/usr/local/etc/singularity/singularity.conf: no such file or directory

[Monolarity]

hi,

I am trying to use an singularity application on our Linux cluster. Our admin has installed in on all nodes and it seems to work:

hpcl:> which singularity
/usr/local/bin/singularity

When I run my application I get an error, since it cannot find the singularity.conf file:

Activating singularity image /fs/.. .snakemake/singularity/file.simg

[31mFATAL: [0m Unable to parse singularity.conf file: open /usr/local/etc/singularity/singularity.conf: no such file or directory

the path doesn't exist, so I wonder how to fix this. Is there a different way to install singularity or to specify the path manually?

Thanks a lot!

[Justin Cook]

Monolarity,

What you are seeing should not happen. Did the admin move the config file after the installation process? During the installation, the path to the configuration file is hard-coded into the singularity binary. So if it was moved afterwards I could see that error occurring.

Thanks,

Justin

[Richard Powell]

If they did move the conf file to a centralized location (we do on our cluster) a symlink needs to be created at the expected location to reflect the centralized location.  Also they should ensure the symlink and the centralized conf are owned by root.  

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[Monolarity]

Thanks! I guess that was the issue. At least our admin seemed to know where the problem was and just fixed it.

Now I am getting:

bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF8)

Is this also related to an similar cause, like folders being removed or so? Or isn‘t this related to singularity anymore?

Thank you!

With locale I get:
>locale
LANG=en_US.UTF-8
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=en_US.UTF-8

[Justin Cook]

Monolarity,

Where is this warning occurring? Could you send the whole command with the output or open an issue on github with it?

Thanks!

Justin

[Sarom Leang]

I had this issue when trying to use ubuntu:16.04 and installing a python package.

I resolved it with:

apt-get install -y locales

echo "LC_ALL=en_US.UTF-8" >> /etc/environment

echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen

echo "LANG=en_US.UTF-8" > /etc/locale.conf

locale-gen en_US.UTF-8

S/

[Monolarity]

Thanks again. seems to work now.

the warning is still there, but does not seem to cause an issue later on.