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sudo port upgrade outdated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>
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