FATAL ERROR singularity build --sandbox test fold_analysis_latest.s if

[wanchun0715]

Hi,

I'm trying to install AlphaPulldown from step 0, and the code ,<ip install -U "jax[cuda12]"> return the error

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
tensorflow 2.14.0 requires ml-dtypes==0.2.0, but you have ml-dtypes 0.5.0 which is incompatible.
Successfully installed jax-0.4.35 ml-dtypes-0.5.0

So I assume the step 0 is successful even through the error showed up.

I have created the file fold_analysis_latest.sif using the code <singularity pull docker://kosinskilab/fold_analysis:latest>, but error show up for the next step code <singularity build --sandbox test fold_analysis_latest.sif>
ERROR: unpackSIF failed: root filesystem extraction failed: extract command failed: WARNING: passwd file doesn't exist in container, not updating
FATAL ERROR:dir_scan: failed to make directory /image/rootfs/ccp4/share/ccp4i/etc/unix, because File exists
FATAL ERROR:dir_scan: failed to make directory /image/rootfs/ccp4/share/ccp4i/etc/unix, because File exists

I deleted the ccp4 files but does not work. Could you please help with this?

Thanks a lot for the help.

Best,
Chun

[DimaMolod]

Hi @wanchun0715
the dependency conflicts should be resolved in the latest AP version. Regarding the singularity, I am not sure what went wrong, just have a couple of ideas to try:
If you have already attempted this build, there might be leftover files in the test directory. Try cleaning up the sandbox directory rm -r test and starting again. You could also try to use --overlay flag instead of --sandbox, but i suspect that something is wrong with your singularity installation (possibly related to #439)

[wanchun0715]

Thank you so much for the suggestion. Looks like I have the same issue as #439, and I use the code: singularity build new_fold_analysis_latest.sif fold_analysis_latest.sif, and it returns as follows:

INFO: Starting build...
INFO: Verifying bootstrap image fold_analysis_latest.sif
WARNING: integrity: signature not found for object group 1
WARNING: Bootstrap image could not be verified, but build will continue.
INFO: Extracting local image...
INFO: Inserting Singularity configuration...
INFO: Creating SIF file...
INFO: Build complete: new_fold_analysis_latest.sif

Hopefully, this also works for analysis.