Performance improvements with smarter handling of raw data

[tpoisot]

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

[tpoisot]

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

[github-actions]

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	GC 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	GC 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