Issue with gcc5 I do not understand. I activated universal option in my /opt/local/etc/macports:
universal_archs arm64 x86_64 I believed that some ports which are x86_64 only may be build and run in emulation. But I have not used +universal for any port yet. I did : sudo port selfupdate sudo port upgrade outdated today. I was not aware I should do "sync" as well. I may try if it helps. Petr ______________________________________________________________ > Od: "Christopher Jones" <[email protected]> > Komu: [email protected] > Datum: 18.04.2021 17:06 > Předmět: Re: Update on Big Sur Problems > > CC: <[email protected], [email protected]> >your basic issue is you are enabling by default the gcc5 variant, i.e. you get > >pmm:~ pet$ port variants atlas >atlas has the variants: > gcc49: build using macports-gcc-4.9 > * conflicts with gcc5 mpclang37 perf >[+]gcc5: build using macports-gcc-5 > * conflicts with gcc49 mpclang37 perf > mpclang37: use mp-clang-3.7 and gfortran > * conflicts with gcc49 gcc5 perf > nofortran: Forgo use of fortran compiler > universal: Build for multiple architectures > >see the [+] against it above…. > >This is not normal, i.e. I get > >Oberon ~/Projects/MacPorts/ports > port variants atlas >atlas has the variants: > gcc49: build using macports-gcc-4.9 > * conflicts with gcc5 mpclang37 perf > gcc5: build using macports-gcc-5 > * conflicts with gcc49 mpclang37 perf > mpclang37: use mp-clang-3.7 and gfortran > * conflicts with gcc49 gcc5 perf > nofortran: Forgo use of fortran compiler > > >Something specific in *your* setup is causing this, and you need to figure out >what it is and remove it. > >b.t.w. are your ports up to date ? I also see in your listing the ‘universal’ >variant which I do not have. I see at > >https://github.com/macports/macports-ports/commits/36a4990f197af54e31881f5e5a59b880c51116dd/math/atlas/Portfile > ><https://github.com/macports/macports-ports/commits/36a4990f197af54e31881f5e5a59b880c51116dd/math/atlas/Portfile> > >there where some changes to the port about this recently. Please run > >sudo port -d selfupdate >sudo port -d sync >sudo port upgrade outdated > >to first make sure you are fully up to date > >Chris > >> On 18 Apr 2021, at 3:57 pm, <[email protected]> <[email protected]> >> wrote: >> >> I am not sure. I do the clean: >> >> pmm:~ pet$ sudo port clean atlas >> ---> Cleaning atlas >> pmm:~ pet$ sudo port install atlas -gcc5 >> Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not >> build correctly. >> Warning: You can install it as part of the Xcode Command Line Tools package >> by running `xcode-select --install'. >> ---> Fetching archive for atlas >> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >> https://packages.macports.org/atlas >> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >> https://cph.dk.packages.macports.org/atlas >> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >> https://lil.fr.packages.macports.org/atlas >> ---> Fetching distfiles for atlas >> ---> Verifying checksums for atlas >> ---> Extracting atlas >> ---> Applying patches to atlas >> ---> Configuring atlas >> Selected C compiler: /usr/bin/clang >> Selected F77 compiler: gfortran5 >> Warning: reinplace s|-no-cpp-precomp||g didn't change anything in >> /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/atlcomp.txt >> Error: Failed to configure atlas: sysctl failed: No such file or directory >> Error: See >> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/main.log >> for details. >> Error: Follow https://guide.macports.org/#project.tickets to report a bug. >> Error: Processing of port atlas failed >> >> >> pmm:~ pet$ sudo port clean atlas >> ---> Cleaning atlas >> pmm:~ pet$ sudo port install atlas >> Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not >> build correctly. >> Warning: You can install it as part of the Xcode Command Line Tools package >> by running `xcode-select --install'. >> ---> Computing dependencies for atlas >> Error: Can't install libgcc9 because conflicting ports are active: >> libgcc-devel >> Error: Follow https://guide.macports.org/#project.tickets to report a bug. >> Error: Processing of port atlas failed >> >> Well, it is strange that in the case of " sudo port install atlas" it does >> not fetch the package again. >> >> pmm:~ pet$ port variants atlas >> atlas has the variants: >> gcc49: build using macports-gcc-4.9 >> * conflicts with gcc5 mpclang37 perf >> [+]gcc5: build using macports-gcc-5 >> * conflicts with gcc49 mpclang37 perf >> mpclang37: use mp-clang-3.7 and gfortran >> * conflicts with gcc49 gcc5 perf >> nofortran: Forgo use of fortran compiler >> universal: Build for multiple architectures >> >> finally I tried to suppress both gcc variants: >> >> pmm:~ pet$ sudo port clean atlas >> Password: >> ---> Cleaning atlas >> pmm:~ pet$ sudo port install atlas -gcc5 -gcc49 >> Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not >> build correctly. >> Warning: You can install it as part of the Xcode Command Line Tools package >> by running `xcode-select --install'. >> ---> Fetching archive for atlas >> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >> https://packages.macports.org/atlas >> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >> https://cph.dk.packages.macports.org/atlas >> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >> https://lil.fr.packages.macports.org/atlas >> ---> Fetching distfiles for atlas >> ---> Verifying checksums for atlas >> ---> Extracting atlas >> ---> Applying patches to atlas >> ---> Configuring atlas >> Selected C compiler: /usr/bin/clang >> Selected F77 compiler: gfortran5 >> Warning: reinplace s|-no-cpp-precomp||g didn't change anything in >> /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/atlcomp.txt >> Error: Failed to configure atlas: sysctl failed: No such file or directory >> Error: See >> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/main.log >> for details. >> Error: Follow https://guide.macports.org/#project.tickets to report a bug. >> Error: Processing of port atlas failed >> >> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/main.log >> is not very long I attached it >> >> Petr >> >> ______________________________________________________________ >>> Od: "Christopher Jones" <[email protected]> >>> Komu: "Lenore Horner" <[email protected]> >>> Datum: 18.04.2021 16:13 >>> Předmět: Re: Update on Big Sur Problems >>> >>> CC: <[email protected]> >>> >>> yes… >>> >>> Your build is not being done from a clean start. Do >>> >>> sudo port clean atlas >>> sudo port install atlas >>> >>> Chris >>> >>>> On 18 Apr 2021, at 2:49 pm, Lenore Horner <[email protected]> >>>> wrote: >>>> I think that just means you need to clean and then retry. >>>>> On Apr 18, 2021, at 09:17, [email protected] wrote: >>>>> I tried also: >>>>> pmm:~ pet$ sudo port install atlas -gcc5 >>>>> Password: >>>>> Error: Requested variants "" do not match those the build was started >>>>> with: "+gcc5". >>>>> Error: Please use the same variants again, or run 'port clean atlas' >>>>> first to remove the existing partially completed build. >>>>> Error: Follow https://guide.macports.org/#project.tickets to report a bug. >>>>> Error: Processing of port atlas failed >>>>> pmm:~ pet$ sudo port clean atlas >>>>> ---> Cleaning atlas >>>>> pmm:~ pet$ sudo port install atlas -gcc5 >>>>> Warning: The macOS 11.2 SDK does not appear to