Performance improvements with smarter handling of raw data #57

tpoisot · 2023-03-04T21:20:27Z

This should make looking for stuff we know is here faster. Hopefully by a lot.

tpoisot · 2023-03-04T21:56:58Z

Turns out that indexing a grouped DF is O(1). This is about to get interesting.

…b/NCBITaxonomy.jl into feature/speedup-groupdb

github-actions · 2023-03-05T03:13:41Z

Benchmark result

Judge result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Time of benchmarks:
- Target: 5 Mar 2023 - 03:10
- Baseline: 5 Mar 2023 - 03:13
Package commits:
- Target: b7dc72
- Baseline: 2a3a84
Julia commits:
- Target: 17cfb8
- Baseline: 17cfb8
Julia command flags:
- Target: None
- Baseline: None
Environment variables:
- Target: None
- Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID	time ratio	memory ratio
`["name finders", "mammals (inclusive)"]`	0.17 (5%) ✅	10.10 (1%) ❌
`["name finders", "mammals"]`	0.00 (5%) ✅	0.06 (1%) ✅
`["name finders", "phage"]`	0.00 (5%) ✅	0.07 (1%) ✅
`["taxon search", "by ID"]`	0.20 (5%) ✅	13.00 (1%) ❌
`["taxon search", "lowercase with finder"]`	0.86 (5%) ✅	1.04 (1%) ❌
`["taxon search", "pan - mammal finder"]`	0.82 (5%) ✅	1.05 (1%) ❌
`["taxon search", "pan - primate finder"]`	0.88 (5%) ✅	1.10 (1%) ❌
`["taxon search", "pan - string annotation"]`	1.06 (5%) ❌	1.00 (1%)
`["taxon search", "scientific with finder"]`	0.82 (5%) ✅	1.05 (1%) ❌
`["taxon search", "with finder"]`	0.85 (5%) ✅	1.05 (1%) ❌
`["traversal", "children"]`	0.41 (5%) ✅	1.00 (1%)
`["traversal", "common ancestor (array)"]`	0.95 (5%) ✅	1.00 (1%)
`["traversal", "common ancestor (pair)"]`	0.84 (5%) ✅	1.00 (1%)
`["traversal", "in root"]`	0.44 (5%) ✅	1.00 (1%)
`["traversal", "lineage"]`	0.88 (5%) ✅	1.00 (1%)
`["utilities", "distance matrix (no allocation)"]`	0.46 (5%) ✅	1.48 (1%) ❌
`["utilities", "distance matrix (pre-allocation)"]`	0.48 (5%) ✅	1.48 (1%) ❌

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

["name finders"]
["taxon search"]
["traversal"]
["utilities"]

Julia versioninfo

Target

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.2 LTS
  uname: Linux 5.15.0-1033-azure #40-Ubuntu SMP Mon Jan 23 20:36:59 UTC 2023 x86_64 x86_64
  CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: 
              speed         user         nice          sys         idle          irq
       #1  2294 MHz       6038 s          0 s        289 s       3044 s          0 s
       #2  2294 MHz       2549 s          0 s        405 s       6301 s          0 s
  Memory: 6.781219482421875 GB (3413.67578125 MB free)
  Uptime: 945.49 sec
  Load Avg:  1.0  1.0  0.73
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, broadwell)
  Threads: 1 on 2 virtual cores

Baseline

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.2 LTS
  uname: Linux 5.15.0-1033-azure #40-Ubuntu SMP Mon Jan 23 20:36:59 UTC 2023 x86_64 x86_64
  CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: 
              speed         user         nice          sys         idle          irq
       #1  2294 MHz       6398 s          0 s        317 s       4678 s          0 s
       #2  2294 MHz       4175 s          0 s        432 s       6667 s          0 s
  Memory: 6.781219482421875 GB (3912.25 MB free)
  Uptime: 1148.55 sec
  Load Avg:  1.0  1.0  0.8
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, broadwell)
  Threads: 1 on 2 virtual cores

