Failed installation on Mac OS Catalina 10.15.4

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dflo...@gmail.com

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May 26, 2020, 1:05:38 PM5/26/20
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Hi,

I tried to install Dedalus on my MacBook (Catalina 10.15.4) using the conda script, but the installation fails when it tries to build the wheel for dedalus. It looks like the issue is with the linker; here's the end of the error message I get:

  ld: unknown option: -platform_version

  clang-10: error: linker command failed with exit code 1 (use -v to see invocation)

  error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1

  ----------------------------------------

  ERROR: Failed building wheel for dedalus

Failed to build dedalus

ERROR: Could not build wheels for dedalus which use PEP 517 and cannot be installed directly


I haven't found topics on this forum addressing the error I am getting. Any ideas on how to fix this error?

Best,
Daniel

Ben Brown

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May 26, 2020, 3:16:25 PM5/26/20
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Daniel,
       I ran into a similar problem recently on Mojave 10.14.6.  We're still tracking down where this comes from and why it's cropping up now.

The problem seems to be a gcc linking command that clang is not understanding.

Could you try doing this:

export CC=gcc

at your terminal, and then run the install_conda.sh script again from that same terminal, and let us know if that fixes the problem?

Thanks,
--Ben

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Daniel Floryan

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May 26, 2020, 4:05:07 PM5/26/20
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Hi Ben,

I tried what you suggested, but I got the same error as before. Maybe this Stack Overflow post will be helpful:


In case it is helpful, here is the output I get from running ld -v in my terminal:

@(#)PROGRAM:ld  PROJECT:ld64-556.6

BUILD 17:57:49 Apr 24 2020

configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em

LTO support using: LLVM version 11.0.3, (clang-1103.0.32.62) (static support for 26, runtime is 26)

TAPI support using: Apple TAPI version 11.0.0 (tapi-1100.0.11)


and here is the output from running clang -v:

Apple clang version 11.0.3 (clang-1103.0.32.62)

Target: x86_64-apple-darwin19.4.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


Best,
Daniel


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annele...@gmail.com

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May 29, 2020, 12:12:06 PM5/29/20
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Hi,

I have the same issue with the installation on Catalina 10.15.4. I tried your fix with no success.

Best,

Anne


On Tuesday, May 26, 2020 at 10:16:25 PM UTC+3, Ben Brown wrote:
Daniel,
       I ran into a similar problem recently on Mojave 10.14.6.  We're still tracking down where this comes from and why it's cropping up now.

The problem seems to be a gcc linking command that clang is not understanding.

Could you try doing this:

export CC=gcc

at your terminal, and then run the install_conda.sh script again from that same terminal, and let us know if that fixes the problem?

Thanks,
--Ben

On Tue, May 26, 2020 at 11:05 AM <dflo...@gmail.com> wrote:
Hi,

I tried to install Dedalus on my MacBook (Catalina 10.15.4) using the conda script, but the installation fails when it tries to build the wheel for dedalus. It looks like the issue is with the linker; here's the end of the error message I get:

  ld: unknown option: -platform_version

  clang-10: error: linker command failed with exit code 1 (use -v to see invocation)

  error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1

  ----------------------------------------

  ERROR: Failed building wheel for dedalus

Failed to build dedalus

ERROR: Could not build wheels for dedalus which use PEP 517 and cannot be installed directly


I haven't found topics on this forum addressing the error I am getting. Any ideas on how to fix this error?

Best,
Daniel

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Keaton Burns

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May 29, 2020, 1:09:47 PM5/29/20
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Hi everyone,

Thanks for the reports — trying to dig into this a bit now.  Can everyone check what version of Xcode they have (highlight Xcode in the finder applications window and check the info on the left), and provide the outputs of both “ld -v” and “clang -v” both in a regular terminal session, and after activating the conda environment built for Dedalus?

