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Singularity error github mac Installation Method Ubuntu 22. Singularity Singularity. 226 I am sorry if this doesn't belong here. When trying to clone the repository, facing 443 timeout issue. We've seen some issues with Mindboggle on clusters over the past year or so, so please let us know if you have success or more difficulties. The networking isn't fun. So I would assume a user would eventually add Singularity in the lustre system (or equivalent, e. Scratch that - the vector theme depends on the default theme, so it would still crash. 0 is the first release in the 4. Saved searches Use saved searches to filter your results more quickly Replace D:\host\path\where\to\ouptut\singularity\image with a path in the host filesystem where your Singularity image will be created. New Features & Functionality. 1, but from what I can see, the semantics of singularity_image_check have changed:. 0) You signed in with another tab or window. Almost certainly this is the issue - --bind /usr Binding all of /usr from the host in to the container will replace all the basic libraries in the container with the versions from the host. If you are modifying Singularity and contributing your changes Saved searches Use saved searches to filter your results more quickly This is fixed in 3. Version of Singularity: 3. sif ping www. In 2. Please also note that there is a 2. 0/24. Are you using that instead of the GTF (which is available here)?I suspect that if you didn't download the prebuillt index (indicated by the . el8. 10. 1 but does not have this patch Ubuntu updated to 5. The programs in the container are expecting the container You signed in with another tab or window. You should try again, and investigate any network issues. Hello, I've compiled singularity 2. com> Date: Monday, December 7, 2020 at 5:08 PM Singularity relies on a package called containers/image to handle fetching of docker/OCI images. If you work on a project related to Singularity, or use Singularity in an interesting workflow, let us know if you'd like to present to the community! This guide is intended for running {Singularity} on a computer where you have root (administrative) privileges, and will install {Singularity} from source code. This method will work for >=v3. 0, rocker/rstudio:devel, and rocker/rstudio:latest on 9/1/2020, none of which allow me to connect via localhost, and if I run these on a compute node the jobs kill Install from source¶. This is extremely useful for ensuring that your code can be run portably on other machines. . FATAL: while loading overlay images: failed If that does not work, then a more involved attempt is to modify the prefs. 0-rc. Version of Singularity What version of Singularity are you using? Run: $ singularity --version singularity-ce version 3. 20. 0 What version of Singularity are you using? Run: $ singularity version 3. From: David Trudgian <notifications@github. stderr file looks like this for me: I'm not familiar with the changes since v2. Everything seemed okay. github. Version of Singularity: $ singularity version singularity version 3. sylabs. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 4 kernel in 18. I have previously downloaded Go and have indicated the path to the libraries and binary files in my . Reload to refresh your session. 2. A fresh, default installation of {Singularity} is configured to connect to the public services available at cloud. I also develop with pygame for mac and i encounter a crash with my bundled app (py2app) that seems related. If you are using the Windows compile, just run singularity. If you have a singularity image, it is pretty straight forward. Variables defined in later files take Saved searches Use saved searches to filter your results more quickly Version of Singularity: What version of Singularity are you using? Run: $ singularity version d5eaf8a+dirty I run a Nextflow pipeline executed using singularity. Hello, Just writing to report that I'm still having trouble getting the most recent version of Finder to work as documented on an HPC cluster via singularity. The provided singularity deb there is also 2. All materials and instructions will be on github (WIP), you can find git in the description under the video Version of Singularity singularity-ce-4. Adding to the circle recipe directly fixed things up. I can not use root since it has hi @crichgriffin, thank you for your interest in dandelion and raising this issue. 00 FROM openjdk:17 ADD https:/ Do you mean you followed the instructions from INSTALL. FATAL: while loading overlay images: failed I have downloaded the git and set name and email variables. This version of RepeatMasker uses a new version of FamDB with a new format. The run_finder job, for me, took several hours to build the images, and then f What steps will reproduce the problem? 1. 4. By default, group-wise co-assembly is disabled, while the computation of group-wise co-abundances is enabled. iMOKA is run solely through an image. 