On Sun, Jul 30, 2017 at 02:36:03PM +0200, Steffen Möller wrote:
>
> Users will not care if it is flatpak, singularity, conda or prefix -
> they want
> all the packages and the packages shall work. What I like about all of these
> efforts is that from what I grasped we will stop caring too much abo
On Tue, Jul 25, 2017 at 12:04:27PM +0200, Florian Weimer wrote:
> But it's not clear if the HPC community wants to run
> containers/namespaces at all.
Exploring the container-less approaches for different but related
purposes[1], I just did what turned out to be a practice test of
installation loc
* Steffen Möller:
> The HPC community does not want to need root privileges to get their
> software installed/used on the HPC setup. This excludes regular
> Debian packages, traditional containers like Docker and chroot
> environments.
So they would rather give the user full file system access on
Hi Simon,
Simon McVittie writes:
> Flatpak's approach to this is to use bind-mounts (in a new mount
> namespace set up by bubblewrap) so that the "app" (the leaf package,
> together with any libraries that are bundled with it) always appears
> to be installed in --prefix=/app, which can safely b
On 30.07.17 13:47, Simon McVittie wrote:
> On Sun, 30 Jul 2017 at 19:34:42 +0900, Benda Xu wrote:
>> As far as I can see, the easiest relocations are those modifiable in a
>> plain text, like configuration file, script shebang, etc. The medium
>> ones are ELF, with which we have tools like patch
On Sun, 30 Jul 2017 at 19:34:42 +0900, Benda Xu wrote:
> As far as I can see, the easiest relocations are those modifiable in a
> plain text, like configuration file, script shebang, etc. The medium
> ones are ELF, with which we have tools like patchelf and chrpath, etc.
> The most difficult part
Hi Steffen,
Steffen Möller writes:
> This is good to hear. While I like all that I read about Gentoo, I do
> not know about how well equipped it is with packages in computational
> biology [edit: I had a look at
> https://packages.gentoo.org/categories/sci-biology and am impressed,
> well done!]
Hi Benda,
On 30.07.17 09:37, Benda Xu wrote:
> Hi Steffen,
>
> Steffen Möller writes:
>
>> I just had a quick look and it seems really nice, indeed! Thank you tons for
>> pointing that out to us. Has anybody already tried that with Debian?
> I am one of a few guys behind that project. Gentoo Pre
Hi Steffen,
Steffen Möller writes:
> I just had a quick look and it seems really nice, indeed! Thank you tons for
> pointing that out to us. Has anybody already tried that with Debian?
I am one of a few guys behind that project. Gentoo Prefix with its own
libc runs on Debian very well, the exp
Quoting Steffen Möller (2017-07-29 18:05:27)
> On 29.07.17 17:51, Jeff wrote:
> > On 29/07/17 17:26, Steffen Möller wrote: >> The HPC community does not want
> > to need root privileges to get their
> >> software installed/used on the HPC setup. This excludes regular >>
> Debian packages, traditio
On 29.07.17 17:51, Jeff wrote:
> On 29/07/17 17:26, Steffen Möller wrote: >> The HPC community does not want
> to need root privileges to get their
>> software installed/used on the HPC setup. This excludes regular >>
Debian packages, traditional containers like Docker and chroot
environments. >
On 29.07.17 17:41, Paul Wise wrote:
> On Sat, Jul 29, 2017 at 11:26 AM, Steffen Möller wrote:
>
>> If flatpak is an answer - great. But from what I get, there is no automated
>> transformation from .deb to it, so we would need to decide for packaging
>> in that different format instead of our reg
On 29/07/17 17:26, Steffen Möller wrote:
> The HPC community does not want to need root privileges to get their
> software installed/used on the HPC setup. This excludes regular
> Debian packages, traditional containers like Docker and chroot environments.
I use a gentoo prefix for stuff like this
On Sat, Jul 29, 2017 at 11:26 AM, Steffen Möller wrote:
> If flatpak is an answer - great. But from what I get, there is no automated
> transformation from .deb to it, so we would need to decide for packaging
> in that different format instead of our regular effort.
We could probably leverage our
On 25.07.17 12:04, Florian Weimer wrote:
> * Simon McVittie:
>
>> On Sat, 22 Jul 2017 at 12:28:04 +0200, Steffen Möller wrote:
>>> And quite some packages in our
>>> distribution do not really need to be installed as root if they were
>>> installed where the user has write permissions. There woul
* Simon McVittie:
> On Sat, 22 Jul 2017 at 12:28:04 +0200, Steffen Möller wrote:
>> And quite some packages in our
>> distribution do not really need to be installed as root if they were
>> installed where the user has write permissions. There would hence be
>> little overhead over what we have no
Quoting Paul Wise (2017-07-22 13:34:46)
> I would wager most Debian packages are not bit-for-bit identical when you
> vary the installation prefix (and Debian build tools don't support doing that
> AFAICT), but you can almost fake user-installable packages using existing
> binary packages using som
Hi,
Niels Thykier wrote:
> Simon McVittie:
> > On Sat, 22 Jul 2017 at 12:28:04 +0200, Steffen Möller wrote:
> >> And quite some packages in our
> >> distribution do not really need to be installed as root if they were
> >> installed where the user has write permissions. There would hence be
> >> l
Simon McVittie:
> On Sat, 22 Jul 2017 at 12:28:04 +0200, Steffen Möller wrote:
>> And quite some packages in our
>> distribution do not really need to be installed as root if they were
>> installed where the user has write permissions. There would hence be
>> little overhead over what we have now.
On Sat, 22 Jul 2017 at 12:28:04 +0200, Steffen Möller wrote:
> And quite some packages in our
> distribution do not really need to be installed as root if they were
> installed where the user has write permissions. There would hence be
> little overhead over what we have now. Should we not somehow
On Sat, Jul 22, 2017 at 8:28 PM, Steffen Möller wrote:
> user-installable packages
That sounds like Flatpak/Snappy/etc.
I would wager most Debian packages are not bit-for-bit identical when
you vary the installation prefix (and Debian build tools don't support
doing that AFAICT), but you can alm
Hello,
There is a fairly new trend out there, best represented by brew.sh and
conda.io, to have user-installable packages. These come very handy in
HPC-near environments or other shared resources that do not grant root
access. In computational biology it is bioconda that is attracting many
users.
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