Target result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Time of benchmark: 5 Mar 2023 - 3:10
Package commit: b7dc72
Julia commit: 17cfb8
Julia command flags: None
Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID	time	memory	allocations
`["name finders", "descendants of Diplectanidae"]`	542.512 ms (5%)	83.34 MiB (1%)	17216
`["name finders", "mammals (inclusive)"]`	6.310 ms (5%)	29.03 MiB (1%)	326
`["name finders", "mammals"]`	30.000 μs (5%)	128.02 KiB (1%)	14
`["name finders", "phage"]`	73.900 μs (5%)	319.88 KiB (1%)	13
`["taxon search", "by ID"]`	827.273 ns (5%)	416 bytes (1%)	19
`["taxon search", "by name"]`	23.640 ms (5%)	441.56 KiB (1%)	28
`["taxon search", "lowercase with finder"]`	159.201 μs (5%)	8.73 KiB (1%)	30
`["taxon search", "pan - all defaults"]`	23.428 ms (5%)	441.56 KiB (1%)	28
`["taxon search", "pan - mammal finder"]`	206.702 μs (5%)	8.58 KiB (1%)	27
`["taxon search", "pan - primate finder"]`	26.600 μs (5%)	5.28 KiB (1%)	28
`["taxon search", "pan - string annotation"]`	3.800 ns (5%)
`["taxon search", "scientific with finder"]`	211.201 μs (5%)	8.58 KiB (1%)	27
`["taxon search", "with finder"]`	216.301 μs (5%)	8.58 KiB (1%)	27
`["traversal", "children"]`	1.371 ms (5%)	309.03 KiB (1%)	22
`["traversal", "common ancestor (array)"]`	40.168 ms (5%)	36.62 KiB (1%)	714
`["traversal", "common ancestor (pair)"]`	11.830 ms (5%)	14.30 KiB (1%)	261
`["traversal", "in root"]`	116.894 ms (5%)	19.98 MiB (1%)	3601
`["traversal", "lineage"]`	5.893 ms (5%)	4.38 KiB (1%)	112
`["traversal", "parent"]`	12.800 μs (5%)	128 bytes (1%)	7
`["utilities", "distance matrix (no allocation)"]`	32.661 ms (5%)	135.33 KiB (1%)	3277
`["utilities", "distance matrix (pre-allocation)"]`	33.230 ms (5%)	135.08 KiB (1%)	3276

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

["name finders"]
["taxon search"]
["traversal"]
["utilities"]

Julia versioninfo

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.2 LTS
  uname: Linux 5.15.0-1033-azure #40-Ubuntu SMP Mon Jan 23 20:36:59 UTC 2023 x86_64 x86_64
  CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: 
              speed         user         nice          sys         idle          irq
       #1  2294 MHz       6038 s          0 s        289 s       3044 s          0 s
       #2  2294 MHz       2549 s          0 s        405 s       6301 s          0 s
  Memory: 6.781219482421875 GB (3413.67578125 MB free)
  Uptime: 945.49 sec
  Load Avg:  1.0  1.0  0.73
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, broadwell)
  Threads: 1 on 2 virtual cores

