Re: Update on Big Sur Problems

[Dave Allured - NOAA Affiliate via macports-users]

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three years out of date.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  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 

Re: Update on Big Sur Problems

[Marius Schamschula]

Indeed, I have not built Atlas for any recent version of macOS due the reason 
Joshua brings up: Atlas is not compatible with kernel micro-sleep. Atlas cannot 
determine accurate timing, and thus its optimizations are inaccurate.

The port has not been updated for this very reason see 
https://trac.macports.org/ticket/54342  
 (June 2017)

The bottomline: Atlas only works with older versions of macOS. There is 
absolutely no point in building it under Big Sur (or Catalina, Mojave…)!

> On Apr 18, 2021, at 1:27 PM, Joshua Root  wrote:
> 
> Christopher Jones wrote:
>> 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.
> 
> AFAICT, this would happen for all users on arm64. 
> 
> 
> Be aware however that last I saw, the atlas maintainer didn't think there had 
> been any recent upstream development of this software, and the auto-tuning 
> that is the main point of atlas didn't work on any recent macOS versions. I 
> don't know if it's even possible to build atlas on arm64, but if it's 
> possible, it's probably not worth it.
> 
> If it doesn't work, it should set supported_archs and/or known_fail 
> appropriately, of course.
> 
> - Josh

Marius
--
Marius Schamschula

Re: Update on Big Sur Problems

[Joshua Root]

Christopher Jones wrote:

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.


AFAICT, this would happen for all users on arm64. 



Be aware however that last I saw, the atlas maintainer didn't think 
there had been any recent upstream development of this software, and the 
auto-tuning that is the main point of atlas didn't work on any recent 
macOS versions. I don't know if it's even possible to build atlas on 
arm64, but if it's possible, it's probably not worth it.


If it doesn't work, it should set supported_archs and/or known_fail 
appropriately, of course.


- Josh

Re: Update on Big Sur Problems

[petr.2006]

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" 
> Komu: petr.2...@centrum.cz
> Datum: 18.04.2021 17:06
> Předmět: Re: Update on Big Sur Problems
>
> CC: 
>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
> 
>
>
>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,   
>> 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 

Re: Update on Big Sur Problems

[Christopher Jones]

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
 


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,   
> 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 

Re: Update on Big Sur Problems

[petr.2006]

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" 
Komu: "Lenore Horner" 
Datum: 18.04.2021 16:13
Předmět: Re: Update on Big Sur Problems

CC: 

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  wrote:

I think that just means you need to clean and then retry.


On Apr 18, 2021, at 09:17, petr.2...@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 

Re: Update on Big Sur Problems

[Christopher Jones]

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  wrote:
> 
> I think that just means you need to clean and then retry.
> 
>> On Apr 18, 2021, at 09:17, petr.2...@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.2...@centrum.cz
>>> Komu: "Christopher Jones" 
>>> Datum: 18.04.2021 15:13
>>> Předmět: Re: Update on Big Sur Problems
>>> 
>>> CC: 
>>> 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: vi...@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" 
 Komu: petr.2...@centrum.cz
 Datum: 18.04.2021 14:34
 Předmět: Re: Update on Big Sur Problems
 
 CC: >>> james.se...@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: vi...@macports.org, GitHub: 

Re: Update on Big Sur Problems

[Lenore Horner]

I think that just means you need to clean and then retry.

> On Apr 18, 2021, at 09:17, petr.2...@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.2...@centrum.cz
>> Komu: "Christopher Jones" 
>> Datum: 18.04.2021 15:13
>> Předmět: Re: Update on Big Sur Problems
>> 
>> CC: 
>> 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: vi...@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" 
>>> Komu: petr.2...@centrum.cz
>>> Datum: 18.04.2021 14:34
>>> Předmět: Re: Update on Big Sur Problems
>>> 
>>> CC: >> james.se...@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: vi...@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 

Re: Update on Big Sur Problems

[petr.2006]

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.2...@centrum.cz
> Komu: "Christopher Jones" 
> Datum: 18.04.2021 15:13
> Předmět: Re: Update on Big Sur Problems
>
> CC: 
>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: vi...@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" 
>> Komu: petr.2...@centrum.cz
>> Datum: 18.04.2021 14:34
>> Předmět: Re: Update on Big Sur Problems
>>
>> CC: > james.se...@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: vi...@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,   
>>> wrote:
>>> 
>>> Hi,
>>> 
>>> pmm:~ pet$ port info sundials2 +atlas
>>> sundials2 @2.7.0_3 (math, devel)
>>> Variants: accelerate, 

Re: Update on Big Sur Problems

[petr.2006]

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: vi...@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" 
> Komu: petr.2...@centrum.cz
> Datum: 18.04.2021 14:34
> Předmět: Re: Update on Big Sur Problems
>
> CC:  james.se...@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: vi...@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,   
>> 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
>>

Re: Update on Big Sur Problems

[Christopher Jones]

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: vi...@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,   
> 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" 
>> Komu: petr.2...@centrum.cz
>> Datum: 18.04.2021 13:08
>> Předmět: Re: Update on Big Sur Problems
>> 
>> CC: > james.se...@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 

Re: Update on Big Sur Problems

[petr.2006]

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" 
> Komu: petr.2...@centrum.cz
> Datum: 18.04.2021 13:08
> Předmět: Re: Update on Big Sur Problems
>
> CC:  james.se...@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.2...@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
>> 
>> 
>> __
>>> Od: 

Re: Update on Big Sur Problems

[Christopher Jones]

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.2...@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
> 
> 
> __
>> Od: "Marius Schamschula" 
>> Komu: "MacPorts Users" 
>> 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  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
>> 
>> 
>> 
>> 
>> 
>> 



smime.p7s
Description: S/MIME cryptographic signature

Re: Update on Big Sur Problems

[petr.2006]

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" 
> Komu: "MacPorts Users" 
> 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  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
>
>
>
>
>
>