Error converting

[egarza]

I'm getting this error when I try to convert the bids/cpac from docker to singularity:

sudo docker run --privileged -ti --rm -v /var/run/docker.sock:/var/run/docke
r.sock -v /home/egarza/MRI/apps/singularity_images:/output singularityware/docker2singularity bids/cpac
Size: 5533 MB for the singularity container
(1/9) Creating an empty image...
Creating a sparse image with a maximum size of 5533MiB...
Using given image size of 5533
Formatting image (/sbin/mkfs.ext3)
Done. Image can be found at: /tmp/bids_cpac-2017-03-29-71120146c4f4.img
(2/9) Importing filesystem...
(3/9) Bootstrapping...
(4/9) Adding run script...
(5/9) Setting ENV variables...
Singularity: sexec (U=0,P=146)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh
(6/9) Adding mount points...
Singularity: sexec (U=0,P=152)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh
(7/9) Fixing permissions...
Singularity: sexec (U=0,P=158)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh
We're running on BusyBox/Buildroot
Singularity: sexec (U=0,P=201)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh
find: `/proc/2/task/2/fd/11': No such file or directory
find: `/proc/2/task/2/fd/11': No such file or directory
find: `/proc/2/task/2/fdinfo/11': No such file or directory
find: `/proc/2/task/2/fdinfo/11': No such file or directory
find: `/proc/2/fd/11': No such file or directory
find: `/proc/2/fd/11': No such file or directory
find: `/proc/2/fdinfo/11': No such file or directory
find: `/proc/2/fdinfo/11': No such file or directory

Any help is appreciated,

Thanks

Eduardo

[chrisgorgo]

This should've been fixed. Are you using the latest version of docker2singularity?

On Aug 1, 2017 9:01 AM, "Eduardo Garza-Villarreal" notifications@github.com wrote:

I'm getting this error when I try to convert the bids/cpac from docker to singularity:

sudo docker run --privileged -ti --rm -v /var/run/docker.sock:/var/run/docke r.sock -v /home/egarza/MRI/apps/singularity_images:/output singularityware/docker2singularity bids/cpac Size: 5533 MB for the singularity container (1/9) Creating an empty image... Creating a sparse image with a maximum size of 5533MiB... Using given image size of 5533 Formatting image (/sbin/mkfs.ext3) Done. Image can be found at: /tmp/bids_cpac-2017-03-29-71120146c4f4.img (2/9) Importing filesystem... (3/9) Bootstrapping... (4/9) Adding run script... (5/9) Setting ENV variables... Singularity: sexec (U=0,P=146)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh (6/9) Adding mount points... Singularity: sexec (U=0,P=152)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh (7/9) Fixing permissions... Singularity: sexec (U=0,P=158)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh We're running on BusyBox/Buildroot Singularity: sexec (U=0,P=201)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh find: /proc/2/task/2/fd/11': No such file or directory find:/proc/2/task/2/fd/11': No such file or directory find: /proc/2/task/2/fdinfo/11': No such file or directory find:/proc/2/task/2/fdinfo/11': No such file or directory find: /proc/2/fd/11': No such file or directory find:/proc/2/fd/11': No such file or directory find: /proc/2/fdinfo/11': No such file or directory find:/proc/2/fdinfo/11': No such file or directory

Any help is appreciated,

Thanks

Eduardo

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[egarza]

Yeah. It should be. I don't actually download docker2singularity, I use the docker version of it, so it should be the latest. Do I give it another try?

[chrisgorgo]

I just tried this and could not replicate. I expect your docker2singularity is out of date. Try updating it via:

docker pull singularityware/docker2singularity

On Tue, Aug 1, 2017 at 10:23 AM, Eduardo Garza-Villarreal < notifications@github.com> wrote:

Yeah. It should be. I don't actually download docker2singularity, I use the docker version of it, so it should be the latest. Do I give it another try?

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[egarza]

Yup, that was the problem. Now it worked.

Thanks, Chris.