- Singularity (itch) (alexander) Mac Os Update
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I’m thrilled to announce support for Mac OS X artifact builds. Artifact builds trade expensivecompile times for (variable) download times and some restrictions on what parts of the Firefoxcodebase can be modified. For Mac OS X, the downloaded binaries are about 100Mb, which might takejust a minute to fetch. The hard restriction is that only the non-compiled parts of the browser canbe developed, which means that artifact builds are really only useful for front-end developers. TheFirefox for Android front-end team has been using artifact builds with great success for almost ayear (see Build Fennec frontend fast with mach artifact! and my other posts on this blog).
I intend to update the MDN documentation and the build bootstrapper (seeBug 1221200) as soon as I can, but in the meantime, here’s a quick start guide.
Singularity (itch) (alexander) Mac Os Update
Since i was using sx os emunand and using sysnand online i skipped the first part of tutorial. And since i already had a hidden partition i skipped the second step and went to copy files. Hidden reality mac os. I downloaded atmosphere and hekate files to root of sd, put payloads into the bootloader payloads folder. Then i created the emuMMC folder and put in the new. Singularity containers let users run applications in a Linux environment of their choosing. Possible uses for Singularity on Biowulf: Run an application that was built for a different distribution of Linux than the host OS. Reproduce an environment to run a workflow created by someone else.
Quick start
You’ll need to have run mach mercurial-setup and installed the mozext extension (see Bug1234912). In your mozconfig file, add the lines
You’ll want to run mach configure again to make sure the change is recognized. This sets--disable-compile-environment and opts you in to running mach artifact installautomatically.
After this, you should find that mach build downloads and installs the required artifactbinaries automatically, based off your current Mercurial commit. To test, just try
After the initial build, incremental mach build DIR should also maintain the state of theartifact binaries — even across hg commit and hg pull && hg update.
You should find that mach build faster works as expected, and that the occasional mach buildbrowser/app/repackage is required.
Restrictions
Oh, so many. Here are some of the major ones:
- Right now, artifact builds are only available to developers working on Mac OS X Desktop builds(Bug 1207890) and Firefox for Android builds. I expect Linux support to follow shortly (trackedin Bug 1236110). Windows support is urgently needed but I don’t yet know how much work it will be(tracked in Bug 1236111).
- Right now, artifact builds are only available to Mercurial users. There’s no hard technicalreason they can’t be made available to git users, and I expect it to happen eventually, but it’snon-trivial and really needs a dedicated git-using engineer to scratch her own itch. This istracked by Bug 1234913.
- Artifact builds don’t allow developing the C++ source code. As soon as you need to change acompiled component, you’ll need a regular build. Unfortunately, things like Telemetry arecompiled (but see tickets like Bug 1206117).
- Artifact builds are somewhat heuristic, in that the downloaded binary artifacts may not correspondto your actual source tree perfectly. That is, we’re not hashing the inputs and mapping to aknown binary: we’re choosing binaries from likely candidates based on your version control statusand pushes to Mozilla automation. Binary mismatches for Fennec builds are rare (but do exist,see, for example, Bug 1222636), but I expect them to be much more common for Desktop builds.Determining if an error is due to an artifact build is a black art. We’ll all have to learn whatthe symptoms look like (often, binary component UUID mismatches) and how to minimize them.
- Support for running tests is limited. I don’t work on Desktop builds myself, so I haven’t reallyexplored this. I expect a little work will be needed to get xpcshell tests running, since we’llneed to arrange for a downloaded xpcshell binary to get to the right place at the right time.Please file a bug if some test suite doesn’t work so that we can investigate.
Troubleshooting
The command that installs binaries is mach artifact install. Start by understanding whathappens when you run
See the troubleshooting section of my older blog postfor more. As a last resort, the Firefox for Android MDN documentationmay be helpful.
Conclusion
Thanks to Gregory Szorc (@indygreg) and Mike Hommey for reviewing this work. Many thanks to MarkFinkle (@mfinkle) for providing paid time for me to pursue this line of work and to the entireFirefox for Android team for being willing guinea pigs.
There’s a huge amount of work to be done here, and I’ve tried to include Bugzilla ticket links sothat interested folks can contribute or just follow along. Dan Minor will be picking up some ofthis artifact build work in the first quarter of 2016.
Mozilla is always making things better for the front-end teams and our valuable contributors! Sullen mac os. Getinvolved with code contribution at Mozilla!
Discussion is best conducted on the dev-builds mailing list and I’m nalexander onirc.mozilla.org/#developers and @ncalexander on Twitter.
Notes
Binding external directories Singularity as an Installation Medium |
Extreme Mobility of Compute
Singularity containers let users run applications in a Linux environment of their choosing.
Possible uses for Singularity on Biowulf:
- Run an application that was built for a different distribution of Linux than the host OS.
- Reproduce an environment to run a workflow created by someone else.
- Run a series of applications (a 'pipeline') that includes applications built on different platforms.
- Run an application from Singularity Hub or Docker Hub on Biowulf without actually installing anything.
Additional Learning Resources
- Class taught by NIH HPC staff:
Example definition files written by the NIH HPC staff
These definition files can all be found on GitHub, and the containers built from them are hosted on Singularity hub.
- RStudio
Additionally, a large number of staff maintained definition files and associated helper scripts can be found at this GitHub repo. These are files that staff members use to install containerized apps on the NIH HPC systems.
Please Note:
Singularity gives you the ability to install and run applications in your own Linux environment with your own customized software stack. With this ability comes the added responsibility of managing your own Linux environment. While the NIH HPC staff can provide guidance on how to create and use singularity containers, we do not have the resources to manage containers for individual users. If you decide to use Singularity, it is your responsibility to build and manage your own containers.
back to topSingularity gives you the ability to install and run applications in your own Linux environment with your own customized software stack. With this ability comes the added responsibility of managing your own Linux environment. While the NIH HPC staff can provide guidance on how to create and use singularity containers, we do not have the resources to manage containers for individual users. If you decide to use Singularity, it is your responsibility to build and manage your own containers.
To use Singularity on Biowulf, you either need to create your own Singularity container, or use one created by someone else. You have several options to build Singularity containers:
- You can build small and medium sized containers on Helix or Biowulf compute nodes using the --remote option. In a nutshell, you must log in and generate a token on the Singularity Container Services and use the command line to copy that token into your environment (using the command singularity remote login SylabsCloud). Once you've done that, the --remote option will allow you to build containers using the Sylabs remote builder.
- If you have a Linux system to which you have root (admin) access, you can install Singularity and build your Singularity container there.
- If you have a very recent Linux system (like Ubuntu >=18) you can build Singularity containers without root access using the --fakeroot option.
- If you don't have a Linux system you could easily install one in a virtual machine using software like VirtualBox, Vagrant, VMware, or Parallels. (If you use a virtual machine be sure to allocate at least 2GB of memory or some of your builds may fail with out of memory errors.)
- You can allocate a cloud instance, to which you will have root access. Install Singularity and build your Singularity container there.
You can find information about installing Singularity on your Linux build system here for 2.x and here for the current 3.x series.
In addition to your own Linux environment, you will also need a definition file to build a Singularity container from scratch. You can find some simple definition files for a variety of Linux distributions in the /example directory of the source code. You can also find a small list of definition files containing popular applications at the top of this page.Detailed documentation about building Singularity container images is available at the Singularity website.
Troubleshooting containers that hang when they run out of memory
back to topA few containers have caused issues on Biowulf by triggering a kernel level bug described in detail here and here. These include fmriprep and nanodisco. The problems follow a predictable pattern:
- The containerized application uses more memory than has been allocated for the job.
- The Out Of Memory (OOM) killer is invoked by the kernel to kill the offending process.
- Other processes that presumably depend on the first process fail to cancel and may enter the D state (awaiting IO).
- Node responses become sluggish as it bogged down with D state processes.
- File system performance may suffer as the container tries repeatedly to communicate with the singularity starter process. Depending on the number of jobs running, this may produce noticeable degracation of file system performance.
