-
Notifications
You must be signed in to change notification settings - Fork 24
How Infernal Programs Scale On Multiple Processors
The Infernal programs cmalign, cmcalibrate, cmsearch and
cmscan support multicore parallelization using POSIX threads. You
can control how many threads are used with the --cpu <n>
command-line option. As of version 1.1.4, the default number of
threads used is the number of CPUs on the host.
The tables below summarize multi-threading performance on experiments run on NCBI hosts for the four multi-threaded infernal programs. This information is provided to give you an idea for how well these programs scale on up to 16 threads. Your mileage may vary.
Infernal v1.1.4 executables were used for the tests.
The cmalign, cmcalibrate and cmsearch tests below use three
models from Rfam 14.7: RF00504 (Glycine), RF00174 (Cobalamin) and
RF01959 (SSU_rRNA_archaea).
The final column in each table shows 'efficiency', which is a measure
of scaling performance defined as the speedup versus --cpu 1 divided
by <n> when run with <n> threads; 1.0 is optimal scaling.
All timings were performed on 2.93 GHz Intel Xeon processors.
The set of Rfam 14.7 seed sequences were aligned to RF00174 (432 sequences) and RF01959 (554 sequences), and the set of Rfam 14.7 full sequences were aligned to RF00504 (4600 sequences).
Example command:
cmalign --cpu 8 -o RF00504.cpu8.stk RF00504.cm RF000504.fa > RF00504.cpu8.cmalign
| Rfam accession | Rfam name | model length | --cpu <n> |
seconds | speedup vs --cpu 1
|
efficiency |
|---|---|---|---|---|---|---|
| RF00504 | Glycine | 94 | 1 | 156.0 | 1.0 | 1.000 |
| RF00504 | Glycine | 94 | 2 | 78.8 | 2.0 | 0.990 |
| RF00504 | Glycine | 94 | 4 | 39.7 | 3.9 | 0.982 |
| RF00504 | Glycine | 94 | 8 | 20.9 | 7.4 | 0.931 |
| RF00504 | Glycine | 94 | 16 | 16.1 | 9.7 | 0.606 |
| RF00174 | Cobalamin | 190 | 1 | 33.2 | 1.0 | 1.000 |
| RF00174 | Cobalamin | 190 | 2 | 16.7 | 2.0 | 0.997 |
| RF00174 | Cobalamin | 190 | 4 | 8.4 | 3.9 | 0.983 |
| RF00174 | Cobalamin | 190 | 8 | 4.6 | 7.3 | 0.907 |
| RF00174 | Cobalamin | 190 | 16 | 3.2 | 10.3 | 0.646 |
| RF01959 | SSU_rRNA_archaea | 1477 | 1 | 739.3 | 1.0 | 1.000 |
| RF01959 | SSU_rRNA_archaea | 1477 | 2 | 377.7 | 2.0 | 0.979 |
| RF01959 | SSU_rRNA_archaea | 1477 | 4 | 191.8 | 3.9 | 0.964 |
| RF01959 | SSU_rRNA_archaea | 1477 | 8 | 117.4 | 6.3 | 0.787 |
| RF01959 | SSU_rRNA_archaea | 1477 | 16 | 104.6 | 7.1 | 0.442 |
Example command:
cmcalibrate --cpu 8 RF00504.cm > RF00504.cmcalibrate
| Rfam accession | Rfam name | model length | --cpu <n> |
seconds | speedup vs --cpu 1
|
efficiency |
|---|---|---|---|---|---|---|
| RF00504 | Glycine | 94 | 1 | 7258.5 | 1.0 | 1.000 |
| RF00504 | Glycine | 94 | 2 | 3443.0 | 2.1 | 1.054 |
| RF00504 | Glycine | 94 | 4 | 1752.1 | 4.1 | 1.036 |
| RF00504 | Glycine | 94 | 8 | 1042.4 | 7.0 | 0.870 |
| RF00504 | Glycine | 94 | 16 | 643.9 | 11.3 | 0.705 |
| RF00174 | Cobalamin | 190 | 1 | 25733.9 | 1.0 | 1.000 |
| RF00174 | Cobalamin | 190 | 2 | 13139.4 | 2.0 | 0.979 |
| RF00174 | Cobalamin | 190 | 4 | 6617.1 | 3.9 | 0.972 |
| RF00174 | Cobalamin | 190 | 8 | 3571.3 | 7.2 | 0.901 |
| RF00174 | Cobalamin | 190 | 16 | 2594.1 | 9.9 | 0.620 |
| RF01959 | SSU_rRNA_archaea | 1477 | 1 | 121525.8 | 1.0 | 1.000 |
| RF01959 | SSU_rRNA_archaea | 1477 | 2 | 61922.0 | 2.0 | 0.981 |
| RF01959 | SSU_rRNA_archaea | 1477 | 4 | 32115.3 | 3.8 | 0.946 |
| RF01959 | SSU_rRNA_archaea | 1477 | 8 | 16642.5 | 7.3 | 0.913 |
| RF01959 | SSU_rRNA_archaea | 1477 | 16 | 11814.6 | 10.3 | 0.643 |
The cmscan tests below use all 4070 Rfam 14.6 models as the target
database with 1000 query archaeal sequences ranging from
length 27 nt to 3,466,370 nt with an average size 26,296 nt (total
number of nucleotides: 26,296,123).
