==== description ====
CD-HIT is a fast program for clustering and comparing large sets of protein or nucleotide sequences. Accelerated for clustering the next generation sequencing data. Software page : [[http://cd-hit.org]] .

==== software version ====
CD-HIT , from Ubuntu 18.04 repo (CD-HIT version 4.7 (built on Jul  1 2017)) . 

==== sbatch example ====
File ''uniprot_sprot.fasta'' (md5sum: 28930f98b76a8475b1d4f8291f2a5833) complete UniProtKB/Swiss-Prot data set in flat file format was downloaded from [[ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/|here]] .

Take notice of ''-M'' option. There is not slurm environment variable that stores value of allocated memory. That is why it is important to remember to make value of allocated for computing job memory (''--mem'') and ''-M'' coherent.

<code>
#!/bin/bash -l
#SBATCH --partition=short
#SBATCH --ntasks=8
#SBATCH --mem 15G

#input filename
FASTAFILE=uniprot_sprot.fasta

#dir with input file and dir for results
INPUTFILEDIR="/workspace/${USER}/uniprot_files/"

#printout to output file some info
echo "cd-hit anthill test"
echo "input_file : " ${FASTAFILE}
echo "date: " `date`
echo "node_name: " `hostname`
echo "cores: " ${SLURM_NPROCS}

#run cdhit computation and remove output files
cd ${INPUTFILEDIR}
cdhit -i ${FASTAFILE} -o out -c 0.9 -n 5 -T ${SLURM_NPROCS} -M 14000
</code>

==== performance tests ====

Bellow results how efficiently cd-hit scales in function of used cores. Each computation were run 3 times separately for each node type ant6nn and type ant0nn.

{{ :anthill:cdhit4.7_anthill_result_001.png?nolink|}}
^ node ^ cores ^ min[s] ^ avg [s] ^ median [s] ^ max[s] ^ efficiency [%] ^
| ant6nn | 1 | 107.66 | 108.18 | 108.21 | 108.78 | 100.00% |
| ant6nn | 2 | 103.79 | 104.00 | 104.02 | 104.16 | 52.01% |
| ant6nn | 4 | 75.78 | 76.11 | 76.21 | 76.29 | 35.50% |
| ant6nn | 8 | 62.15 | 62.18 | 62.17 | 62.26 | 21.76% |
| ant6nn | 10 | 57.41 | 58.53 | 58.92 | 59.10 | 18.36% |

^ node ^ cores ^ min[s] ^ avg [s] ^ median [s] ^ max[s] ^ efficiency [%] ^
| ant00n | 1 | 150.84 | 160.29 | 151.97 | 178.35 | 100.00% |
| ant00n | 2 | 154.55 | 158.30 | 155.96 | 170.05 | 48.72% |
| ant00n | 4 | 114.23 | 117.90 | 116.52 | 127.71 | 32.61% |
| ant00n | 8 | 92.79 | 108.49 | 99.84 | 139.51 | 19.03% |
| ant00n | 10 | 90.37 | 96.00 | 96.08 | 104.37 | 15.82% |
| ant00n | 14 | 84.71 | 88.76 | 88.17 | 94.25 | 12.31% |
| ant00n | 16 | 82.85 | 88.40 | 90.33 | 92.43 | 10.52% |
| ant00n | 21 | 80.98 | 86.11 | 88.26 | 89.28 | 8.20% |
| ant00n | 28 | 78.94 | 89.15 | 91.17 | 93.79 | 5.95% | 

*) ant6nn = ant602 and ant604, ant00n = ant007 and ant008 \\
*) efficiency as ''t1 / ( cores * tn )'' ( where t1 is computation time at one core, tn is computation time on N cores ) \\
*) command run ''cdhit -i ${FASTAFILE} -o out -c 0.9 -n 5 -T ${SLURM_NPROCS} -M 14000'' on file ''uniprot_sprot.fasta (md5sum: 28930f98b76a8475b1d4f8291f2a5833)''