Wrongly reported: No space left on device

[Michał T. Lorenc]

Hi,

Despite my laptop has more than 30 GB free I Singularity reported No space left on device:

Building Singularity image...
tar: ./usr/local/envs/3d-dna/lib/libicui18n.a: Wrote only 2048 of 10240 bytes
tar: ./usr/local/envs/3d-dna/lib/lib: Cannot mkdir: No space left on device

I used the following commands:

docker run --rm -it --privileged -v $(pwd):/work deephorizons/singularity sh
cd work
singularity create 3d-dna.img
singularity bootstrap 3d-dna.img Singularity

What did I miss?

Thank you in advance.

Michal

[Joana Chavez]

Hello Michal, is your container using a ext3 file system? I would suggest running it with a sandbox if that's the case. Ext3 has an allotted amount of space which you might be exceeding, whereas a sandbox has much space. Other possibility would be to expand your image using image expand ( see this -> https://www.sylabs.io/guides/2.6/user-guide/appendix.html?highlight=image%20expand#image-expand )

If you would like to run it with a sandbox instead you could do so: sudo singularity build --sandbox new_container old_container

Joana

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[Michał T. Lorenc]

Hi Joana,

I tried to use sandbox (singularity build --sandbox 3d-dna-sandbox Singularity) but now I got

Errors were encountered while processing:
 /tmp/apt-dpkg-install-gpR3vj/061-linux-libc-dev_4.9.110-3+deb9u4_amd64.deb
 /tmp/apt-dpkg-install-gpR3vj/112-manpages-dev_4.10-2_all.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
ABORT: Aborting with RETVAL=255

with this Singularity file:

BootStrap: docker
From: debian:stretch-backports

%help
  A container with 3d-dna

%environment
  PATH=/opt/conda/bin:$PATH


%post
  apt-get update && apt-get -y upgrade
  apt-get -y install \
    build-essential \
    wget \
    bzip2 \
    ca-certificates \
    libglib2.0-0 \
    libxext6 \
    libsm6 \
    libxrender1 \
    git

  rm -rf /var/lib/apt/lists/*
  apt-get clean

  # download and install Miniconda
  echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh
  wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
    /bin/bash Miniconda2-latest-Linux-x86_64.sh -bfp /usr/local/

  rm -rf Miniconda2-latest-Linux-x86_64.sh

  # add bioconda channels
  conda config --add channels defaults
  conda config --add channels conda-forge
  conda config --add channels bioconda
  conda update conda
 
  # install 3d-dna dependecies
  conda create -y --name 3d-dna lastz=1.0.4 openjdk=8.0.152 gawk=4.2.1 coreutils=8.30 parallel=20180522 python=2.7 numpy=1.15.1 scipy=1.1.0 matplotlib=2.2.3
  conda clean --all --yes

  # install 3d-dna
  git clone https://github.com/theaidenlab/3d-dna.git

%runscript
   exec conda activate 3d-dna

What did I miss?

Thank you in advance,

Michal

[Jafaruddin Lie]

You might not have enough space in the docker container to build the singularity container.

Maybe try setting the Singularity build environment to a local directory that you mount into Docker? (http://singularity.lbl.gov/build-environment)

Another thing, since you have the Singularity file, why not just build it using Singularity on your local PC?

If that's not possible, you can always try Singularity Hub (https://singularity-hub.org/) to build.

[Michał T. Lorenc]

I use docker because I am unsing a mac and I think singularity is not avaible for mac.

Before using Singularity Hub I would prefere to do it locally because of testsing the container.

How is it possible to check how much space the docker container has? The Singularity contaner get build on a docker volume which has 30 GB available.

Thank you in advance,

Michal

[Michał T. Lorenc]

I used the wrong command to create the image. The correct one was singularity build 3d-dna.simg Singularity .

Thank you for your help.

Michal