be installed. Ports may >>>>> not build correctly. >>>>> Warning: You can install it as part of the Xcode Command Line Tools >>>>> package by running `xcode-select --install'. >>>>> ---> Fetching archive for atlas >>>>> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >>>>> https://packages.macports.org/atlas >>>>> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >>>>> https://cph.dk.packages.macports.org/atlas >>>>> ---> Attempting to fetch atlas-3.10.2_2.darwin_20.arm64.tbz2 from >>>>> https://lil.fr.packages.macports.org/atlas >>>>> ---> Fetching distfiles for atlas >>>>> ---> Attempting to fetch atlas3.10.2.tar.bz2 from >>>>> https://distfiles.macports.org/atlas >>>>> ---> Attempting to fetch lapack-3.6.0.tgz from >>>>> https://distfiles.macports.org/atlas ---> Verifying checksums for atlas >>>>> ---> Extracting atlas >>>>> ---> Applying patches to atlas >>>>> ---> Configuring atlas >>>>> Selected C compiler: /usr/bin/clang >>>>> Selected F77 compiler: gfortran5 >>>>> Warning: reinplace s|-no-cpp-precomp||g didn't change anything in >>>>> /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/atlcomp.txt >>>>> Error: Failed to configure atlas: sysctl failed: No such file or directory >>>>> Error: See >>>>> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/main.log >>>>> for details. >>>>> Error: Follow https://guide.macports.org/#project.tickets to report a bug. >>>>> Error: Processing of port atlas failed >>>>> ______________________________________________________________ >>>>>> Od: [email protected] >>>>>> Komu: "Christopher Jones" <[email protected]> >>>>>> Datum: 18.04.2021 15:13 >>>>>> Předmět: Re: Update on Big Sur Problems >>>>>> CC: <[email protected]> >>>>>> pmm:~ pet$ port info atlas >>>>>> atlas @3.10.2_2 (math) >>>>>> Variants: gcc49, [+]gcc5, mpclang37, nofortran, universal >>>>>> Description: Provides a complete BLAS and LAPACK API. >>>>>> ATLAS achieves performance on par with machine-specific >>>>>> tuned libraries. >>>>>> Homepage: http://math-atlas.sourceforge.net/ >>>>>> Build Dependencies: gcc5 >>>>>> Library Dependencies: libgcc, libgcc6 >>>>>> Platforms: darwin >>>>>> License: BSD >>>>>> Maintainers: Email: [email protected], GitHub: Veence >>>>>> pmm:~ pet$ port rdeps atlas >>>>>> The following ports are dependencies of atlas @3.10.2_2+gcc5: >>>>>> gcc5 >>>>>> xz >>>>>> libiconv >>>>>> gperf >>>>>> gettext >>>>>> ncurses >>>>>> cctools >>>>>> gmp >>>>>> isl18 >>>>>> ld64 >>>>>> ld64-xcode >>>>>> zlib >>>>>> libmpc >>>>>> mpfr >>>>>> gcc_select >>>>>> libgcc6 >>>>>> isl >>>>>> libgcc7 >>>>>> libgcc8 >>>>>> libgcc9 >>>>>> libgcc >>>>>> libgcc10 >>>>>> pmm:~ pet$ ______________________________________________________________ >>>>>>> Od: "Christopher Jones" <[email protected]> >>>>>>> Komu: [email protected] >>>>>>> Datum: 18.04.2021 14:34 >>>>>>> Předmět: Re: Update on Big Sur Problems >>>>>>> CC: <[email protected], [email protected], >>>>>>> [email protected]> >>>>>>> So the issue is with atlas, it is forcing the use of gcc5, which will >>>>>>> never work on M1 machines. >>>>>>> please run >>>>>>> port info atlas >>>>>>> port rdeps atlas >>>>>>> I am not sure why you get >>>>>>> atlas >>>>>>> gcc5 >>>>>>> isl18 >>>>>>> libgcc6 >>>>>>> libgcc7 >>>>>>> libgcc8 >>>>>>> libgcc9 >>>>>>> libgcc >>>>>>> libgcc10 >>>>>>> below, as on my Intel macOS11 machine I don’t see this in the dep tree >>>>>>> for atlas >>>>>>> Oberon ~/Projects/MacPorts/ports > port info atlas atlas @3.10.2_2 >>>>>>> (math) >>>>>>> Variants: gcc49, gcc5, mpclang37, nofortran >>>>>>> Description: Provides a complete BLAS and LAPACK API. >>>>>>> ATLAS achieves performance on par with >>>>>>> machine-specific tuned