6 . I came up with This tutorial will introduce you to Singularity, a containerization system for scientific computing environments that is available on many scientific computing clusters. What's your assessment? Hi, The idea of Singularity is that you have nothing to install it provides a full image of the software and its dependencies. Does the underlying filesystem matter significantly? Obviously Singularity will be used on HPCs where there are two filesystems usually: Lustre with vast storage and a "home" filesystem with only like 5-10 GB per user. Is this available on singularity yet? Last time I checked you guys mentioned that you are working on it. Pass in custom mount points as an evironment variable -e MOUNTPOINTS=/home /work /scratch to Commands that run, or otherwise execute containers (shell, exec) can take an --nv option, which will setup the container's environment to use an NVIDIA GPU and the basic CUDA libraries to run a CUDA enabled application. dat file (you may have to create it) and set the theme=vector. Other installation options, including building an RPM package and installing {Singularity} without root privileges, are discussed in the Closing as a duplicate as above - discussion can continue on #3634. Version of Singularity: singularity version 3. ESMValTool v2. /run_singularity to start singularity. In v2. I'm trying to run Singularity containers with the working directory on a mounted filesystem backed by Google Drive, via rclone mount. 2) for MacOS X (11. If this is the case, try manually assigning the index starting from index 0 and work your way up. - Issues · sylabs/singularity Checkout Code from Git . IIRC Mac defaults to 192. img MY_COMMAND is just a way to execute a command which is within the Singularity image. 5) docker container. tag: GitHub tags form the basis for releases, so installing Contribute to fohofmann/manuals development by creating an account on GitHub. 2 series, including various new features. Description: I cannot execute singularity build file. I doubt this extra piece of info is useful, but just in case, the new_species. If you already have part of the data such as the . You may try whether port 22 is open using lsof -i:22 or telnet localhost 22 in the singularity shell. If I run singularity build --fakeroot --fix-perms sscha-with-quippy. Config the hosts' firewall. Thanks for For Mac, the beta Singularity Desktop product was deprecated a while back, due to the complexities of shipping and maintaining a working Linux Virtual Machine configuration to run Singularity inside of. 1) on Apple Silicon (MacBook Pro 13-inch, M1, 2020). But I admit it is far from "good". This group information can be used for group-wise co-assembly with MEGAHIT or SPAdes and/or to compute co-abundances for the binning step with MetaBAT2. 1 Expected behavior Compile a Docker container from Docker Hub and assemble it into a Singularity container. Basically, singularity exec hicpro_devel_ubuntu. js): This sample payload makes a GET request to the root directory ('/') and shows the server response using the fetch API. Version of Singularity: What version of Singularity are you using? 3. I'll have a look at getting a conda environment together. com should ping facebook Actual behavior ping: socket: Operation not permitted [ 1. Installed vagrant-scp plugin to share the resources from host. Aim. md @m-mews we cannot reproduce it on our end, and we actually don't need permutation testing in our current pipeline using fine-mapping to follow up on marginal assocaitions. 1 Expected behavior What did you expect to see when you do? Okay, so I am working Hi there, I'm using singularity version 3. 04 (jammy) DEB package with dpkg. Reach out via email to: thesingularity. The recipe requires access to brew which is My school recently installed singularity on a cluster I have access to, and I would like to try it, but I'm unable to create any images because I don't have sudo privileges. The goal of this payload is to function as example request to make additional contributions as easy as possible. It also skips as no associated ranking_debug. Singularity runs under linux OS. On Linux and most Unix-like other platforms, running python3 -m singularity in the git checkout will start the game (or simply singularity if installed via a Linux distribution). Follow these instructions to run singularity on macOS Ventura @arm64. tar cannot copy these files to the new image with the correct permissions if it is executed as a normal user. Replace ubuntu:14. You can shut the VM down using the command ‘vagrant halt’ when you no longer need it. If you have multiple devices, it might incorrectly pick the wrong one. simg of the edX / TUDelft / Delftx Hello Real World with ROS. If you want to use a different version of Singularity, or want to get more familiar with how Vagrant and VirtualBox work, you can build your own Vagrant Box from scratch. git commit -m "short message about updates" Once you are done with your edits, save and commit your code using step #3 and then push your changes: git push. The following commands will install Singularity from the GitHub repo to /usr/local. If one of these errors is reported, it is best to check the installation of Singularity and ensure that I am trying to install Singularity on my MacOS but it doesn't seem to pick up which singularity or singularity --version: Main Attempt: Install using Homebrew (and install Home Singularity on your Mac via Vagrant. 1). This note will be visible to only you. Some resources that I consulted although none of them presented a self ERROR : User namespace not supported, and program not running privileged. 1-468-gb034a40-dirty Expected behavior $ singularity instance start Default. Actual behavior While storing Yeah, I'd check on your side first, especially since it is mesos executor. def file on an HPC cluster. 88 TETools contains RepeatMasker 4. sh. sif www $ echo $? 