Latest Ubuntu 18.04 update: kernel doesn't support the compression algorithm #5466
Comments
|
Hi. We need a bit more information here:
Thanks. |
|
Sure thing, @dctrud. I'm providing the Container definition # singularity docks
Bootstrap: docker
#From: tensorflow/tensorflow:2.1.0-gpu-py3-jupyter
#From: nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04
From: ubuntu:18.04
%labels
LAYER base
AUTHOR rrs
VERSION v0.3.0
%help
%environment
export LANG='en_US.UTF-8'
export LANGUAGE='en_US.UTF-8'
export LC_ALL='en_US.UTF-8'
export GO_VER=1.13.4
export OS=linux
export ARCH=amd64
export CUDA_VER=10.1
export DEV_PATH=/opt/dev
export RUSTUP_HOME=$DEV_PATH/rust
export CARGO_HOME=$DEV_PATH/rust
export CARGO_BIN=$CARGO_HOME/bin
. $RUSTUP_HOME/env
export HASKELL_HOME=$DEV_PATH/haskell
export HASKELL_BIN=$HASKELL_HOME/bin
export CABAL_HOME=$HASKELL_HOME/cabal
export CABAL_CONFIG=$CABAL_HOME/config
export AGDA_HOME=$HASKELL_HOME/agda
export IDRIS_HOME=$HASKELL_HOME/idris
export ELM_HOME=$HOME
export PATH=$CARGO_BIN:$HASKELL_BIN:$ELM_HOME:/opt/conda/bin:/usr/local/cuda/bin:/usr/local/go/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/extras/CUPTI/lib64
export OCAML_HOME=$DEV_PATH/ocaml
%post
# build the setup
#
# https://sylabs.io/guides/3.5/user-guide/persistent_overlays.html
#
################################################################################
# BASIC SYSTEM
########################################
# infrastructure
apt update -y && \
apt install -y --no-install-recommends software-properties-common && \
add-apt-repository ppa:kelleyk/emacs && \
apt update -y && apt upgrade -y && \
apt install -y --no-install-recommends \
build-essential \
default-jre \
dialog \
cmake \
make \
gcc \
g++ \
curl \
wget \
gnupg \
sudo \
ca-certificates \
libjpeg-dev \
libpng-dev \
libev-dev \
libxkbcommon-x11-0 \
redis-server \
emacs26 \
libopenmpi-dev \
pkg-config \
openssh-client \
zip unzip \
git \
feh \
locales \
bubblewrap
########################################
# basic OS dev tools
TZ=America/Los_Angeles
ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
apt update -y --fix-missing && \
DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata && \
apt install -y --no-install-recommends \
python ruby ruby-dev gem xclip \
libnss3-dev libgtk-3-0 libxtst6 libxss-dev libxss1 \
libgraphviz-dev graphviz
#################################################################################
# sublime text
wget -qO - https://download.sublimetext.com/sublimehq-pub.gpg | sudo apt-key add -
sudo apt-add-repository "deb https://download.sublimetext.com/ apt/stable/"
apt install -y --no-install-recommends \
sublime-text
#################################################################################
locale-gen en_US.UTF-8
################################################################################
# LANGUAGES and DEV TOOLS
export DEV_PATH=/opt/dev
########################################
# Node + Optic API stuff
curl -sL https://deb.nodesource.com/setup_12.x | bash && sudo apt update -y
apt install -y nodejs libsecret-1-dev libssl-dev
npm config set python /usr/bin/python
npm install -g gulp gulp-cli
npm install @useoptic/cli -g
apt autoremove -y && apt clean
#################################################################################
# OCaml
add-apt-repository ppa:avsm/ppa && apt update -y && \
apt install -y --no-install-recommends opam m4
# NOTES and links
# https://github.com/ocaml/infrastructure/wiki/Containers#package-sandboxing
# users will have to redo all this
# init with --disable-sandboxing
# https://github.com/janestreet/install-ocaml
opam init
opam update -uy
opam install -y core merlin utop ocp-indent
opam install -y async core js_of_ocaml js_of_ocaml-ppx merlin utop ocp-indent
####################################################
# ELM
export ELM_HOME=$DEV_PATH/elm
mkdir -p $ELM_HOME
cd $ELM_HOME
curl -L -o elm.gz https://github.com/elm/compiler/releases/download/0.19.1/binary-for-linux-64-bit.gz
gunzip elm.gz
chmod +x elm
npm install -g elm-test elm-oracle elm-format @elm-tooling/elm-language-server
###################################################
# Haskell
# https://cabal.readthedocs.io/en/latest/index.html
export HASKELL_HOME=$DEV_PATH/haskell
export HASKELL_BIN=$HASKELL_HOME/bin
export CABAL_HOME=$HASKELL_PATH/cabal
export CABAL_CONFIG=$CABAL_PATH/config
mkdir -p $HASKELL_HOME
mkdir -p $HASKELL_BIN
mkdir -p $CABAL_HOME
apt install cabal-install -y --no-install-recommends
cabal user-config update
cabal update
apt install -y --no-install-recommends \
libicu-dev libtinfo-dev libgmp-dev netbase
curl -sSL https://get.haskellstack.org/ | sh
###################################################
# Idris
export IDRIS_HOME=$HASKELL_HOME/idris
mkdir -p $IDRIS_HOME
cd $IDRIS_HOME
cabal sandbox init
cabal install idris --prefix=$HASKELL_HOME --bindir=$HASKELL_BIN
###################################################
# Agda
# export AGDA_HOME=$HASKELL_HOME/agda
#
# mkdir -p $AGDA_HOME
# cd $AGDA_HOME
# cabal sandbox init
# cabal install 'alex >=3.1.0 && <3.2.0 || ==3.2.1 || >=3.2.3' --prefix=$HASKELL_HOME --bindir=$HASKELL_BIN
# cabal install alex happy Agda --prefix=$HASKELL_HOME --bindir=$HASKELL_BIN
###################################################
# Rust
# https://doc.rust-lang.org/book/ch01-01-installation.html#installing-rustup-on-linux-or-macos
export RUSTUP_HOME=$DEV_PATH/rust
export CARGO_HOME=$DEV_PATH/rust
export CARGO_BIN=$CARGO_HOME/bin
mkdir -p $RUSTUP_HOME
mkdir -p $CARGO_HOME
mkdir -p $CARGO_BIN
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
. $CARGO_HOME/env
#################################################################################
# make everything writable
chmod -R a+rwx $DEV_PATH
%files
# copy local files
%startscript
# in the container; instance creation
%runscript
# in the container; run
%test
# run test code |
|
Not sure if this is the same issue but this is localized to one compute node. There's something off with They don't exist: A reboot will likely fix this but is there another option? |
|
This repository is closed. Please create a new issue in https://github.com/apptainer/apptainer with all your OS particulars |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Version of Singularity:
What version of Singularity are you using? Run:
A container that previously used to work (pre Ubuntu update) suddenly does not work. Rebuilding the container does not help.
Expected behavior
Container starts.
Actual behavior
Error is printed out.
Steps to reproduce this behavior
Updated Ubuntu 18.04 yesterday.
What OS/distro are you running
How did you install Singularity
Source.
The text was updated successfully, but these errors were encountered: