Is there a way to auto-pass environment variables to the container?

[Jonathan Greenberg]

I'm still a bit confused about how environment variables are passed to the containers.  Say I want to make sure some environment variable I've assigned my global environment "MOO" available in the container "automatically" (not tacking it to the singularity exec statement) -- how do I go about doing this?

--j

[Thomas Hartmann]

Hi Jonathan,

if you create a Singularity container natively, you can add environment
variables in your Singularity file with the enironment flag, e.g.

%environment
MYFOOVAR="somevalue"
MYBAZVAR=23

Else, if you have imported a container from Docker or so, you maybe can
trick it by creating a sandboxed version and add an env-script to

yoursandbox.d/.singularity.d/env/99-mystuff.sh

(there should be a hidden .singularity/ directory in a container, where
Singularity keeps its info)

Cheers,
Thomas

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[Jason Stover]

Hi,

As mentioned you can use the %environment section in the DEF file.
If you need to pass changing values, you can do something like:

export SINGULARITYENV_MOO="cow"

Then when you run singularity, you should have the "MOO" variable
available to you. Just prefix whatever with "SINGULARITYENV_" ... i.e.
SINGULARITYENV_MY_VAR ... for "MY_VAR".

-J

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[Jonathan Greenberg]

Hmm, so is "TMPDIR" a protected name?  The MOO -> cow thing worked properly, but:

export SINGULARITYENV_MOO="cow" 

export SINGULARITYENV_TMPDIR=/pathto/scratch/$USER

echo $SINGULARITYENV_MOO

cow

echo $SINGULARITYENV_TMPDIR

/pathto/scratch/jgreenberg

Now in Singularity:

singularity shell ~/gearslaboratory-gears-singularity-master-gears-general.simg

echo $MOO

cow

echo $TMPDIR

TMPDIR

Not working!  Thoughts?

--j

> > <mailto:singularity+unsub...@lbl.gov>.

[Jason Stover]

No, not protected. That should work. I'm not getting that at least...

$ echo $TMPDIR

$ export SINGULARITYENV_TMPDIR="/lala/tmp"
$ /usr/local/singularity/2.5.1/bin/singularity shell ~/images/ubuntu-latest.img
Singularity ubuntu-latest.img:~> echo $TMPDIR
/lala/tmp

-J

>> > > <mailto:singularity...@lbl.gov>.

[Thomas Hartmann]

hmmm, can you grep in your container, if maybe another script
sets/overwrites TMPDIR?

grep -ri TMPDIR /.singularity.d/env

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[Jonathan Greenberg]

The grep (from inside the container) returns:

/.singularity.d/env/90-environment.sh:    TMPDIR=TMPDIR

/.singularity.d/env/90-environment.sh:    export TMPDIR TMP TEMP

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[Jonathan Greenberg]

AH.  Got it.  I had (don't remember why):

%environment

    TMPDIR=TMPDIR

    TMP=TMP

    TEMP=TEMP

    export TMPDIR TMP TEMP 

in my container def.  Fixing it now!

--j