Singularity (itch) (alexnerd) Mac Os Update
format. You can perform this conversion on a compute node using the following command:Please contact [email protected] with questions. back to topBinding a directory to your Singularity container allows you to access files in a host system directory from within your container. By default, Singularity will bind your $HOME directory (along with a few other directories such as /tmp and /dev). You can also bind other directories into your Singularity container yourself.The process is described in detail in the Singularity documentation.
While $HOME is bound to the container by default, there are several filesystems on the NIH HPC systems that you may also want to include.Furthermore, if you are running a job and have allocated local scratch space, you might like to bind mount your lscratch directory to /tmp in the container.
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The following command opens a shell in a container while bind-mounting your data directory, /fdb, /scratch, and /lscratch into the same path inside the containerIf you have access to shared data directories, you'll want to add them to the list as well (for example, /data/$USER,/data/mygroup1,/data/mygroup2,/fdb,..).or, using the environment variable:If you would like to store this in ~/.bashrc, you can also automatically bind /lscratch/$SLURM_JOB_ID to /tmp inside the container depending on whether a local scratch allocation is detected:When you share this container, your colleagues here and elsewhere can bind their own corresponding directories to these same mountpoints.
NIH HPC Staff recommendations for bind mounts on Biowulf
back to topWhen building containers for use on Biowulf, there are two steps you should take to ensure that users of the container can read and write data to all normal directories. These are the same steps that NIH HPC staff take when containerizing applications for general use.
Step 1. Add directories and symlinks at build time
Data directories hosted on the GPFS file system rely on a series of symbolic links. Singularity can't follow these symlinks if they don't exist within the container, so you need to create them at build time. Other data directories can be automatically created within the container by recent versions of Singularity, but it's still a good idea to create them.
Include the following lines in the %post section of your definition file.Creating the directories above is probably not necesary with modern versions of Singularity, but there may be situations in which they are needed and having those directories within the container will not hurt anything. This code snippet also creates more symbolic links to /gpfs/gsfs*than actually exist on Biowulf. This serves to 'future-proof' the container because more of these links will be added to the Biowulf system as more GPFS storage is added to the system.
Step 2. Set the --bind option or the SINGULARITY_BIND variable appropriately at run time
Use the following option/argument pair when you run your container.Or set the SINGULARITY_BINDPATH environment variable before running your container like so.Following these steps will allow you to access all relevant Biowulf directories from within your container.
Singularity as an Installation Medium: faking a native installation
One use case of Singularity is to transparently use software in a container as through it were directly installed on the host system.To accomplish this on our systems, you need to be aware of the shared filesystem locations and bind mount the corresponding directories inside the container, which is more complicated than it seems because we use symbolic links to refer to some of our network storage systems.As a result, you will need to specify some directories in addition to the ones you use directly to ensure that the symbolic link destinations are also bound into the container.
If you wanted to take advantage of a Debian package this way and use it to install software into your home directory, for example samtools and bcftools, you would use a definition file, Singularity, with these contents:This defines a container based on the space-efficient 'slim' Debian images from Docker Hub, installs the samtools and bcftools packages, and then creates the necessary symbolic links to our GPFS mounts to be able to use the container transparently.
After finalizing the definition file, you can proceed to build the container (of course, on a system where you have sudo or root access):
You can then set up your installation prefix (here, it's $HOME/opt/hts) as follows, making use of symbolic links and a wrapper script:where the wrapper script wrap looks like:wrap checks to see how it was called, then passes that same command to the container after appropriately setting SINGULARITY_BINDPATH.
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So if you have added the installation prefix $HOME/opt/hts/bin to your PATH, then calling samtools or bcftools will run those programs from within your container.And because we have arranged to bind mount all the necessary filesystems into the container, the path names you provide for input and output into the programs will be available to the container in the same way.
back to topSingularity cannot be run on the Biowulf login node.
