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bilke/apptainer_guix.diff

Last active June 21, 2024 08:03
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guix image vs sif image
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apptainer_guix.diff
--- A/app.kaleidoscope.kaleidoscope_dynamic_file_617227C8-FE8D-4D0C-8F51-5161DB889ADF-20755-00000016AA95D574.txt
+++ B/app.kaleidoscope.kaleidoscope_dynamic_file_67BD825E-33FF-4752-9F52-F615F0486C23-20755-00000016E195C82B.txt
@@ -3,6 +3,12 @@
DEBUG SetBinaryPath() Setting binary path to /usr/lib/apptainer/bin:/home/bilke/.config/guix/current/bin:/opt/homebrew/Caskroom/miniconda/base/bin:/home/bilke/.local/bin:/home/bilke/.yarn/bin:/home/bilke/.config/yarn/global/node_modules/.bin:/home/bilke/.config/bilke/bin:./node_modules/.bin:/home/bilke/.config/bin:/usr/local/bin:/usr/local/sbin:/opt/local/bin:/home/bilke/.guix-profile/bin:/home/bilke/.config/guix/current/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/opt/cuda/bin:/opt/cuda/nsight_compute:/opt/cuda/nsight_systems/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/bilke/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
DEBUG SetBinaryPath() Using that path for all binaries
DEBUG handleConfDir() /home/bilke/.apptainer already exists. Not creating.
+DEBUG getCacheParentDir() environment variable APPTAINER_CACHEDIR not set, using default image cache
+DEBUG parseURI() Parsing docker://alpine into reference
+DEBUG getDockerRefDigest() docker.GetDigest source image digest for docker://alpine:latest is b89d9c93e9ed3597455c90a0b88a8bbb5cb7188438f70953fede212a0c4394e0
+DEBUG getDockerRefDigest() docker.GetDigest digest for docker://alpine:latest is 9e0b381511b17908ab0ab45978fcb104966d1f2d0edc95075593bb700d4cc323
+DEBUG getRefDigest() GetManifest digest for docker://alpine:latest is 9e0b381511b17908ab0ab45978fcb104966d1f2d0edc95075593bb700d4cc323
+INFO pull() Using cached SIF image
DEBUG setUmask() Saving umask 0022 for propagation into container
VERBOSE useSuid() Unprivileged installation: using user namespace
DEBUG checkEncryptionKey() Checking for encrypted system partition
@@ -10,9 +16,7 @@
DEBUG Init() Check for sandbox image format
DEBUG Init() sandbox format initializer returned: not a directory image
DEBUG Init() Check for sif image format
+DEBUG Init() sif image format detected
-DEBUG Init() sif format initializer returned: SIF magic not found
-DEBUG Init() Check for squashfs image format
-DEBUG Init() squashfs image format detected
DEBUG setCgroups() Recording rootless XDG_RUNTIME_DIR / DBUS_SESSION_BUS_ADDRESS
VERBOSE setKeyIfNotAlreadyOverridden()Forwarding APPTAINERENV_BAR as BAR environment variable
DEBUG SetContainerEnv() Forwarding USER environment variable
@@ -104,9 +108,7 @@
DEBUG Init() Check for sandbox image format
DEBUG Init() sandbox format initializer returned: not a directory image
DEBUG Init() Check for sif image format
+DEBUG Init() sif image format detected
-DEBUG Init() sif format initializer returned: SIF magic not found
-DEBUG Init() Check for squashfs image format
-DEBUG Init() squashfs image format detected
DEBUG setSessionLayer() Using overlay because it is not disabled
DEBUG PrepareConfig() image driver is fuseapps
VERBOSE wait_child() stage 1 exited with status 0
@@ -114,8 +116,6 @@
DEBUG cleanup_fd() Close file descriptor 4
DEBUG cleanup_fd() Close file descriptor 5
DEBUG cleanup_fd() Close file descriptor 6
-DEBUG cleanup_fd() Close file descriptor 7
-DEBUG cleanup_fd() Close file descriptor 8
DEBUG init() Set child signal mask
DEBUG init() Create socketpair for master communication channel
DEBUG init() Create RPC socketpair for communication between stage 2 and RPC server
