrandr=1.5.2-3 libxrender=0.9.10-4 libxshmfence=1.3-2 libxss=1.2.3-3 libxt=1.2.1-1 libxtst=1.2.3-4 libxxf86vm=1.1.4-4 libyaml=0.2.5-1 libyuv=r2212+dfaf7534-2 linux-libre=5.13.8-1 llvm-libs=12.0.1-4 lz4=1:1.9.3-2 lzo=2.10-3 m17n-db=1.8.0-3 m17n-lib=1.8.0-10 m4=1.4.19-1 make=4.3-3 med-openmpi=4.1.0-1 mesa=21.2.1-1 metis=5.1.0.p10-2 mpfr=4.1.0.p13-1 mtdev=1.1.6-1 mumps=5.4.1-3 ncurses=6.2-2 npth=1.6-3 openblas=0.3.17-1 opencl-headers=2:2021.04.29-1 opencl-mesa=21.2.2-1 openmp=12.0.1-1 openmpi=4.1.1-2 openrc=0.42.1-7 openrc-init=0.42.1-7 openrc-net=0.42.1-7 openssh=8.8p1-1 openssl=1.1.1.l-1 opus=1.3.1-2 p11-kit=0.24.0-1.nonsystemd1 pango=1:1.48.10-1 patch=2.7.6-8 pciutils=3.7.0-1 pcre=8.45-1 pcre2=10.37-1 perl=5.34.0-2 perl-error=0.17029-3 perl-mailtools=2.21-5 perl-timedate=2.33-3 petsc-git= 3.15.4.39.g3348d10f62a-1 pinentry=1.1.1-1 pixman=0.40.0-1 pkgconf=1.8.0-1 popt=1.18-1 procps-ng=3.3.17-1 psmisc=23.4-1 pybind11=2.7.1-1 python=3.9.7-1 python-appdirs=1.4.4-3 python-dijitso=2019.1.0-1 python-dolfin=2019.1.0.post0-1 python-ffc=2019.1.0-2 python-fiat=2019.1.0-1 python-gmpy2=2.1.0rc1-1 python-more-itertools =8.10.0-1 python-mpi4py=3.0.3-3 python-mpmath=1.2.1-2 python-numpy=1.21.2-1 python-ordered-set=4.0.2-3 python-packaging=20.9-2 python-pkgconfig=1.5.5-1 python-ply=3.11-7 python-pyparsing=2.4.7-3 python-setuptools=1:57.4.0-2 python-six=1.16.0-1 python-sympy=1.8-1 python-ufl=2019.1.0-1 rav1e=0.4.1-1 readline=8.1.001-1 rest=0.8.1-3 rhash=1.4.2-1 rpcbind=1.2.6-1 rpcbind-openrc=20170927-3 run-parts=5.4-1 scalapack=2.1.0-1 scotch=6.0.6-1 sed=4.8-1 shadow=4.8.1-4 sowing=1.1.26-2 speex=1.2.0-3 speexdsp=1.2.0-2 sqlite=3.36.0-1 sudo=1.9.8-1 suitesparse=5.10.1-1 superlu=5.2.2-2 svt-av1=0.8.7-1 syslog-ng=3.33.1-1 syslog-ng-openrc=20170927-3 tar=1.34-1 tbb=2020.3-1 tcl=8.6.11-1 tdb=1.4.5-1 texinfo=6.8-2 tk=8.6.11.1-1 tlp=1.3.1-2 tlp-openrc=20201202-1 tzdata=2021a-2 util-linux=2.36-4.nonsystemd1 util-linux-libs=2.36-4.nonsystemd1 which=2.21-5 x265=3.5-1 xcb-proto=1.14.1-3 xf86-input-libinput=1.1.0-1 xkeyboard-config=2.33-2 xorg-fonts-encodings=1.0.5-2 xorg-server=1.20.13-2 xorg-server-common=1.20.13-2 xorg-setxkbmap=1.3.2-2 xorg-xauth=1.1-2 xorg-xinit=1.4.1-3 xorg-xkbcomp=1.4.5-1 xorg-xmodmap=1.0.10-2 xorg-xrdb=1.2.1-1 xorgproto=2021.4-1 xz=5.2.5-1 zlib=1:1.2.11-4 zstd=1.5.0-1 acl=2.3.1-1 adobe-source-code-pro-fonts=2.038ro+1.058it+1.018var-1 at-spi2-atk=2.38.0-1 at-spi2-core=2.40.3-1 atk=2.36.0-1 attr=2.5.1-1 audit=3.0.4-1 autoconf=2.71-1 automake=1.16.4-1 avahi=0.8+22+gfd482a7-1 avahi-openrc=20201202-1 base=2-2.parabola1.nonsystemd3 bash=5.1.008-1 binutils=2.36.1-3 bison=3.7.6-1 boost=1.76.0-1 boost-libs=1.76.0-1 bzip2=1.0.8-4 ca-certificates=20210603-1 ca-certificates-mozilla=3.70-1 ca-certificates-utils=20210603-1 cairo=1.17.4-5 cantarell-fonts=1:0.301-1 cblas=3.10.0-1 cgns=4.1.2-1 chrony=4.1-1 chrony-openrc=20201202-1 chrpath=0.16-3 clang=12.0.1-1 cmake=3.21.3-1 