libraries. >>>>>>> Homepage: http://math-atlas.sourceforge.net/ >>>>>>> Extract Dependencies: lbzip2 >>>>>>> Platforms: darwin >>>>>>> License: BSD >>>>>>> Maintainers: Email: [email protected], GitHub: Veence >>>>>>> Oberon ~/Projects/MacPorts/ports > port rdeps atlas >>>>>>> The following ports are dependencies of atlas @3.10.2_2: >>>>>>> lbzip2 >>>>>>> Are you perhaps forcing the use of a gcc5 variant in some way ? >>>>>>> Please check trac for an existing ticket against atlas, and if it does >>>>>>> not exist create one. >>>>>>> In the meantime I suggest you try without using the atlas variant. >>>>>>> Chris >>>>>>>> On 18 Apr 2021, at 12:25 pm, <[email protected]> >>>>>>>> <[email protected]> wrote: >>>>>>>> Hi, >>>>>>>> pmm:~ pet$ port info sundials2 +atlas >>>>>>>> sundials2 @2.7.0_3 (math, devel) >>>>>>>> Variants: accelerate, +atlas, clang11, clangdevel, debug, >>>>>>>> doc, examples, g95, gccdevel, [+]gfortran, >>>>>>>> [+]mpich, openblas, openmpi, universal >>>>>>>> Description: SUNDIALS consists of the following five solvers: >>>>>>>> CVODE solves initial value problems for ordinary >>>>>>>> differential equation (ODE) systems. CVODES solves >>>>>>>> ODE systems and includes sensitivity analysis >>>>>>>> capabilities (forward and adjoint). IDA solves >>>>>>>> initial value problems for differential-algebraic >>>>>>>> equation (DAE) systems. IDAS solves DAE systems and >>>>>>>> includes sensitivity analysis capabilities >>>>>>>> (forward and adjoint). KINSOL solves nonlinear >>>>>>>> algebraic systems. >>>>>>>> Homepage: https://computing.llnl.gov/projects/sundials >>>>>>>> Build Dependencies: cmake, gcc-devel >>>>>>>> Library Dependencies: SuiteSparse_KLU, libgcc-devel, mpich-default, >>>>>>>> atlas >>>>>>>> Conflicts with: sundials >>>>>>>> Platforms: darwin >>>>>>>> License: BSD >>>>>>>> Maintainers: none >>>>>>>> pmm:~ pet$ port rdeps sundials2 +atlas >>>>>>>> The following ports are dependencies of sundials2 >>>>>>>> @2.7.0_3+atlas+gfortran+mpich: >>>>>>>> cmake >>>>>>>> libcxx >>>>>>>> xz >>>>>>>> libiconv >>>>>>>> gperf >>>>>>>> gettext >>>>>>>> ncurses >>>>>>>> curl >>>>>>>> pkgconfig >>>>>>>> libidn2 >>>>>>>> libunistring >>>>>>>> perl5 >>>>>>>> perl5.28 >>>>>>>> db48 >>>>>>>> gdbm >>>>>>>> readline >>>>>>>> texinfo >>>>>>>> help2man >>>>>>>> p5.28-locale-gettext >>>>>>>> perl5.30 >>>>>>>> autoconf >>>>>>>> m4 >>>>>>>> automake >>>>>>>> libtool >>>>>>>> xattr >>>>>>>> unzip >>>>>>>> libpsl >>>>>>>> python39 >>>>>>>> bzip2 >>>>>>>> expat >>>>>>>> libedit >>>>>>>> libffi >>>>>>>> expect >>>>>>>> tcl >>>>>>>> dejagnu >>>>>>>> openssl >>>>>>>> zlib >>>>>>>> sqlite3 >>>>>>>> python_select >>>>>>>> python3_select >>>>>>>> glib2 >>>>>>>> libxml2 >>>>>>>> icu >>>>>>>> pcre >>>>>>>> zstd >>>>>>>> lz4 >>>>>>>> curl-ca-bundle >>>>>>>> libarchive >>>>>>>> lzo2 >>>>>>>> libuv >>>>>>>> gcc-devel >>>>>>>> cctools >>>>>>>> gmp >>>>>>>> isl >>>>>>>> ld64 >>>>>>>> ld64-xcode >>>>>>>> libmpc >>>>>>>> mpfr >>>>>>>> gcc_select >>>>>>>> libgcc-devel >>>>>>>> SuiteSparse_KLU >>>>>>>> SuiteSparse_config >>>>>>>> SuiteSparse_AMD >>>>>>>> SuiteSparse_BTF >>>>>>>> SuiteSparse_COLAMD >>>>>>>> mpich-default >>>>>>>> mpi_select >>>>>>>> mpi-doc >>>>>>>> atlas >>>>>>>> gcc5 >>>>>>>> isl18 >>>>>>>> libgcc6 >>>>>>>> libgcc7 >>>>>>>> libgcc8 >>>>>>>> libgcc9 >>>>>>>> libgcc >>>>>>>> libgcc10 >>>>>>>> pmm:~ pet$ ps: without +atlas sundials2 installs successfully >>>>>>>> pmm:~ pet$ uname -a >>>>>>>> Darwin pmm.