Ripserer.jl
Ripserer.jl copied to clipboard
Published
20 hours ago •
mtsch
mtsch
Better homology
- Improvements to the homology algorithm:
- compute infinite intervals by tracking potential birth simplex candidates.
- use these candidates to stop the reduction early if possible.
- Some code reorganization.
Benchmark result
Judge result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmarks:
- Target: 3 Apr 2024 - 11:49
- Baseline: 3 Apr 2024 - 11:52
- Package commits:
- Target: b8bcc5
- Baseline: 3f2d63
- Julia commits:
- Target: bd47ec
- Baseline: bd47ec
- 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 :x:), while a ratio less
than 1.0 denotes a possible improvement (marked with :white_check_mark:). 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 |
|---|---|---|
["homology", "klein200.pts"] |
0.99 (5%) | 0.92 (1%) :white_check_mark: |
["homology", "lena1024.dipha"] |
1.12 (5%) :x: | 0.96 (1%) :white_check_mark: |
["homology", "sphere100.pts"] |
1.01 (5%) | 0.95 (1%) :white_check_mark: |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Target
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 3242 MHz 959 s 0 s 106 s 3429 s 0 s
#2 3225 MHz 975 s 0 s 103 s 3414 s 0 s
#3 2445 MHz 1233 s 0 s 127 s 3125 s 0 s
#4 2445 MHz 846 s 0 s 108 s 3533 s 0 s
Memory: 15.606498718261719 GB (13659.140625 MB free)
Uptime: 451.75 sec
Load Avg: 1.1 0.95 0.45
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Baseline
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 3240 MHz 1424 s 0 s 129 s 4676 s 0 s
#2 2601 MHz 1544 s 0 s 124 s 4559 s 0 s
#3 2445 MHz 1652 s 0 s 147 s 4420 s 0 s
#4 3243 MHz 1106 s 0 s 126 s 4989 s 0 s
Memory: 15.606498718261719 GB (13653.24609375 MB free)
Uptime: 625.43 sec
Load Avg: 1.07 0.99 0.56
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Target result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmark: 3 Apr 2024 - 11:49
- Package commit: b8bcc5
- Julia commit: bd47ec
- 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 |
|---|---|---|---|---|
["alpha", "klein500.pts"] |
7.421 s (5%) | 193.447 ms | 2.72 GiB (1%) | 25741846 |
["alpha", "torus10k.pts"] |
2.146 s (5%) | 37.549 ms | 828.85 MiB (1%) | 7915108 |
["cubical", "bonsai64.dipha"] |
1.435 s (5%) | 16.900 ms | 299.73 MiB (1%) | 284200 |
["cubical", "lena2048.dipha"] |
4.023 s (5%) | 322.999 ms | 1.62 GiB (1%) | 4275722 |
["homology", "klein200.pts"] |
8.120 ms (5%) | 2.87 MiB (1%) | 9101 | |
["homology", "lena1024.dipha"] |
1.827 s (5%) | 150.267 ms | 446.60 MiB (1%) | 1201341 |
["homology", "sphere100.pts"] |
108.167 ms (5%) | 34.44 MiB (1%) | 135726 | |
["rips", "dense", "dragon2000.pts"] |
2.073 s (5%) | 132.218 ms | 281.87 MiB (1%) | 11410 |
["rips", "dense", "fract-r.dist"] |
12.679 s (5%) | 270.361 ms | 1.98 GiB (1%) | 5106 |
["rips", "dense", "o3_1024.pts"] |
2.576 s (5%) | 26.745 ms | 288.30 MiB (1%) | 6123 |
["rips", "sparse", "alpha_4_sphere_2000.spdist"] |
4.143 s (5%) | 366.54 MiB (1%) | 8662 | |
["rips", "sparse", "dragon2000.pts"] |
2.368 s (5%) | 126.077 ms | 312.23 MiB (1%) | 7407 |
["rips", "sparse", "fract-r.dist"] |
14.534 s (5%) | 277.619 ms | 1.98 GiB (1%) | 4079 |
["rips", "sparse", "o3_1024.pts"] |
1.975 s (5%) | 135.032 ms | 296.22 MiB (1%) | 4070 |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 3242 MHz 959 s 0 s 106 s 3429 s 0 s
#2 3225 MHz 975 s 0 s 103 s 3414 s 0 s
#3 2445 MHz 1233 s 0 s 127 s 3125 s 0 s