Baseline result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Time of benchmark: 5 Mar 2023 - 3:13
Package commit: 2a3a84
Julia commit: 17cfb8
Julia command flags: None
Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID	time	memory	allocations
`["name finders", "mammals (inclusive)"]`	37.579 ms (5%)	2.87 MiB (1%)	308
`["name finders", "mammals"]`	28.427 ms (5%)	2.21 MiB (1%)	309
`["name finders", "phage"]`	30.845 ms (5%)	4.72 MiB (1%)	307
`["taxon search", "by ID"]`	4.171 μs (5%)	32 bytes (1%)	2
`["taxon search", "by name"]`	24.566 ms (5%)	441.19 KiB (1%)	11
`["taxon search", "lowercase with finder"]`	184.299 μs (5%)	8.36 KiB (1%)	13
`["taxon search", "pan - all defaults"]`	24.208 ms (5%)	441.19 KiB (1%)	11
`["taxon search", "pan - mammal finder"]`	253.102 μs (5%)	8.20 KiB (1%)	10
`["taxon search", "pan - primate finder"]`	30.400 μs (5%)	4.81 KiB (1%)	9
`["taxon search", "pan - string annotation"]`	3.600 ns (5%)
`["taxon search", "scientific with finder"]`	256.003 μs (5%)	8.20 KiB (1%)	10
`["taxon search", "with finder"]`	253.502 μs (5%)	8.20 KiB (1%)	10
`["traversal", "children"]`	3.370 ms (5%)	309.03 KiB (1%)	22
`["traversal", "common ancestor (array)"]`	42.311 ms (5%)	36.62 KiB (1%)	714
`["traversal", "common ancestor (pair)"]`	14.076 ms (5%)	14.30 KiB (1%)	261
`["traversal", "in root"]`	266.300 ms (5%)	19.98 MiB (1%)	3601
`["traversal", "lineage"]`	6.702 ms (5%)	4.38 KiB (1%)	112
`["traversal", "parent"]`	12.900 μs (5%)	128 bytes (1%)	7
`["utilities", "distance matrix (no allocation)"]`	71.043 ms (5%)	91.41 KiB (1%)	1446
`["utilities", "distance matrix (pre-allocation)"]`	69.377 ms (5%)	91.16 KiB (1%)	1445

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

["name finders"]
["taxon search"]
["traversal"]
["utilities"]

Julia versioninfo

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.2 LTS
  uname: Linux 5.15.0-1033-azure #40-Ubuntu SMP Mon Jan 23 20:36:59 UTC 2023 x86_64 x86_64
  CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: 
              speed         user         nice          sys         idle          irq
       #1  2294 MHz       6398 s          0 s        317 s       4678 s          0 s
       #2  2294 MHz       4175 s          0 s        432 s       6667 s          0 s
  Memory: 6.781219482421875 GB (3912.25 MB free)
  Uptime: 1148.55 sec
  Load Avg:  1.0  1.0  0.8
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, broadwell)
  Threads: 1 on 2 virtual cores

Runtime information

Runtime Info
BLAS #threads	1
`BLAS.vendor()`	`openblas64`
`Sys.CPU_THREADS`	2

lscpu output:

Architecture:                    x86_64
CPU op-mode(s):                  32-bit, 64-bit
Address sizes:                   46 bits physical, 48 bits virtual
Byte Order:                      Little Endian
CPU(s):                          2
On-line CPU(s) list:             0,1
Vendor ID:                       GenuineIntel
Model name:                      Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz
CPU family:                      6
Model:                           79
Thread(s) per core:              1
Core(s) per socket:              2
Socket(s):                       1
Stepping:                        1
BogoMIPS:                        4589.37
Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase bmi1 hle avx2 smep bmi2 erms invpcid rtm rdseed adx smap xsaveopt md_clear
Hypervisor vendor:               Microsoft
Virtualization type:             full
L1d cache:                       64 KiB (2 instances)
L1i cache:                       64 KiB (2 instances)
L2 cache:                        512 KiB (2 instances)
L3 cache:                        50 MiB (1 instance)
NUMA node(s):                    1
NUMA node0 CPU(s):               0,1
Vulnerability Itlb multihit:     KVM: Mitigation: VMX unsupported
Vulnerability L1tf:              Mitigation; PTE Inversion
Vulnerability Mds:               Mitigation; Clear CPU buffers; SMT Host state unknown
Vulnerability Meltdown:          Mitigation; PTI
Vulnerability Mmio stale data:   Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown
Vulnerability Retbleed:          Not affected
Vulnerability Spec store bypass: Vulnerable
Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:        Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected
Vulnerability Srbds:             Not affected
Vulnerability Tsx async abort:   Mitigation; Clear CPU buffers; SMT Host state unknown