0 $ singularity instanc Describe the bug When making a namespace as an unprivileged user, either the UID in the namespace is mapped to 0 or something else. dirty When go to run or shell a singularity container, build on a Linux system and runs fine on multiple linux distros and singularity versions The script may or may not link to the correct device index. 1 address. json is found. The --writable option will put the container into a file system with a predefined mount of extra buffer space. 0. You signed in with another tab or window. g7427b73f1. 04, with all the software required to run the HybPiper pipeline (including some additional functionality, see below for details), as well Hi there, I'm using singularity version 3. 8. docker run --privileged Version of Singularity: Singularity 3. I have the same error, also trying to get things running via singularity, trying test1. This Gist describes the steps needed to install Singularity in a Parallels-Desktop-and-vagrant-managed arm64-compatible virtual machine on a MacBook Pro with an M1 Pro chip. 5. E. img file. Now open the GitHub repo web page. Version of Singularity: What version of Singularity are you using? Run: $ singularity --version singularity/3. You should run this once for each independent contig in your dataset, producing one SMC++ output file per $ singularity pull docker://ubuntu:latest INFO: Converting OCI blobs to SIF format INFO: Starting build Getting image source signatures Copying blob d72e567cc804 done Copying blob 0f3630e5ff08 done Copying blob b6a83d81d1f4 done Copying config bbea2a0436 done Writing manifest to image destination Storing signatures 2020/10/20 17:24:18 info unpack Singularity Python is a python module and command line tool to provide helpers for working with Singularity containers, specifically providing functions to visualize, package, and compare containers. FATAL: container creation failed: mount /opt/foo->/opt/foo error: while mounting /opt Version of Singularity: $ singularity --version singularity version 3. For this comparison I built a singularity images from rocker/rstudio:4. 1 Describe the bug I am trying to install singularity in an HPC environment. g. git add . As this chip is arm64 based, it turned out rather tricky. 2) go version go1. Each sample has an associated group ID (see input specifications). Version of Singularity: What version of Singularity are you using? Run: singularity-ce version 4. SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, GitHub community articles Repositories. - installing_singularity_on_macbook_pro_m1_pro. But, I can run glxinfo and glxgears. The compilation on both hosts was uneventful, and in both I us You signed in with another tab or window. sif) I get the following error: ERROR : Unknown image format/type: tracker. Hi Chris, Generally, packaging Desktop for a package manager like conda would be a challenge, as I'm not sure they support including binaries that need privilege (such as xhyve does to start a VM)? The permission denied is strange - did you do anything with sudo or change permissions? sudo would have gone to roots home, so I'm not sure what might have happened. Keywords for someone searching: this was needed to use hrwros-09. 9. ind, which is the pre-built index for TEcount (available here). Singularity container for EIC Fun4All allows any user to run the EIC RCF/SDCC environment with the nightly builds on your local computers or on external high-performance computing clusters. If you only want to use these public services, all you need to do is obtain an authentication token, which you then Remove the original pip install MACS line from the dockerfile. Also, the http. This is the default for docker and podman runs that we tested on. But in 2. 0-rc2 on MacOS Expected behavior singularity exec container. For simplicity, there is also a sh wrapper . 1 and Ubuntu 18. e. smc. data. x series and includes a security fix that is not in 2. 4 but every time I run the script below, I get into an error. 64. To keep it consistent with v2 behavior, and because singularity knows that the container needs to be rebuilt with new layer or not, I think it should be singularity's responsibility to make sure that it handles concurrent executions of the same container, in my humble opinion - probably by making other Version of Singularity: 3. I noticed that your snakemake is referring to the hg38_rmsk_TE. The problem is the OpenSSH update 7. 12. simg. com> Reply-To: hpcng/singularity <reply@reply. Hi, I am trying to install Singularity on a Macbook Pro M1 MacOS BigSur 11. H If that does not work, then a more involved attempt is to modify the prefs. Inferring CNV from Single-Cell RNA-Seq. Needed to install libarchive-dev as well. It is now possible to use multiple environment variable files using the --env-file flag, files can be specified as a comma-separated list or by using the flag multiple times. 658. MacOS moves quickly, security changes often affect these types of environments, and the Intel / ARM split recently adds complexity. 3. 0 Dear developers, I'm trying to build a singularity container from a . You signed out in another tab or window. The singularity version is: singularity --version singularity version 3. It will access Docker Version of Singularity: I downloaded Singularity Desktop for macOS (Beta Release v0. What is the expected output? What do you see instead? If run from the windowing system, the application bounces in the dock You signed in with another tab or window. You can easily redirect IO, use pipes, pass arguments, and access files, sockets, and ports on the host system from within a container. Hi, Thank you for your interest in the software. The following are a list of brief examples and tutorials generated by the Singularity community for using docker2singularity. 