#4 2445 MHz 846 s 0 s 108 s 3533 s 0 s
Memory: 15.606498718261719 GB (13659.140625 MB free)
Uptime: 451.75 sec
Load Avg: 1.1 0.95 0.45
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Baseline result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmark: 3 Apr 2024 - 11:52
- Package commit: 3f2d63
- Julia commit: bd47ec
- 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 |
|---|---|---|---|---|
["alpha", "klein500.pts"] |
7.502 s (5%) | 202.511 ms | 2.72 GiB (1%) | 25741846 |
["alpha", "torus10k.pts"] |
2.099 s (5%) | 35.666 ms | 828.85 MiB (1%) | 7915108 |
["cubical", "bonsai64.dipha"] |
1.457 s (5%) | 17.191 ms | 299.73 MiB (1%) | 284200 |
["cubical", "lena2048.dipha"] |
4.063 s (5%) | 327.377 ms | 1.62 GiB (1%) | 4275722 |
["homology", "klein200.pts"] |
8.200 ms (5%) | 3.11 MiB (1%) | 9100 | |
["homology", "lena1024.dipha"] |
1.632 s (5%) | 35.319 ms | 466.16 MiB (1%) | 1201338 |
["homology", "sphere100.pts"] |
106.862 ms (5%) | 36.06 MiB (1%) | 135724 | |
["rips", "dense", "dragon2000.pts"] |
2.080 s (5%) | 134.606 ms | 281.87 MiB (1%) | 11410 |
["rips", "dense", "fract-r.dist"] |
12.748 s (5%) | 276.644 ms | 1.98 GiB (1%) | 5106 |
["rips", "dense", "o3_1024.pts"] |
2.619 s (5%) | 137.419 ms | 288.30 MiB (1%) | 6123 |
["rips", "sparse", "alpha_4_sphere_2000.spdist"] |
4.118 s (5%) | 366.54 MiB (1%) | 8662 | |
["rips", "sparse", "dragon2000.pts"] |
2.353 s (5%) | 118.978 ms | 312.23 MiB (1%) | 7407 |
["rips", "sparse", "fract-r.dist"] |
14.573 s (5%) | 276.561 ms | 1.98 GiB (1%) | 4079 |
["rips", "sparse", "o3_1024.pts"] |
1.990 s (5%) | 136.552 ms | 296.22 MiB (1%) | 4070 |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 3240 MHz 1424 s 0 s 129 s 4676 s 0 s
#2 2601 MHz 1544 s 0 s 124 s 4559 s 0 s
#3 2445 MHz 1652 s 0 s 147 s 4420 s 0 s
#4 3243 MHz 1106 s 0 s 126 s 4989 s 0 s
Memory: 15.606498718261719 GB (13653.24609375 MB free)
Uptime: 625.43 sec
Load Avg: 1.07 0.99 0.56
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (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: 4890.84
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 invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves 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 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
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 |
![github-actions[bot] avatar](https://avatars.githubusercontent.com/in/15368?v=4 "Published by a pub.dev verified publisher"){kind=small}
Benchmark result
Judge result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmarks:
- Target: 3 Apr 2024 - 11:57
- Baseline: 3 Apr 2024 - 12:00
- Package commits:
- Target: f56efb
- Baseline: 3f2d63
- Julia commits:
- Target: bd47ec
- Baseline: bd47ec
- 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 :x:), while a ratio less
than 1.0 denotes a possible improvement (marked with :white_check_mark:). 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 |
|---|---|---|
["homology", "klein200.pts"] |
0.98 (5%) | 0.92 (1%) :white_check_mark: |
["homology", "lena1024.dipha"] |
1.05 (5%) :x: | 0.96 (1%) :white_check_mark: |
["homology", "sphere100.pts"] |
0.95 (5%) :white_check_mark: | 0.95 (1%) :white_check_mark: |
["rips", "dense", "o3_1024.pts"] |
0.94 (5%) :white_check_mark: | 1.00 (1%) |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Target
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 2445 MHz 1068 s 0 s 103 s 2485 s 0 s
