Qsiprep image create EOF Error

Software Support
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1

Summary of what happened:

I am using a singularity container to create an image. I get an EOF error as detailed below.

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity build qsiprep-0.22.1.sif docker://pennbbl/qsiprep:0.22.1

Environment (Docker, Singularity / Apptainer, custom installation):

Running with singularity.

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

bids-validator@1.14.6

Relevant log outputs (up to 20 lines):

"FATAL:   While performing build: conveyor failed to get: Error initializing source oci:/PHShome/mw1264/.singularity/cache/blob:c175102aa4bfa07d5015f9d80406019c7e5529d529df2996640f299a5cf0bc38: Error writing blob: unexpected EOF"

Screenshots / relevant information:

image
image1132×595 153 KB

As you can see in the screenshots, the copying of blobs is taking place till around 400 MB, after which it just stops and moves to the next blob. I do have around 500 MB of space in my home directory which is maybe why. I was wondering if there is a way to specify where the image can be built. I have also tried with other qsiprep versions but get the same error.

Thanks!

2

Hi @mwalvekar, and welcome to neurostars!

You can move your singularity cache to a place with more space, then symlink from your home directory to that new location, e.g.:

mv ~/.singularity /new/place/
ln -s /new/place/.singularity ~/.singularity

Best,
Steven

3

Hi @Steven

Thanks for responding!

I tried that way and unfortunately that doesn’t seem to work. I get the same error.

FATAL: While performing build: conveyor failed to get: Error initializing source oci:/PHShome/mw1264/.singularity/cache/blob:c175102aa4bfa07d5015f9d80406019c7e5529d529df2996640f299a5cf0bc38: Error writing blob: unexpected EOF

It still seems initialize in the directory .singularity was initially setup in even though I did symlink. I had to remove the previous .singularity directory from my home directory for the symlink to work, or else I would get this error. ln: failed to create symbolic link ‘/PHShome/mw1264/.singularity/.singularity’: File exists

When I look at the folders in my home directory now with ls -la, it says:
lrwxrwxrwx. 1 mw1264 mw1264 39 Sep 17 14:04 .singularity -> /new/place/.singularity

Which does seem to hint at some connection. I just don’t know which way it means to say that connection has been made.

Let me know,
Thanks!
Mihir

4

You should replace /new/place with the actual name of where you want the data to go to. Depending on your filesystem, /new/place might not exist or be a place you have write permissions to. It also looks like it is trying to make a link at /PHShome/mw1264/.singularity/.singularity, when it should be just at /PHShome/mw1264/.singularity. You can also try clearing out the singularity cache and trying again.