• 成功例

[hoge@gpu1 ~]$ cat test.def

BootStrap: docker

From: ubuntu:20.04

 

%post

    apt-get update

    DEBIAN_FRONTEND=noninteractive \

    apt-get install -y \

        vim

 

[hoge@gpu1 ~]$

 

[hoge@gpu1 ~]$ apptainer build –fakeroot test.sif test.def

INFO:    Starting build…

Getting image source signatures

Copying blob ca1778b69356 done

Copying config 88bd689171 done

Writing manifest to image destination

Storing signatures

2023/05/31 12:21:19  info unpack layer: sha256:ca1778b6935686ad781c27472c4668fc61ec3aeb85494f72deb1921892b9d39e

INFO:    Running post scriptlet

+ apt-get update

Get:1 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]

Get:2 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]

Get:3 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [1053 kB]

Get:4 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]

Get:5 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [2274 kB]

Get:6 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]

Get:7 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [28.5 kB]

Get:8 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [2731 kB]

Get:9 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB]

Get:10 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1275 kB]

Get:11 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB]

Get:12 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB]

Get:13 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [31.2 kB]

Get:14 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [3226 kB]

Get:15 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [2449 kB]

Get:16 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1351 kB]

Get:17 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [55.2 kB]

Get:18 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [28.6 kB]

Fetched 26.7 MB in 6s (4215 kB/s)

Reading package lists… Done

+ DEBIAN_FRONTEND=noninteractive apt-get install -y vim

Reading package lists… Done

Building dependency tree

Reading state information… Done

The following additional packages will be installed:

alsa-topology-conf alsa-ucm-conf file libasound2 libasound2-data libcanberra0 libexpat1 libgpm2 libltdl7

libmagic-mgc libmagic1 libmpdec2 libogg0 libpython3.8 libpython3.8-minimal libpython3.8-stdlib libreadline8

libsqlite3-0 libssl1.1 libtdb1 libvorbis0a libvorbisfile3 mime-support readline-common sound-theme-freedesktop

vim-common vim-runtime xxd xz-utils

Suggested packages:

libasound2-plugins alsa-utils libcanberra-gtk0 libcanberra-pulse gpm readline-doc ctags vim-doc vim-scripts

The following NEW packages will be installed:

alsa-topology-conf alsa-ucm-conf file libasound2 libasound2-data libcanberra0 libexpat1 libgpm2 libltdl7

libmagic-mgc libmagic1 libmpdec2 libogg0 libpython3.8 libpython3.8-minimal libpython3.8-stdlib libreadline8

libsqlite3-0 libssl1.1 libtdb1 libvorbis0a libvorbisfile3 mime-support readline-common sound-theme-freedesktop vim

vim-common vim-runtime xxd xz-utils

0 upgraded, 30 newly installed, 0 to remove and 5 not upgraded.

Need to get 15.0 MB of archives.

After this operation, 70.6 MB of additional disk space will be used.

Get:1 http://archive.ubuntu.com/ubuntu focal/main amd64 libmagic-mgc amd64 1:5.38-4 [218 kB]

Get:2 http://archive.ubuntu.com/ubuntu focal/main amd64 libmagic1 amd64 1:5.38-4 [75.9 kB]

Get:3 http://archive.ubuntu.com/ubuntu focal/main amd64 file amd64 1:5.38-4 [23.3 kB]

Get:4 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libexpat1 amd64 2.2.9-1ubuntu0.6 [74.6 kB]

Get:5 http://archive.ubuntu.com/ubuntu focal/main amd64 libmpdec2 amd64 2.4.2-3 [81.1 kB]

Get:6 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu2.19 [1321 kB]

Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8-minimal amd64 3.8.10-0ubuntu1~20.04.7 [717 kB]

Get:8 http://archive.ubuntu.com/ubuntu focal/main amd64 mime-support all 3.64ubuntu1 [30.6 kB]

Get:9 http://archive.ubuntu.com/ubuntu focal/main amd64 readline-common all 8.0-4 [53.5 kB]

Get:10 http://archive.ubuntu.com/ubuntu focal/main amd64 libreadline8 amd64 8.0-4 [131 kB]

Get:11 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsqlite3-0 amd64 3.31.1-4ubuntu0.5 [549 kB]

Get:12 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8-stdlib amd64 3.8.10-0ubuntu1~20.04.7 [1675 kB]

Get:13 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 xxd amd64 2:8.1.2269-1ubuntu5.14 [52.4 kB]

Get:14 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 vim-common all 2:8.1.2269-1ubuntu5.14 [87.2 kB]

Get:15 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 xz-utils amd64 5.2.4-1ubuntu1.1 [82.6 kB]

