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ATLAS application :
A few errors, tried everything I can
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Send message Joined: 17 Feb 17 Posts: 42 Credit: 2,589,736 RAC: 0 ![]() ![]() |
Hi, A few errors on multiple machines, Ubuntu 20.04. [2021-03-04 08:18:44] [31mFATAL: [0m while extracting /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img: root filesystem extraction failed: extract command failed: exit status 1 https://lhcathome.cern.ch/lhcathome/result.php?resultid=304481909 And this one. [2021-03-04 13:04:23] [31mFATAL: [0m container creation failed: mount ->/var error: can't remount /var: operation not permitted https://lhcathome.cern.ch/lhcathome/result.php?resultid=304481865 No idea how to go about fixing these. |
Send message Joined: 2 May 07 Posts: 2174 Credit: 171,550,712 RAC: 167,014 ![]() ![]() ![]() |
have the same info from CentOS8. After installing singularity from OS - Tasks are running well. https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=5613 |
Send message Joined: 17 Feb 17 Posts: 42 Credit: 2,589,736 RAC: 0 ![]() ![]() |
have the same info from CentOS8. Thank you. I did sudo apt-get install singularity, so we'll see what happens. thanks |
Send message Joined: 15 Nov 14 Posts: 602 Credit: 24,371,321 RAC: 0 ![]() ![]() |
Thank you. I did sudo apt-get install singularity, so we'll see what happens. I think you get an old version that way, though I have not tried it recently. It might work. You can get the latetest version by following these instructions: https://sylabs.io/guides/3.0/user-guide/installation.html Note that you have to install GO first. The following works for me on Ubuntu 18.04/20.04. Not all versions of GO and Singularity work for me, but these do. You can find the latest versions as indicated. Install GO (check latest version at https://pkg.go.dev/golang.org/dl#pkg-subdirectories): export VERSION=1.15.2 OS=linux ARCH=amd64 && \ wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \ sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \ rm go$VERSION.$OS-$ARCH.tar.gz echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \ echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \ source ~/.bashrc go get -u github.com/golang/dep/cmd/dep ----------------------------------------------------------------------------------- Install Singularity (check latest version at https://github.com/hpcng/singularity/releases): export VERSION=3.6.4 && # adjust this as necessary \ mkdir -p $GOPATH/src/github.com/sylabs && \ cd $GOPATH/src/github.com/sylabs && \ wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \ tar -xzf singularity-${VERSION}.tar.gz && \ cd ./singularity && \ ./mconfig ./mconfig && \ make -C ./builddir && \ sudo make -C ./builddir install Check Version: singularity --version |
Send message Joined: 17 Feb 17 Posts: 42 Credit: 2,589,736 RAC: 0 ![]() ![]() |
Thank you. I did sudo apt-get install singularity, so we'll see what happens. Thanks so much. I'll give this a try if the above method fails. Bought two year old but new Ryzen 5 3600's. They'll be a marked improvement over what I have currently, especially in the summer. |
Send message Joined: 17 Feb 17 Posts: 42 Credit: 2,589,736 RAC: 0 ![]() ![]() |
Thank you. I did sudo apt-get install singularity, so we'll see what happens. It seems as though most of this is well above my head and knowledge. Or maybe it's simply paid work followed by 'free work and troubleshooting' as it were. Things still don't appear to be functioning correctly. I do not appear to be out of memory. Have switched over to Rosetta, for now, until I can troubleshoot this and get it functional. Will start with one machine at a time. I may reinstall Ubuntu 20.04 from scratch and go through everything again. At this point I'm not sure what else to try. The most frustrating part - I have not done anything different on the machines that are able to complete these tasks versus the ones that are not, to my knowledge, so I'm at a loss as to where to begin. |
Send message Joined: 15 Nov 14 Posts: 602 Credit: 24,371,321 RAC: 0 ![]() ![]() |
It seems as though most of this is well above my head and knowledge. Or maybe it's simply paid work followed by 'free work and troubleshooting' as it were. Well I just tried it on a new Ubuntu 20.04.2 machine, and it didn't work for me either, if that makes you feel any better. After considerable trial-and-error and searching I found that this worked. I will reserve commenting on the Linux "developers" for another occasion. First: install Dependencies: sudo apt-get update && sudo apt-get install -y \ build-essential \ libssl-dev \ uuid-dev \ libgpgme11-dev \ squashfs-tools \ libseccomp-dev \ wget \ pkg-config \ git \ cryptsetup Second: install GO sudo apt install git sudo snap install go --classic sudo echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \ echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \ source ~/.bashrc go get -u github.com/golang/dep/cmd/dep (wait for the download!) Check version: go version Third install Singularity (latest version at https://github.com/hpcng/singularity/releases, though this works for me): For reference, see: https://sylabs.io/guides/3.7/user-guide/quick_start.html go get -d github.com/sylabs/singularity export VERSION=3.7.2 && \ wget https://github.com/hpcng/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \ tar -xzf singularity-${VERSION}.tar.gz && \ cd singularity ./mconfig && \ make -C ./builddir && \ sudo make -C ./builddir install Check Version: singularity --version |
![]() ![]() Send message Joined: 7 Jan 07 Posts: 41 Credit: 16,032,260 RAC: 18 ![]() ![]() |
@Jim1348 : Thanks for the tip As I always prioritize packages over sources, I modified your process as follow : Needed dependencies for both cases : build-essential uuid-dev squashfs-tools wget pkg-config Modified process validated on Ubuntu 20.04.2.
$ sudo apt install golang (2) Modified PATH without /usr/local/go/bin : $ sudo echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \ $ echo 'export PATH=${PATH}:${GOPATH}/bin' >> ~/.bashrc && \ $ source ~/.bashrc $ go get -u github.com/golang/dep/cmd/dep $ go version go version go1.13.8 linux/amd64
$ echo 'deb http://deb.debian.org/debian buster-backports main contrib non-free'|sudo tee -a /etc/apt/sources.list $ sudo apt update $ sudo apt install -t buster-backports golang $ sudo sed -i '$d' /etc/apt/sources.list $ sudo apt update (2) Modified PATH without /usr/local/go/bin : $ sudo echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \ $ echo 'export PATH=${PATH}:${GOPATH}/bin' >> ~/.bashrc && \ $ source ~/.bashrc $ go get -u github.com/golang/dep/cmd/dep $ go version go version go1.14 linux/amd64
$ singularity --version singularity version 3.7.3 |
![]() ![]() Send message Joined: 7 Jan 07 Posts: 41 Credit: 16,032,260 RAC: 18 ![]() ![]() |
Latest improvements : PATH does not need to be modified since we use package for Go : $ sudo echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \ $ source ~/.bashrc This command is useless since we install Singularity from the tarball : go get -d github.com/sylabs/singularity |
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