2. Hi, first of all thanks for your assistance. It can't find "hits" even with a cut-off of 100. Alternatively, Here I got the same crash here. See #5434 Skip to the content. 3 Expected behavior I am using --bind=/opt/foo to bind a directory during build. I typed singularity in the command window to verify that the installation was successful. def The build crashes Option 2: Download the latest development code. AI-powered developer platform Available add-ons Note that as of version 1. Ensure that the /dev/nvidiaX device entries are available inside the container, so that the GPU cards in the host are accessible. The xhost + was to allow connections to the X server you may not need that (And that opens it wide open as well). facebook. Scratch that - the vector theme depends on the default theme, Version of Singularity: 3. 1. gz chr1 Pop1:S1,S2 This command will parse data for the contig chr1 for samples S1 and S2 which are members of population Pop1. At Replace D:\host\path\where\to\ouptut\singularity\image with a path on the host filesystem where your Singularity image will be created. When the UID is mapped to 0 singularity thinks it is root, and tries to perform operations that it may not be permitted to do even if it's not technically root. 2-119. Fidler and nlmixr2 users, I have trouble fitting the following model with the data attached here. 6, and What steps will reproduce the problem? 1. For my game it crash at run. What the --nv flag does, is it takes the host libraries (which can be driver dependent), and bind mounts them into the container on run. Version of Singularity singularity-ce version 4. ind in the file extension), then you might need to go into Ok, I finally got around to testing this and I can confirm that using rstudio-version 1. 14. x86_64 singularity: symbol lookup error: singularity: undef What steps will reproduce the problem? 1. When installing from source, you can decide to install from either a tag, a release branch, or from the master branch. 11. 1) here. 0 the mksquashfs procs and mem limits were not applied to all mksquashfs calls. It includes specifics about the base OS to build or the base container to start from, as well as software to install, environment variables to set at runtime, files to Ah figured it out - it indeed was the kernel, and the issue was that the machine (ubuntu 20. bashrc profile. There is a sudo make install, is that what you mean?It is expected that you will run the make as non-root, then make install as root. Other distributions use the same or different I'm trying to build the singularity image with the latest cloned lbann repo on commit 8ec2d00. md? It doesn't have a sudo make. 0 (top of tree as of 11/5) Expected behavior successful sandbox build from singularity image Actual behavior FATAL: While performing build: packer failed to pack: exec: "u Heya, did you find a fix for this? I am having the same issue. GitHub Gist: instantly share code, notes, and snippets. You switched accounts on another tab or window. 2-96. 5042 creates working singularity images. Unless the host is an identical linux distro / version and has all the libraries the container needs under /usr then this will cause major problems. Version of Singularity: What version of Singularity are you using? Run: $ singularity --version Installed via EPEL: apptainer-1. 04 with the docker image name you wish to convert (it will be pulled from Docker Hub if it does not exist on your host system). Sylabs introduced Singularity Container Services (SCS) to enable users to Create container images, Secure them, and Share them with others. allValidPairs files for instance, you should be able to Hi Dr. By default it has kernel. MAFFT) singularity container is very handy as the end user just need to install singularity and download the container without having to care for installing dependencies or setting environment variables. This bug has been fixed in conda, but the problem reported here will only be fixed once we release a new I am having the exact same issue and have removed the python game but there is no package called "singularity-ce" and despite installing singularity from the source, it won't run commands under singularity. You may receive streaming errors with each attempt: If you will be making changes to the source code, and submitting PRs, you should install golangci-lint, which is the linting tool used in the SingularityCE project to ensure code consistency. sif Singularity_new. com Be sure to include "Hacking the Universe" in the subject line, so that the email doesn't get overlooked. Every pull request must pass the golangci-lint checks, and these will be run automatically before attempting to merge the code. 3 Expected behavior I'm trying to pull a docker container with singularity in a nextflow pipeline. It's got to do with numba being unable to create its default cache in your compute environment/location when scanpy is being imported. I attempted to use the "singularity pull" command, but that created a cache in my home directory, and it turns out we have a relatively low capacity in our home directories. Write a paragraph or two about how you would like to contribute. Singularity container for ECCE@EIC Fun4All allows any user to run the EIC RCF/SDCC environment with the nightly builds on your local computers or on external high-performance computing clusters. Other notes Singularity has worked fine for converting and running You signed in with another tab or window. Now it's singularity_image_check(struct image_object *image), implemented by When I try to run the provided singularity image (tracker. ssh-keygen(1): write OpenSSH format private keys by default instead of using OpenSSL's PEM format. A brief introduction to singularity is available here. Steps to reproduce: Follow official documention. SingularityCE 4. See here for default NUMBA_CACHE_DIR locations. I'm glad you were able to spot the issue (missing the command). 