Cpu Property	Value
Brand	Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz
Vendor	:Intel
Architecture	:Broadwell
Model	Family: 0x06, Model: 0x4f, Stepping: 0x01, Type: 0x00
Cores	2 physical cores, 2 logical cores (on executing CPU)
	No Hyperthreading hardware capability detected
Clock Frequencies	Not supported by CPU
Data Cache	Level 1:3 : (32, 256, 51200) kbytes
	64 byte cache line size
Address Size	48 bits virtual, 46 bits physical
SIMD	256 bit = 32 byte max. SIMD vector size
Time Stamp Counter	TSC is accessible via `rdtsc`
	TSC increased at every clock cycle (non-invariant TSC)
Perf. Monitoring	Performance Monitoring Counters (PMC) are not supported
Hypervisor	Yes, Microsoft

github-actions · 2025-03-12T16:49:08Z

Benchmark result

Judge result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Time of benchmarks:
- Target: 12 Mar 2025 - 16:46
- Baseline: 12 Mar 2025 - 16:49
Package commits:
- Target: 54ff16
- Baseline: b64570
Julia commits:
- Target: 8561cc
- Baseline: 8561cc
Julia command flags:
- Target: None
- Baseline: None
Environment variables:
- Target: None
- Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID	time ratio	memory ratio
`["name finders", "mammals (inclusive)"]`	0.10 (5%) ✅	7.87 (1%) ❌
`["name finders", "mammals"]`	0.00 (5%) ✅	0.05 (1%) ✅
`["name finders", "phage"]`	0.00 (5%) ✅	0.06 (1%) ✅
`["taxon search", "by ID"]`	0.16 (5%) ✅	13.00 (1%) ❌
`["taxon search", "lowercase with finder"]`	0.94 (5%) ✅	1.08 (1%) ❌
`["taxon search", "pan - mammal finder"]`	0.85 (5%) ✅	1.08 (1%) ❌
`["taxon search", "pan - primate finder"]`	0.98 (5%)	1.71 (1%) ❌
`["taxon search", "scientific with finder"]`	0.84 (5%) ✅	1.08 (1%) ❌
`["taxon search", "with finder"]`	0.93 (5%) ✅	1.08 (1%) ❌
`["traversal", "children"]`	0.53 (5%) ✅	1.00 (1%)
`["traversal", "in root"]`	0.54 (5%) ✅	1.00 (1%)
`["utilities", "distance matrix (no allocation)"]`	0.54 (5%) ✅	1.65 (1%) ❌
`["utilities", "distance matrix (pre-allocation)"]`	0.54 (5%) ✅	1.65 (1%) ❌

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

["name finders"]
["taxon search"]
["traversal"]
["utilities"]

Julia versioninfo

Target

Julia Version 1.11.4
Commit 8561cc3d68d (2025-03-10 11:36 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.2 LTS
  uname: Linux 6.8.0-1021-azure #25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       1905 s          0 s        172 s       5209 s          0 s
       #2     0 MHz       3361 s          0 s        228 s       3723 s          0 s
       #3     0 MHz       1627 s          0 s        149 s       5472 s          0 s
       #4     0 MHz       1457 s          0 s        144 s       5661 s          0 s
  Memory: 15.61526870727539 GB (13669.92578125 MB free)
  Uptime: 737.31 sec
  Load Avg:  1.02  1.18  0.76
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline

Julia Version 1.11.4
Commit 8561cc3d68d (2025-03-10 11:36 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.2 LTS
  uname: Linux 6.8.0-1021-azure #25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       2002 s          0 s        191 s       6403 s          0 s
       #2     0 MHz       4410 s          0 s        254 s       3960 s          0 s
       #3     0 MHz       1703 s          0 s        174 s       6667 s          0 s
       #4     0 MHz       1500 s          0 s        161 s       6910 s          0 s
  Memory: 15.61526870727539 GB (13777.296875 MB free)
  Uptime: 868.58 sec
  Load Avg:  1.05  1.13  0.8
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Target result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Time of benchmark: 12 Mar 2025 - 16:46
Package commit: 54ff16
Julia commit: 8561cc
Julia command flags: None
Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID	time	GC time	memory	allocations
`["name finders", "descendants of Diplectanidae"]`	133.425 ms (5%)	3.511 ms	90.67 MiB (1%)	17823
`["name finders", "mammals (inclusive)"]`	2.617 ms (5%)		32.86 MiB (1%)	431
`["name finders", "mammals"]`	6.526 μs (5%)		142.45 KiB (1%)	14
`["name finders", "phage"]`	21.591 μs (5%)		400.33 KiB (1%)	14
`["taxon search", "by ID"]`	647.152 ns (5%)		416 bytes (1%)	20
`["taxon search", "by name"]`	16.654 ms (5%)		495.02 KiB (1%)	30
`["taxon search", "lowercase with finder"]`	189.115 μs (5%)		5.08 KiB (1%)	37
`["taxon search", "pan - all defaults"]`	15.255 ms (5%)		495.02 KiB (1%)	30
`["taxon search", "pan - mammal finder"]`	165.681 μs (5%)		4.83 KiB (1%)	30
`["taxon search", "pan - primate finder"]`	18.385 μs (5%)		1.12 KiB (1%)	30
`["taxon search", "pan - string annotation"]`	3.095 ns (5%)
`["taxon search", "scientific with finder"]`	169.769 μs (5%)		4.83 KiB (1%)	30
`["taxon search", "with finder"]`	187.722 μs (5%)		4.83 KiB (1%)	30
`["traversal", "children"]`	293.234 μs (5%)		324.55 KiB (1%)	24
`["traversal", "common ancestor (array)"]`	30.416 ms (5%)		30.53 KiB (1%)	712
`["traversal", "common ancestor (pair)"]`	10.426 ms (5%)		11.41 KiB (1%)	257
`["traversal", "in root"]`	23.009 ms (5%)	581.057 μs	22.88 MiB (1%)	3876
`["traversal", "lineage"]`	5.278 ms (5%)		4.23 KiB (1%)	115
`["traversal", "parent"]`	11.812 μs (5%)		128 bytes (1%)	7
`["utilities", "distance matrix (no allocation)"]`	26.487 ms (5%)		106.22 KiB (1%)	3203
`["utilities", "distance matrix (pre-allocation)"]`	26.464 ms (5%)		105.95 KiB (1%)	3201

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

["name finders"]
["taxon search"]
["traversal"]
["utilities"]

