At OIST we have two separate sections that deal with computing-related things.
The IT Division handles everything around administrative IT, laptops and end-user devices, OIST accounts, and office systems. You contact them for printers, laptop issues, account issues, VPN, desktop software and so on. The contact email is it-help@oist.jp.
We at the Scientific Computing and Data Analysis section manage HPC clusters, large-scale storage, scientific software and licenses, the OIST campus-wide network and similar. Come to us for anything related to this kind of thing. Contact us at ask-scda@oist.jp.
You may have a problem that could be either for IT or for us at SCDA. Don’t worry! Take your best guess. We’ll all make sure it ends up with the right people.
Welcome to OIST! We hope you’ll like it here.
You have an OIST account. The account name usually looks something like “sam-vimes” - your first and last name, connected with a hyphen. When you log in to Office365, you add the OIST domain to it: “sam-vimes@oist.jp”.
Your email address is usually “sam.vimes@oist.jp” - your first and last name connected with a dot. It’s very easy to confuse your email address and OIST account name! Your account has a hyphen (“-“) and your email address a dot (“.”).
Many of you will be a unit leader, research staff (researchers, postdocs, technicians and so on) or Core Facilities staff. You belong to your research unit or section and generally have access to everything at OIST.
If you are a student or intern you belong to the Graduate School. To get access to your research unit storage you typically have to ask your unit leader for access.
A visiting researcher that has an OIST account and belongs to a research unit has the same access as regular research staff.
Administrative staff belong to the administrative side, not to research, and generally has no access to computing, research software or storage facilities at OIST.
“OIST-public” lets you get online without any authentication. But as the name says, it’s a public network with no access to any internal OIST websites or systems.
“OIST” and “OIST-2.4g” are internal networks. You need to authenticate with your OIST account and password. The details of doing this for Windows, Mac and Linux is covered on this page: Connect to OIST Wifi (IT section)
Wired connection: If you want speed and low latency, you probably want a wired Ethernet connection. Like with Wifi you need to authenticate with your OIST ID and password. The details for Windows, Mac and Linux are here: Connect to OIST Network (IT Section)
Your unit has storage available on Bucket for research data. The unit likely also has space on Flash and Work for running jobs on the HPC clusters; and perhaps other systems as well. You can find how to use these on our page on transferring data
By law, all research data must be stored at the university for a period of at least ten years. At OIST you do this by having a copy of the data on Bucket. Bucket is highly reliable and backed up, so we recommend that you use it to store all your research data.
Note that Bucket is only for research data. Do not use it to backup your laptop; for administrative files; or for anything personal.
If you are a postdoc, staff researcher or similar you are employed directly in your unit, and you automatically have access to these storage systems.
If you are a student you belong to the Graduate School, not to a unit. You need to ask your unit leader to enable access for you.
If you are a unit leader, look here for details on how to do manage the unit storage.
Other storage you may hear about or want to use include:
Flash and Work You use these when running jobs on the HPC clusters. They’re very fast but small. Don’t store data there other than when you run a job on the cluster.
Comspace Per-unit storage where you have fine control over access. You mount it on your desktop as a remote folder. Especially good for data you want only a subset of members to access or see.
HPAcquire Used to transfer data from instruments, typically to Bucket or to your computer. This isolates instruments from the wider network, helping them stay secure.
You can find more information on storage here.
You have a personal OneDrive storage area where you can store data and share it with other users at OIST, similar to Dropbox.
Using Teams you can access OneDrive and your calendar; chat directly with other OIST users; and create collaboration teams for your unit, research projects or other things.
Your unit can also have a Sharepoint site that is appropriate for unit doducments, internal web sites, published or in-progress papers, sensitive administrative files and other, mostly non-research data.
You can get an OIST Dropbox account. But it’s only for collaborating with researchers outside OIST.
Store research data on Bucket. For sharing files within the unit, please use OneDrive. Administrative documents go into Sharepoint. You can also get storage on Comspace; this gives you fine-grained constrol over access and permissions. You can collaborate with external users using a Sharepoint Access Package.
Why do we discourage the use of Dropbox?
OIST no longer provide Slack. It proved to be cost-prohibitive. For any internal communication, please use Teams.
In principle, we promote the use of and provide open source software where possible and reasonable1. However, we recognize that it’s not always practical, and so we also provide a number of commercial scientific software packages; on the cluster, on remote workstations, and for desktop use.
Our provided software, and how to get access, is listed on this page.
Access Requrirements
The license terms differ for each package. Some may only be allowed on OIST-provided devices; others may disallow using VPN or using it when away from campus. Check the terms of each software carefully.