2 from source on two different hosts, both running redhat clones, although of different versions. 1 - You will need to use 3. gpfs). Here is the problem. Topics Trending Collections Enterprise Enterprise platform. x is not actively supported any more. I download the source for Linux (i got pygame installed) and the game run fine on Mac from Source. 04. I first built it using $ singularity buil You signed in with another tab or window. prox You signed in with another tab or window. Substitute with a pip install from the local corrected MACS directory (reference the pip local installs lower in the dockerfile). gd61d61e2 Expected behavior Pulling singularity image docker://mono:5. 1 as a bug meant that in 3. 6 release of Singularity, which is the last in the 2. 0 Expected behavior Trying to run hello-world. Remember that the VM is running in the background because we started it via the command vagrant up. rclone mount Moore_L A {Singularity} Definition File (or "def file" for short) is like a set of blueprints explaining how to build a custom container. 9 Describe the bug A clear and concise description of what the bug is. 3-jammy Describe the bug I have a Dockerfile built and uploaded to my Docker Hub account at bskubi/juicer_tools:2. x this worked properly because we did priv escalation on import. What is the expected output? What do you see instead? If run from the windowing system, the application bounces in the dock Ok I solved the issue. This is technically not a bug. Singularity runs on Linux natively and can also be run on Windows and Mac through virtual machines (VMs). Adding the which package, was just for my usage on the ldd command. Everything pertaining to the technological singularity and related topics, e. 0-1. Have you set any *_PATH variables in your environment - or do you have anything like a conda To simplify running HybPiper, I’ve provided a Singularity container based on the Linux distribution Ubuntu 22. 6. io. unprivileged_userns_clone=0 which causes the clone call with the CLONE_USERNS flag to fail. "export VM=sylabs/singularity Run the container: sudo singularity shell --writable --net --network-args "portmap=2226:22/tcp" <sandbox_path> SSH uses tcp so that there is nothing to do with udp. 5-8. Convert your VCF(s) to the SMC++ input format with vcf2smc: $ smc++ vcf2smc my. Containers allow you to package the environment that your code depends on inside of a portable unit. If you have an example of your own, please let us know! docker2singularity-demo: an example of using Version of Singularity What version of Singularity are you using? Run: $ singularity --version singularity-ce version 3. Install from source¶. tag: GitHub tags form the basis for releases, so installing You signed in with another tab or window. Must be done with DHCP because the framework needs to assign a I wanted to install Singularity on my M1 Pro (Ventura 13. 7. Meeting details are posted in Github Discussions, and recordings made available at the Sylabs YouTube Channel. The --nv flag will:. {Singularity}’s :ref:`command line interface <cli>` allows you to build and interact with containers transparently. This README contains instructions for modifying the files available to the TETools container, but the README file in the FamDB repository contains more information on the format itself. I am having issues with pulling a singularity image. @zklaus As far as I understand, there is a bug in the conda version included in the stable (i. The aim is to create a singularity container that installs some packages, then clones a custom package from a git repo and makes it. vcf. If you are looking for the Singularity Python client to pull, build, and otherwise wrap Singularity functions, then please see the repository singularity-cli for the spython module. Solutions using VirtualBox did not work for me, as VirtualBox is available for the arm64-architecture, but no sylabs vm-box. You should commit your work to the branch whenever you have working code or whenever you stop working on it using: git add . 168. The original image contains root owned files and directories. el7 on a CentOS Linux 7 system. Hi Terry - This isn't likely related to #3874 - in that one once the correct package is installed from the right repo on RHEL8 all works as expected. gz out/chr1. If there is a difference between mconfig finding things and make not then it might be something in your environment. Run Endgame: Singularity v0. I've previously encountered this issue, but can't exactly remember how i dealt with it. Please consider the following: Is this issue a duplicate, or has it been fixed/implemented since being added? Is the issue still relevant to the current state of Singularity's functionality? Singularity supports the following attack payloads: Basic fetch request (simple-fetch-get. 5 darwin/amd64 Expected behavior Run a container Actual