Get:16 http://archive.ubuntu.com/ubuntu focal/main amd64 alsa-topology-conf all 1.2.2-1 [7364 B]

Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 alsa-ucm-conf all 1.2.2-1ubuntu0.13 [27.0 kB]

Get:18 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libasound2-data all 1.2.2-2.1ubuntu2.5 [20.1 kB]

Get:19 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libasound2 amd64 1.2.2-2.1ubuntu2.5 [335 kB]

Get:20 http://archive.ubuntu.com/ubuntu focal/main amd64 libltdl7 amd64 2.4.6-14 [38.5 kB]

Get:21 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libtdb1 amd64 1.4.5-0ubuntu0.20.04.1 [44.2 kB]

Get:22 http://archive.ubuntu.com/ubuntu focal/main amd64 libogg0 amd64 1.3.4-0ubuntu1 [24.0 kB]

Get:23 http://archive.ubuntu.com/ubuntu focal/main amd64 libvorbis0a amd64 1.3.6-2ubuntu1 [87.0 kB]

Get:24 http://archive.ubuntu.com/ubuntu focal/main amd64 libvorbisfile3 amd64 1.3.6-2ubuntu1 [16.1 kB]

Get:25 http://archive.ubuntu.com/ubuntu focal/main amd64 sound-theme-freedesktop all 0.8-2ubuntu1 [384 kB]

Get:26 http://archive.ubuntu.com/ubuntu focal/main amd64 libcanberra0 amd64 0.30-7ubuntu1 [38.1 kB]

Get:27 http://archive.ubuntu.com/ubuntu focal/main amd64 libgpm2 amd64 1.20.7-5 [15.1 kB]

Get:28 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8 amd64 3.8.10-0ubuntu1~20.04.7 [1626 kB]

Get:29 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 vim-runtime all 2:8.1.2269-1ubuntu5.14 [5875 kB]

Get:30 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 vim amd64 2:8.1.2269-1ubuntu5.14 [1241 kB]

Fetched 15.0 MB in 1min 24s (177 kB/s)

debconf: delaying package configuration, since apt-utils is not installed

Selecting previously unselected package libmagic-mgc.

(Reading database … 4126 files and directories currently installed.)

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Unpacking libmagic-mgc (1:5.38-4) …

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Adding ‘diversion of /usr/share/vim/vim81/doc/help.txt to /usr/share/vim/vim81/doc/help.txt.vim-tiny by vim-runtime’

Adding ‘diversion of /usr/share/vim/vim81/doc/tags to /usr/share/vim/vim81/doc/tags.vim-tiny by vim-runtime’

Unpacking vim-runtime (2:8.1.2269-1ubuntu5.14) …

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Unpacking vim (2:8.1.2269-1ubuntu5.14) …

Setting up libexpat1:amd64 (2.2.9-1ubuntu0.6) …

Setting up libgpm2:amd64 (1.20.7-5) …

Setting up libogg0:amd64 (1.3.4-0ubuntu1) …

Setting up mime-support (3.64ubuntu1) …

Setting up alsa-ucm-conf (1.2.2-1ubuntu0.13) …

Setting up libmagic-mgc (1:5.38-4) …

Setting up libtdb1:amd64 (1.4.5-0ubuntu0.20.04.1) …

Setting up libssl1.1:amd64 (1.1.1f-1ubuntu2.19) …

Setting up libsqlite3-0:amd64 (3.31.1-4ubuntu0.5) …

Setting up libmagic1:amd64 (1:5.38-4) …

Setting up file (1:5.38-4) …

Setting up xxd (2:8.1.2269-1ubuntu5.14) …

Setting up libasound2-data (1.2.2-2.1ubuntu2.5) …

Setting up vim-common (2:8.1.2269-1ubuntu5.14) …

Setting up xz-utils (5.2.4-1ubuntu1.1) …

update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode

update-alternatives: warning: skip creation of /usr/share/man/man1/lzma.1.gz because associated file /usr/share/man/man1/xz.1.gz (of link group lzma) doesn’t exist

update-alternatives: warning: skip creation of /usr/share/man/man1/unlzma.1.gz because associated file /usr/share/man/man1/unxz.1.gz (of link group lzma) doesn’t exist

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Setting up libvorbis0a:amd64 (1.3.6-2ubuntu1) …