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 >>>>>>>> 00:06:51 PST 2021; root:xnu-7195.81.3~1/RELEASE_ARM64_T8101 arm64 >>>>>>>> Petr >>>>>>>> ______________________________________________________________ >>>>>>>>> Od: "Christopher Jones" <[email protected]> >>>>>>>>> Komu: [email protected] >>>>>>>>> Datum: 18.04.2021 13:08 >>>>>>>>> Předmět: Re: Update on Big Sur Problems >>>>>>>>> CC: <[email protected], [email protected], >>>>>>>>> [email protected]> >>>>>>>>> Hi, >>>>>>>>> Any port that forces the use of gcc10 or older on M1 macs cannot >>>>>>>>> work, as these gcc versions are never going to be supported on these >>>>>>>>> machines. Even gcc11 support seems unlikely at this time, so for a >>>>>>>>> while gccdevel is likely going to be the only supported version on >>>>>>>>> these machines, which currently uses a special fork of the gcc >>>>>>>>> mainline by the primary Darwin maintainer with experimental M1 >>>>>>>>> support. >>>>>>>>> However, ports using the compilers PG should automatically use >>>>>>>>> gccdevel, so we need to see why the port below is trying to install >>>>>>>>> libgcc9, as this is incorrect. Please show what >>>>>>>>> port info sundials2 +atlas >>>>>>>>> and >>>>>>>>> port rdeps sundials2 +atlas >>>>>>>>> Finally, if you want this to get fixed you need to follow the final >>>>>>>>> instructions below and submit a trac ticket for the issue. >>>>>>>>> Chris >>>>>>>>>> On 18 Apr 2021, at 11:40 am, [email protected] wrote: >>>>>>>>>> Hello, >>>>>>>>>> I run "sudo port selfupdate" and "sudo port upgrade outdated" >>>>>>>>>> occasionally and I see that there are updates and improvements. >>>>>>>>>> Which is nice. >>>>>>>>>> Yes, gcc-devel is pulled by default, it includes fortran and it >>>>>>>>>> seems to work. >>>>>>>>>> However I am experiencing problems with some packages which need >>>>>>>>>> other version which is ether not available for arm64 or it is >>>>>>>>>> conflict with gcc-devel . >>>>>>>>>> Just as an example, I tried to install cantera and it wants >>>>>>>>>> sundials2 +atlas >>>>>>>>>> but : >>>>>>>>>> sudo port install sundials2 +atlas >>>>>>>>>> Warning: The macOS 11.2 SDK does not appear to be installed. Ports >>>>>>>>>> may not build correctly. >>>>>>>>>> Warning: You can install it as part of the Xcode Command Line Tools >>>>>>>>>> package by running `xcode-select --install'. >>>>>>>>>> ---> Computing dependencies for sundials2 >>>>>>>>>> Error: Can't install libgcc9 because conflicting ports are active: >>>>>>>>>> libgcc-devel >>>>>>>>>> Error: Follow https://guide.macports.org/#project.tickets to report >>>>>>>>>> a bug. >>>>>>>>>> Error: Processing of port sundials2 failed >>>>>>>>>> And I am finished at this point. >>>>>>>>>> Petr >>>>>>>>>> ______________________________________________________________ >>>>>>>>>>> Od: "Marius Schamschula" <[email protected]> >>>>>>>>>>> Komu: "MacPorts Users" <[email protected]> >>>>>>>>>>> Datum: 17.04.2021 20:50 >>>>>>>>>>> Předmět: Re: Update on Big Sur Problems >>>>>>>>>>> James, >>>>>>>>>>> gcc-devel works fine on M1 macs. E.g. I’ve used it to install >>>>>>>>>>> octave. >>>>>>>>>>>> On Apr 17, 2021, at 1:05 PM, James Secan <[email protected]> >>>>>>>>>>>> wrote: >>>>>>>>>>>> I just checked the MacPorts wiki page for Big Sur problems and >>>>>>>>>>>> noted that it hasn’t been updated for three months (at least >>>>>>>>>>>> that’s what the wiki page says). With the possibility that new M1 >>>>>>>>>>>> iMacs might show up soon can you provide a short update on where >>>>>>>>>>>> things stand vis-a-vis Big Sur and M1-based Macs? I’m most >>>>>>>>>>>> interested in where things stand on the gcc compiler package >>>>>>>>>>>> (gfortran in particular). >>>>>>>>>>>> Thanks. >>>>>>>>>>>> Jim >>>>>>>>>>>> Seattle, WA >>>>>>>>>>> Marius >>>>>>>>>>> -- >>>>>>>>>>> Marius Schamschula >>>>>>>>>>> Marius >>>>>>>>>>> -- >>>>>>>>>>> Marius Schamschula >>> >>> >> <main.log> > > >
