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Atmosphere FAQ

Where should I put save data on my Atmosphere Instance?

When doing work in Atmosphere, you will likely bring data into instances from the CyVerse Data Store, your local system, or another data source. However, within the instance, where should you put your data?

There are a several instance storage options within an instance, each with different considerations:

  • Instance volume (usually mounted as /vol_c )
  • Instance scratch directory, /scratch
  • FUSE-mount your Data Store directory
  • Home directory /home

Each solution will be briefly described below.

Instance Volume

Larger storage, good performance, durable, not accessible outside of Atmosphere

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An instance volume, often referred to as simply “volume”, is a durable, long-term storage option that can only be used within Atmosphere instances. This is a reasonable storage solution for larger data sets that will be used within Atmosphere for many weeks or months. We recommend backing up your data to your Data Store home directory.


Note: A volume can be attached to one instance at a time, much like a virtual USB drive.

Instance Scratch Directory /scratch

Storage size according to instance size, high performance, ephemeral, not accessible outside of Atmosphere

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Every instance will have a ephemeral disk that is stored under /scratch, and its storage size is defined by the size of the instance. The ephemeral disk only exists while the instance is active, and any data stored within this directory may be deleted when the instances is inactive (i.e. suspended, stopped, or shelved). This is a reasonable place for intermediate files or interim “work” before moving it to a long term storage (1. CyVerse Data Store, 2. an attached volume).

FUSE-mount your Data Store directory

Large storage, low performance, extremely durable, accessible with CyVerse’s ecosystem

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You can mount your Data Store home directory within your instance through FUSE. This method of access is convenient within certain limits. Performance may degrade if there are too many concurrent file access (e.g. several dozen concurrent files accessed simultaneously) or the files are too large (e.g. 100 Gb+).

Home directory /home

Small storage, high performance, ephemeral, and not accessible outside of Atmosphere

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The /home directory, the directory which you see when you login to an instance, will have limited disk space, whatever is configured for the image. This directory should also be considered temporary, if the instance is deleted or imaged. Unlike the scratch directory, the home directory will persist if the instance becomes inactive.

Viewing attached volumes and scratch

A command that will help see what is mounted & available is df. The example below uses the -h option for storage reporting in more human readable form, see details Below

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$ df -h

Filesystem      Size  Used Avail Use% Mounted on
/dev/vda1        20G  2.6G   17G  14% /
none            4.0K     0  4.0K   0% /sys/fs/cgroup
udev            7.9G   12K  7.9G   1% /dev
tmpfs           1.6G  412K  1.6G   1% /run
none            5.0M     0  5.0M   0% /run/lock
none            7.9G     0  7.9G   0% /run/shm
none            100M     0  100M   0% /run/user
/dev/vdb        158G   60M  150G   1% /scratch
/dev/vdc         64G   52M   61G   1% /vol_c

This instance has a 65 GB attached volume mounted at /vol_c and over 150GB available under /scratch.

One approach to deciding might be:

“Using /scratch” would fit if my analysis likely to “start” with the large dataset (30 fastq of 150 GB). Then, various tools are run that produce new data. Once those are complete, only a smaller set of outputs will be retained. In this case, we use /scratch for computing intermediate files and only keep outputs.

“Attaching a volume” would fit if my analysis likely to begin with a common input. Then, an analysis (or many) are performed. Once complete, the results are the input to “periodic” analysis or refined over time.

In the end, any of the storage options mentioned in this article can be used for performing analysis. It is a matter of evaluating what data needs to be retained or the performance requirements. The CyVerse Data Store, or a Volume, are the most durable options for keeping data.

How do I manage disk space on my Atmosphere Instance?

A recent change in Atmosphere “relocated” ephemeral storage mounted within the instance’s filesystem.

Previously, Atmosphere would mount the ephemeral storage under the home directory, /home. This allowed you to automatically have a larger temporary, working space when you established a remote connection via SSH or VNC. This temporary space is relative to the “instance size” you selected on launch.

Due to the nature of ephemeral storage, namely that this storage may be erased when the instance is not active, Atmosphere now mounts this storage onto /scratch. You are welcome to use /scratch if you need additional storage for active analysis or work.

See details below:

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        $ df -h
Filesystem      Size  Used Avail Use% Mounted on
udev             16G     0   16G   0% /dev
tmpfs           3.2G  8.7M  3.2G   1% /run
/dev/vda1        20G  4.9G   15G  26% /
tmpfs            16G     0   16G   0% /dev/shm
tmpfs           5.0M     0  5.0M   0% /run/lock
tmpfs            16G     0   16G   0% /sys/fs/cgroup
/dev/vdb        237G   15G  210G   7% /scratch
tmpfs           3.2G     0  3.2G   0% /run/user/0


It is important to note is that data under /scratch will not persist when shelving an instance. Also, instances which are in a suspended or stopped state may ultimately be shelved if the instance is inactive for too long. This consideration should be weighed when choosing where to put data. If a higher durability guarantee is required (or desired) within the instance, then store data in a volume. You can also backup and restore your data to the CyVerse Data Store.

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