compiler-rt=12.0.1-2 coreutils=8.32-1 cppunit=1.15.1-2 curl=7.78.0-1 cython=0.29.24-1 db=5.3.28-5 dbus=1.12.20-1.nonsystemd2 dconf=0.40.0-1 desktop-file-utils=0.26-1 diffutils=3.8-1 ding-libs=0.6.1-3 dnssec-anchors=20190629-3 dolfin=2019.1.0.post0-4 e2fsprogs=1.46.4-1 eigen=3.4.0-1 elfutils=0.185-1 emacs=27.2-1 esysusers=248.3-1 etmpfiles=248.3-1 eudev=3.2.9-1 eudev-libudev=3.2.9-1 expat=2.4.1-1 fakeroot=1.26-1 fftw=3.3.10-1 file=5.40-5 filesystem=2020.09.03-1.nonsystemd1 findutils=4.8.0-1 flac=1.3.3-3 flex=2.6.4-3 fontconfig=2:2.13.94-1 freetype2=2.11.0-3 fribidi=1.0.10-1 gawk=5.1.0-1 gc=8.0.4-4 gcc=11.1.0-1 gcc-fortran=11.1.0-1 gcc-libs=11.1.0-1 gd=2.3.3-1 gdb-common=11.1-1 gdbm=1.21-1 gdk-pixbuf2=2.42.6-2 gentoo-functions=0.12-1 gettext=0.21-1 giflib=5.2.1-2 git=2.33.0-1 gl2ps=1.4.2-2 glib-networking=1:2.68.2-1 glib2=2.68.4-1 glibc=2.33-5 glibc-openrc=20170927-3 glu=9.0.2-1 gmp=6.2.1-1 gnupg=2.2.29-1 gnutls=3.7.2-2 gpgme=1.16.0-1 gpm=1.20.7.r38.ge82d1a6-4 gpm-openrc=20201202-1 graphite=1:1.3.14-1 grep=3.6-1 groff=1.22.4-6 gssproxy=0.8.4-1 gtk3=1:3.24.30-2 guile=2.2.7-1 gzip=1.11-1 harfbuzz=2.9.1-1 hdf5-openmpi=1.12.0-2 hdparm=9.62-1 hwids=20210613-1 hwloc=2.5.0-1 hypre=2.18.2-1 icu=69.1-1 iso-codes=4.7.0-1 jansson=2.13.1-1 json-c=0.15-1 json-glib=1.6.6-1 jsoncpp=1.9.4-1 kbd=2.4.0-2 kexec-tools=2.0.21-1 keyutils=1.6.3-1 kmod=29-1 krb5=1.19.2-1 lapack=3.10.0-1 lcms2=2.12-1 ldns=1.7.1-2 libaec=1.0.5-1 libarchive=3.5.2-1 libassuan=2.5.5-1 libasyncns=0.8+3+g68cd5af-3 libavif=0.9.2-1 libcanberra=0.30+2+gc0620e4-5 libcap=2.56-1 libcap-ng=0.8.2-3 libclc=12.0.1-1 libcloudproviders=0.3.1-2 libcolord=1.4.5-4 libcroco=0.6.13-2 libdaemon=0.14-5 libdatrie=0.2.13-1 libde265=1.0.8-1 libdrm=2.4.107-1 libedit=20210714_3.1-1 libelf=0.185-1 libelogind=246.10-2 libepoxy=1.5.9-1 libevdev=1.11.0-1 libevent=2.1.12-1 libffi=3.3-4 libfontenc=1.1.4-3 libgcrypt=1.9.4-1 libglvnd=1.3.3-1 libgpg-error=1.42-1 libgudev=237-1 libheif=1.12.0-1 libical=3.0.10-1 libice=1.0.10-3 libidn2=2.3.2-1 libinput=1.18.1-1 libjpeg-turbo=2.1.1-1 libksba=1.6.0-1 libmnl=1.0.4-3 libmpc=1.2.1-1 libnsl=2.0.0-1 libogg=1.3.5-1 libomxil-bellagio=0.9.3-3 libp11-kit=0.24.0-1.nonsystemd1 libpcap=1.10.1-1 libpciaccess=0.16-2 libpng=1.6.37-3 libpsl=0.21.1-1 )
or
depends=('dolfin=2019.1.0.post0' 'mpfr'
librsvg libsasl libseccomp libsecret libsm libsoup libssh2 libtasn1 libthai libtiff libtirpc libtool libunistring libunwind libuv libx11 libxau libxaw libxcb libxcomposite libxcrypt libxcursor libxdamage libxdmcp libxext libxfixes libxfont2 libxft libxi libxinerama libxkbcommon libxkbfile libxml2 libxmu libxpm libxrandr libxrender libxshmfence libxss libxt libxtst libxxf86vm libyaml libyuv linux-libre llvm-libs lz4 lzo m17n-db m17n-lib m4 make med-openmpi mesa metis mpfr mtdev mumps ncurses npth openblas opencl-headers opencl-mesa openmp openmpi openrc openrc-init openrc-net openssh openssl opus p11-kit pango patch