Ruddle
NOTICE: We plan to permanently decommission the ycga-ba filesystem on Sept 16, 2019. See here for details.
Ruddle is named for Frank Ruddle, a Yale geneticist who was a pioneer in genetic engineering and the study of developmental genetics.
Ruddle is intended for use only on projects related to the Yale Center for Genome Analysis; Please do not use this cluster for other projects. If you have any questions about this policy, please contact us.
Hardware
Ruddle is made up of several kinds of compute nodes. The Features column below lists the features that can be used to request different node types using the --constraints flag (see our Slurm documentation for more details). The RAM listed below is the amount of memory available for jobs.
Warning
Care should be taken if when scheduling your job if you are running programs/libraries optimized for specific hardware. See the guide on how to compile software for specific guidance.
Compute Node Configurations
| Count | CPU | CPU Cores | RAM | Features |
|---|---|---|---|---|
| 12 | 4x AMD Opteron 6276 | 32 | 499G | bulldozer, opteron-6276 |
| 155 | 2x E5-2660 v3 | 20 | 121G | haswell, avx2, E5-2660_v3, oldest |
| 2 | 4x E7-4809 v3 | 32 | 1507G | haswell, avx2, E7-4809_v3 |
Slurm Partitions
Nodes on the clusters are organized into partitions, to which you submit your jobs with Slurm. The default resource requests for all jobs is 1 core and 5GB of memory per core. The general partition is where most batch jobs should run, and is the default if you don't specify a partition. The interactive partition is dedicated to jobs with which you need ongoing interaction. The bigmem partition contains our largest memory nodes; only jobs that cannot be satisfied by general should run here. The scavenge partition allows you to run preemptable jobs on more resources than normally allowed. For more information about scavenge, see the Scavenge documentation.
The limits listed below are for all running jobs combined. Per-node limits are bound by the node types, as described in the hardware table.
| Partition | Group Limits | User Limits | Walltime Default/Max | Node Type (count) |
|---|---|---|---|---|
| general* | 400 CPUs, 2000 G RAM | 300 CPUs, 1800 G RAM | 7d/30d | E5-2660_v3 (155) |
| interactive | 20 CPUs, 256 G RAM | 1d/2d | E5-2660_v3 (155) | |
| bigmem | 32 CPUs, 1507 G RAM | 1d/7d | opteron-6276 (12), E7-4809_v3 1507G (2) | |
| scavenge | 800 CPUs, 5120 G RAM | 1d/7d | all |
* default
Access Sequencing Data
To avoid duplication of data and to save space that counts against your quotas, we suggest that you make soft links to your sequencing data rather than copying them:
ln -s /path/to/sequece_data /path/to/your_link
Tip
Original sequence data are archived pursuant to the YCGA retention policy. For long-running projects we recommend you keep a personal backup of your sequence files. If you need to retrieve archived sequencing data, please see our guide on how to do so.
To find the location of the sequence files on the storage, look at the URL that you were sent from YCGA.
fullPath Starts With |
Root Path on Ruddle |
|---|---|
gpfs_illumina/sequencer |
/gpfs/ycga/illumina/sequencer |
ba_sequencers |
/ycga-ba/ba_sequencers |
sequencers |
/gpfs/ycga/sequencers/panfs/sequencers |
For example, if the sample link you received is:
http://sysg1.cs.yale.edu:2011/gen?fullPath=sequencers2/sequencerV/runs/131107_D00306_0096... etc
The path on the cluster to the data is:
/gpfs/ycga/sequencers/panfs/sequencers2/sequencerV/runs/131107_D00306_0096... etc
Public Datasets
We host datasets of general interest in a loosely organized directory tree in /gpfs/ycga/datasets:
├── annovar
│ └── humandb
├── db
│ └── blast
├── genomes
│ ├── Aedes_aegypti
│ ├── Bos_taurus
│ ├── Chelonoidis_nigra
│ ├── Danio_rerio
│ ├── Gallus_gallus
│ ├── hisat2
│ ├── Homo_sapiens
│ ├── Macaca_mulatta
│ ├── Monodelphis_domestica
│ ├── Mus_musculus
│ ├── PhiX
│ └── tmp
└── hisat2
└── mouse
If you would like us to host a dataset or questions about what is currently available, please email hpc@yale.edu.
Storage
Ruddle has access to two filesystems. /gpfs/ycga is Ruddle's filesystem where home, project, and scratch60 directories are located. /ycga-ba stores legacy data. For more details on the different storage spaces, see our Cluster Storage documentation.
You can check your current storage usage & limits by running the getquota command. Note that the per-user usage breakdown only update once daily..
Warning
Files stored in scratch60 are purged if they are older than 60 days. You will receive an email alert one week before they are deleted.
| Partition | Root Directory | Storage | File Count | Backups |
|---|---|---|---|---|
| home | /gpfs/ycga/home |
125G/user | 500,000 | Yes |
| project | /gpfs/ycga/project |
4T/group | 5,000,000 | No |
| scratch60 | /gpfs/ycga/scratch60 |
10T/group | 5,000,000 | No |