Farnam
Farnam is a shared-use resource for the Yale School of Medicine (YSM). It consists of a variety of compute nodes networked over ethernet and mounts several shared filesystems.
The Farnam Cluster is named for Louise Whitman Farnam, the first woman to graduate from the Yale School of Medicine, class of 1916.
Upcoming Farnam Retirement
After more than six years in service, we will be retiring the Farnam HPC cluster in mid 2023. Farnam is being replaced with the new HPC cluster, McCleary. For more information and updates see the McCleary announcement page.
Access the Cluster
Once you have an account, the cluster can be accessed via ssh or through the Open OnDemand web portal.
System Status and Monitoring
For system status messages and the schedule for upcoming maintenance, please see the system status page. For a current node-level view of job activity, see the cluster monitor page (VPN only).
Partitions and Hardware
Farnam is made up of several kinds of compute nodes. We group them into (sometimes overlapping) Slurm partitions meant to serve different purposes. By combining the --partition and --constraint Slurm options you can more finely control what nodes your jobs can run on.
Job Submission Rate Limits
Job submissions are limited to 200 jobs per hour. See the Rate Limits section in the Common Job Failures page for more info.
Public Partitions
See each tab below for more information about the available common use partitions.
Use the general partition for most batch jobs. This is the default if you don't specify one with --partition.
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the general partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 30-00:00:00 |
| Maximum CPUs per group | 400 |
| Maximum memory per group | 2.50T |
| Maximum CPUs per user | 200 |
| Maximum memory per user | 1280G |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 68 | E5-2660_v3 | 20 | 117 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, common |
Use the interactive partition to jobs with which you need ongoing interaction. For example, exploratory analyses or debugging compilation.
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=06:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the interactive partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 1-00:00:00 |
| Maximum CPUs per user | 20 |
| Maximum memory per user | 256G |
| Maximum running jobs per user | 2 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 83 | E5-2660_v3 | 20 | 117 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, common |
Use the transfer partition to stage data for your jobs to and from cluster storage.
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the transfer partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 1-00:00:00 |
| Maximum running jobs per user | 2 |
| Maximum CPUs per job | 1 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 2 | E5-2660_v3 | 20 | 117 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, common |
Use the gpu partition for jobs that make use of GPUs. You must request GPUs explicitly with the --gpus option in order to use them. For example, --gpus=gtx1080ti:2 would request 2 GeForce GTX 1080Ti GPUs per node.
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
GPU jobs need GPUs!
Jobs submitted to this partition do not request a GPU by default. You must request one with the --gpus option.
Job Limits
Jobs submitted to the gpu partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 2-00:00:00 |
| Maximum CPUs per user | 32 |
| Maximum GPUs per user | 12 |
| Maximum memory per user | 256G |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | GPU Type | GPUs/Node | vRAM/GPU (GB) | Node Features |
|---|---|---|---|---|---|---|---|
| 1 | 6240 | 36 | 370 | a100 | 4 | 40 | cascadelake, avx2, avx512, 6240, doubleprecision, common, bigtmp, a100 |
| 2 | 5222 | 8 | 181 | rtx5000 | 4 | 16 | cascadelake, avx2, avx512, 5222, doubleprecision, common, bigtmp, rtx5000 |
| 5 | E5-2637_v4 | 8 | 119 | gtx1080ti | 4 | 11 | broadwell, avx2, E5-2637_v4, singleprecision, common, gtx1080ti |
| 2 | E5-2660_v3 | 20 | 119 | k80 | 4 | 12 | haswell, avx2, E5-2660_v3, doubleprecision, common, k80 |
Use the gpu_devel partition to debug jobs that make use of GPUs, or to develop GPU-enabled code.
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=00:10:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
GPU jobs need GPUs!
Jobs submitted to this partition do not request a GPU by default. You must request one with the --gpus option.
Job Limits
Jobs submitted to the gpu_devel partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 02:00:00 |
| Maximum submitted jobs per user | 1 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | GPU Type | GPUs/Node | vRAM/GPU (GB) | Node Features |
|---|---|---|---|---|---|---|---|
| 1 | E5-2623_v4 | 8 | 57 | gtx1080ti | 4 | 11 | broadwell, avx2, E5-2623_v4, singleprecision, common, gtx1080ti |
Use the bigmem partition for jobs that have memory requirements other partitions can't handle.
