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Merged
merged 23 commits into from
Aug 14, 2020
Merged

First version of a Prefix installation #4

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a06ffdc
Updated README
bedroge Jun 30, 2020
4488047
Our bootstrap script
bedroge Jun 30, 2020
fab0dbf
Build file for Singularity container
bedroge Jun 30, 2020
fcea440
Update README.md
bedroge Jun 30, 2020
3ec0dde
Update README.md
bedroge Jun 30, 2020
51d6847
use https for distfiles.prefix.bitzolder.nl (to avoid 403 errors when…
boegel Jul 2, 2020
c05a920
Merge pull request #6 from boegel/install_prefix
bedroge Jul 2, 2020
99c7663
Updated README
bedroge Jul 2, 2020
27dfe5c
Renamed def file
bedroge Jul 2, 2020
df7ffb5
Improved def file
bedroge Jul 2, 2020
fa16ba4
Renamed some files in README
bedroge Jul 2, 2020
348e9fb
Merge branch 'install_prefix' of github.com:EESSI/compatibility-layer…
bedroge Jul 2, 2020
28e7ae4
Merge branch 'master' into install_prefix
bedroge Jul 2, 2020
28eb4d9
fix determining shell in bootstrap_startscript, take into account tha…
boegel Jul 2, 2020
224a0b1
Merge pull request #7 from boegel/install_prefix
bedroge Jul 2, 2020
c5af17a
Added bootstrap fix to README
bedroge Jul 2, 2020
e63649c
Update README.md
bedroge Jul 2, 2020
c832839
Updated bootstrap script to latest gentoo git commit
bedroge Jul 3, 2020
244eae9
Updated README
bedroge Jul 3, 2020
cf24792
Updated README
bedroge Jul 3, 2020
52e40a9
Update README.md
bedroge Jul 3, 2020
890d2fc
Update singularity-bootstrap-prefix.def
bedroge Jul 13, 2020
1bcc647
add linebreak/indentation
bedroge Jul 13, 2020
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34 changes: 28 additions & 6 deletions README.md
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Expand Up @@ -11,12 +11,36 @@ An alternative would be the [NixOS](https://nixos.org/).
### Prerequisites

The bootstrap process will need a clean environment with a compiler (the system version of gcc will do). It also is very sensitive to
the environment, so setup a user with unset CFFLAGS, CFLAGS, LDFLAGS, PKG_CONFIG_PATH and the always harmful LD_LIBRARY_PATH variables.
EESSI provides a singularity container for this.
the environment, so setup a user with unset `CFFLAGS`, `CFLAGS`, `LDFLAGS`, `PKG_CONFIG_PATH` and the always harmful `LD_LIBRARY_PATH` variables.

EESSI provides a Singularity container for this.

### Building the Singularity container
The provided Singularity definition file can be used to build a container with a clean environment:
```
sudo singularity build bootstrap-prefix.sif singularity-bootstrap-prefix.def
```

### Bootstrapping Gentoo Prefix
Gentoo Prefix provides a bootstrap script to build the prefix. See [Gentoo Prefix Bootstrap](https://wiki.gentoo.org/wiki/Project:Prefix/Bootstrap)
or build and use the singularity container. After starting the bootstrap have a long coffee...
Gentoo Prefix provides a bootstrap script to build the prefix, see [Gentoo Prefix Bootstrap](https://wiki.gentoo.org/wiki/Project:Prefix/Bootstrap).
We forked [this version](https://gitweb.gentoo.org/repo/proj/prefix.git/tree/scripts/bootstrap-prefix.sh?id=e77fd01734f21ec2e9c985c28ba4eb30c1b2bc9d)
and made some modifications. See issue [#8](https://github.com/EESSI/compatibility-layer/issues/8) for more details.

You can run our version of the bootstrap script (see `bootstrap-prefix.sh`) inside the Singularity container by executing:
```
singularity run bootstrap-prefix.sif
```
or simply:
```
./bootstrap-prefix.sif
```

If you want to run your own version of the bootstrap script, use:
```
singularity exec bootstrap-prefix.sif ./bootstrap-prefix.sh
```

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@peterstol peterstol Jun 30, 2020

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The installation path can also be set in the environment as $EPREFIX

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@bedroge bedroge Jun 30, 2020

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Haven't tried this myself (does that also skip the other questions about wishing the script luck?), but added a note about it.

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@peterstol peterstol Jul 1, 2020

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It does not skip the questions, but saves time typing

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@boegel boegel Jul 2, 2020

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And it avoids accidentally installing to a different location... :)

+1 for defining $EPREFIX up front

I also had to do this, because some /etc/profile.d scripts in the system I'm playing on define $LD_LIBRARY_PATH & co:

export SHELL="/bin/bash --norc --noprofile

The Prefix bootstrap script gives up when it sees things like $LD_LIBRARY_PATH and $CPATH defined in a freshly created shell.

After starting the bootstrap have a long coffee...

### Adding EESSI overlay
Additional packages are added in the EESSI overlay, which is based on ComputeCanada.
Expand All @@ -36,5 +60,3 @@ Sync the overlay
```
emerge --sync
```


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