wget from inside the container

[vesbes]

Dear *,

Just started playing with this container technology ... what I ride!

I'm trying to move from VM's to containers on HPC environment and thus Singularity is a perfect match.

Congrats ladies and gents.

Trying to install software in a container but I'm stuck with a 'wget' cmd. The link works just fine on my build box but when called from inside the container it seems to fail. I also tried containers of different sizes to ensure it was not a space problem, still the same.

Any help to put me on the right track is appreciated.

Cheers,

vb

vagrant@vagrant-ubuntu-trusty-64:~$ sudo singularity create -s 1024 gromacs.img

vagrant@vagrant-ubuntu-trusty-64:~$ sudo singularity bootstrap gromacs.img gromacs.def

Cache folder set to /home/vagrant/.singularity/docker
... snip ...

Running hooks in /etc/ca-certificates/update.d...

done.

/bin/sh: 7: wget http://ftp.gromacs.org/pub/gromacs/gromacs-2016.3.tar.gz: not found

WARNING: Something may have gone wrong. %post script exited with non-zero status.

vagrant@vagrant-ubuntu-trusty-64:~$ singularity exec gromacs.img df -h

Filesystem      Size  Used Avail Use% Mounted on

/dev/loop0      976M  392M  534M  43% /

/dev/sda1        40G  3.4G   35G   9% /tmp

tmpfs            49M  356K   49M   1% /etc/resolv.conf

udev            241M   12K  241M   1% /dev

Bootstrap: docker

From: ubuntu:latest

 

%setup

    # commands to be executed on host outside container during bootstrap

 

%post

    # commands to be executed inside container during bootstrap Pre-requisites installs

    apt-get -y update

    apt-get -y install build-essential wget cmake

    # Download and uncompress gmx

    wget http://ftp.gromacs.org/pub/gromacs/gromacs-2016.3.tar.gz

 

%runscript

    # commands to be executed when the container runs

 

%test

    # commands to be executed within container at close of bootstrap process

[tin h]

Vesbes, 

You can indeed install wget and have it run inside your container like the way you have specified.  I have done so to install anaconda and it worked for me.

From your error, it seems to complain that wget is not installed in your container, but you have specified to do so.

The interesting part is I would expect the error to be "wget: command not found".

But in your output it included the URL as well.   Could there be some non-print character between your wget and the http, thus confusing the system as it treated it as one long convoluted command?

Other than that, I have tended to use "--force-yes" option in apt-get.  Perhaps that may help you as well.

Good luck!

Tin

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[vanessa s]

Hey vesbes! I think this might be related to running in Vagrant. Could you re-run the bootstrap and add --debug to give the full output?

sudo singularity --debug bootstrap gromacs.img gromacs.def

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Vanessa Villamia Sochat
Stanford University '16

(603) 321-0676

[vesbes]

Hi Tin, Vanessa

Thanks for the prompt reply.

The issue was a hidden character in the wget command (probably introduced when I did copy/past of that specific cmd line).

Just great.

Cheers,

N.

[vanessa s]

Awesome! Glad you caught it. Never can know what's hiding in copy pastes these days... or excel cells for that matter.

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