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the bigmem partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 3-00:00:00 |
| Maximum CPUs per user | 32 |
| Maximum memory per user | 1505G |
| Maximum running jobs per user | 2 |
| Maximum nodes per job | 1 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 3 | 6240 | 36 | 1505 | cascadelake, avx2, avx512, 6240, nogpu, common, bigtmp |
| 2 | E7-4809_v3 | 32 | 1505 | haswell, avx2, E7-4809_v3, nogpu, common |
Use the scavenge partition to run preemptable jobs on more resources than normally allowed. For more information about scavenge, see the Scavenge documentation.
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
GPU jobs need GPUs!
Jobs submitted to this partition do not request a GPU by default. You must request one with the --gpus option.
Job Limits
Jobs submitted to the scavenge partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 7-00:00:00 |
| Maximum CPUs per user | 800 |
| Maximum memory per user | 5T |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | GPU Type | GPUs/Node | vRAM/GPU (GB) | Node Features |
|---|---|---|---|---|---|---|---|
| 1 | 6240 | 36 | 181 | cascadelake, avx2, avx512, 6240, nogpu, standard, pi, bigtmp | |||
| 1 | 6240 | 36 | 370 | a100 | 4 | 40 | cascadelake, avx2, avx512, 6240, doubleprecision, common, bigtmp, a100 |
| 3 | 6240 | 36 | 1505 | cascadelake, avx2, avx512, 6240, nogpu, common, bigtmp | |||
| 5 | E5-2637_v4 | 8 | 119 | gtx1080ti | 4 | 11 | broadwell, avx2, E5-2637_v4, singleprecision, common, gtx1080ti |
| 1 | E5-2623_v4 | 8 | 57 | gtx1080ti | 4 | 11 | broadwell, avx2, E5-2623_v4, singleprecision, common, gtx1080ti |
| 16 | E5-2660_v3 | 20 | 119 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, pi | |||
| 85 | E5-2660_v3 | 20 | 117 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, common | |||
| 2 | E7-4809_v3 | 32 | 1505 | haswell, avx2, E7-4809_v3, nogpu, common | |||
| 3 | E5-2660_v3 | 20 | 119 | k80 | 4 | 12 | haswell, avx2, E5-2660_v3, doubleprecision, pi, k80 |
| 2 | E5-2660_v3 | 20 | 119 | k80 | 4 | 12 | haswell, avx2, E5-2660_v3, doubleprecision, common, k80 |
Use the scavenge_gpu partition to run preemptable jobs on more GPU resources than normally allowed. For more information about scavenge, see the Scavenge documentation.
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
GPU jobs need GPUs!
Jobs submitted to this partition do not request a GPU by default. You must request one with the --gpus option.
Job Limits
Jobs submitted to the scavenge_gpu partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 2-00:00:00 |
| Maximum GPUs per user | 64 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | GPU Type | GPUs/Node | vRAM/GPU (GB) | Node Features |
|---|---|---|---|---|---|---|---|
| 1 | 6240 | 36 | 370 | a100 | 4 | 40 | cascadelake, avx2, avx512, 6240, doubleprecision, common, bigtmp, a100 |
| 5 | E5-2637_v4 | 8 | 119 | gtx1080ti | 4 | 11 | broadwell, avx2, E5-2637_v4, singleprecision, common, gtx1080ti |
| 1 | E5-2623_v4 | 8 | 57 | gtx1080ti | 4 | 11 | broadwell, avx2, E5-2623_v4, singleprecision, common, gtx1080ti |
| 3 | E5-2660_v3 | 20 | 119 | k80 | 4 | 12 | haswell, avx2, E5-2660_v3, doubleprecision, pi, k80 |
| 2 | E5-2660_v3 | 20 | 119 | k80 | 4 | 12 | haswell, avx2, E5-2660_v3, doubleprecision, common, k80 |
Private Partitions
With few exceptions, jobs submitted to private partitions are not considered when calculating your group's Fairshare. Your group can purchase additional hardware for private use, which we will make available as a pi_groupname partition. These nodes are purchased by you, but supported and administered by us. After vendor support expires, we retire compute nodes. Compute nodes can range from $10K to upwards of $50K depending on your requirements. If you are interested in purchasing nodes for your group, please contact us.