Non-scientific software, such as PDF viewers and image editors is provided by the IT division. You can find their portal page here: The OIST IT Division
OIST has a Github enterprise account. This lets you safely store source code and work with it with other unit and OIST members in private, without having to pay for your own subscription.
To get access, follow the instructions here.
In short, you need a personal github account. You submit the Github ID for that account, and you then get access to the OIST enterprise repository.
A cluster is a large computing system made up of dozens or hundreds of individual nodes, or computers. They’re connected in a fast network and able to work together on a single large computing problem. You use them when you need more speed or more memory than your local desktop an provide.
We have two main systems here at OIST:
Deigo2 is our main HPC cluster. It has about 66 000 cores, and is used for most general scientific computing. More information about Deigo is here.
Saion3 is our GPU cluster. It has over 150 GPUs in a mix of P100, V100 and A100 GPUs. Mostly used for GPU-related data analysis and model training. More information about Saion is here.
We also have DCV, remote Windows workstations, mostly for running certain visualization software that need a lot of resources and a fast connection to the storage.
Computing is provided to OIST members free of charge, and on an equal basis.
All OIST members get access to the Deigo “compute” partition4 with 2000 cores for up to 4 days; the “short” partition with 4000 cores for 2 hours; and the Saion “test-gpu” partition with two GPUs for up to 8 hours.
You can apply for access from this page; choose “Open Resources”.
There are also several restricted partitions. Again, they are free to use, but you need to show that you need them before you get access. You can apply for them from the same request page as above, through “Restricted Resources”.
Our main page on using the computing resources is here.
In brief, you access the clusters with SSH. You can use modules of preinstalled software or elect to install software for yourself. Use SLURM to allocate resources and run your jobs.
We have periodic training on using the clusters; we have daily Open Hours for direct help; and you can email us at ask-scda@oist.jp for any issues or questions.
We provide elabFTW for research units. It’s an online alternative to paper lab notebooks, with better support for collaboration, adding images and video and more.
You can contact us with email at ask-scda@oist.jp, or go to ask-scda.oist.jp for any questions or requests.
We have general documentation and application forms at scda-answers and HPC-specific documentation here at scda-guide.
We have Open Hours every weekday from 15:30—17:30 in Lab 2, room B648; and on Zoom.
We also provide training courses with a basic introduction for new users three times a year (around September/October; January/February; and May), and a selection of more advanced courses on an occasional basis.
We have a bioninformatics specialist offering one-on-one consultation and training courses for all your bioinformatics needs. Contact ask-scda@oist.jp for more information.
If you want to explore your data graphically, need an illustration for a publication, or an animation showing your work, contact us for our scientific data visualization and illustration services.
When you leave OIST, your account will be suspended, and you will lose access to OIST resources.
When you change roles — from student to Postdoc for instance — you will usually get a new OIST account. Your old account will lose access to OIST resources and you will have to manually get them for your new one. See below for more.
Your PI can apply for an account extension on your behalf. But it has to be done well before your account expires. Don’t delay.
You need to arrange a copy of your data well before you leave. We have no way to provide your data for you; you need to do this yourself. Once your account is disabled you can not retreive your data.
For larger amounts of data we recommend that you transfer it directly to your new place of work directly if at all possible. It’s more reliable than a hard disk, and if the transfer fails you know it and can redo the parts that failed. Large data sets can take days or weeks, so please get started early!
Please clean up the data in your unit storage. Your unit leader and your coworkers will thank you5! Let your unit leader know what data is important; what data could be archived; and what can be discarded.
You will lose access to your Dropbox account. Make sure you have a local copy of the data beforehand.
You will lose access to all OIST-licensed software when you leave. If you have important data stored in a closed format used by such software, make sure to export it into an open format while you still have access. This is one reason we recommend open source software when possible.
You lose access to all HPC systems. We can not give you any access to computing or storage without an active OIST account.
Your old account will lose access to everything as above. You need to reapply for resources again with your new account.
Note that your new role at OIST may have different restrictions than your old one. HPC resources, licensed software and Dropbox are only available to OIST researchers, for instance, not to administration or to OIST incubators.
Let us know that you are switching accounts and reapply for access. We can move your old home folder to your new one, and make sure the files are owned by the New You™.
Let us know which files and folders you want to change owner to your new account. We can’t unfortunately do a global search and replace.
If you have any questions, email us at ask-scda@oist.jp or come to our Open Hours.
Open Source, like Open Science, is overall good for reproducibility and accountability, in addition to being good for your wallet. It’s also freely accessible off campus, and after you leave OIST. ↩
named after Erythrina Variegata, the official flower of Okinawa. ↩
named after an early Okinawan ruler. ↩
Clusters are divided into partitions for specific uses. ↩
This is a good way to make sure you get invited to future parties. ↩