pciutils pcre pcre2 perl perl-error perl-mailtools perl-timedate petsc-git= 3.15.4.39.g3348d10f62a-1 pinentry pixman pkgconf popt procps-ng psmisc pybind11 python python-appdirs python-dijitso python-dolfin python-ffc python-fiat python-gmpy2 python-more-itertools python-mpi4py python-mpmath python-numpy python-ordered-set python-packaging python-pkgconfig python-ply python-pyparsing python-setuptools python-six python-sympy python-ufl rav1e readline rest rhash rpcbind rpcbind-openrc run-parts scalapack scotch sed shadow sowing speex speexdsp sqlite sudo suitesparse superlu svt-av1 syslog-ng syslog-ng-openrc tar tbb tcl tdb texinfo tk tlp tlp-openrc tzdata util-linux util-linux-libs which x265 xcb-proto xf86-input-libinput xkeyboard-config xorg-fonts-encodings xorg-server xorg-server-common xorg-setxkbmap xorg-xauth xorg-xinit xorg-xkbcomp xorg-xmodmap xorg-xrdb xorgproto xz zlib zstd acl adobe-source-code-pro-fonts at-spi2-atk at-spi2-core atk attr audit autoconf automake avahi avahi-openrc base bash binutils bison boost boost-libs bzip2 ca-certificates ca-certificates-mozilla ca-certificates-utils cairo cantarell-fonts cblas cgns chrony chrony-openrc chrpath clang cmake compiler-rt coreutils cppunit curl cython db dbus dconf desktop-file-utils diffutils ding-libs dnssec-anchors dolfin e2fsprogs eigen elfutils emacs esysusers etmpfiles eudev eudev-libudev expat fakeroot fftw file filesystem findutils flac flex fontconfig freetype2 fribidi gawk gc gcc gcc-fortran gcc-libs gd gdb-common gdbm gdk-pixbuf2 gentoo-functions gettext giflib git gl2ps glib-networking glib2 glibc glibc-openrc glu gmp gnupg gnutls gpgme gpm gpm-openrc graphite grep groff gssproxy gtk3 guile gzip harfbuzz hdf5-openmpi hdparm hwids hwloc hypre icu iso-codes jansson json-c json-glib jsoncpp kbd kexec-tools keyutils kmod krb5 lapack lcms2 ldns libaec libarchive libassuan libasyncns libavif libcanberra libcap libcap-ng libclc libcloudproviders libcolord libcroco libdaemon libdatrie libde265 libdrm libedit libelf libelogind libepoxy libevdev libevent libffi libfontenc libgcrypt libglvnd libgpg-error libgudev libheif libical libice libidn2 libinput libjpeg-turbo libksba libmnl libmpc libnsl libogg libomxil-bellagio libp11-kit libpcap libpciaccess libpng libpsl)
entshuld commented on 2022-04-07 17:53 (UTC)
Hello @carlosal1015, did you see the list which is below of all the software which may be needed? have you tried installing CMake? Can you report back if installing it helps? Thanks.
sigvald commented on 2021-09-30 07:01 (UTC)
@entshuld: Thank you. Your efforts are much appreciated. I added you as maintainer for this package, so you can update dependency requirements in the PKGBUILD file as needed. I think where the newest versions of the dependencies work, we should allow those versions to be used. Where older (or specific) versions are required, this can be specified in the PKGBUILD.
