Error while running the first command on Docker "docker: failed to register layer"

[Mtay316]

Hi , First of all I wanted to say thank you for making this amazing method that can solve lots of distortion correction problems on dataset without reverse gradient. Your work is so precious.

I tried to run your method on my data and what I did is to run the following command:

sudo docker run --rm \ -v $(pwd)/INPUTS/:/INPUTS/ \ -v $(pwd)/OUTPUTS:/OUTPUTS/ \ -v /usr/local/freesurfer:/extra/freesurfer/license.txt \ --user $(id -u):$(id -g) \ leonyichencai/synb0-disco:v3.0 Password: Unable to find image 'leonyichencai/synb0-disco:v3.0' locally v3.0: Pulling from leonyichencai/synb0-disco

As you mentioned in your instruction, as a Mac user I opened my Docker and in the setting I increased the Memory to 40 GB and CPUs to 8 , Swap is 1 GB and Disk Image size is 59.6 GB.

After running the command , I can see all of the downloading goes complete, apart from the biggest one with 12.38 GB. I can see it goes up to 10 GB and then it drops out and showing this error:

docker: failed to register layer: Error processing tar file(exit status 1): write /extra/fsl/bin/fdt_matrix_merge: no space left on device. See 'docker run --help'.

Could you please help me how to sort out this issue?

Big thanks, Maryam

[Diffusion-MRI]

Could you copy the full output or error log? That will help us debug where the error occurs.

Thank you.

[Mtay316]

This is everything :

Unable to find image 'leonyichencai/synb0-disco:v3.0' locally v3.0: Pulling from leonyichencai/synb0-disco 6abc03819f3e: Pull complete 05731e63f211: Pull complete 0bd67c50d6be: Pull complete af74ea47daf5: Pull complete 1183f58ddb5d: Extracting [==================================================>] 12.38GB/12.38GB bffc45fdfb6e: Download complete 76e5d712b7df: Download complete a8616262ab23: Download complete c02c7de5bd7b: Download complete 96ae328f242e: Download complete 59c27ab8fec6: Download complete 727a3d6a1614: Download complete 224d00df44f6: Download complete f8395e755e56: Download complete ad0f643c8349: Download complete d6d717c50894: Download complete 9332719043ff: Download complete f8b462257835: Download complete docker: failed to register layer: Error processing tar file(exit status 1): write /extra/fsl/bin/fdt_matrix_merge: no space left on device. See 'docker run --help'.

[Diffusion-MRI]

This is an error downloading the image. It seems as if you have run out of space on your hard drive? It may be worth downloading on a disk space that you know contains plenty of space (10-12Gb).

[Mtay316]

Could you please tell me how to do that? I am not that familiar with Docker. My Hard drive has 2 TB space and still 0.5 TB space left there. I don't know which part of the command to change to download it on a disk space

[Diffusion-MRI]

That should be plenty of space. I would try the pulling the docker again (which is the first thing done when you do 'docker run'). It only needs to download once, then all other 'docker run' calls will be much more quick because it will not need to redownload the container.

[Mtay316]

I tried again, and this time I logged in the Docker page and found "leonyichencai/synb0-disco" and pulled the docker command from there "docker pull leonyichencai/synb0-disco"

After running this command , I got this error :

Using default tag: latest latest: Pulling from leonyichencai/synb0-disco 6abc03819f3e: Pull complete 05731e63f211: Pull complete 0bd67c50d6be: Pull complete af74ea47daf5: Pull complete 1183f58ddb5d: Extracting [==================================================>] 12.38GB/12.38GB bffc45fdfb6e: Download complete 76e5d712b7df: Download complete a8616262ab23: Download complete c02c7de5bd7b: Download complete 96ae328f242e: Download complete 59c27ab8fec6: Download complete 727a3d6a1614: Download complete 224d00df44f6: Download complete f8395e755e56: Download complete ad0f643c8349: Download complete d6d717c50894: Download complete 9332719043ff: Download complete f8b462257835: Download complete failed to register layer: Error processing tar file(exit status 1): write /extra/fsl/bin/fdt_matrix_merge: no space left on device

Seems like downloading the image is not a problem this time but space is still an issue. What do I need to add to the command to define the space on my hard drive ?

[Mtay316]

In order to check how much space can be reclaimed due to unused images, I ran this command:

docker system df

And what I got was:

TYPE TOTAL ACTIVE SIZE RECLAIMABLE Images 3 2 24.74GB 11.23GB (45%) Containers 4 0 122kB 122kB (100%) Local Volumes 0 0 0B 0B Build Cache 36 0 6.237GB 6.237GB

And because RECLAIMABLE amount was greater than zero then I ran command:

docker system prune -a

and it cleaned up all the unused space.

Now I am running "docker pull leonyichencai/synb0-disco " again. I hope it works this time

[Mtay316]

Fortunately It worked and space problem is solved. Thanks