PI Partitions (click to expand)
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
GPU jobs need GPUs!
Jobs submitted to this partition do not request a GPU by default. You must request one with the --gpus option.
Job Limits
Jobs submitted to the pi_gerstein_gpu partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | GPU Type | GPUs/Node | vRAM/GPU (GB) | Node Features |
|---|---|---|---|---|---|---|---|
| 3 | E5-2660_v3 | 20 | 119 | k80 | 4 | 12 | haswell, avx2, E5-2660_v3, doubleprecision, pi, k80 |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_jadi partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 365-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 3 | E5-2660_v3 | 20 | 117 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, common |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_kleinstein partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 3 | E5-2660_v3 | 20 | 119 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, pi |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_krauthammer partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 1 | E5-2660_v3 | 20 | 119 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, pi |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_ma partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 2 | E5-2660_v3 | 20 | 119 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, pi |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_ohern partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 3 | E5-2660_v3 | 20 | 119 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, pi |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_sigworth partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 1 | E5-2660_v3 | 20 | 119 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, pi |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_sindelar partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 1 | E5-2660_v3 | 20 | 119 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, pi |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_townsend partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 5 | E5-2660_v3 | 20 | 119 | haswell, avx2, E5-2660_v3, nogpu, standard, oldest, pi |
Request Defaults
Unless specified, your jobs will run with the following options to salloc and sbatch options for this partition.
--time=1-00:00:00 --nodes=1 --ntasks=1 --cpus-per-task=1 --mem-per-cpu=5120
Job Limits
Jobs submitted to the pi_tucci partition are subject to the following limits:
| Limit | Value |
|---|---|
| Maximum job time limit | 14-00:00:00 |
Available Compute Nodes
Requests for --cpus-per-task and --mem can't exceed what is available on a single compute node.
| Count | CPU Type | CPUs/Node | Memory/Node (GiB) | Node Features |
|---|---|---|---|---|
| 1 | 6240 | 36 | 181 | cascadelake, avx2, avx512, 6240, nogpu, standard, pi, bigtmp |
Public Datasets
We host datasets of general interest in a loosely organized directory tree in /gpfs/gibbs/data:
├── alphafold-2.3
├── alphafold-2.2 (deprecated)
├── alphafold-2.0 (deprecated)
├── annovar
│ └── humandb
├── cryoem
├── db
│ ├── annovar
│ ├── blast
│ ├── busco
│ └── Pfam
└── genomes
├── 1000Genomes
├── 10xgenomics
├── Aedes_aegypti
├── Chelonoidis_nigra
├── Danio_rerio
├── Drosophila_melanogaster
├── hisat2
├── Homo_sapiens
├── Mus_musculus
├── PhiX
└── Saccharomyces_cerevisiae
If you would like us to host a dataset or questions about what is currently available, please contact us.
Storage
Farnam has access to a number of GPFS filesystems. /gpfs/ysm is Farnam's primary filesystem where Home, Project, and Scratch60 directories are located. 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. Your ~/project and ~/scratch60 directories are shortcuts. Get a list of the absolute paths to your directories with the mydirectories command. If you want to share data in your Project or Scratch directory, see the permissions page.
For information on data recovery, see the Backups and Snapshots documentation.
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. Artificial extension of scratch file expiration is forbidden without explicit approval from the YCRC. Please purchase storage if you need additional longer term storage.
| Partition | Root Directory | Storage | File Count | Backups | Snapshots |
|---|---|---|---|---|---|
| home | /gpfs/ysm/home |
125GiB/user | 500,000 | Yes | >=2 days |
| project | /gpfs/ysm/project |
1TiB/group, increase to 4TiB on request | 5,000,000 | No | >=2 days |
| scratch60 | /gpfs/ysm/scratch60 |
20TiB/group | 15,000,000 | No | >=2 days |