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Molecular Science Computing User Policies

1.0 Support Policies
1.1 Contacting MSC Support Staff

1.1.1 Required citation In the event of a problem, contact the MSC Support staff:

2.0 User Policies
2.1 Acknowledgement of EMSL in published work

2.1.1 Required citation Any use of the computing resources of the MSC must be properly acknowledged in publications using the following citation: (http://www.emsl.pnl.gov/root/publications/acknowledgement/)

2.2 MSC Lack-of-Use policy

2.2.1 The purpose of this policy is to ensure the efficient use of MSC computing resources, MSC management will be monitoring all computer project accounts frequently.

2.2.2 Project Inactivity Any projects that have had no usage (computer time used) for two months will be notified for lack-of-use.

2.2.3 User Inactivity

3.0 System Usage Policies
3.1 Disk usage

3.1.1 Purpose of this policy is to define the uses of the files systems available at the MSC. The MSC provides users with four disk storage options:

3.1.2 Jobs must be run from /dtemp or /scratch. Jobs running from the /home file system can cause system degradation either because too many files are being accessed simultaneously or by exceeding disk storage capacity.

3.1.3 The /dtemp file system is for temporary storage. The MSC will periodically delete "stale" files from the /dtemp subdirectories. A "stale" file is one that has not been accessed within the last 60 days. For longer term storage of important files, the user should move them from /dtemp to NWfs (www.emsl.pnl.gov/capabilities/computing/howto/nwfs_policies.jsp).

3.1.4 Do not submit jobs from /home Jobs running from the /home file system can cause system degradation either because too many files are being accessed simultaneously or by exceeding disk storage capacity.

3.1.5 Appropriate use of /home

4.0 Jobs Policies
4.1 Job Submission Policy

4.1.1 The primary objective of EMSL's Molecular Science Computing capability is to provide teraflop computing resources for large scale computational needs associated with environmental problems as given in the Mission Statement of our sponsor (http://www.science.doe.gov/ober/ober_top.html), the Office of Biological & Environmental Research (http://www.science.doe.gov/Program_Offices/BER.htm). The job scheduling policy has been established to provide higher priorities to large jobs that cannot be run on local clusters or other HPC systems not designed for computational chemistry code. To maximize system flexibility, all batch jobs are submitted in identical fashion. The job scheduler controls the allocation of compute nodes to the users job and will place the job in one of seven available queues: tiny, small, medium, large, and extra-large (xl). This allocation is governed by a number of queue constraints. All queue constraint values must be satisfied or the job will go into "BatchHold" until deleted. For information on MSC User policies, please see User Policies

4.1.2 Job Policy Constraints: The total number of jobs a person can have running depends on Chinook user activity. While busy with many users:

4.1.3 Jobs must be run from the batch queue rather than the login node.

4.1.4 Job queue default values limit the time a single job with a particular number of nodes can have.

Queue Name Number of Nodes in a Single Job Time Limit Notes
Extra Large (XL) 256 - 1100 24 wall-clock hours These jobs (xl) will be placed ahead of the jobs in the queues below, i.e., they will receive highest priority.
Large 128 - 255 48 wall-clock hours These jobs (large) will be placed ahead of the jobs in the queues below, i.e., they will receive higher priority.
Normal 2 - 127 48 wall-clock hours These jobs, medium and small will be used to backfill with the larger queues.
Short 1 - 4 30 wall clock minutes This is a test or interactive queue, with only 16 nodes in this (short) queue. A maximum limit of 4 nodes/job may be used.
Long 2 - 16 96 wall clock hours This is referred to as the "long queue" as it has the most wall clock hours of any queue.

4.1.5 Jobs larger than 1,100 nodes can be run when needed. We ask that you first contact your Science Point-of-Contact (your PI should know who that is) to make arrangements. Or you may send an e-mail to mscf-consulting@emsl.pnl.gov with details on what is required. Your large job may qualify as a SIGHTS job (see below).

4.1.6 Idle Queue: {This queue has not been implemented on Chinook pending further investigation.}

4.2 Special Purpose Queue (SIGHTS Jobs)

4.2.1 The purpose of this policy In addition to the queue limitations mentioned above the users can request access to a special purpose queue called Scientific Impact Generated by High Teraflop Simulations (SIGHTS). The SIGHTS queue is for compute jobs that require resources beyond the normal queue limits for Chinook, and serve uniquely impactful cutting-edge OBER/EMSL mission science opportunities which cannot be performed at any other computing facility. SIGHTS jobs should require the use of 1600 nodes or more, up to Chinook's capacity of 2130 nodes. SIGHTS jobs should not be sent to the Chinook queue until approval is given by the appropriate MSC staff. SIGHTS jobs can be submitted anytime after approval and will be tended by an MSC scientific consultant and operations personnel to improve the chance for successful completion. When a scheduled outage is planned, a SIGHTS request must be submitted by 12 noon on the day before the scheduled outage.

4.2.2 Access to the SIGHTS is by request only and is subject to time availability. All requests are submitted to the MSC consulting group for review. In your request please provide a short (one-two page) description of what you plan to do and how you plan on doing it. If your request is accepted, and you do not have an active EMSL Usage System project, you will need to submit your accepted request to the EMSL User Portal. Then a consultant will be assigned to the job and will work with you to be sure the job is ready. The consultants and operations staff will watch all SIGHTS jobs to be sure they are running correctly. Details about SIGHTS jobs are:

4.2.3 To be eligible as a SIGHTS job, the science completed must have a high expectation of being published in a high-impact journal upon successful completion. Time used during the SIGHTS job will not be deducted from your project account.