There's a rather large chain of dependencies for FEniCS. python-dolfin depends on dolfin, which again depends on petsc, and so on. If you need to change the PKGBUILD for any of the other packages (that I maintain), just let me know.
entshuld commented on 2021-09-30 01:05 (UTC) (edited on 2021-09-30 01:07 (UTC) by entshuld)
@sigvald I was able to build, install and run in a virtual machine. Then, I used those same packages in my system and they work. I am guessing that it has to do with some cache or residual configuration. At this point, I think that I could help to maintain the package, if you want.
This is not the full list in the system, but should suffice to know what is needed to compile:
| acl | 2.3.1-1 | | librsvg | 2:2.50.7-1 |
| adobe-source-code-pro-fonts | 2.038ro+1.058it+1.018var-1 | | libsasl | 2.1.27-3 |
| at-spi2-atk | 2.38.0-1 | | libseccomp | 2.5.2-1 |
| at-spi2-core | 2.40.3-1 | | libsecret | 0.20.4-1 |
| atk | 2.36.0-1 | | libsm | 1.2.3-2 |
| attr | 2.5.1-1 | | libsoup | 2.74.0-1 |
| audit | 3.0.4-1 | | libssh2 | 1.9.0-3 |
| autoconf | 2.71-1 | | libtasn1 | 4.17.0-1 |
| automake | 1.16.4-1 | | libthai | 0.1.28-2 |
| avahi | 0.8+22+gfd482a7-1 | | libtiff | 4.3.0-1 |
| avahi-openrc | 20201202-1 | | libtirpc | 1.3.2-1 |
| base | 2-2.parabola1.nonsystemd3 | | libtool | 2.4.6+42+gb88cebd5-16 |
| bash | 5.1.008-1 | | libunistring | 0.9.10-3 |
| binutils | 2.36.1-3 | | libunwind | 1.5.0-1 |
| bison | 3.7.6-1 | | libuv | 1.42.0-1 |
| boost | 1.76.0-1 | | libx11 | 1.7.2-1 |
| boost-libs | 1.76.0-1 | | libxau | 1.0.9-3 |
| bzip2 | 1.0.8-4 | | libxaw | 1.0.14-1 |
| ca-certificates | 20210603-1 | | libxcb | 1.14-1 |
| ca-certificates-mozilla | 3.70-1 | | libxcomposite | 0.4.5-3 |
| ca-certificates-utils | 20210603-1 | | libxcrypt | 4.4.25-1 |
| cairo | 1.17.4-5 | | libxcursor | 1.2.0-2 |
| cantarell-fonts | 1:0.301-1 | | libxdamage | 1.1.5-3 |
| cblas | 3.10.0-1 | | libxdmcp | 1.1.3-3 |
| cgns | 4.1.2-1 | | libxext | 1.3.4-3 |
| chrony | 4.1-1 | | libxfixes | 6.0.0-1 |
| chrony-openrc | 20201202-1 | | libxfont2 | 2.0.5-1 |
| chrpath | 0.16-3 | | libxft | 2.3.4-1 |
| clang | 12.0.1-1 | | libxi | 1.7.10-3 |
| cmake | 3.21.3-1 | | libxinerama | 1.1.4-3 |
| compiler-rt | 12.0.1-2 | | libxkbcommon | 1.3.1-1 |
| coreutils | 8.32-1 | | libxkbfile | 1.1.0-2 |
| cppunit | 1.15.1-2 | | libxml2 | 2.9.12-2 |
| curl | 7.78.0-1 | | libxmu | 1.1.3-2 |
| cython | 0.29.24-1 | | libxpm | 3.5.13-2 |
| db | 5.3.28-5 | | libxrandr | 1.5.2-3 |
| dbus | 1.12.20-1.nonsystemd2 | | libxrender | 0.9.10-4 |
| dconf | 0.40.0-1 | | libxshmfence | 1.3-2 |
| desktop-file-utils | 0.26-1 | | libxss | 1.2.3-3 |
| diffutils | 3.8-1 | | libxt | 1.2.1-1 |
| ding-libs | 0.6.1-3 | | libxtst | 1.2.3-4 |
| dnssec-anchors | 20190629-3 | | libxxf86vm | 1.1.4-4 |
| dolfin | 2019.1.0.post0-4 | | libyaml | 0.2.5-1 |
| e2fsprogs | 1.46.4-1 | | libyuv | r2212+dfaf7534-2 |