#2 2445 MHz 1347 s 0 s 120 s 2190 s 0 s
#3 3270 MHz 963 s 0 s 127 s 2580 s 0 s
#4 3242 MHz 707 s 0 s 103 s 2848 s 0 s
Memory: 15.606498718261719 GB (13683.07421875 MB free)
Uptime: 369.09 sec
Load Avg: 1.19 1.04 0.51
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Baseline
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 2582 MHz 1283 s 0 s 116 s 4037 s 0 s
#2 2445 MHz 1603 s 0 s 144 s 3691 s 0 s
#3 2445 MHz 1725 s 0 s 146 s 3581 s 0 s
#4 3241 MHz 1235 s 0 s 129 s 4075 s 0 s
Memory: 15.606498718261719 GB (13635.31640625 MB free)
Uptime: 547.48 sec
Load Avg: 1.03 1.03 0.61
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Target result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmark: 3 Apr 2024 - 11:57
- Package commit: f56efb
- Julia commit: bd47ec
- 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 |
|---|---|---|---|---|
["alpha", "klein500.pts"] |
7.630 s (5%) | 199.761 ms | 2.72 GiB (1%) | 25741846 |
["alpha", "torus10k.pts"] |
2.164 s (5%) | 39.933 ms | 828.85 MiB (1%) | 7915108 |
["cubical", "bonsai64.dipha"] |
1.489 s (5%) | 21.423 ms | 299.73 MiB (1%) | 284200 |
["cubical", "lena2048.dipha"] |
4.103 s (5%) | 333.912 ms | 1.62 GiB (1%) | 4275722 |
["homology", "klein200.pts"] |
8.027 ms (5%) | 2.87 MiB (1%) | 9101 | |
["homology", "lena1024.dipha"] |
1.779 s (5%) | 151.255 ms | 446.60 MiB (1%) | 1201341 |
["homology", "sphere100.pts"] |
105.618 ms (5%) | 34.44 MiB (1%) | 135726 | |
["rips", "dense", "dragon2000.pts"] |
2.107 s (5%) | 145.828 ms | 281.87 MiB (1%) | 11410 |
["rips", "dense", "fract-r.dist"] |
13.659 s (5%) | 287.129 ms | 1.98 GiB (1%) | 5106 |
["rips", "dense", "o3_1024.pts"] |
2.533 s (5%) | 29.541 ms | 288.30 MiB (1%) | 6123 |
["rips", "sparse", "alpha_4_sphere_2000.spdist"] |
4.100 s (5%) | 366.54 MiB (1%) | 8662 | |
["rips", "sparse", "dragon2000.pts"] |
2.353 s (5%) | 123.388 ms | 312.23 MiB (1%) | 7407 |
["rips", "sparse", "fract-r.dist"] |
14.847 s (5%) | 286.042 ms | 1.98 GiB (1%) | 4079 |
["rips", "sparse", "o3_1024.pts"] |
2.065 s (5%) | 143.599 ms | 296.22 MiB (1%) | 4070 |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 2445 MHz 1068 s 0 s 103 s 2485 s 0 s
#2 2445 MHz 1347 s 0 s 120 s 2190 s 0 s
#3 3270 MHz 963 s 0 s 127 s 2580 s 0 s
#4 3242 MHz 707 s 0 s 103 s 2848 s 0 s
Memory: 15.606498718261719 GB (13683.07421875 MB free)
Uptime: 369.09 sec
Load Avg: 1.19 1.04 0.51
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Baseline result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmark: 3 Apr 2024 - 12:0
- Package commit: 3f2d63
- Julia commit: bd47ec
- 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 |
|---|---|---|---|---|
["alpha", "klein500.pts"] |
7.581 s (5%) | 223.598 ms | 2.72 GiB (1%) | 25741846 |
["alpha", "torus10k.pts"] |
2.115 s (5%) | 39.649 ms | 828.85 MiB (1%) | 7915108 |
["cubical", "bonsai64.dipha"] |
1.499 s (5%) | 16.636 ms | 299.73 MiB (1%) | 284200 |
["cubical", "lena2048.dipha"] |
4.290 s (5%) | 337.823 ms | 1.62 GiB (1%) | 4275722 |
["homology", "klein200.pts"] |
8.193 ms (5%) | 3.11 MiB (1%) | 9100 | |
["homology", "lena1024.dipha"] |
1.691 s (5%) | 35.135 ms | 466.16 MiB (1%) | 1201338 |
["homology", "sphere100.pts"] |
111.525 ms (5%) | 36.06 MiB (1%) | 135724 | |
["rips", "dense", "dragon2000.pts"] |
2.146 s (5%) | 142.872 ms | 281.87 MiB (1%) | 11410 |
["rips", "dense", "fract-r.dist"] |