To run a Singularity container image on Biowulf interactively, you need to allocate an interactive session, and load the Singularity module. In this sample session (user input in bold), an Ubuntu 16.04 Singularity container is downloaded and run from Docker Hub. If you want to run a local Singularity container instead of downloading one, just replace the DockerHub URL with the path to your container image file. Note that you need to exit your Singularity container as well as your allocated interactive Slurm session when you are done. In between the space mac os.
Expand the tab below to view a demo of interactive Singularity usage.
- space - play / pause
- f - toggle fullscreen mode
- arrow keys(←/→) - rewind 5 seconds / fast-forward 5 seconds
- 0, 1, 2 .. 9 - jump to 0%, 10%, 20% .. 90%
- copy and paste text from movie
In this example, singularity will be used to run a TensorFlow example in an Ubuntu 16.04 container. (User input in bold).
First, create a container image on a machine where you have root privileges. These commands were run on a Google Cloud VM instance running an Ubuntu 16.04 image, and the Singularity container was created using this definition file that includes a TensorFlow installation.
Next, copy the TensorFlow script that you want to run into your home directory, or another directory that will be visible from within the container at runtime. (See 'binding external directories' above). In this case, this example script from the TensorFlow website was copied to /home/$USER, and the container was moved to the user's data directory
Then ssh to Biowulf and write a batch script to run the singularity command similar to this:
Submit the job like so:
After the job finishes executing you should see the following output in the slurm*.out file.
Expand the tab below to watch a quick demo of Singularity in batch mode.
- space - play / pause
- f - toggle fullscreen mode
- arrow keys(←/→) - rewind 5 seconds / fast-forward 5 seconds
- 0, 1, 2 .. 9 - jump to 0%, 10%, 20% .. 90%
- copy and paste text from movie
With the release of Singularity v2.3 it is no longer necessary to install NVIDIA drivers into your Singularity container to access the GPU on a host node. If you still want the deprecated gpu4singularity script that was used to install NVIDIA drivers within containers for use on our GPU nodes you can find it on GitHub.
Now, you can simply use the --nv option to grant your containers GPU support at runtime. Consider the following example in which we will download some TensorFlow models to the user's home directory and then run the latest TensorFlow container from DockerHub to train a model on the MNIST handwritten digit data set using a GPU node.
Expand the tab below to see a demo of installing and using GPU support in a Singularity container.
- space - play / pause
- f - toggle fullscreen mode
- arrow keys(←/→) - rewind 5 seconds / fast-forward 5 seconds
- 0, 1, 2 .. 9 - jump to 0%, 10%, 20% .. 90%
- copy and paste text from movie
Singularity can import, bootstrap, and even run Docker images directly from Docker Hub. For instance, the following commands will start an Ubuntu container running on a compute node with no need for a definition file or container image!And, of course, we remember to set SINGULARITY_BINDPATH appropriately to be able to access all our files.In this instance the container is ephemeral. It will disappear as soon as you exit the shell. If you wanted to actually download the container from Docker Hub, you could use the pull command like so:This feature gives you instant access to 100,000+ pre-built container images. You can even use a Docker Hub container as a starting point in a definition file.
In this example, we will create a Singularity container image starting from the official continuumio miniconda container on Docker Hub. Then we'll install a number of RNASeq tools. This would allow us to write a pipelinewith, for example, Snakemake and distribute it along with theimage to create an easily shared, reproducible workflow. This definition file also installs a runscript enabling us to treat our container like an executable.
Assuming this file is called rnaseq.def, we can create a Singularity container called rnaseq on our build system with the following commands:
This image contains miniconda and our rnaseq tools and can be called directly as an executable like so:
After copying the image to the NIH HPC systems, allocate an sinteractivesession and test it there
This could be used with a Snakemake file like this
Expand the tab below to see an example of creating a Singularity container to be used as an executable from a Docker image on DockerHub.
- space - play / pause
- f - toggle fullscreen mode
- arrow keys(←/→) - rewind 5 seconds / fast-forward 5 seconds
- 0, 1, 2 .. 9 - jump to 0%, 10%, 20% .. 90%
- copy and paste text from movie