| eigen | 3.4.0-1 | | linux-libre | 5.13.8-1 |
| elfutils | 0.185-1 | | llvm-libs | 12.0.1-4 |
| emacs | 27.2-1 | | lz4 | 1:1.9.3-2 |
| esysusers | 248.3-1 | | lzo | 2.10-3 |
| etmpfiles | 248.3-1 | | m17n-db | 1.8.0-3 |
| eudev | 3.2.9-1 | | m17n-lib | 1.8.0-10 |
| eudev-libudev | 3.2.9-1 | | m4 | 1.4.19-1 |
| expat | 2.4.1-1 | | make | 4.3-3 |
| fakeroot | 1.26-1 | | med-openmpi | 4.1.0-1 |
| fftw | 3.3.10-1 | | mesa | 21.2.1-1 |
| file | 5.40-5 | | metis | 5.1.0.p10-2 |
| filesystem | 2020.09.03-1.nonsystemd1 | | mpfr | 4.1.0.p13-1 |
| findutils | 4.8.0-1 | | mtdev | 1.1.6-1 |
| flac | 1.3.3-3 | | mumps | 5.4.1-3 |
| flex | 2.6.4-3 | | ncurses | 6.2-2 |
| fontconfig | 2:2.13.94-1 | | npth | 1.6-3 |
| freetype2 | 2.11.0-3 | | openblas | 0.3.17-1 |
| fribidi | 1.0.10-1 | | opencl-headers | 2:2021.04.29-1 |
| gawk | 5.1.0-1 | | opencl-mesa | 21.2.2-1 |
| gc | 8.0.4-4 | | openmp | 12.0.1-1 |
| gcc | 11.1.0-1 | | openmpi | 4.1.1-2 |
| gcc-fortran | 11.1.0-1 | | openrc | 0.42.1-7 |
| gcc-libs | 11.1.0-1 | | openrc-init | 0.42.1-7 |
| gd | 2.3.3-1 | | openrc-net | 0.42.1-7 |
| gdb-common | 11.1-1 | | openssh | 8.8p1-1 |
| gdbm | 1.21-1 | | openssl | 1.1.1.l-1 |
| gdk-pixbuf2 | 2.42.6-2 | | opus | 1.3.1-2 |
| gentoo-functions | 0.12-1 | | p11-kit | 0.24.0-1.nonsystemd1 |
| gettext | 0.21-1 | | pango | 1:1.48.10-1 |
| giflib | 5.2.1-2 | | patch | 2.7.6-8 |
| git | 2.33.0-1 | | pciutils | 3.7.0-1 |
| gl2ps | 1.4.2-2 | | pcre | 8.45-1 |
| glib-networking | 1:2.68.2-1 | | pcre2 | 10.37-1 |
| glib2 | 2.68.4-1 | | perl | 5.34.0-2 |
| glibc | 2.33-5 | | perl-error | 0.17029-3 |
| glibc-openrc | 20170927-3 | | perl-mailtools | 2.21-5 |
| glu | 9.0.2-1 | | perl-timedate | 2.33-3 |
| gmp | 6.2.1-1 | | petsc-git | 3.15.4.39.g3348d10f62a-1 |
| gnupg | 2.2.29-1 | | pinentry | 1.1.1-1 |
| gnutls | 3.7.2-2 | | pixman | 0.40.0-1 |
| gpgme | 1.16.0-1 | | pkgconf | 1.8.0-1 |
| gpm | 1.20.7.r38.ge82d1a6-4 | | popt | 1.18-1 |
| gpm-openrc | 20201202-1 | | procps-ng | 3.3.17-1 |
| graphite | 1:1.3.14-1 | | psmisc | 23.4-1 |
| grep | 3.6-1 | | pybind11 | 2.7.1-1 |
| groff | 1.22.4-6 | | python | 3.9.7-1 |
| gssproxy | 0.8.4-1 | | python-appdirs | 1.4.4-3 |
| gtk3 | 1:3.24.30-2 | | python-dijitso | 2019.1.0-1 |
| guile | 2.2.7-1 | | python-dolfin | 2019.1.0.post0-1 |
| gzip | 1.11-1 | | python-ffc | 2019.1.0-2 |
| harfbuzz | 2.9.1-1 | | python-fiat | 2019.1.0-1 |
| hdf5-openmpi | 1.12.0-2 | | python-gmpy2 | 2.1.0rc1-1 |
| hdparm | 9.62-1 | | python-more-itertools | 8.10.0-1 |
| hwids | 20210613-1 | | python-mpi4py | 3.0.3-3 |
| hwloc | 2.5.0-1 | | python-mpmath | 1.2.1-2 |
| hypre | 2.18.2-1 | | python-numpy | 1.21.2-1 |
| icu | 69.1-1 | | python-ordered-set | 4.0.2-3 |
| iso-codes | 4.7.0-1 | | python-packaging | 20.9-2 |
| jansson | 2.13.1-1 | | python-pkgconfig | 1.5.5-1 |
| json-c | 0.15-1 | | python-ply | 3.11-7 |
| json-glib | 1.6.6-1 | | python-pyparsing | 2.4.7-3 |
