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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:
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
Transferring files securely to OSC involves understanding which commands/applications to use and which directory to use.
As we migrate to Slurm from Torque/Moab, there will be necessary software environment changes.
Decommissioning old MVAPICH2 versions
Old MVAPICH2 including
mvapich2/2.2 and its variants do not support Slurm very well due to its life span, so we will remove the following versions:
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. This 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.
To manage a project, navigate to Project -> List Projects and select the blue button on the left of the appropriate project.
This article discusses memory tuning strategies for VASP.
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.
This article focuses on debugging strategies for C/C++ codes, but many are applicable to other languages as well.
Rubber Duck Debugging
This approach is a great starting point. Say you have written some code, and it does not do what you expect it to do. You have stared at it for a few minutes, but you cannot seem to spot the problem.
OSC has entered an agreement with OSU College of Medicine (CoM) to provide dedicated compute services. Researchers from CoM will have access to Pitzer cluster, whose hardware is described below.
Pitzer node specifications for CoM dedicated compute are:
This document is obsoleted and kept as a reference to previous Pitzer programming environment. Please refer to here for the latest version.