Julia versioninfo

Julia Version 1.11.4
Commit 8561cc3d68d (2025-03-10 11:36 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.2 LTS
  uname: Linux 6.8.0-1021-azure #25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       1905 s          0 s        172 s       5209 s          0 s
       #2     0 MHz       3361 s          0 s        228 s       3723 s          0 s
       #3     0 MHz       1627 s          0 s        149 s       5472 s          0 s
       #4     0 MHz       1457 s          0 s        144 s       5661 s          0 s
  Memory: 15.61526870727539 GB (13669.92578125 MB free)
  Uptime: 737.31 sec
  Load Avg:  1.02  1.18  0.76
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Time of benchmark: 12 Mar 2025 - 16:49
Package commit: b64570
Julia commit: 8561cc
Julia command flags: None
Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID	time	memory	allocations
`["name finders", "mammals (inclusive)"]`	25.560 ms (5%)	4.18 MiB (1%)	345
`["name finders", "mammals"]`	19.470 ms (5%)	2.59 MiB (1%)	343
`["name finders", "phage"]`	20.869 ms (5%)	6.31 MiB (1%)	340
`["taxon search", "by ID"]`	3.939 μs (5%)	32 bytes (1%)	2
`["taxon search", "by name"]`	16.149 ms (5%)	494.64 KiB (1%)	12
`["taxon search", "lowercase with finder"]`	200.929 μs (5%)	4.70 KiB (1%)	19
`["taxon search", "pan - all defaults"]`	15.315 ms (5%)	494.64 KiB (1%)	12
`["taxon search", "pan - mammal finder"]`	195.719 μs (5%)	4.45 KiB (1%)	12
`["taxon search", "pan - primate finder"]`	18.745 μs (5%)	672 bytes (1%)	10
`["taxon search", "pan - string annotation"]`	3.095 ns (5%)
`["taxon search", "scientific with finder"]`	201.971 μs (5%)	4.45 KiB (1%)	12
`["taxon search", "with finder"]`	201.189 μs (5%)	4.45 KiB (1%)	12
`["traversal", "children"]`	555.686 μs (5%)	324.55 KiB (1%)	24
`["traversal", "common ancestor (array)"]`	30.523 ms (5%)	30.53 KiB (1%)	712
`["traversal", "common ancestor (pair)"]`	10.463 ms (5%)	11.41 KiB (1%)	257
`["traversal", "in root"]`	42.676 ms (5%)	22.88 MiB (1%)	3876
`["traversal", "lineage"]`	5.292 ms (5%)	4.23 KiB (1%)	115
`["traversal", "parent"]`	11.882 μs (5%)	128 bytes (1%)	7
`["utilities", "distance matrix (no allocation)"]`	49.199 ms (5%)	64.50 KiB (1%)	1373
`["utilities", "distance matrix (pre-allocation)"]`	49.155 ms (5%)	64.23 KiB (1%)	1371

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

["name finders"]
["taxon search"]
["traversal"]
["utilities"]

Julia versioninfo

Julia Version 1.11.4
Commit 8561cc3d68d (2025-03-10 11:36 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 24.04.2 LTS
  uname: Linux 6.8.0-1021-azure #25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1     0 MHz       2002 s          0 s        191 s       6403 s          0 s
       #2     0 MHz       4410 s          0 s        254 s       3960 s          0 s
       #3     0 MHz       1703 s          0 s        174 s       6667 s          0 s
       #4     0 MHz       1500 s          0 s        161 s       6910 s          0 s
  Memory: 15.61526870727539 GB (13777.296875 MB free)
  Uptime: 868.58 sec
  Load Avg:  1.05  1.13  0.8
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Runtime information

Runtime Info
BLAS #threads	2
`BLAS.vendor()`	`lbt`
`Sys.CPU_THREADS`	4

lscpu output:

Architecture:                         x86_64
CPU op-mode(s):                       32-bit, 64-bit
Address sizes:                        48 bits physical, 48 bits virtual
Byte Order:                           Little Endian
CPU(s):                               4
On-line CPU(s) list:                  0-3
Vendor ID:                            AuthenticAMD
Model name:                           AMD EPYC 7763 64-Core Processor
CPU family:                           25
Model:                                1
Thread(s) per core:                   2
Core(s) per socket:                   2
Socket(s):                            1
Stepping:                             1
BogoMIPS:                             4890.85
Flags:                                fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves user_shstk clzero xsaveerptr rdpru arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload umip vaes vpclmulqdq rdpid fsrm
Virtualization:                       AMD-V
Hypervisor vendor:                    Microsoft
Virtualization type:                  full
L1d cache:                            64 KiB (2 instances)
L1i cache:                            64 KiB (2 instances)
L2 cache:                             1 MiB (2 instances)
L3 cache:                             32 MiB (1 instance)
NUMA node(s):                         1
NUMA node0 CPU(s):                    0-3
Vulnerability Gather data sampling:   Not affected
Vulnerability Itlb multihit:          Not affected
Vulnerability L1tf:                   Not affected
Vulnerability Mds:                    Not affected
Vulnerability Meltdown:               Not affected
Vulnerability Mmio stale data:        Not affected
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed:               Not affected
Vulnerability Spec rstack overflow:   Vulnerable: Safe RET, no microcode
Vulnerability Spec store bypass:      Vulnerable
Vulnerability Spectre v1:             Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:             Mitigation; Retpolines; STIBP disabled; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds:                  Not affected
Vulnerability Tsx async abort:        Not affected