| jsoncpp | 1.9.4-1 | | python-setuptools | 1:57.4.0-2 |
| kbd | 2.4.0-2 | | python-six | 1.16.0-1 |
| kexec-tools | 2.0.21-1 | | python-sympy | 1.8-1 |
| keyutils | 1.6.3-1 | | python-ufl | 2019.1.0-1 |
| kmod | 29-1 | | rav1e | 0.4.1-1 |
| krb5 | 1.19.2-1 | | readline | 8.1.001-1 |
| lapack | 3.10.0-1 | | rest | 0.8.1-3 |
| lcms2 | 2.12-1 | | rhash | 1.4.2-1 |
| ldns | 1.7.1-2 | | rpcbind | 1.2.6-1 |
| libaec | 1.0.5-1 | | rpcbind-openrc | 20170927-3 |
| libarchive | 3.5.2-1 | | run-parts | 5.4-1 |
| libassuan | 2.5.5-1 | | scalapack | 2.1.0-1 |
| libasyncns | 0.8+3+g68cd5af-3 | | scotch | 6.0.6-1 |
| libavif | 0.9.2-1 | | sed | 4.8-1 |
| libcanberra | 0.30+2+gc0620e4-5 | | shadow | 4.8.1-4 |
| libcap | 2.56-1 | | sowing | 1.1.26-2 |
| libcap-ng | 0.8.2-3 | | speex | 1.2.0-3 |
| libclc | 12.0.1-1 | | speexdsp | 1.2.0-2 |
| libcloudproviders | 0.3.1-2 | | sqlite | 3.36.0-1 |
| libcolord | 1.4.5-4 | | sudo | 1.9.8-1 |
| libcroco | 0.6.13-2 | | suitesparse | 5.10.1-1 |
| libdaemon | 0.14-5 | | superlu | 5.2.2-2 |
| libdatrie | 0.2.13-1 | | svt-av1 | 0.8.7-1 |
| libde265 | 1.0.8-1 | | syslog-ng | 3.33.1-1 |
| libdrm | 2.4.107-1 | | syslog-ng-openrc | 20170927-3 |
| libedit | 20210714_3.1-1 | | tar | 1.34-1 |
| libelf | 0.185-1 | | tbb | 2020.3-1 |
| libelogind | 246.10-2 | | tcl | 8.6.11-1 |
| libepoxy | 1.5.9-1 | | tdb | 1.4.5-1 |
| libevdev | 1.11.0-1 | | texinfo | 6.8-2 |
| libevent | 2.1.12-1 | | tk | 8.6.11.1-1 |
| libffi | 3.3-4 | | tlp | 1.3.1-2 |
| libfontenc | 1.1.4-3 | | tlp-openrc | 20201202-1 |
| libgcrypt | 1.9.4-1 | | tzdata | 2021a-2 |
| libglvnd | 1.3.3-1 | | util-linux | 2.36-4.nonsystemd1 |
| libgpg-error | 1.42-1 | | util-linux-libs | 2.36-4.nonsystemd1 |
| libgudev | 237-1 | | which | 2.21-5 |
| libheif | 1.12.0-1 | | x265 | 3.5-1 |
| libical | 3.0.10-1 | | xcb-proto | 1.14.1-3 |
| libice | 1.0.10-3 | | xf86-input-libinput | 1.1.0-1 |
| libidn2 | 2.3.2-1 | | xkeyboard-config | 2.33-2 |
| libinput | 1.18.1-1 | | xorg-fonts-encodings | 1.0.5-2 |
| libjpeg-turbo | 2.1.1-1 | | xorg-server | 1.20.13-2 |
| libksba | 1.6.0-1 | | xorg-server-common | 1.20.13-2 |
| libmnl | 1.0.4-3 | | xorg-setxkbmap | 1.3.2-2 |
| libmpc | 1.2.1-1 | | xorg-xauth | 1.1-2 |
| libnsl | 2.0.0-1 | | xorg-xinit | 1.4.1-3 |
| libogg | 1.3.5-1 | | xorg-xkbcomp | 1.4.5-1 |
| libomxil-bellagio | 0.9.3-3 | | xorg-xmodmap | 1.0.10-2 |
| libp11-kit | 0.24.0-1.nonsystemd1 | | xorg-xrdb | 1.2.1-1 |
| libpcap | 1.10.1-1 | | xorgproto | 2021.4-1 |
| libpciaccess | 0.16-2 | | xz | 5.2.5-1 |
| libpng | 1.6.37-3 | | zlib | 1:1.2.11-4 |
| libpsl | 0.21.1-1 | | zstd | 1.5.0-1 |
entshuld commented on 2021-09-28 16:24 (UTC)
Thanks @sigvald. Indeed, I tried with both PETSc 3.14.5--which is what the CMake log said was the requirement (PETSc>=3.14.5), and the current PETSc 3.15.4 (installed through Git sources). I don't have SLEPc, but that was an optional requirement, so I removed it from the PKGBUILD.
