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The Farnam Cluster is named for Louise Whitman Farnam, the first woman to graduate from the Yale School of Medicine, class of 1916.

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.


Farnam 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. GPUs listed can be requested with the --gres flag, e.g. --gres=gpu:gtx1080ti:2 would request 2 GeForce GTX 1080Ti GPUs per node. See the Request Compute Resources page for more info.


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 Node Type CPU CPU Cores RAM GPU Features
59 Dell PowerEdge M620 2x E5-2670 16 121G sandybridge, E5-2670, nogpu, standard, oldest
14 Dell PowerEdge M915 4x AMD Opteron 6276 32 507G bulldozer, opteron-6276
117 Lenovo nx360h 2x E5-2660 v3 20 121G haswell, avx2, E5-2660_v3, nogpu, standard
5 Lenovo nx360h w/GPUs 2x E5-2660 v3 20 121G 2x k80 (2GPUs/k80) haswell, avx2, E5-2660_v3, doubleprecision
38 Lenovo nx360b 2x E5-2680 v4 28 246G broadwell, avx2, E5-2680_v4, nogpu, standard
3 Lenovo nx360b w/GPUs 2x E5-2660 v4 28 246G 2x p100 broadwell, avx2, E5-2660_v4, doubleprecision
2 Lenovo sd530 2x Gold 6132 28 184G skylake, avx2, avx512, 6132, nogpu, standard
1 Lenovo sd530 2x Gold 6132 28 751G skylake, avx2, avx512, 6132, nogpu
1 Thinkmate GPX XT4 (gpu_devel) 2x E5-2623 v4 8 58G 4x gtx1080ti broadwell, avx2, E5-2623_v4, singleprecision
20 Thinkmate GPX XT4 2x E5-2637 v4 8 121G 4x gtx1080ti broadwell, avx2, E5-2637_v4, singleprecision
1 Thinkmate GPX XT4 2x E5-2637 v4 8 121G 4x titanv broadwell, avx2, E5-2637_v4, singleprecision
2 Lenovo 3850X6 4x E7-4809 v3 32 1507G haswell, avx2, E7-4809_v3, nogpu
1 Lenovo 3850X6 4x E7-4820 v4 40 1507G broadwell, avx2, E7-4820_v4, nogpu

Slurm Partitions

Nodes on the clusters are organized into partitions, to which you submit your jobs with Slurm.

Public Partitions

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 gpu_devel partition is a single node meant for testing or compiling GPU accelerated code, and the gpu partition is where normal GPU jobs should run. 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 (number)
general* 400 CPUs, 2560 G RAM 200 CPUs, 1280 G RAM 1d/30d m620 (34), nx360h (94)
interactive 20 CPUs, 256 G RAM 1d/2d m620 (34), nx360h (94)
bigmem 2 jobs, 32 CPUs, 1532 G RAM 1d/7d m915 (9), 3850X6 (2)
gpu_devel 1 job 10min/2hr GPX XT4 gtx1080ti (1)
gpu 32 CPUs, 256 G RAM 1d/2d nx360h k80 (2), GPX XT4 gtx1080ti (10)
scavenge 800 CPUs, 5120 G RAM 1d/7d all

* default

Private Partitions

Private partitions contain nodes acquired by specific research groups. Full access to these partitions is granted at the discretion of the owner. Contact us if your group would like to purchase nodes.

Partition Walltime default/max Node type (number)
pi_breaker 1d/14d nx360b (24)
pi_cryoem 1d/∞ GPX XT4 gtx1080ti (10)
pi_deng 1d/14d nx360b (1)
pi_gerstein 1d/14d m915 (2), nx360b (11), sd530 (3), 3850X6 (1)
pi_gerstein_gpu 1d/14d nx360h k80 (3), nx360b p100 (2), GPX XT4 titanv (1)
pi_gruen 1d/14d nx360b (1)
pi_jadi 1d/14d nx360b (2)
pi_kleinstein 1d/14d m915 (1), nx360h (3)
pi_krauthammer 1d/14d nx360h (1)
pi_ma 1d/14d nx360h (2)
pi_ohern 1d/14d m620 (6), nx360h (3)
pi_sigworth 1d/14d nx360h (1)
pi_sindelar 1d/14d m620 (4), m915 (1), nx360h (1)
pi_strobel 1d/14d m915 (1)
pi_townsend 1d/14d nx360h (5)
pi_zhao 1d/14d m620 (17), m915 (1)

Public Datasets

We host datasets of general interest in a loosely organized directory tree in /gpfs/ysm/datasets:

├── cryoem
├── db
│   ├── annovar
│   └── blast
└── genomes
    ├── 1000Genomes
    ├── 10xgenomics
    ├── Aedes_aegypti
    ├── Chelonoidis_nigra
    ├── Danio_rerio
    ├── 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 email


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. Note that the per-user usage breakdown only update once daily.


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/ysm/home 125G/user 500,000 Yes
project /gpfs/ysm/project 4T/group 5,000,000 No
scratch60 /gpfs/ysm/scratch60 10T/group 5,000,000 No