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 ChrisOn 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 libgcc10pmm:~ pet$______________________________________________________________Od: "Christopher Jones" <[email protected]> Komu: [email protected] Datum: 18.04.2021 14:34 Předmět: Re: Update on Big Sur Problems CC: <[email protected], [email protected], [email protected]> So the issue is with atlas, it is forcing the use of gcc5, which will never work on M1 machines. please run port info atlas port rdeps atlas I am not sure why you get atlas gcc5 isl18 libgcc6 libgcc7 libgcc8 libgcc9 libgcc libgcc10 below, as on my Intel macOS11 machine I don’t see this in the dep tree for atlasOberon ~/Projects/MacPorts/ports > port info atlas atlas @3.10.2_2 (math)Variants: gcc49, gcc5, mpclang37, nofortran Description: Provides a complete BLAS and LAPACK API. ATLAS achieves performance on par with machine-specific tuned libraries. Homepage: http://math-atlas.sourceforge.net/ Extract Dependencies: lbzip2 Platforms: darwin License: BSD Maintainers: Email: [email protected], GitHub: Veence Oberon ~/Projects/MacPorts/ports > port rdeps atlas The following ports are dependencies of atlas @3.10.2_2: lbzip2 Are you perhaps forcing the use of a gcc5 variant in some way ? Please check trac for an existing ticket against atlas, and if it does not exist create one. In the meantime I suggest you try without using the atlas variant. ChrisOn 18 Apr 2021, at 12:25 pm, <[email protected]> <[email protected]> wrote: Hi, pmm:~ pet$ 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 libgcc10pmm:~ 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. ChrisOn 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, WAMarius -- Marius Schamschula Marius -- Marius Schamschula
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