The compilation of the Dolfin package goes well, but the error that I see is when trying to import it. I have tried with both the -git and the non-git packages of the FEniCS dependencies from AUR. I will give it a shot again in a virtual machine to see if it has to do with my system.
Thanks for the list from Conda, I do have it, and was able to run Dolfin by installing Miniconda and creating a working environment with it. As I said, unfortunately, this is not a real option for me. Installation with pip isn't either. I also tried to roll back and forth the Git sources of Dolfin (there is no 2019 tag that I can check out, and the structure of the tar-ball is very different. The other sources do have the tag).
I was planning to look at the Conda recipe to check how exactly they built it as well.
sigvald commented on 2021-09-28 07:16 (UTC)
@entshuld: I believe the FEniCS packages (dolfin, python-ffc, python-ufl and so forth) should be correct if they're installed from AUR. The dependency requirements are such that you must have exactly the right version, i.e., version 2019.1.0 of all these packages.
Just looking at your error message, I suspect either an error with PETSc, or with your Python 3.9 environment. The latest version of PETSc and SLEPc in here is 3.15. The most recent versions I know works is PETSc 3.13.6 and SLEPc 3.13.4. It could be that this is unrelated, but perhaps worth a shot downgrading to version 3.13? Beware that SLEPc needs to be of the same major and minor version number as PETSc, but the patch number (the last number in the version) can be different.
Here is a list from one of my Conda environments where FEniCS 2019 works as it should:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
backcall 0.2.0 pyhd3eb1b0_0
binutils_impl_linux-64 2.33.1 he6710b0_7
binutils_linux-64 2.33.1 h9595d00_15
blas 2.17 openblas conda-forge
boost-cpp 1.72.0 h8e57a91_0 conda-forge
bzip2 1.0.8 h7b6447c_0
ca-certificates 2021.1.19 h06a4308_1
certifi 2020.12.5 py38h06a4308_0
cmake 3.19.6 h973ab73_0
cycler 0.10.0 py38_0
dbus 1.13.18 hb2f20db_0
decorator 5.0.5 pyhd3eb1b0_0
doxygen 1.9.1 hb166930_0 conda-forge
eigen 3.3.9 h4bd325d_1 conda-forge
expat 2.3.0 h2531618_2
fenics 2019.1.0 py38hce46ccb_12 conda-forge
fenics-dijitso 2019.1.0 py38h578d9bd_20 conda-forge
fenics-dolfin 2019.1.0 py38h4764ffe_12 conda-forge
fenics-ffc 2019.1.0 py38h578d9bd_20 conda-forge
fenics-fiat 2019.1.0 py38h578d9bd_20 conda-forge
fenics-libdolfin 2019.1.0 h6459f4c_12 conda-forge
fenics-ufl 2019.1.0 py38h578d9bd_20 conda-forge
fontconfig 2.13.1 h6c09931_0
freetype 2.10.4 h5ab3b9f_0
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_15
glib 2.63.1 h5a9c865_0
gmp 6.2.1 h2531618_2
gmpy2 2.0.8 py38hd5f6e3b_3
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_15
hdf5 1.10.6 mpi_mpich_ha7d0aea_1 conda-forge
hypre 2.18.2 hc98498a_1 conda-forge
icu 64.2 he1b5a44_1 conda-forge
ipython 7.22.0 py38hb070fc8_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
jedi 0.17.0 py38_0
jpeg 9d h36c2ea0_0 conda-forge
kiwisolver 1.3.1 py38h2531618_0
krb5 1.18.2 h173b8e3_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.33.1 h53a641e_7
libblas 3.8.0 17_openblas conda-forge
libcblas 3.8.0 17_openblas conda-forge