Cpu Property	Value
Brand	AMD EPYC 7763 64-Core Processor
Vendor	:AMD
Architecture	:Unknown
Model	Family: 0xaf, Model: 0x01, Stepping: 0x01, Type: 0x00
Cores	16 physical cores, 16 logical cores (on executing CPU)
	No Hyperthreading hardware capability detected
Clock Frequencies	Not supported by CPU
Data Cache	Level 1:3 : (32, 512, 32768) kbytes
	64 byte cache line size
Address Size	48 bits virtual, 48 bits physical
SIMD	256 bit = 32 byte max. SIMD vector size
Time Stamp Counter	TSC is accessible via `rdtsc`
	TSC runs at constant rate (invariant from clock frequency)
Perf. Monitoring	Performance Monitoring Counters (PMC) are not supported
Hypervisor	Yes, Microsoft

tpoisot added 5 commits March 4, 2023 15:59

🛑 sanitize the download/extract step

57d3c10

🚮 only check the local checksum after making sure the archive is here

c854aca

✨ build step cleaned up

eae7618

⚙️ move the code to read the taxonomy out of the main file

1683801

⚡ only keep two taxo dbs

36306cf

tpoisot added 21 commits March 4, 2023 16:57

➕ Downloads (tmp. Revise)

9340b85

⚡ speedy lookup by ID

b65d0dd

⚙️ use filter in namefilter

4933e83

⚙️ keep division code

dd430bc

⚡ direct lookup for rank

efd0902

🐛 namefilter from df filter

b276c7b

🐛 index by tuple

518faa9

⚡ update some benchmarks

276de15

⚡ update the speed of namefinders

1e81706

⚡ minimize memory footprint of the table

c749b0d

Merge branch 'main' into feature/speedup-groupdb

4db9187

🐛 make taxon work with abstract dfs

01a7ca7

Merge branch 'feature/speedup-groupdb' of https://github.com/PoisotLa…

87a95f2

…b/NCBITaxonomy.jl into feature/speedup-groupdb

🦆 make sure name is a String

3ebcc5a

🚧 allow missings

46f8a52

🐛 return data frame for filtering on multiple divisions

79e2dde

⚡ authority

de7c441

⚡ nametools

2653d79

🦆 remove all union{missing} from the taxonomy table

9180a31

⚡ pre-split the division table

4a04f30

🦆 remove Abstract from strings

a1599a7

PoisotLab deleted a comment from github-actions bot Mar 5, 2023

⚡ taxon by id speedup

3eda3e7

PoisotLab deleted a comment from github-actions bot Mar 5, 2023

Merge branch 'main' into feature/speedup-groupdb

bc82012

Performance improvements with smarter handling of raw data #57

Are you sure you want to change the base?

Performance improvements with smarter handling of raw data #57

Conversation

tpoisot commented Mar 4, 2023

tpoisot commented Mar 4, 2023

github-actions bot commented Mar 5, 2023

Judge result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Results

Benchmark Group List

Julia versioninfo

Target

Baseline

Target result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Results

Benchmark Group List

Julia versioninfo

Baseline result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Results

Benchmark Group List

Julia versioninfo

Runtime information

github-actions bot commented Mar 12, 2025

Judge result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Results

Benchmark Group List

Julia versioninfo

Target

Baseline

Target result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Results

Benchmark Group List

Julia versioninfo

Baseline result

Benchmark Report for /home/runner/work/NCBITaxonomy.jl/NCBITaxonomy.jl

Job Properties

Results

Benchmark Group List

Julia versioninfo

Runtime information