@@ -132,9 +132,9 @@
VERBOSE create_namespace() Create mount namespace
VERBOSE init() Spawn RPC server
DEBUG func1() executablePath is /usr/lib/apptainer/bin/starter
-DEBUG func1() executablePath is /usr/lib/apptainer/bin/starter
DEBUG func1() starter was not relocated from /usr/lib
DEBUG func1() Install prefix is /usr
+DEBUG func1() executablePath is /usr/lib/apptainer/bin/starter
DEBUG func1() starter was not relocated from /usr/lib
DEBUG func1() Install prefix is /usr
DEBUG startup() apptainer runtime engine selected
@@ -151,7 +151,7 @@
DEBUG setupOverlayLayout() Creating overlay SESSIONDIR layout
DEBUG addRootfsMount() Mount rootfs in read-only mode
DEBUG addRootfsMount() Image type is 4096
+DEBUG addRootfsMount() Mounting block [squashfs] image: /home/bilke/.apptainer/cache/oci-tmp/9e0b381511b17908ab0ab45978fcb104966d1f2d0edc95075593bb700d4cc323
-DEBUG addRootfsMount() Mounting block [squashfs] image: /gnu/store/v27n3gwdl3hn01bmm1ad4z1jkw51cz1r-bash-coreutils-squashfs-pack.gz.squashfs
DEBUG addKernelMount() Checking configuration file for 'mount proc'
DEBUG addKernelMount() Adding proc to mount list
VERBOSE addKernelMount() Default mount: /proc:/proc
@@ -176,7 +176,7 @@
DEBUG create() Mount all
DEBUG mountGeneric() Mounting tmpfs to /var/lib/apptainer/mnt/session
DEBUG func2() Starting image driver fuseapps
+DEBUG Mount() Executing /usr/bin/squashfuse_ll -f -o allow_other,ro,uid=40841,gid=4623,offset=36864 /proc/self/fd/3 /var/lib/apptainer/mnt/session/rootfs
-DEBUG Mount() Executing /usr/bin/squashfuse_ll -f -o allow_other,ro,uid=40841,gid=4623 /proc/self/fd/3 /var/lib/apptainer/mnt/session/rootfs
DEBUG Mount() /var/lib/apptainer/mnt/session/rootfs mounted in 25ms
DEBUG createCwdDir() Using /home/bilke as current working directory
DEBUG mountGeneric() Mounting overlay to /var/lib/apptainer/mnt/session/final
@@ -184,9 +184,14 @@
DEBUG mountGeneric() Remounting /var/lib/apptainer/mnt/session/final
DEBUG setPropagationMount() Set RPC mount propagation flag to SLAVE
VERBOSE Passwd() Checking for template passwd file: /var/lib/apptainer/mnt/session/rootfs/etc/passwd
+VERBOSE Passwd() Creating passwd content
+VERBOSE Passwd() Creating template passwd file and injecting user data: /var/lib/apptainer/mnt/session/rootfs/etc/passwd
+DEBUG addIdentityMount() Adding /etc/passwd to mount list
+VERBOSE addIdentityMount() Default mount: /etc/passwd:/etc/passwd
-WARNING addIdentityMount() passwd file doesn't exist in container, not updating
VERBOSE Group() Checking for template group file: /var/lib/apptainer/mnt/session/rootfs/etc/group
+VERBOSE Group() Creating group content
+DEBUG addIdentityMount() Adding /etc/group to mount list
+VERBOSE addIdentityMount() Default mount: /etc/group:/etc/group
-WARNING addIdentityMount() group file doesn't exist in container, not updating
DEBUG mountGeneric() Mounting /dev to /var/lib/apptainer/mnt/session/final/dev
DEBUG mountGeneric() Mounting /etc/localtime to /var/lib/apptainer/mnt/session/final/etc/localtime
DEBUG mountGeneric() Remounting /var/lib/apptainer/mnt/session/final/etc/localtime
@@ -202,10 +207,12 @@
VERBOSE func1() Default mount: /tmp:/tmp
VERBOSE func1() Default mount: /var/tmp:/var/tmp
DEBUG mountGeneric() Mounting /tmp to /var/lib/apptainer/mnt/session/final/tmp
+DEBUG mountGeneric() Remounting /var/lib/apptainer/mnt/session/final/tmp
-WARNING mountGeneric() Skipping mount /tmp [tmp]: /tmp doesn't exist in container
DEBUG mountGeneric() Mounting /var/tmp to /var/lib/apptainer/mnt/session/final/var/tmp
+DEBUG mountGeneric() Remounting /var/lib/apptainer/mnt/session/final/var/tmp
-WARNING mountGeneric() Skipping mount /var/tmp [tmp]: /var/tmp doesn't exist in container
