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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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Importing the docker image into a singularity container #134

Closed mivanyo closed 5 years ago

mivanyo commented 6 years ago

I had been able to pull the docker image into a singularity last August. Now I have tried to do the same with the new Mindboggle release but it fails to import one of the gzipped tar files. How can this problem be fixed? The error message is shown below.

singularity pull --name mindboggle.img docker://nipy/mindboggle ... gzip: .../.singularity/docker/sha256:61172108f568b5ecb62997b5180da846b9ac0e2000cd2d086b7da3c0d8b95e71.tar.gz: unexpected end of file /bin/tar: Unexpected EOF in archive /bin/tar: Unexpected EOF in archive /bin/tar: Error is not recoverable: exiting now ERROR : Tar did not return successful

mivanyo commented 6 years ago

By way of additional information; the singularity version is 2.3.1 and I've tried using both the pull and import sub-commands but both have failed with the identical error.

satra commented 6 years ago

@mivanyo - this is an error typical with running out of storage space.

i can check with 2.3.1 later, but here is the output with 2.4

$ singularity pull --name mindboggle.img docker://nipy/mindboggle
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
Docker image path: index.docker.io/nipy/mindboggle:latest
Cache folder set to /dev/shm/satra/docker
[25/25] |===================================| 100.0% 
Importing: base Singularity environment
Importing: /dev/shm/satra/docker/sha256:693502eb7dfbc6b94964ae66ebc72d3e32facd981c72995b09794f1e87bac184.tar.gz
Importing: /dev/shm/satra/docker/sha256:a3782c2efb4188af8b56f4001efae6f76b337d21f3c1b58c73d484b1cf1f4b72.tar.gz
Importing: /dev/shm/satra/docker/sha256:9cb32b776a4064ce43ac5e6cc5abd317a5dba0fd5a0d842c21e73587b468d804.tar.gz
Importing: /dev/shm/satra/docker/sha256:e539f5722cd5086ddd1b5bf2324fe74e9e4f398cc9298b9f9d6f31ac5a7ab8bc.tar.gz
Importing: /dev/shm/satra/docker/sha256:b4690d4047c60224d5230518591790ef488f7b77775ce8e4dfe202bf08bca030.tar.gz
Importing: /dev/shm/satra/docker/sha256:121dc465f5c667aae08854250881e709b95511d9767551675da33f2801a77501.tar.gz
Importing: /dev/shm/satra/docker/sha256:c352772bbcfd800bdfb76ce627eb1a18b2cf5e70411ba0f74ea7672ba3d68047.tar.gz
Importing: /dev/shm/satra/docker/sha256:eeda14d1c42137239ad40b8081df1e48df93ce70cc6777edb388e40582cd104d.tar.gz
Importing: /dev/shm/satra/docker/sha256:0057b9e76c8a523a63a6418fdfc9580811083be2a505468a24eaf06348151f9b.tar.gz
Importing: /dev/shm/satra/docker/sha256:e63bd87d75ddf5bea921b03aad03f39d4c3e5557a759fde329bce4b96e44685b.tar.gz
Importing: /dev/shm/satra/docker/sha256:055904fbc069100f2cc1071176cbb732a79e8976ddfb8d5def11594b53bbadbf.tar.gz
Importing: /dev/shm/satra/docker/sha256:d336770b8a83a8c3b76fb3d8449ba0e7a82b5080cff817f1e721afba4820be69.tar.gz
Importing: /dev/shm/satra/docker/sha256:d61dbef85c7dfcaa0de7e2e221a5b88549f5be6e819609c436e80694cf89699b.tar.gz
Importing: /dev/shm/satra/docker/sha256:ffc7c70a135f12321a08b7e20e854955ea32441050770bb1caf87c1b25c671fc.tar.gz
Importing: /dev/shm/satra/docker/sha256:17bb7ee465e185ca7d95b67e9a98b171290ee9447259fabb620b809f1bd90618.tar.gz
Importing: /dev/shm/satra/docker/sha256:1312b14dd00db5468deb266f9c230075d97180ff0324c10ea2c5c6b2c54257e3.tar.gz
Importing: /dev/shm/satra/docker/sha256:79b2678810091976967c5e40984a89eec3ab1db0c654c4a02f6ceb91a8304458.tar.gz
Importing: /dev/shm/satra/docker/sha256:11af8c286d07428bce339dbeba2ef117e3d339f0cd175db4b5caaee2e292d761.tar.gz
Importing: /dev/shm/satra/docker/sha256:61172108f568b5ecb62997b5180da846b9ac0e2000cd2d086b7da3c0d8b95e71.tar.gz
Importing: /dev/shm/satra/docker/sha256:ab70cd89acdacaa8e32ad69faa3431e352e43223a78fbb88b55c7e14879d4373.tar.gz
Importing: /dev/shm/satra/docker/sha256:d06d6aefef13bd321bd94db90c1a2a3efb460276ea693ff2eccc467b43029566.tar.gz
Importing: /dev/shm/satra/docker/sha256:6c8015a048f48ea66df3b727d126fb8262c3b3f19c34c333a7764527c6888b67.tar.gz
Importing: /dev/shm/satra/docker/sha256:72fe0d30d99c6522d62ff46f3737defd0ef5cb28b0928525774b8b9b2bc5e292.tar.gz
Importing: /dev/shm/satra/docker/sha256:2568adc748a4b97eba7f6c1d5e0ad4eb8c4997211844a251094b102127e88c27.tar.gz
Importing: /dev/shm/satra/docker/sha256:3451124a5b8a8ff8b67c3085f64f3d086aa6b5b5f0d98524caa7d5ac2cf31441.tar.gz
Importing: /dev/shm/satra/metadata/sha256:b0e3e9ac94459a9d422293ec79baf69c6a6e835feebebc79dd882cf54abb92d9.tar.gz
WARNING: Building container as an unprivileged user. If you run this container as root
WARNING: it may be missing some functionality.
Building Singularity image...
Singularity container built: /dev/shm/satra/mindboggle.img
Cleaning up...
binarybottle commented 6 years ago

@mivanyo -- Did @satra's suggestion to increase storage space fix the problem?

binarybottle commented 6 years ago

@mivanyo -- Did you resolve this issue, or do you need further assistance?

binarybottle commented 5 years ago

@mivanyo -- Perhaps the recently resolved issue #159 will help you create a Singularity container?

binarybottle commented 5 years ago

@mivanyo -- I will assume that this issue was due to running out of storage space and will consider it resolved.