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Profile mehari #430
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profilingProfiling was done with an explicit [profile.profiling]
inherits = "release"
debug = true on a machine with the following specs CPU: quad core Intel Xeon E5-1630 v3 (-MT MCP-)
speed/min/max: 1621/1200/3800 MHz Kernel: 6.5.0-28-generic x86_64
Mem: 9386.1/64180.0 MiB (14.6%) Storage: 685.61 GiB (26.7% used) Procs: 337
Drives:
Local Storage: total: 685.61 GiB used: 182.78 GiB (26.7%)
ID-1: /dev/sda vendor: Samsung model: MZ7LN256HCHP-00000 size: 238.47 GiB # hosts /, /home
ID-2: /dev/sdb model: MZ7KH480HAHQ0D3 size: 447.13 GiB # hosts mehari DB flamegraphOnly uses the first 1M records from the input file ( invocationcargo flamegraph --profile profiling --bin mehari -- annotate seqvars --path-db /mnt/data/mehari/0.21.0/db --path-input-vcf tests/data/annotate/seqvars/NA-12878WGS_dragen.first1M.vcf.gz --path-output-vcf /tmp/NA-12878WGS_dragen.first1M.annotated.vcf.gz --path-input-ped data/FAM_BE_10.sup.ped result
dhatOnly uses the first 100k records from the input file ( invocationcargo run --profile profiling --features dhat-heap --bin mehari -- annotate seqvars --path-db /mnt/data/mehari/0.21.0/db --path-input-vcf tests/data/annotate/seqvars/NA-12878WGS_dragen.first100k.vcf.gz --path-output-vcf /tmp/NA-12878WGS_dragen.first100k.annotated.vcf.gz --path-input-ped data/FAM_BE_10.sup.ped resultdhat-heap.json (view in dhat-viewer) cozFigure out reasonable scopes before running coz. |
At the moment, my reading of this is roughly:
|
caching |
Setting |
Using noodles |
@tedil impressive 50% time saved! |
Is your feature request related to a problem? Please describe.
We need to understand, which code paths influence mehari performance.
Describe the solution you'd like
Use
flamegraph
,DHAT
to understand code paths and allocations. Add a branch withcoz
support. Look into https://crates.io/crates/criterion.Describe alternatives you've considered
None
Additional context
This is the basis for additional work.
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