Sherlock, a shared resource#
Sherlock is a shared compute cluster available for use by all Stanford faculty members and their research teams to support sponsored research.
Sherlock is a resource for research
Sherlock is not suitable for course work, class assignments or general-use training sessions.
Users interested in using computing resources in such contexts are encouraged to investigate FarmShare, Stanford’s community computing environment, which is primarily intended for supporting coursework.
It is open to the Stanford community as a computing resource to support departmental or sponsored research, thus a faculty member's sponsorship is required for all user accounts.
Please note that your use of this system falls under the "Computer and Network Usage Policy", as described in the Stanford Administrative Guide. In particular, sharing authentication credentials is strictly prohibited. Violation of this policy will result in termination of access to Sherlock.
Sherlock has been designed, deployed, and is maintained and operated by the Stanford Research Computing Center (SRCC) staff. The SRCC is a joint effort of the Dean of Research and IT Services to build and support a comprehensive program to advance computational research at Stanford.
Sherlock has been initially purchased and supported with seed funding from Stanford's Provost. It comprises a set of freely available compute nodes, a few specific resources such as large-memory machines and GPU servers, as well as the associated networking equipment and storage. These resources can be used to run computational codes and programs, and are managed through a job scheduler using a fair-share algorithm.
Data risk classification#
Low and Moderate Risk data
Sherlock is approved for computing with Low and Moderate Risk data only.
High Risk data
Sherlock is NOT approved to store or process HIPAA, PHI, PII nor any kind of High Risk data. The system is approved for computing with Low and Moderate Risk data only, and is not suitable to process High Risk data.
Users are responsible for ensuring the compliance of their own data.
For more information about data risk classifications, see the Information Security Risk Classification page.
Investing in Sherlock#
For users who need more than casual access to a shared computing environment, Sherlock also offers Faculty members the possibility to invest in additional, dedicated computing resources.
Unlike traditional clusters, Sherlock is a collaborative system where the majority of nodes are purchased and shared by the cluster users. When a user (typically a PI) purchases one or more nodes, they become an owner. Owners choose from a standard set of server configurations supported by SRCC staff (known as the Sherlock catalog) to add to the cluster.
When they're not in use, PI-purchased compute nodes can be used by other owners. This model also allows Sherlock owners to benefit from the scale of the cluster by giving them access to more compute nodes than their individual purchase, which gives them much greater flexibility than owning a standalone cluster.
The majority of Sherlock nodes are owners nodes
The vast majority of Sherlock's compute nodes have been purchased by individual PIs and groups, and PI purchases are the main driver behind the rapid expansion of the cluster, which went from 120 nodes to more than 1,000 nodes in less than 3 years.
The resource scheduler configuration works like this:
- owners and their research teams get immediate and exclusive access to the resources they purchased,
- when those nodes are idle, other owners can use them,
- when the purchasing owners want to use their resources, jobs from other owners that may be running on them are preempted (ie. killed and re-queued).
This provides a way to get more resources to run less important jobs in the background, while making sure that an owner always gets immediate access to his/her own nodes.
Participating owners also have shared access to the public, shared Sherlock nodes, along with everyone else.
Benefits to owners include:
- no wait time in queue with immediate and exclusive access to the purchased nodes
- access to more resources with the possibility to submit jobs to the other owners' nodes when they're not in use
Compared to hosting and managing computing resources on your own, purchasing nodes on Sherlock provides:
- data center hosting, including backup power and cooling
- system configuration, maintenance and administration
- hardware diagnostics and repairs
Those benefits come in addition to the other Sherlock advantages:
- access to high-performance, large parallel scratch storage space
- access to snapshot'ed, replicated, enterprise-class storage space
- optimized software stack, especially tailored for a range of research needs
- tools to build and install additional software applications as needed
- user support
Being an owner on Sherlock is different from traditional server hosting.