13.388 s (5%) | 294.759 ms | 1.98 GiB (1%) | 5106 |
["rips", "dense", "o3_1024.pts"] |
2.687 s (5%) | 145.082 ms | 288.30 MiB (1%) | 6123 |
["rips", "sparse", "alpha_4_sphere_2000.spdist"] |
4.284 s (5%) | 366.54 MiB (1%) | 8662 | |
["rips", "sparse", "dragon2000.pts"] |
2.344 s (5%) | 121.669 ms | 312.23 MiB (1%) | 7407 |
["rips", "sparse", "fract-r.dist"] |
14.991 s (5%) | 298.351 ms | 1.98 GiB (1%) | 4079 |
["rips", "sparse", "o3_1024.pts"] |
2.099 s (5%) | 143.919 ms | 296.22 MiB (1%) | 4070 |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 2582 MHz 1283 s 0 s 116 s 4037 s 0 s
#2 2445 MHz 1603 s 0 s 144 s 3691 s 0 s
#3 2445 MHz 1725 s 0 s 146 s 3581 s 0 s
#4 3241 MHz 1235 s 0 s 129 s 4075 s 0 s
Memory: 15.606498718261719 GB (13635.31640625 MB free)
Uptime: 547.48 sec
Load Avg: 1.03 1.03 0.61
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (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: 4890.86
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 invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves 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 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
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 |
Benchmark result
Judge result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmarks:
- Target: 3 Apr 2024 - 20:31
- Baseline: 3 Apr 2024 - 20:34
- Package commits:
- Target: 1b04ee
- Baseline: 3f2d63
- Julia commits:
- Target: bd47ec
- Baseline: bd47ec
- 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 :x:), while a ratio less
than 1.0 denotes a possible improvement (marked with :white_check_mark:). 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 |
|---|---|---|
["cubical", "bonsai64.dipha"] |
0.85 (5%) :white_check_mark: | 1.00 (1%) |
["cubical", "lena2048.dipha"] |
0.79 (5%) :white_check_mark: | 1.00 (1%) |
["homology", "klein200.pts"] |
1.01 (5%) | 0.92 (1%) :white_check_mark: |
["homology", "lena1024.dipha"] |
1.00 (5%) | 0.96 (1%) :white_check_mark: |
["homology", "sphere100.pts"] |
0.97 (5%) | 0.95 (1%) :white_check_mark: |
["rips", "sparse", "dragon2000.pts"] |
0.87 (5%) :white_check_mark: | 1.00 (1%) |
["rips", "sparse", "fract-r.dist"] |
0.90 (5%) :white_check_mark: | 1.00 (1%) |
["rips", "sparse", "o3_1024.pts"] |
0.92 (5%) :white_check_mark: | 1.00 (1%) |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Target
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 3242 MHz 1168 s 0 s 111 s 3594 s 0 s
#2 3267 MHz 1111 s 0 s 112 s 3667 s 0 s
#3 2445 MHz 973 s 0 s 119 s 3785 s 0 s
#4 2589 MHz 802 s 0 s 120 s 3966 s 0 s
Memory: 15.606498718261719 GB (13602.51171875 MB free)
Uptime: 491.41 sec
Load Avg: 1.14 1.0 0.47
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Baseline
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 3162 MHz 2085 s 0 s 136 s 4485 s 0 s
#2 2445 MHz 1826 s 0 s 131 s 4765 s 0 s
#3 3229 MHz 1124 s 0 s 133 s 5451 s 0 s
#4 3243 MHz 832 s 0 s 144 s 5743 s 0 s
Memory: 15.606498718261719 GB (13597.375 MB free)
Uptime: 674.81 sec
Load Avg: 1.04 1.02 0.58
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Target result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmark: 3 Apr 2024 - 20:31
- Package commit: 1b04ee
- Julia commit: bd47ec
- 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 |
|---|---|---|---|---|
["alpha", "klein500.pts"] |
7.470 s (5%) | 264.297 ms | 2.72 GiB (1%) | 25741846 |
["alpha", "torus10k.pts"] |
