Update on Big Sur Problems
Dave Allured - NOAA Affiliate
dave.allured at noaa.gov
Mon Apr 19 00:02:43 UTC 2021
Petr, you originally said you wanted cantera. All this trouble with
sundials2, atlas, etc. is because the cantera port at v2.3.0 is more than
three years out of date. Many versions have passed. Sundials2 (v2.7.0)
and atlas should both be considered obsolete ports as far as modern
machines are concerned.
Cantera source is in current and robust maintenance. Mac OS is
actively supported. It uses sundials -- NOT sundials2 -- which is also
actively maintained and up to date on Macports, at v5.7.0. Leave behind
all this old sundials2, atlas, gcc5. I recommend that you update port
cantera to current version 2.5.1, or file an update request ticket. From
the looks of cantera upstream install docs, it looks like there may be some
work involved.
On Sun, Apr 18, 2021 at 8:57 AM <petr.2006 at centrum.cz> 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" <jonesc at hep.phy.cam.ac.uk>
> > Komu: "Lenore Horner" <LenoreHorner at sbcglobal.net>
> > Datum: 18.04.2021 16:13
> > Předmět: Re: Update on Big Sur Problems
> >
> > CC: <macports-users at lists.macports.org>
> >
> >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 <LenoreHorner at sbcglobal.net>
> wrote:
> >>
> >> I think that just means you need to clean and then retry.
> >>
> >>> On Apr 18, 2021, at 09:17, petr.2006 at centrum.cz 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: petr.2006 at centrum.cz
> >>>> Komu: "Christopher Jones" <jonesc at hep.phy.cam.ac.uk>
> >>>> Datum: 18.04.2021 15:13
> >>>> Předmět: Re: Update on Big Sur Problems
> >>>>
> >>>> CC: <macports-users at lists.macports.org>
> >>>> 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: vince at macports.org, 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" <jonesc at hep.phy.cam.ac.uk>
> >>>>> Komu: petr.2006 at centrum.cz
> >>>>> Datum: 18.04.2021 14:34
> >>>>> Předmět: Re: Update on Big Sur Problems
> >>>>>
> >>>>> CC: <lists at schamschula.com, macports-users at lists.macports.org,
> james.secan at gmail.com>
> >>>>>
> >>>>> 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: vince at macports.org, 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, <petr.2006 at centrum.cz> <
> petr.2006 at centrum.cz> 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" <jonesc at hep.phy.cam.ac.uk>
> >>>>>>> Komu: petr.2006 at centrum.cz
> >>>>>>> Datum: 18.04.2021 13:08
> >>>>>>> Předmět: Re: Update on Big Sur Problems
> >>>>>>>
> >>>>>>> CC: <lists at schamschula.com, macports-users at lists.macports.org,
> james.secan at gmail.com>
> >>>>>>> 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, petr.2006 at centrum.cz 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
>
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