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Pitzer
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
We have licensed applications such as ansys, abaqus, and Schrodinger. These applications have a license server with a limited number of licenses, and you need to check out the licenses when you use the software each time. One problem is that the job scheduler, Slurm, doesn't communicate with the license server. As a result, a job can be launched even there are not enough licenses available, and it fails due to insufficient licenses.
Charge account
- Used to group projects together.
- A PI may have multiple charge accounts, but it is preferred to limit the amount to one unless there is reason to group different projects.
- Institutions may use charge accounts to group PI charge accounts together
- (e.g. group all college of engineering PI charge accounts under college of engineering charge account)
Owens, Pitzer
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Availability and Restrictions
The following versions of Trinity are available on OSC clusters:
Owens
This document is obsoleted and kept as a reference to previous Owens programming environment. Please refer to here for the latest version.
Securely transferring files at OSC
Files containing personal health information (PHI) must be encrypted when they are stored (at rest) and when they are transferred between networked systems (in transit).
Transferring files securely to OSC involves understanding which commands/applications to use and which directory to use.
Owens
As we migrate to Slurm from Torque/Moab, there will be necessary software environment changes.
Decommissioning old MVAPICH2 versions
Old MVAPICH2 including mvapich2/2.1, mvapich2/2.2 and its variants do not support Slurm very well due to its life span, so we will remove the following versions:
Owens, Pitzer
OSC clients who are affiliated with Ohio State can deploy their own endpoint on a server using OSU subscriptions. Please follow the steps below:
Manage users on a project
The PI of a project can manage the users on their projects. Note, that PIs are not automatically added as authorized users under their project(s).
Managing users on the project includes inviting, adding and removing users to the project as well as increasing a user's privileges on a project so that they can assist with the management of it.
Owens, Pitzer
This article discusses memory tuning strategies for VASP.
Data Distribution
Typically the first approach for memory sensitive VASP issues is to tweak the data distribution (via NCORE or NPAR). The information at https://www.vasp.at/wiki/index.php/NPAR covers a variety of machines. OSC has fast communications via Infiniband.
