ARM Architecture Support (Apple Silicon)

[oxygen311]

Hello!

I tried to run this tool with M1 MacBook on Mac OS. Unfortunately, it did not work.

Installation via conda install -c bioconda colord shows error:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - colord

Current channels:

  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

I decided to try to compile it by myself. brew install gcc@10 also leads to the error:

(base) alexey@Alexeys-MacBook-Pro:~$ brew install gcc@10
gcc@10: The x86_64 architecture is required for this software.
Error: gcc@10: An unsatisfied requirement failed this build.

I managed to install gcc and edit the makefile to find and use it. But finally I've got a compilation error:

(base) alexey@Alexeys-MacBook-Pro:~/Downloads/colord$ make
/opt/homebrew/bin/g++ -Wall -O3 -std=c++17 -static-libgcc -static-libstdc++ -pthread  -I src/colord/../common/libs/zlib -I src/colord/libs/kmc_api -I src/colord/libs/edlib -I src/colord/libs/CLI11 -c src/colord/timer.cpp -o src/colord/timer.o
/opt/homebrew/bin/g++ -Wall -O3 -std=c++17 -static-libgcc -static-libstdc++ -pthread  -I src/colord/../common/libs/zlib -I src/colord/libs/kmc_api -I src/colord/libs/edlib -I src/colord/libs/CLI11 -c src/colord/stats_collector.cpp -o src/colord/stats_collector.o
/opt/homebrew/bin/g++ -Wall -O3 -std=c++17 -static-libgcc -static-libstdc++ -pthread  -I src/colord/../common/libs/zlib -I src/colord/libs/kmc_api -I src/colord/libs/edlib -I src/colord/libs/CLI11 -c src/colord/reads_sim_graph.cpp -o src/colord/reads_sim_graph.o
In file included from src/colord/kmer_filter.h:26,
                 from src/colord/reads_sim_graph.h:21,
                 from src/colord/reads_sim_graph.cpp:19:
src/colord/hs.h:21:10: fatal error: mmintrin.h: No such file or directory
   21 | #include <mmintrin.h>
      |          ^~~~~~~~~~~~
compilation terminated.
make: *** [src/colord/reads_sim_graph.o] Error 1

It seems the problem is because of using SSE commands which are implemented only under x64/x86 architecture. I think a possible solution is sse2neon but I am not sure it's the best and universal solution.

Later I can check using of this tool under ARM Linux.

[marekkokot]

Hi,

thanks! We are working on adding support for ARM to our software, but I'm not able to promise when it will be ready for this project. We will do our best.

[oxygen311]

@marekkokot

Thank you for the info! Will wait for support.

Tested on ARM64 Linux (Ubuntu), and got the same error:

parallels@ubuntu-linux-22-04-desktop:~/Downloads/colord$ make
g++ -Wall -O3 -std=c++17 -static -Wl,--whole-archive -lstdc++fs -lpthread -Wl,--no-whole-archive  -I src/colord/../common/libs/zlib -I src/colord/libs/kmc_api -I src/colord/libs/edlib -I src/colord/libs/CLI11 -c src/colord/reads_sim_graph.cpp -o src/colord/reads_sim_graph.o
In file included from src/colord/kmer_filter.h:26,
                 from src/colord/reads_sim_graph.h:21,
                 from src/colord/reads_sim_graph.cpp:19:
src/colord/hs.h:21:10: fatal error: mmintrin.h: No such file or directory
   21 | #include <mmintrin.h>
      |          ^~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:92: src/colord/reads_sim_graph.o] Error 1