Segmentation fault errors when running a docker image

[Diego Ortega Del Vecchyo]

Hello Singularity community,

I am learning how to use Singularity and I am trying to use it on my Mac. I was making some tests trying to execute a command from a docker image. With docker I did the following to download and run one simple command:

ucbvpn-209-149:Programitas vicentediegoortegadelvecchyo$ docker pull cmonjeau/im_clam

Using default tag: latest

latest: Pulling from cmonjeau/im_clam

Digest: sha256:3f80ad1c02c43767269161fadbc3dc5216427d3d2348803b9e2bb2672b0cb9d3

Status: Image is up to date for cmonjeau/im_clam:latest

ucbvpn-209-149:Programitas vicentediegoortegadelvecchyo$ docker run -it --rm cmonjeau/im_clam /opt/im_clam/cmc_stateSpace 3 3

n1: 3 n2: 3 nstates: 268

0 0 0 0 || 0 3 0 0 

3 0 0 0 || 0 0 0 0 

0 0 0 0 || 0 0 0 0 

0 0 0 0 || 0 0 0 0 

-----------

So things were working well there. On the other hand, I tried to install singularity following the instructions from http://singularity.lbl.gov/install-mac . When I tried to download a docker image and make it run, I got a segmentation fault error:

vagrant@vagrant:~$ sudo singularity build im_clam_2.img docker://cmonjeau/im_clam

Docker image path: index.docker.io/cmonjeau/im_clam:latest

Cache folder set to /root/.singularity/docker

Importing: base Singularity environment

Importing: /root/.singularity/docker/sha256:693502eb7dfbc6b94964ae66ebc72d3e32facd981c72995b09794f1e87bac184.tar.gz

Importing: /root/.singularity/docker/sha256:4e72165269eb76a55576d8e4c63244419dd8450c7a20bd89d8a2b5dcfc6c1a46.tar.gz

Importing: /root/.singularity/docker/sha256:0cbcfa14b6e0fb3ee380e3b819abacb953b13b0258815a2f1a0cfc51923e6c77.tar.gz

Importing: /root/.singularity/docker/sha256:80b6f7236a3953a185c5cc3b5dc0e9172ddda6a74661c1a7d99640c3a0e74bc7.tar.gz

Importing: /root/.singularity/docker/sha256:18ca2f7eb40dcbcbca7eaa8d85110e083affd7c545ebb69109be42b4f29463d8.tar.gz

Importing: /root/.singularity/docker/sha256:868c469dbfe980dc2f07f1fa4cb49e3cb0ed432c1e14b21669409e3095fc95b2.tar.gz

Importing: /root/.singularity/docker/sha256:62bdc35b210390ae920d55c994abadf5875123f43575b9701637235cdb2fe835.tar.gz

Importing: /root/.singularity/docker/sha256:96e60b719a598f393577db6063787766396a1e3043f20fd7d7fabbb8ee994d0a.tar.gz

Importing: /root/.singularity/docker/sha256:41270ce51037852092cf7b3cb07dbad24932d843d88582c312a63fbf92fa8896.tar.gz

Importing: /root/.singularity/docker/sha256:e83c7eabbe91e424ded5b358191d126ca686500c34803f727472ed09e9ceafaa.tar.gz

Importing: /root/.singularity/docker/sha256:4659d5d6efdbabe8a2044066066106c51121107219e286d312e23a12abfdc4f2.tar.gz

Importing: /root/.singularity/docker/sha256:7f042e511ba3e0cc9a9aec314a0b87774de0ecaafe958387e4926c6456c6e7d6.tar.gz

Importing: /root/.singularity/docker/sha256:c3986ea8d9e61ed59d660b899d1da61130d268a7a7a2c58ba77befd46e896215.tar.gz

Importing: /root/.singularity/metadata/sha256:84dcadd4ebc7fbaaa6732db68bcdb98c917db0ecf98f6bf80a46190e7621c27e.tar.gz

Building Singularity image...

Singularity container built: im_clam_2.img

Cleaning up...

vagrant@vagrant:~$ singularity exec im_clam_2.img /opt/im_clam/cmc_stateSpace 3 3

Segmentation fault (core dumped)

Does anyone know how to solve this problem? Thanks a lot!

[v]

Could you try the command with --debug to see if there is anything meaningful to be learned? it might have to do with being in a Vagrant image. What exactly does that software do?

I am testing this on linux, and using pull instead of build:

singularity pull --name im_clam_2.img docker://cmonjeau/im_clam
singularity exec $SCRATCH/.singularity/im_clam_2.img /opt/im_clam/cmc_stateSpace 3 3

The above works for me, I get a crapton of 0 0 0 0 matrix type things printed. So I think it's likely being inside the Vagrant box on a Mac that is the issue. Do you have access to a linux server?

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Vanessa Villamia Sochat
Stanford University '16

(603) 321-0676