Biowulf High Performance Computing at the NIH
hhsuite on Biowulf

The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).


Important Notes

hhblits and hhsearch need to do many random file access and read operations. The central file systems (i.e. /data, /scratch, or /fdb) will not perform well under this type of load. This means that running against the database directly stored on /fdb will not be performant. In addition it may tax the file system enough to also slow down other user's computations. We therefore recommend to copy the database to be searched to lscratch. In particular, nodes with SSD storage should be used. This means that the ideal usage pattern for large hhblits/hhsearch jobs is to allocate a node (or nodes) exclusively, copy the database to lscratch, and then run all computations on that node.

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 --constraint=ssd3200 --gres=lscratch:100 --cpus-per-task=10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load hhsuite
[+] Loading gcc  7.3.0  ... 
[+] Loading openmpi 3.0.0  for GCC 7.3.0 
[+] Loading hhsuite  3.3.0 
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 46116226]$ cp -r /fdb/hhsuite/uniprot20_2016_02 .
[user@cn3144 46116226]$ hhblits \
 -i /fdb/hhsuite/test-data/query.a3m \
 -d uniprot20_2016_02/uniprot20_2016_02 \
 -o query.hhr

- 17:04:47.198 INFO: Searching 8290206 column state sequences.

- 17:04:47.723 INFO: /fdb/hhsuite/test-data/query.a3m is in A2M, A3M or FASTA format

- 17:04:47.794 INFO: Iteration 1

- 17:04:48.727 INFO: Prefiltering database

- 17:06:47.000 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 302479
[user@cn3144 46116226]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

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

set -e

module load hhsuite
cd /lscratch/$SLURM_JOB_ID
cp -r /fdb/hhsuite/uniprot20_2016_02 .

hhblits -i /fdb/hhsuite/test-data/query.seq \
  -d ./uniprot20_2016_02/uniprot20_2016_02 \
  -cpu $SLURM_CPUS_PER_TASK -o test.hhr \
  -oa3m test.a3m -n 6

hhmake -i test.a3m -o test.hhm test.hhm test_addss.hhm -hmm
cp test* /path/to/output/dir

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --gres=lscratch:100 [--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. hhblits.swarm). For example:

cp -r /fdb/hhsuite/uniprot20_2016_02 /lscratch/$SLURM_JOB_ID \
&& hhblits -i sample1.seq -d /lscratch/$SLURM_JOB_ID/uniprot20_2016_02/uniprot20_2016_02 -cpu $SLURM_CPUS_PER_TASK -o sample1.hhr
cp -r /fdb/hhsuite/uniprot20_2016_02 /lscratch/$SLURM_JOB_ID \
&& hhblits -i sample2.seq -d /lscratch/$SLURM_JOB_ID/uniprot20_2016_02/uniprot20_2016_02 -cpu $SLURM_CPUS_PER_TASK -o sample2.hhr
cp -r /fdb/hhsuite/uniprot20_2016_02 /lscratch/$SLURM_JOB_ID \
&& hhblits -i sample3.seq -d /lscratch/$SLURM_JOB_ID/uniprot20_2016_02/uniprot20_2016_02 -cpu $SLURM_CPUS_PER_TASK -o sample3.hhr
cp -r /fdb/hhsuite/uniprot20_2016_02 /lscratch/$SLURM_JOB_ID \
&& hhblits -i sample4.seq -d /lscratch/$SLURM_JOB_ID/uniprot20_2016_02/uniprot20_2016_02 -cpu $SLURM_CPUS_PER_TASK -o sample4.hhr

Submit this job using the swarm command.

swarm -f hhblits.swarm [-g #] -t 6 --gres=lscratch:100 --module hhsuite
-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).
--gres lscratch:# Number of gigabytes of local scratch space required for each process
--module hhsuite Loads the hhsuite module for each subjob in the swarm