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Add test case for repetitive values in batchextraction#186

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Add test case for repetitive values in batchextraction#186
felixcremer wants to merge 1 commit intomainfrom
fc/polygonbatchextract

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@felixcremer felixcremer commented Oct 12, 2022

This is a first testitem for the extraction of multiple pixels from the same site.

Currently using a Table with a column with repeating values just goes through and returns a YAXArray with a repetitive site Axis.
I would propose to return a dataset which has as cubes the different entries in the :site column and as axis values the longitude and latitude combinations.
This would also make working with Shapefiles much nicer, because you could use the CubeTable interface to generate the subsetting table.

This is a nice workflow, which could be enhanced by returning a cube per unique polygon value and it would also be good to have the ability to subset with all parts of the CubeTable at the same time.

julia> freqmasklarge  = cubefromshape(freqpath, getAxis("Y",allcube), getAxis("X", allcube), wrap=nothing)
julia> ctlarge = CubeTable(polygons = freqmasklarge)
julia> ctlargefiltered = TableOperations.filter.(x-> !ismissing(x.polygons),ctlarge)
julia> allcube[ctlargefiltered[1]]

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Benchmark result

Judge result

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

Job Properties

  • Time of benchmarks:
    • Target: 12 Oct 2022 - 15:32
    • Baseline: 12 Oct 2022 - 15:33
  • Package commits:
    • Target: f9fc21
    • Baseline: cd8cc6
  • Julia commits:
    • Target: 36034a
    • Baseline: 36034a
  • 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
["mapslices", "small"] 0.01 (5%) ✅ 0.16 (1%) ✅

Benchmark Group List

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

  • ["mapslices"]

Julia versioninfo

Target

Julia Version 1.8.2
Commit 36034abf260 (2022-09-29 15:21 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 20.04.5 LTS
  uname: Linux 5.15.0-1020-azure #25~20.04.1-Ubuntu SMP Thu Sep 1 19:20:56 UTC 2022 x86_64 x86_64
  CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: 
              speed         user         nice          sys         idle          irq
       #1  2095 MHz        938 s          0 s        153 s       1266 s          0 s
       #2  2095 MHz       1183 s          0 s        272 s        917 s          0 s
  Memory: 6.781253814697266 GB (4721.01171875 MB free)
  Uptime: 242.34 sec
  Load Avg:  1.47  1.07  0.47
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  Threads: 1 on 2 virtual cores

Baseline

Julia Version 1.8.2
Commit 36034abf260 (2022-09-29 15:21 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 20.04.5 LTS
  uname: Linux 5.15.0-1020-azure #25~20.04.1-Ubuntu SMP Thu Sep 1 19:20:56 UTC 2022 x86_64 x86_64
  CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: 
              speed         user         nice          sys         idle          irq
       #1  2095 MHz       1274 s          0 s        166 s       1298 s          0 s
       #2  2095 MHz       1220 s          0 s        274 s       1259 s          0 s
  Memory: 6.781253814697266 GB (4667.93359375 MB free)
  Uptime: 280.46 sec
  Load Avg:  1.26  1.06  0.49
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  Threads: 1 on 2 virtual cores

Target result

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

Job Properties

  • Time of benchmark: 12 Oct 2022 - 15:32
  • Package commit: f9fc21
  • Julia commit: 36034a
  • 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
["mapslices", "small"] 200.970 ms (5%) 1.931 ms 326.03 MiB (1%) 91534

Benchmark Group List

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

  • ["mapslices"]

Julia versioninfo

Julia Version 1.8.2
Commit 36034abf260 (2022-09-29 15:21 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 20.04.5 LTS
  uname: Linux 5.15.0-1020-azure #25~20.04.1-Ubuntu SMP Thu Sep 1 19:20:56 UTC 2022 x86_64 x86_64
  CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: 
              speed         user         nice          sys         idle          irq
       #1  2095 MHz        938 s          0 s        153 s       1266 s          0 s
       #2  2095 MHz       1183 s          0 s        272 s        917 s          0 s
  Memory: 6.781253814697266 GB (4721.01171875 MB free)
  Uptime: 242.34 sec
  Load Avg:  1.47  1.07  0.47
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  Threads: 1 on 2 virtual cores

Baseline result

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

Job Properties

  • Time of benchmark: 12 Oct 2022 - 15:33
  • Package commit: cd8cc6
  • Julia commit: 36034a
  • 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
["mapslices", "small"] 14.483 s (5%) 986.022 ms 1.93 GiB (1%) 30746014

Benchmark Group List

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

  • ["mapslices"]

Julia versioninfo

Julia Version 1.8.2
Commit 36034abf260 (2022-09-29 15:21 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 20.04.5 LTS
  uname: Linux 5.15.0-1020-azure #25~20.04.1-Ubuntu SMP Thu Sep 1 19:20:56 UTC 2022 x86_64 x86_64
  CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: 
              speed         user         nice          sys         idle          irq
       #1  2095 MHz       1274 s          0 s        166 s       1298 s          0 s
       #2  2095 MHz       1220 s          0 s        274 s       1259 s          0 s
  Memory: 6.781253814697266 GB (4667.93359375 MB free)
  Uptime: 280.46 sec
  Load Avg:  1.26  1.06  0.49
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  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
Byte Order:                      Little Endian
Address sizes:                   46 bits physical, 48 bits virtual
CPU(s):                          2
On-line CPU(s) list:             0,1
Thread(s) per core:              1
Core(s) per socket:              2
Socket(s):                       1
NUMA node(s):                    1
Vendor ID:                       GenuineIntel
CPU family:                      6
Model:                           85
Model name:                      Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz
Stepping:                        4
CPU MHz:                         2095.210
BogoMIPS:                        4190.42
Hypervisor vendor:               Microsoft
Virtualization type:             full
L1d cache:                       64 KiB
L1i cache:                       64 KiB
L2 cache:                        2 MiB
L3 cache:                        35.8 MiB
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:          Vulnerable
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
Vulnerability Srbds:             Not affected
Vulnerability Tsx async abort:   Mitigation; Clear CPU buffers; SMT Host state unknown
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 mpx avx512f avx512dq rdseed adx smap clflushopt avx512cd avx512bw avx512vl xsaveopt xsavec xsaves md_clear
Cpu Property Value
Brand Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz
Vendor :Intel
Architecture :Skylake
Model Family: 0x06, Model: 0x55, Stepping: 0x04, 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, 1024, 36608) kbytes
64 byte cache line size
Address Size 48 bits virtual, 46 bits physical
SIMD 512 bit = 64 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

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