From d046a6cc123d51031e4e10ec5ce271fc3b617c59 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Thu, 7 Nov 2024 14:57:23 +0100 Subject: [PATCH 1/5] add note on docker with Apple Silicon --- README.rst | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/README.rst b/README.rst index db40d0420..1ced88793 100644 --- a/README.rst +++ b/README.rst @@ -189,6 +189,20 @@ and ``--tmp-outdir-prefix`` to somewhere under ``/Users``:: $ cwl-runner --tmp-outdir-prefix=/Users/username/project --tmpdir-prefix=/Users/username/project wc-tool.cwl wc-job.json + +Docker default platform on macOS with Apple Silicon +=================================================== + +If macOS cwltool users want to run tools/workflows that reference software containers that only support amd64 (64-bit x86), but they have an Apple Silicon (aarch64/arm64) CPU, +they run into the error `WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested`. + +To circumvent this, export the following environment variable before executing the `cwltool`: + +`export DOCKER_DEFAULT_PLATFORM=linux/amd64` + +To automatically enable this variable in new shells, this can be added to the respective shell profiles (e.g. `~/.zshrc`, `~/.bash_profile`). + + Using uDocker ============= From f9aeabc011716d742cc6f047ee76f02ddb0b4814 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Thu, 7 Nov 2024 14:59:02 +0100 Subject: [PATCH 2/5] fix backticks --- README.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index 1ced88793..c11502111 100644 --- a/README.rst +++ b/README.rst @@ -194,13 +194,13 @@ Docker default platform on macOS with Apple Silicon =================================================== If macOS cwltool users want to run tools/workflows that reference software containers that only support amd64 (64-bit x86), but they have an Apple Silicon (aarch64/arm64) CPU, -they run into the error `WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested`. +they run into the error ``WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested``. To circumvent this, export the following environment variable before executing the `cwltool`: -`export DOCKER_DEFAULT_PLATFORM=linux/amd64` +``export DOCKER_DEFAULT_PLATFORM=linux/amd64`` -To automatically enable this variable in new shells, this can be added to the respective shell profiles (e.g. `~/.zshrc`, `~/.bash_profile`). +To automatically enable this variable in new shells, this can be added to the respective shell profiles (e.g. ``~/.zshrc``, ``~/.bash_profile``). Using uDocker From 7424dbbd2abae4ab88c32e50723961ad71e1c08c Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Thu, 7 Nov 2024 14:59:54 +0100 Subject: [PATCH 3/5] style --- README.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index c11502111..ba2c45919 100644 --- a/README.rst +++ b/README.rst @@ -194,7 +194,9 @@ Docker default platform on macOS with Apple Silicon =================================================== If macOS cwltool users want to run tools/workflows that reference software containers that only support amd64 (64-bit x86), but they have an Apple Silicon (aarch64/arm64) CPU, -they run into the error ``WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested``. +they run into the error: + +``WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested``. To circumvent this, export the following environment variable before executing the `cwltool`: From 9da5ce22348cb3e6f42b020f2797f65a432a2cf8 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Thu, 7 Nov 2024 15:40:02 +0100 Subject: [PATCH 4/5] tweaks --- README.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index ba2c45919..58195d5f7 100644 --- a/README.rst +++ b/README.rst @@ -193,16 +193,16 @@ and ``--tmp-outdir-prefix`` to somewhere under ``/Users``:: Docker default platform on macOS with Apple Silicon =================================================== -If macOS cwltool users want to run tools/workflows that reference software containers that only support amd64 (64-bit x86), but they have an Apple Silicon (aarch64/arm64) CPU, +If macOS users want to run CWL tools/workflows using ``cwltool`` with Docker and their software containers only have support for amd64 (64-bit x86) CPUs, but they have an Apple Silicon (aarch64/arm64) CPU, they run into the error: -``WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested``. + WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested. -To circumvent this, export the following environment variable before executing the `cwltool`: +To fix this, export the following environment variable before executing `cwltool`: ``export DOCKER_DEFAULT_PLATFORM=linux/amd64`` -To automatically enable this variable in new shells, this can be added to the respective shell profiles (e.g. ``~/.zshrc``, ``~/.bash_profile``). +To automically have this variable set in the future, add the same command to ones respective shell profile (e.g. ``~/.zshrc``, ``~/.bash_profile``). Using uDocker From 16743188aa70f2d54f301a86bdf38c3fb4d096c3 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Thu, 7 Nov 2024 17:07:12 +0100 Subject: [PATCH 5/5] fix my typo --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 58195d5f7..dce55fc95 100644 --- a/README.rst +++ b/README.rst @@ -202,7 +202,7 @@ To fix this, export the following environment variable before executing `cwltool ``export DOCKER_DEFAULT_PLATFORM=linux/amd64`` -To automically have this variable set in the future, add the same command to ones respective shell profile (e.g. ``~/.zshrc``, ``~/.bash_profile``). +To automatically have this variable set in the future, add the same command to ones respective shell profile (e.g. ``~/.zshrc``, ``~/.bash_profile``). Using uDocker