Thanks,
-Keaton
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Daniel Floryan

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May 29, 2020, 1:49:10 PM5/29/20
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Xcode version: 11.5

ld -v in regular terminal session:

@(#)PROGRAM:ld  PROJECT:ld64-556.6

BUILD 17:57:49 Apr 24 2020

configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em

LTO support using: LLVM version 11.0.3, (clang-1103.0.32.62) (static support for 26, runtime is 26)

TAPI support using: Apple TAPI version 11.0.0 (tapi-1100.0.11)


clang -v in regular terminal session:

Apple clang version 11.0.3 (clang-1103.0.32.62)

Target: x86_64-apple-darwin19.4.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


ld -v with dedalus conda environment activated:

@(#)PROGRAM:ld  PROJECT:ld64-556.6

BUILD 17:57:49 Apr 24 2020

configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em

LTO support using: LLVM version 11.0.3, (clang-1103.0.32.62) (static support for 26, runtime is 26)

TAPI support using: Apple TAPI version 11.0.0 (tapi-1100.0.11)


clang -v with dedalus conda environment activated:

clang version 10.0.0 

Target: x86_64-apple-darwin19.4.0

Thread model: posix

InstalledDir: /opt/anaconda3/envs/dedalus/bin




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Keaton Burns

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May 29, 2020, 6:23:38 PM5/29/20
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Hi Daniel,

Thanks.  All inside the conda environment, can you also check the outputs of “$CC -v” and “$LD -v”, and send along txt files with the outputs of “conda list” and "python3 -m pip install --no-cache dedalus -v”?

Thanks!
-Keaton

Daniel Floryan

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May 29, 2020, 6:46:03 PM5/29/20
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Hi Keaton,

Output of "$CC -v" with dedalus conda environment activated:

clang version 10.0.0 

Target: x86_64-apple-darwin13.4.0

Thread model: posix

InstalledDir: /opt/anaconda3/envs/dedalus/bin


Output of "$LD -v" with dedalus conda environment activated:

@(#)PROGRAM:ld  PROJECT:ld64-450.3

BUILD 02:41:06 May 15 2020

configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em (tvOS)

LTO support using: LLVM version 10.0.0 (static support for 26, runtime is 26)

TAPI support using: Apple TAPI version 10.0.0 (tapi-1000.10.8)


I've attached two text files with the outputs of the commands you asked for. Both were executed while the dedalus conda environment was activated. 

Best,
Daniel

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condaList.txt
pipInstall.txt

Keaton Burns

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May 29, 2020, 7:51:55 PM5/29/20
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Ok, so conda ships compilers now, and it looks like it may be an issue with clang 10 vs clang 9 provided by conda.  Can you try this updated install script which forces conda to use clang 9?  Make sure to delete the old conda environment or modify the script to pick a new environment name.

Thanks,
-Keaton
install_conda_clang9.sh

Daniel Floryan

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May 29, 2020, 9:12:32 PM5/29/20
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Success! The installation succeeded and I was able to execute one of the example scripts. Here's the info about the compiler and linker that are being used in the dedalus environment now.

Output of "$CC -v" with dedalus conda environment activated:

clang version 9.0.1 

Target: x86_64-apple-darwin13.4.0

Thread model: posix

InstalledDir: /opt/anaconda3/envs/dedalus/bin


Output of "$LD -v" with dedalus conda environment activated:

@(#)PROGRAM:ld  PROJECT:ld64-450.3

BUILD 23:46:44 Jan 25 2020

configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em (tvOS)

LTO support using: LLVM version 9.0.1 (static support for 24, runtime is 24)

TAPI support using: Apple TAPI version 10.0.0 (tapi-1000.10.8)


Thanks for your help!

Best,
Daniel

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Anne Le Blanc

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May 30, 2020, 4:43:00 AM5/30/20
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Hi Keaton,

Works fine, thanks for your help !

Anne

Keaton Burns

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May 30, 2020, 1:40:16 PM5/30/20
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Great, thanks again for the reports.  The install script online should now be updated with these fixes.
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