libcurl 7.71.1 h20c2e04_1
libedit 3.1.20210216 h27cfd23_1
libffi 3.2.1 hf484d3e_1007
libgcc-ng 9.3.0 h2828fa1_18 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.8.0 17_openblas conda-forge
liblapacke 3.8.0 17_openblas conda-forge
libopenblas 0.3.10 h5a2b251_0
libpng 1.6.37 hbc83047_0
libssh2 1.9.0 h1ba5d50_1
libstdcxx-ng 9.3.0 h6de172a_18 conda-forge
libtiff 4.2.0 h85742a9_0
libuuid 1.0.3 h1bed415_2
libuv 1.40.0 h7b6447c_0
libwebp-base 1.2.0 h27cfd23_0
libxcb 1.14 h7b6447c_0
libxml2 2.9.10 hee79883_0 conda-forge
llvm-openmp 11.1.0 h4bd325d_1 conda-forge
lz4-c 1.9.3 h2531618_0
matplotlib 3.3.4 py38h06a4308_0
matplotlib-base 3.3.4 py38h62a2d02_0
metaplot 1.1.0 pypi_0 pypi
metis 5.1.0 hf484d3e_4
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.2 hb69a4c5_1
mpi 1.0 mpich
mpi4py 3.0.3 py38h028fd6f_0
mpich 3.3.2 hc856adb_0
mpmath 1.2.1 py38h06a4308_0
mshr 2019.1.0 py38hf9f41d3_3 conda-forge
mumps-include 5.2.1 8 conda-forge
mumps-mpi 5.2.1 h1f24c91_8 conda-forge
ncurses 6.2 he6710b0_1
numpy 1.19.2 py38h6163131_0
numpy-base 1.19.2 py38h75fe3a5_0
olefile 0.46 py_0
openssl 1.1.1k h27cfd23_0
packaging 20.9 pypi_0 pypi
parmetis 4.0.3 h9f7b9cf_1005 conda-forge
parso 0.8.2 pyhd3eb1b0_0
pcre 8.44 he6710b0_0
petsc 3.13.6 h82b89f7_0 conda-forge
petsc4py 3.13.0 py38h8c4a8b4_3 conda-forge
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 8.2.0 py38he98fc37_0
pint 0.17 pypi_0 pypi
pip 21.0.1 py38h06a4308_0
pkg-config 0.29.2 h1bed415_8
pkgconfig 1.5.2 py38h06a4308_0
prompt-toolkit 3.0.17 pyh06a4308_0
ptscotch 6.0.9 h294ddb0_1 conda-forge
ptyprocess 0.7.0 pyhd3eb1b0_2
pybind11 2.6.0 py38hbe0434c_0 conda-forge
pybind11-global 2.6.0 pypi_0 pypi
pygments 2.8.1 pyhd3eb1b0_0
pyparsing 2.4.7 pyhd3eb1b0_0
pyqt 5.9.2 py38h05f1152_4
python 3.8.2 hcf32534_0
python-dateutil 2.8.1 pyhd3eb1b0_0
python_abi 3.8 1_cp38 conda-forge
qt 5.9.7 h0c104cb_3 conda-forge
readline 8.1 h27cfd23_0
rhash 1.4.1 h3c74f83_1
scalapack 2.0.2 hfacbc1e_1008 conda-forge
scipy 1.6.2 py38hf56f3a7_0
scotch 6.0.9 h0eec0ba_1 conda-forge
setuptools 52.0.0 py38h06a4308_0
sip 4.19.13 py38he6710b0_0
six 1.15.0 py38h06a4308_0
slepc 3.13.4 ha8d41fe_0 conda-forge
slepc4py 3.13.0 py38hdebec43_2 conda-forge
sqlite 3.35.4 hdfb4753_0
suitesparse 5.6.0 h717dc36_0 conda-forge
superlu 5.2.1 hfe2efc7_1207 conda-forge
superlu_dist 6.2.0 h5e15a89_2 conda-forge
sympy 1.7.1 py38h06a4308_0
tbb 2020.3 hfd86e86_0
tk 8.6.10 hbc83047_0
tornado 6.1 py38h27cfd23_0
traitlets 5.0.5 pyhd3eb1b0_0
wcwidth 0.2.5 py_0
wheel 0.36.2 pyhd3eb1b0_0
xz 5.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.5 h9ceee32_0
Although you're not planning to use Conda, it can give you an idea of which versions of dependencies should work well with FEniCS 2019.
Hope this helps :)
Pinned Comments
entshuld commented on 2021-09-30 01:05 (UTC) (edited on 2021-09-30 01:07 (UTC) by entshuld)
@sigvald I was able to build, install and run in a virtual machine. Then, I used those same packages in my system and they work. I am guessing that it has to do with some cache or residual configuration. At this point, I think that I could help to maintain the package, if you want.
This is not the full list in the system, but should suffice to know what is needed to compile: