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Nix HPC

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Nix for High Perfomance Computing clusters18 Servers

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3 Apr 2023
@jb:vk3.wtf@jb:vk3.wtfI prepopulate a nix store in project/scratch area with a copy of nix then bind mount it in the container so it's writable20:53:52
@jb:vk3.wtf@jb:vk3.wtfThe singularity image I use is completely empty, really just using singularity to bind mount as there's no namespaces20:54:42
4 Apr 2023
@tpw_rules:matrix.orgtpw_rulesi've done hax with singularity too. i need to document them sometime03:43:20
@ryantalo:matrix.orgRyan SwartHave you benched the performance profile of nix-in-singularity? How close is it to native?09:28:23
@jb:vk3.wtf@jb:vk3.wtfno i haven't but i expect it to be close to native as it's just a bunch of binds handled by the kernel11:39:46
@ss:someonex.netSomeoneSerge (UTC+U[-12,12])

@jbedo do you also disable the sandbox?

I suppose what I'm seeing is nix trying to set up mount namespaces for the builds, but idk:

Singularity> nix-shell -p gh
error: executing shell '/nix/store/k4j76vg58c6j90s8l46kx3843vysx732-bash-interactive-5.2-p15/bin/bash': No such file or directory
Singularity> nix shell nixpkgs#gh
error: setting up a private mount namespace: Operation not permitted
Singularity>
17:00:50
6 Apr 2023
@ryantalo:matrix.orgRyan Swart Ok, managed to get things building + running using the singularity method jbedo described; alas inode limits are killing me now. It seems that nix build nixpkgs#hello is essentially evaluating every nix package for some reason; why would /nix/store/tmp-1759374-1/x/pkgs/development/python-modules/qimage2ndarray be getting built for a simple c binary otherwise... 02:12:15
@jb:vk3.wtf@jb:vk3.wtf
In reply to @ss:someonex.net

@jbedo do you also disable the sandbox?

I suppose what I'm seeing is nix trying to set up mount namespaces for the builds, but idk:

Singularity> nix-shell -p gh
error: executing shell '/nix/store/k4j76vg58c6j90s8l46kx3843vysx732-bash-interactive-5.2-p15/bin/bash': No such file or directory
Singularity> nix shell nixpkgs#gh
error: setting up a private mount namespace: Operation not permitted
Singularity>
yeah i disable sandbox and a few other things that don't work on luster (WAL & luster.lov ACL)
02:47:49
@jb:vk3.wtf@jb:vk3.wtf
In reply to @ryantalo:matrix.org
Ok, managed to get things building + running using the singularity method jbedo described; alas inode limits are killing me now. It seems that nix build nixpkgs#hello is essentially evaluating every nix package for some reason; why would /nix/store/tmp-1759374-1/x/pkgs/development/python-modules/qimage2ndarray be getting built for a simple c binary otherwise...
it shouldn't be building anything you don't need, but it does need to unpack nixpkgs which might be your problem since there's quite a lot of files
02:49:23
7 Apr 2023
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24 Apr 2023
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1 May 2023
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2 May 2023
@twesterhout:matrix.org@twesterhout:matrix.org Hello, has anybody managed to run MPI-aware applications via nix-portable or Nixie on an HPC cluster where Nix isn't installed? Single-node executables work fine, but I'm struggling to do anything with multi-node stuff. Currently trying to go through Singularity with pkgs.singularity-tools, but no luck so far. So if anybody has an example, that'd very much appreciated. 07:33:55
18 May 2023
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20 May 2023
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@shamrocklee:matrix.orgShamrockLee (Yueh-Shun Li)
In reply to @twesterhout:matrix.org
Hello, has anybody managed to run MPI-aware applications via nix-portable or Nixie on an HPC cluster where Nix isn't installed? Single-node executables work fine, but I'm struggling to do anything with multi-node stuff. Currently trying to go through Singularity with pkgs.singularity-tools, but no luck so far. So if anybody has an example, that'd very much appreciated.
I'm not familliar with MPI. Does it rely on certain device file or top-level directory?
12:49:27
21 May 2023
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23 May 2023
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26 May 2023
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27 May 2023
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7 Jun 2023
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12 Jun 2023
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13 Jun 2023
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21 Jun 2023
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25 Jun 2023
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25 Jul 2023
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27 Jul 2023
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