DEBUG mountGeneric() Mounting /var/lib/apptainer/mnt/session/etc/resolv.conf to /var/lib/apptainer/mnt/session/final/etc/resolv.conf
+DEBUG mountGeneric() Mounting /var/lib/apptainer/mnt/session/etc/passwd to /var/lib/apptainer/mnt/session/final/etc/passwd
+DEBUG mountGeneric() Mounting /var/lib/apptainer/mnt/session/etc/group to /var/lib/apptainer/mnt/session/final/etc/group
VERBOSE addCwdMount() /home/bilke found within container
DEBUG create() Chroot into /var/lib/apptainer/mnt/session/final
DEBUG Chroot() Hold reference to host / directory
@@ -230,18 +237,24 @@
VERBOSE startup() Execute stage 2
DEBUG StageTwo() Entering stage 2
DEBUG StartProcess() Setting umask in container to 0022
+DEBUG sylogBuiltin() Sourcing /.singularity.d/env/01-base.sh
+DEBUG sylogBuiltin() Sourcing /.singularity.d/env/10-docker2singularity.sh
DEBUG sylogBuiltin() Sourcing /.singularity.d/env/90-environment.sh
+DEBUG sylogBuiltin() Sourcing /.singularity.d/env/94-appsbase.sh
+DEBUG sylogBuiltin() Sourcing /.singularity.d/env/95-apps.sh
+DEBUG sylogBuiltin() Sourcing /.singularity.d/env/99-base.sh
+DEBUG sylogBuiltin() Sourcing /.singularity.d/env/99-runtimevars.sh
DEBUG sylogBuiltin() Running action command exec
DEBUG PostStartProcess() Post start process
APPTAINER_APPNAME=
APPTAINER_BIND=
APPTAINER_COMMAND=exec
+APPTAINER_CONTAINER=/home/bilke/.apptainer/cache/oci-tmp/9e0b381511b17908ab0ab45978fcb104966d1f2d0edc95075593bb700d4cc323
-APPTAINER_CONTAINER=/gnu/store/v27n3gwdl3hn01bmm1ad4z1jkw51cz1r-bash-coreutils-squashfs-pack.gz.squashfs
APPTAINER_ENVIRONMENT=/.singularity.d/env/91-environment.sh
+APPTAINER_NAME=9e0b381511b17908ab0ab45978fcb104966d1f2d0edc95075593bb700d4cc323
-APPTAINER_NAME=v27n3gwdl3hn01bmm1ad4z1jkw51cz1r-bash-coreutils-squashfs-pack.gz.squashfs
AUTOJUMP_ERROR_PATH=/home/bilke/.local/share/autojump/errors.log
AUTOJUMP_SOURCED=1
+BAR=FOO
-BASH_LOADABLES_PATH=/gnu/store/sikdbpaxb1n1hy13qag22xp7qbkabw18-profile/lib/bash
CMAKE_GENERATOR=Ninja
CPM_SOURCE_CACHE=/cache/cpm
CUDA_PATH=/opt/cuda
@@ -256,6 +269,7 @@
INFOPATH=/home/bilke/.config/guix/current/share/info:
LANG=en_US.UTF-8
LC_ALL=en_US.UTF-8
+LD_LIBRARY_PATH=/.singularity.d/libs
LOGNAME=bilke
MAIL=/var/spool/mail/bilke
MKLROOT=/opt/intel/oneapi/mkl/latest
@@ -264,7 +278,7 @@
OLDPWD=/home/bilke
OMP_NUM_THREADS=1
OMP_THREAD_LIMIT=32
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-PATH=/gnu/store/sikdbpaxb1n1hy13qag22xp7qbkabw18-profile/bin
PETSC_DIR=/opt/petsc/linux-c-opt
PIP_REQUIRE_VIRTUALENV=true
PROMPT_COMMAND=PS1="Apptainer> "; unset PROMPT_COMMAND
@@ -274,9 +288,9 @@
SHELL=/bin/zsh
SHLVL=1
SINGULARITY_BIND=
+SINGULARITY_CONTAINER=/home/bilke/.apptainer/cache/oci-tmp/9e0b381511b17908ab0ab45978fcb104966d1f2d0edc95075593bb700d4cc323
-SINGULARITY_CONTAINER=/gnu/store/v27n3gwdl3hn01bmm1ad4z1jkw51cz1r-bash-coreutils-squashfs-pack.gz.squashfs
SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh
+SINGULARITY_NAME=9e0b381511b17908ab0ab45978fcb104966d1f2d0edc95075593bb700d4cc323
-SINGULARITY_NAME=v27n3gwdl3hn01bmm1ad4z1jkw51cz1r-bash-coreutils-squashfs-pack.gz.squashfs
SSH_AUTH_SOCK=/tmp/ssh-XXXXp2P4lX/agent.2082651
SSH_CLIENT=141.65.34.101 50577 22
SSH_CONNECTION=141.65.34.101 50577 141.65.34.85 22
@@ -300,6 +314,6 @@
DEBUG CleanupContainer() Cleanup container
DEBUG umount() Umount /var/lib/apptainer/mnt/session/final
DEBUG umount() Umount /var/lib/apptainer/mnt/session/rootfs
+DEBUG stop() Waiting for squashfuse_ll pid 2084123 to exit
-DEBUG stop() Waiting for squashfuse_ll pid 2083970 to exit
DEBUG Master() Child exited with exit status 0
\ No newline at end of file
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