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grst / containerize-conda

Turn an existing conda environment into a Singularity container
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cannot stat 'packed_environment.tar.gz': No such file or directory #3

Open kenhanscombe opened 2 years ago

kenhanscombe commented 2 years ago

Hi,

Any idea why the packed environment file can't be found on the host?

Using singularity build --remote ... and I get:

INFO:    Access Token Verified!
INFO:    Token stored in /root/.singularity/remote.yaml
INFO:    Remote "default" now in use.
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:a2abf6c4d29d43a4bf9fbb769f524d0fb36a2edab49819c1bf3e76f409f953ea
Copying blob sha256:c256cb8a03f53bc258cce8c545ce0d4fd1f17cf695dfd11aa550f602a020e181
Copying blob sha256:96470ebef4adc6521c81f93d2437e182de590faa6efdcc38a83484b502f46d6c
Copying config sha256:397371bbd8abbd2f471f36b0af8aa3b7e9b04929f45f2540af55deec18240dce
Writing manifest to image destination
Storing signatures
2022/02/25 16:47:10  info unpack layer: sha256:a2abf6c4d29d43a4bf9fbb769f524d0fb36a2edab49819c1bf3e76f409f953ea
2022/02/25 16:47:12  info unpack layer: sha256:c256cb8a03f53bc258cce8c545ce0d4fd1f17cf695dfd11aa550f602a020e181
2022/02/25 16:47:14  info unpack layer: sha256:96470ebef4adc6521c81f93d2437e182de590faa6efdcc38a83484b502f46d6c
INFO:    Copying packed_environment.tar.gz to /packed_environment.tar.gz
FATAL:   While performing build: unable to copy files from host to container fs: while copying [packed_environment.tar.gz] to /tmp/build-temp-649033200/rootfs/packed_environment.tar.gz: exit status 1: /bin/cp: cannot stat 'packed_environment.tar.gz': No such file or directory
FATAL:   While performing build: build image size <= 0

Is it something to do with the remote build. (Both the packed_environment.tar.gz file and the Singularity file are in the working directory)

Thanks

grst commented 2 years ago

I have no experience with remote builds... but since the packed_environment.tar.gz is a local file I'm not sure a remote build can work in this case. Any reason you can't build it locally?

kenhanscombe commented 2 years ago

I'm using --remote because it's on an HPC cluster not set up to use --fakeroot. I can't find anything in singularity documentation that indicates source files in the current directory (working directory with defintion file) should be specified differently in the %files section for --remote builds. I see what you're saying about it being a local file and a remote build. I'll try copy the file across in the %setup section.