easybuild_bootstrap.sh - modulecmd' command is not available. about easybuild-life-sciences HOT 6 CLOSED

i have been using this runlist using the prox command:

petersen@rhino3:~$ cat runlists/easybuild.runlist
sudo apt-get install -y curl
sudo adduser --disabled-password --gecos "" eb
sudo sh -c "echo 'eb ALL=(ALL:ALL) NOPASSWD:ALL' > /etc/sudoers.d/zz_eb"
echo "please switch to user eb and then run:"
echo "curl -s https://raw.githubusercontent.com/FredHutch/easybuild-life-sciences/master/easybuild_bootstrap.sh | bash"

petersen@rhino3:~$ prox --runlist runlists/easybuild.runlist new newbox

from easybuild-life-sciences.

This line in the EasyBuild modulefile (/app/easybuild/modules/all/EasyBuild/:

setenv EASYBUILD_MODULES_TOOL "Lmod"

Should be telling EasyBuild to use Lmod, not Environment Modules. Check that is being implemented.

Also, is your VM mounting /app? That will collide.

from easybuild-life-sciences.

Ok will try, no it is not mounting /app

On Oct 22, 2016, at 12:12 PM, Ben McGough <[email protected]mailto:[email protected]> wrote:

This line in the EasyBuild modulefile (/app/easybuild/modules/all/EasyBuild/:

setenv EASYBUILD_MODULES_TOOL "Lmod"

Should be telling EasyBuild to use Lmod, not Environment Modules. Check that is being implemented.

Also, is your VM mounting /app? That will collide.

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from easybuild-life-sciences.

I set it via export ... and it worked

But the bootstrapping script already contains this...should that not work?

setenv EASYBUILD_MODULES_TOOL "Lmod"

Dirk

From: Petersen, Dirk
Sent: Saturday, October 22, 2016 12:43 PM
To: FredHutch/easybuild-life-sciences [email protected]
Cc: FredHutch/easybuild-life-sciences [email protected]; Author [email protected]
Subject: Re: [FredHutch/easybuild-life-sciences] easybuild_bootstrap.sh - modulecmd' command is not available. (#11)

Ok will try, no it is not mounting /app

On Oct 22, 2016, at 12:12 PM, Ben McGough <[email protected]mailto:[email protected]> wrote:

This line in the EasyBuild modulefile (/app/easybuild/modules/all/EasyBuild/:

setenv EASYBUILD_MODULES_TOOL "Lmod"

Should be telling EasyBuild to use Lmod, not Environment Modules. Check that is being implemented.

Also, is your VM mounting /app? That will collide.

You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHubhttps://github.com//issues/11#issuecomment-255547914, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABXJB4ytMUUij7N2qI4wPIX6cCbNrxHlks5q2mAxgaJpZM4Kd6wM.

from easybuild-life-sciences.

This was due to the EasyBuild 2.8.2 bootstrap script actually bootstrapping EasyBuild 2.9.0, so you were not using the carefully constructed modulefile /easybuild/modules/all/EasyBuild/2.8.2, but the generic one /easybuild/modules/all/EasyBuild/2.9.0.

The script has been update to expect 2.9.0, but this will break again when the next version of EasyBuild is released, so we are not done with this issue.

Ben McGough
System Administrator / Center IT - Scientific Computing / 206.667.7818 / [email protected] / Fred Hutch / Cures Start Here

----- Original Message -----
From: "Dirk Petersen" [email protected]
To: "FredHutch/easybuild-life-sciences" [email protected]
Cc: "Benjamin E McGough" [email protected], "Comment" [email protected]
Sent: Tuesday, October 25, 2016 11:25:39 AM
Subject: Re: [FredHutch/easybuild-life-sciences] easybuild_bootstrap.sh - modulecmd' command is not available. (#11)

I set it via export ... and it worked

But the bootstrapping script already contains this...should that not work?

setenv EASYBUILD_MODULES_TOOL "Lmod"

Dirk

From: Petersen, Dirk
Sent: Saturday, October 22, 2016 12:43 PM
To: FredHutch/easybuild-life-sciences [email protected]
Cc: FredHutch/easybuild-life-sciences [email protected]; Author [email protected]
Subject: Re: [FredHutch/easybuild-life-sciences] easybuild_bootstrap.sh - modulecmd' command is not available. (#11)

Ok will try, no it is not mounting /app

On Oct 22, 2016, at 12:12 PM, Ben McGough <[email protected]mailto:[email protected]> wrote:

This line in the EasyBuild modulefile (/app/easybuild/modules/all/EasyBuild/:

setenv EASYBUILD_MODULES_TOOL "Lmod"

Should be telling EasyBuild to use Lmod, not Environment Modules. Check that is being implemented.

Also, is your VM mounting /app? That will collide.

You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHubhttps://github.com//issues/11#issuecomment-255547914, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABXJB4ytMUUij7N2qI4wPIX6cCbNrxHlks5q2mAxgaJpZM4Kd6wM.

You are receiving this because you commented.
Reply to this email directly or view it on GitHub:
#11 (comment)

from easybuild-life-sciences.

Script was 'delivered' - closing out.

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