Biowulf High Performance Computing at the NIH
cellphonedb on Biowulf

A publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive --cpus-per-task=4 --mem=16G --gres=lscratch:10
salloc.exe: Pending job allocation 41538656
salloc.exe: job 41538656 queued and waiting for resources
salloc.exe: job 41538656 has been allocated resources
salloc.exe: Granted job allocation 41538656
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3114 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn3114 ~]$ cd /data/$USER

[user@cn3114 user]$ git clone
Cloning into 'cellphonedb'...
remote: Enumerating objects: 15, done.
remote: Counting objects: 100% (15/15), done.
remote: Compressing objects: 100% (14/14), done.
remote: Total 9381 (delta 1), reused 4 (delta 1), pack-reused 9366
Receiving objects: 100% (9381/9381), 61.54 MiB | 24.54 MiB/s, done.
Resolving deltas: 100% (7066/7066), done.
Checking out files: 100% (368/368), done.

[user@cn3114 user]$ cd cellphonedb/in/example_data/

[user@cn3114 example_data]$ module load cellphonedb
[+] Loading cellphonedb  2.1.1  on cn3114
[+] Loading gcc  7.3.0  ...
[+] Loading GSL 2.4 for GCC 7.2.0 ...
[-] Unloading gcc  7.3.0  ...
[+] Loading gcc  7.3.0  ...
[+] Loading openmpi 3.0.2  for GCC 7.3.0
[+] Loading ImageMagick  7.0.8  on cn3114
[+] Loading HDF5  1.10.4
[+] Loading pandoc  2.1.1  on cn3114
[+] Loading R 3.6.0

[user@cn3114 example_data]$ cellphonedb method statistical_analysis test_meta.txt test_counts.txt
[ ][APP][08/11/19-18:25:15][WARNING] Latest local available version is `v2.0.0`, using it
[ ][APP][08/11/19-18:25:15][WARNING] User selected downloaded database `v2.0.0` is available, using it
[ ][CORE][08/11/19-18:25:15][INFO] Initializing SqlAlchemy CellPhoneDB Core

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load cellphonedb
cd /data/$USER/cellphonedb/in/example_data/
cellphonedb method statistical_analysis test_meta.txt test_counts.txt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. cellphonedb.swarm). For example:

cellphonedb method analysis 1meta.txt 1counts.txt 
cellphonedb method analysis 2meta.txt 2counts.txt 
cellphonedb method analysis 3meta.txt 3counts.txt 
cellphonedb method analysis 4meta.txt 4counts.txt 

Submit this job using the swarm command.

swarm -f cellphonedb.swarm [-g #] [-t #] --module cellphonedb
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module cellphonedb Loads the cellphonedb module for each subjob in the swarm