In particular, purchasing your own compute nodes on Sherlock will NOT allow:
root access: owner nodes on Sherlock are still managed by SRCC in accordance with Stanford's Minimum Security Standards. Although users are welcome to install (or request) any software they may need, purchasing compute nodes on Sherlock does not allow
root access to the nodes.
running permanent services: permanent processes such as web servers or databases can only run on owner nodes through the scheduler, using recurring or persistent. Purchasing compute nodes on Sherlock does not provide a way to run anything that couldn't run on publicly-available nodes.
direct network connectivity from the outside world: owners' nodes are connected to the Sherlock's internal network and are not directly accessible from the outside, which means that they can't host public services like web or application servers.
bypassing the scheduler: jobs running on owners' nodes still need to be submitted to the scheduler. Direct shell access to the nodes is not possible outside of scheduled interactive sessions.
hardware modifications: the hardware components of purchased nodes cannot be changed, removed, swapped or upgraded during the nodes' service lifetime.
persistent local storage: local storage space provided on the compute nodes is only usable for the duration of a job and cannot be used to store long-term data.
additional storage space: purchasing compute nodes on Sherlock does not provide additional storage space. Please note that SRCC does offer the possibility for PIs to purchase their own storage space on Oak, for their long-term research data needs.
The research computing landscape evolves very quickly, and to both accommodate growth and technological advances, it's necessary to adapt the Sherlock environment to these evolutions.
Every year or so, a new generation of processors is released, which is why, over a span of several years, multiple generations of CPUs and GPUs make their way into Sherlock. This provides users with access to the latest features and performance enhancements, but it also adds some heterogeneity to the cluster, which is important to keep in mind when compiling software and requesting resources to run them.
Another key component of Sherlock is the interconnect network that links all of Sherlock's compute nodes together and act as a backbone for the whole cluster. This network fabric is of finite capacity, and based on the individual networking switches characteristics and the typical research computing workflows, it can accommodate up to about 850 compute nodes.
As nodes get added to Sherlock, the number of available ports decreases, and at some point, the fabric gets full and no more nodes can be added. Sherlock reached that stage for the first time in late 2016, which prompted the installation of a whole new fabric, to allow for further system expansion.
This kind of evolution is the perfect opportunity to upgrade other components too: management software, ancillary services architecture and user applications. In January 2017, those components were completely overhauled and a new, completely separate cluster was kick-started, using using a different set of hardware and software, while conserving the same storage infrastructure, to ease the transition process.
After a transition period, the older Sherlock hardware, compute and login nodes, have been be merged in the new cluster, and from a logical perspective (connection, job scheduling and computing resources), nodes attached to each of the fabrics have been reunited to form a single cluster again.
As Sherlock continues to evolve and grow, the new fabric will also approach capacity again, and the same process will happen again to start the next generation of Sherlock.
Maintenances and upgrades#
The SRCC institutes a monthly scheduled maintenance window on Sherlock, to ensure optimal operation, avoid potential issues and prepare for future expansions. This window will be used to make hardware repairs, software and firmware updates, and perform general manufacturer recommended maintenance on our environment.
As often as possible, maintenance tasks are performed in a rolling, non-disruptive fashion, but downtimes are sometimes an unfortunate necessity to allow disruptive operations that can't be conducted while users are working on the system.
As often as possible, maintenances will take place on the first Tuesday of every month, from 08:00 to 12:00 Pacific time (noon), and will be announced 2 weeks in advance, through the usual communication channels.
In case an exceptional amount of work is required, the maintenance window could be extended to 10 hours (from 08:00 to 18:00).
During these times, access to Sherlock will be unavailable, login will be disabled and jobs won't run. A reservation will be placed in the scheduler so running jobs can finish before the maintenance, and jobs that wouldn't finish by the maintenance window would be pushed after it.
Q: Why doing maintenances at all?
A: Due to the scale of our computing environment and the increasing complexity of the systems we deploy, it is prudent to arrange for a regular time when we can comfortably and without pressure fix problems or update facilities with minimal impact to our customers. Most, if not all, major HPC centers have regular maintenance schedules. We also need to enforce the Minimum Security rules instituted by the Stanford Information Security Office, which mandate deployment of security patches in a timely manner.
Q: Why Tuesdays 08:00-12:00? Why not do this late at night?
A: We have observed that the least busy time for our services is at the beginning of the week in the morning hours. Using this time period should not interrupt most of our users. If the remote possibility of a problem that extends past the scheduled downtime occurs, we would have our full staff fresh and available to assist in repairs and quickly restore service.
Q: I have jobs running, what will happen to them?
A: For long-running jobs, we strongly recommend checkpointing your results on a periodic basis. Besides, we will place a reservation in the scheduler for each maintenance that would prevent jobs to run past it. This means that the scheduler will only allow jobs to run if they can finish by the time the maintenance starts. If you submit a long job soon before the maintenance, it will be delayed until after the maintenance. That will ensure that no work is lost when the maintenance starts.