Example command:
cmscan --verbose --cpu 8 Rfam.cm arc.n1000.fa > Rfam.arc.n1000.cpu8.cmscan
--cpu <n> |
seconds | speedup vs --cpu 1
|
efficiency |
|---|---|---|---|
| 1 | 70338.5 | 1.0 | 1.000 |
| 2 | 38464.1 | 1.8 | 0.914 |
| 4 | 21286.6 | 3.3 | 0.826 |
| 8 | 14590.8 | 4.8 | 0.603 |
| 16 | 10113.7 | 7.0 | 0.435 |
Example command:
cmsearch --cpu 8 RF00504.cm arc.fa > RF00504.arc.cpu8.cmsearch
| Rfam accession | Rfam name | model length | --cpu <n> |
seconds | speedup vs --cpu 1
|
efficiency |
|---|---|---|---|---|---|---|
| RF00504 | Glycine | 94 | 1 | 156.4 | 1.0 | 1.000 |
| RF00504 | Glycine | 94 | 2 | 79.3 | 2.0 | 0.986 |
| RF00504 | Glycine | 94 | 4 | 39.2 | 4.0 | 0.998 |
| RF00504 | Glycine | 94 | 8 | 22.5 | 6.9 | 0.868 |
| RF00504 | Glycine | 94 | 16 | 15.9 | 9.8 | 0.614 |
| RF00174 | Cobalamin | 190 | 1 | 430.7 | 1.0 | 1.000 |
| RF00174 | Cobalamin | 190 | 2 | 221.7 | 1.9 | 0.971 |
| RF00174 | Cobalamin | 190 | 4 | 112.3 | 3.8 | 0.959 |
| RF00174 | Cobalamin | 190 | 8 | 72.9 | 5.9 | 0.739 |
| RF00174 | Cobalamin | 190 | 16 | 74.5 | 5.8 | 0.361 |
| RF01959 | SSU_rRNA_archaea | 1477 | 1 | 3827.1 | 1.0 | 1.000 |
| RF01959 | SSU_rRNA_archaea | 1477 | 2 | 1940.1 | 2.0 | 0.986 |
| RF01959 | SSU_rRNA_archaea | 1477 | 4 | 1024.9 | 3.7 | 0.934 |
| RF01959 | SSU_rRNA_archaea | 1477 | 8 | 617.8 | 6.2 | 0.774 |
| RF01959 | SSU_rRNA_archaea | 1477 | 16 | 522.3 | 7.3 | 0.458 |
The cmsearch tests below use each of the three Rfam models as
queries against target database of 20,512 archaeal sequences ranging from
length 16 nt to 5,180,745 nt with an average size 33,026 nt (total
number of nucleotides: 677,428,174).
Rfam 14.7 CM file: http://ftp.ebi.ac.uk/pub/databases/Rfam/14.7/Rfam.cm.gz
Rfam 14.7 seed alignments: http://ftp.ebi.ac.uk/pub/databases/Rfam/14.7/Rfam.seed.gz
RF00504 'full' sequence file: http://ftp.ebi.ac.uk/pub/databases/Rfam/14.7/fasta_files/RF00504.fa.gz
xref: notebook/22_0310_inf_df_num_threads