Setting up libltdl7:amd64 (2.4.6-14) …

Setting up alsa-topology-conf (1.2.2-1) …

Setting up sound-theme-freedesktop (0.8-2ubuntu1) …

Setting up libasound2:amd64 (1.2.2-2.1ubuntu2.5) …

Setting up libmpdec2:amd64 (2.4.2-3) …

Setting up vim-runtime (2:8.1.2269-1ubuntu5.14) …

Setting up readline-common (8.0-4) …

Setting up libpython3.8-minimal:amd64 (3.8.10-0ubuntu1~20.04.7) …

Setting up libreadline8:amd64 (8.0-4) …

Setting up libvorbisfile3:amd64 (1.3.6-2ubuntu1) …

Setting up libpython3.8-stdlib:amd64 (3.8.10-0ubuntu1~20.04.7) …

Setting up libcanberra0:amd64 (0.30-7ubuntu1) …

Setting up libpython3.8:amd64 (3.8.10-0ubuntu1~20.04.7) …

Setting up vim (2:8.1.2269-1ubuntu5.14) …

update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/vim (vim) in auto mode

update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/vimdiff (vimdiff) in auto mode

update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/rvim (rvim) in auto mode

update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/rview (rview) in auto mode

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update-alternatives: warning: skip creation of /usr/share/man/it/man1/editor.1.gz because associated file /usr/share/man/it/man1/vim.1.gz (of link group editor) doesn’t exist

update-alternatives: warning: skip creation of /usr/share/man/ja/man1/editor.1.gz because associated file /usr/share/man/ja/man1/vim.1.gz (of link group editor) doesn’t exist

update-alternatives: warning: skip creation of /usr/share/man/pl/man1/editor.1.gz because associated file /usr/share/man/pl/man1/vim.1.gz (of link group editor) doesn’t exist

update-alternatives: warning: skip creation of /usr/share/man/ru/man1/editor.1.gz because associated file /usr/share/man/ru/man1/vim.1.gz (of link group editor) doesn’t exist

update-alternatives: warning: skip creation of /usr/share/man/man1/editor.1.gz because associated file /usr/share/man/man1/vim.1.gz (of link group editor) doesn’t exist

Processing triggers for libc-bin (2.31-0ubuntu9.9) …

INFO:    Creating SIF file…

INFO:    Build complete: test.sif

[hoge@gpu1 ~]$

[hoge@gpu1 ~]$ apptainer shell test.sif

INFO:    underlay of /etc/localtime required more than 50 (75) bind mounts

Apptainer> cat /etc/os-release

NAME=”Ubuntu”

VERSION=”20.04.6 LTS (Focal Fossa)”

ID=ubuntu

ID_LIKE=debian

PRETTY_NAME=”Ubuntu 20.04.6 LTS”

VERSION_ID=”20.04″

HOME_URL=”https://www.ubuntu.com/”

SUPPORT_URL=”https://help.ubuntu.com/”

BUG_REPORT_URL=”https://bugs.launchpad.net/ubuntu/”

PRIVACY_POLICY_URL=”https://www.ubuntu.com/legal/terms-and-policies/privacy-policy”

VERSION_CODENAME=focal

UBUNTU_CODENAME=focal

Apptainer> exit

exit

[hoge@gpu1 ~]$

 

• エラー発生例

[ki@gpu1 ~]$ cat test.def

BootStrap: docker

From: ubuntu:20.04

 

%post

    apt-get update

    DEBIAN_FRONTEND=noninteractive \

    apt-get install -y \

        vim

 

[ki@gpu1 ~]$

[ki@gpu1 ~]$ apptainer build –fakeroot test.sif test.def

INFO:    User not listed in /etc/subuid, trying root-mapped namespace

INFO:    The %post section will be run under fakeroot

INFO:    Starting build…

Getting image source signatures

Copying blob ca1778b69356 skipped: already exists

Copying config 88bd689171 done

Writing manifest to image destination

Storing signatures

2023/05/31 13:11:44  info unpack layer: sha256:ca1778b6935686ad781c27472c4668fc61ec3aeb85494f72deb1921892b9d39e

INFO:    Running post scriptlet

/.singularity.d/libs/faked: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33′ not found (required by /.singularity.d/libs/faked)

/.singularity.d/libs/faked: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34′ not found (required by /.singularity.d/libs/faked)

fakeroot: error while starting the `faked’ daemon.

/.singularity.d/libs/fakeroot: 1: kill: Usage: kill [-s sigspec | -signum | -sigspec] [pid | job]… or

kill -l [exitstatus]

FATAL:   While performing build: while running engine: exit status 1

[ki@gpu1 ~]$

 

apptainerのマニュアルのNFSの章を参照すると、いろいろと制約が記載されています。

Lustre / GPFS / PanFSなんかも似たような制約があるようです。

このエラーは、そういった制約のせいです。

最初に示した成功例は、/homeがローカルのxfs上に存在している場合です。

/homeがNFS等の場合に発生するエラーです。

apptainerの制約です。