behavior Silently fail Steps to It's not a 127. To download the most recent development code, you should use Git and do the following: We are working hard on 'rebuilding' the Singularity community, and a major task on the agenda is finding out what issues are still outstanding. We are working hard on 'rebuilding' the Singularity community, and a major task on the agenda is finding out what issues are still outstanding. exe. This recipe demonstrates how to run Singularity on your Mac via Vagrant and Ubuntu. The great thing is that exactly the same container is available for direct download with both Docker and This might have been an issue with your network connection, or the Go module proxy service. To install an older tagged release see older versions of the docs. Here we cover several different methods of installing Singularity (>=v3. Please don't include any personal information such as legal names or email addresses. Contribute to broadinstitute/infercnv development by creating an account on GitHub. I will close the ticket for now. System specification: macOS Si Hi @kridsadakorn until now we have had some issues uploading our pipeline containers to a Singularity registry. rclone mount Moore_L Hello, This is a templated response that is being sent out to all open issues. Received an error running the following under Docker Desktop (3. But in macOS, it require another layer of virtual machine to generate a linux environment first (read more on Singularity docs). AI, human enhancement, etc. Follow the installation instructions. I am using a corporate machine, can this be the issue. 04) wasn't being used from the orb. tag: GitHub tags form the basis for releases, so installing . The home for gaming on Mac machines! Here you will find resources, information, and a great community of gamers. The only other thing I can think of is that we did make some improvements as to when shell mode is set to true/false in later Singularity versions, that may also be impacting how the mesos docker executor is running the command (very possible you need the full path to python as @petrovicboban Node-sass singularity bus error 10. Make sure sshd is running inside the container. But i'm quite busy for the next month or so, so it might take a while. gtf. 149837] reboot: Power do The root user within the container has write permissions and is able to change parameters for Cell Ranger as required. You can run programs inside a container as if they were running on your host system. We will release more detailed trans workflow recommendation when i get a chance to document that with inputs from @grennfp. ged79a2e1 When running As our scripts/pipelines often relies on several other scripts and external tools (e. research@gmail. Option 2: Vagrant Box from Scratch. In a very simple task (which is just a Bash script, see below) Singularity You signed in with another tab or window. The user needs to have permission to do things with the custom package, and ideally it would sit in the home directory of the singularity user, but that seems more difficult than I had anticipated. Maximum 100 characters, markdown supported. sif ABORT : Retval = 255 What can I do? Version of Singularity: $ singularity --version singularity version 3. 0-alpha. 0 on macOS (10. Previously, I had no trouble fitting using the same model and the same data. 30. In this case, the host is running Debian 10 (buster). The easiest approach would be using the container within a Unbuntu VirtualBox. You are simply consuming that extra buffer space after the build which is why the sandbox works properly. Options: -d, --debug print debugging information (highest verbosity) -h, --help help for singularity --nocolor print without color output (default False) -q, --quiet suppress normal output -s, --silent only print errors -v, --verbose print additional information Available Commands: build Build a Singularity image cache Manage the local cache capability Manage Linux capabilities for users and This also occurs on our lab's HPC environment using a different singularity install singularity-ce version 3. 1, it was singularity_image_check(FILE *image_fp) and returned -1 if the file was not a valid Singularity image. Hi Fuyou, It's a shame that they won't install that for you. This is followed by development updates & discussion, before open questions. Previously, I had my o The text was updated successfully, but these errors were encountered: It's using git submodules Most importantly, is it possible to legally distribute the macOS version of singularity? The EULA suggests it might not be? Sort of You can distribute the Sigularity code/xhyve all you want. Can you include a run with full debug info singularity -d , your kernel version, and the output of your /proc/self/mountinfo?It looks like there is a standard format for entries in that file that we are either incorrectly parsing or incorrectly output on your system Reporting that this worked with Singularity 2. sif on my Mac with Vargant VM installed. . docker2signularity uses the Docker deamon located on the host system. Hi @mshaikh786, this looks like an issue with parsing /proc/self/mountinfo. However, with the migration of the pipeline to Nextflow DSL2 we will be using Biocontainers to obtain all of the software containers for the pipeline. SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure. 4 we are stepping back from priv escalation wherever possible to reduce attack surface. oofts xittl jvz sssqv axdr bcokc wehtdj bdvvnn ekdyat gurbbww