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cypress/Cellranger-ARC: = Run Cellranger-ARC on Cypress = See ...: = Run Cellranger-ARC on Cypress = See [https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/using/mkfastq Generating FASTQs with cellranger-arc mkfastq]. This page to show how to run Cellranger-ARC with [https://support.10xgenomics.com/single-c ...; By fuji — 09/04/2026 03:49:35 PM
Workshops/JobCheckpointing/Examples: [[PageOutline]] = Job Checkpointing Examples = == Overview == ...: ... b would be in violation of Tulane Information Technology's [https://it.tulane.edu/acceptable-use-policy Acceptable Use Policy], including your '''consent to monitor''' your use of Cypress. == Before you adopt checkpointing == '''Before you adopt a checkpointing workflow''', make a determinatio ...; By Carl Baribault — 09/03/2026 11:44:42 AM
Workshops/JobCheckpointing: [[PageOutline]] = HPC Workshop Spring 2026 = = Module 8 of 8 - Job ...: ... (See "backfill scheduling" in [https://slurm.schedmd.com/sched_config.html|SLURM Scheduling Configuration Guide]. * '''More checkpointed jobs can run simultaneously''' due to strict limits enforced by Cypress, LONI, and most other production clusters. * See '''--qos=n ...; By Carl Baribault — 09/03/2026 11:35:20 AM
Workshops/JobCheckpointing/Examples/R: [[PageOutline]] = R Checkpointing Example = Here is an example of ...: ... (For file editing with '''nano''' on Cypress, see [[https://wiki.hpc.tulane.edu/trac/wiki/cypress/FileEditingSoftware/Example|File Editing Example]].) * [wiki://Workshops/JobCheckpointing/Examples#checkpoint_submitter.sh checkpoint_submitter.sh] * [wiki://Workshops/JobCheckpointing/Exa ...; By Carl Baribault — 09/02/2026 03:46:59 PM
Workshops/JobCheckpointing/Examples/Python: [[PageOutline]] = Python Checkpointing Example = == Python ...: ... (For file editing with '''nano''' on Cypress, see [[https://wiki.hpc.tulane.edu/trac/wiki/cypress/FileEditingSoftware/Example|File Editing Example]].) * [wiki://Workshops/JobCheckpointing/Examples#checkpoint_submitter.sh checkpoint_submitter.sh] * [wiki://Workshops/JobCheckpointing/Exa ...; By Carl Baribault — 09/02/2026 03:09:35 PM
Workshops/JobParallelism/BeforeRunningYourJob: [[PageOutline]] = Before running your job = Before you run your ...: ... ed Vector Extensions (AVX), 256-bit vector processor ||See [https://wiki.hpc.tulane.edu/trac/wiki/cypress#MathLibraries Math Libraries] || ||Multithreaded (shared memory) ||OpenMP ||1 Node, >=2 cores ||See [wiki:cypress/Programming/OpenMp OpenMP] || ||Problem domain decomposition ||MPI ...; By Carl Baribault — 09/02/2026 11:50:59 AM
Workshops/JobParallelism/AfterYourJobHasCompleted: [[PageOutline]] = After your job has completed - determining ...: ... * '''seff''' (See [https://github.com/SchedMD/slurm/tree/master/contribs/seff seff on github].) On LONI QB4 cluster: {{{ [loniID@qbd2 ~]$ seff -h Usage: seff [Options] <Jobid> Options: -h Help menu -v Version - ...; By Carl Baribault — 09/02/2026 02:41:13 AM
cypress/Singularity: [[PageOutline]] = Singularity = '''The current installation of ...: ... ''' == About Singularity == [https://sylabs.io/ Singularity] allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. === Advantages For Using Containers * '''Platform Mobility''' - You can build a con ...; By Carl Baribault — 09/01/2026 01:12:15 PM
cypress/SingularityRecipes: [[PageOutline]] = Build Singularity Containers from Recipes = ...: ... * You can build a Singularity container from a recipe on [https://cloud.sylabs.io/builder Sylabs Cloud]. * On Cypress, use the provided '''singularity pull...''' command to construct the image file from the cloud such as the following, substituting your chosen values for '''sylabsID''', '''myColl ...; By Carl Baribault — 09/01/2026 11:40:42 AM
cypress/SingularityDockerhub: [[PageOutline]] = Build Singularity Containers from Dockerhub = ...: ... Build Singularity Containers from Dockerhub = [https://www.docker.com/ Docker] is a container virtualization environment that can establish development or runtime environments without modifying the environment of the base operating system. It runs on Mac and Windows. == Use CentOS 7 ...; By Carl Baribault — 09/01/2026 11:06:52 AM

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