2.112 s (5%) | 38.700 ms | 828.85 MiB (1%) | 7915108 |
["cubical", "bonsai64.dipha"] |
1.500 s (5%) | 40.600 ms | 299.73 MiB (1%) | 284200 |
["cubical", "lena2048.dipha"] |
4.089 s (5%) | 336.289 ms | 1.62 GiB (1%) | 4275722 |
["homology", "klein200.pts"] |
8.377 ms (5%) | 2.87 MiB (1%) | 9101 | |
["homology", "lena1024.dipha"] |
1.811 s (5%) | 154.752 ms | 446.60 MiB (1%) | 1201341 |
["homology", "sphere100.pts"] |
106.693 ms (5%) | 34.44 MiB (1%) | 135726 | |
["rips", "dense", "dragon2000.pts"] |
2.084 s (5%) | 137.886 ms | 281.87 MiB (1%) | 11410 |
["rips", "dense", "fract-r.dist"] |
12.981 s (5%) | 283.632 ms | 1.98 GiB (1%) | 5106 |
["rips", "dense", "o3_1024.pts"] |
2.483 s (5%) | 28.189 ms | 288.30 MiB (1%) | 6123 |
["rips", "sparse", "alpha_4_sphere_2000.spdist"] |
4.110 s (5%) | 366.54 MiB (1%) | 8662 | |
["rips", "sparse", "dragon2000.pts"] |
2.363 s (5%) | 123.547 ms | 312.23 MiB (1%) | 7407 |
["rips", "sparse", "fract-r.dist"] |
14.621 s (5%) | 285.797 ms | 1.98 GiB (1%) | 4079 |
["rips", "sparse", "o3_1024.pts"] |
1.986 s (5%) | 138.836 ms | 296.22 MiB (1%) | 4070 |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 3242 MHz 1168 s 0 s 111 s 3594 s 0 s
#2 3267 MHz 1111 s 0 s 112 s 3667 s 0 s
#3 2445 MHz 973 s 0 s 119 s 3785 s 0 s
#4 2589 MHz 802 s 0 s 120 s 3966 s 0 s
Memory: 15.606498718261719 GB (13602.51171875 MB free)
Uptime: 491.41 sec
Load Avg: 1.14 1.0 0.47
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Baseline result
Benchmark Report for /home/runner/work/Ripserer.jl/Ripserer.jl
Job Properties
- Time of benchmark: 3 Apr 2024 - 20:34
- Package commit: 3f2d63
- Julia commit: bd47ec
- 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 |
|---|---|---|---|---|
["alpha", "klein500.pts"] |
7.683 s (5%) | 441.825 ms | 2.72 GiB (1%) | 25741846 |
["alpha", "torus10k.pts"] |
2.127 s (5%) | 37.902 ms | 828.85 MiB (1%) | 7915108 |
["cubical", "bonsai64.dipha"] |
1.763 s (5%) | 21.381 ms | 299.73 MiB (1%) | 284200 |
["cubical", "lena2048.dipha"] |
5.168 s (5%) | 426.174 ms | 1.62 GiB (1%) | 4275722 |
["homology", "klein200.pts"] |
8.291 ms (5%) | 3.11 MiB (1%) | 9100 | |
["homology", "lena1024.dipha"] |
1.811 s (5%) | 153.981 ms | 466.16 MiB (1%) | 1201338 |
["homology", "sphere100.pts"] |
109.512 ms (5%) | 36.06 MiB (1%) | 135724 | |
["rips", "dense", "dragon2000.pts"] |
2.090 s (5%) | 147.300 ms | 281.87 MiB (1%) | 11410 |
["rips", "dense", "fract-r.dist"] |
13.068 s (5%) | 305.215 ms | 1.98 GiB (1%) | 5106 |
["rips", "dense", "o3_1024.pts"] |
2.613 s (5%) | 148.274 ms | 288.30 MiB (1%) | 6123 |
["rips", "sparse", "alpha_4_sphere_2000.spdist"] |
4.297 s (5%) | 366.54 MiB (1%) | 8662 | |
["rips", "sparse", "dragon2000.pts"] |
2.703 s (5%) | 177.690 ms | 312.23 MiB (1%) | 7407 |
["rips", "sparse", "fract-r.dist"] |
16.256 s (5%) | 344.683 ms | 1.98 GiB (1%) | 4079 |
["rips", "sparse", "o3_1024.pts"] |
2.155 s (5%) | 154.842 ms | 296.22 MiB (1%) | 4070 |
Benchmark Group List
Here's a list of all the benchmark groups executed by this job:
-
["alpha"] -
["cubical"] -
["homology"] -
["rips", "dense"] -
["rips", "sparse"]
Julia versioninfo
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
Ubuntu 22.04.4 LTS
uname: Linux 6.5.0-1016-azure #16~22.04.1-Ubuntu SMP Fri Feb 16 15:42:02 UTC 2024 x86_64 x86_64
CPU: AMD EPYC 7763 64-Core Processor:
speed user nice sys idle irq
#1 3162 MHz 2085 s 0 s 136 s 4485 s 0 s
#2 2445 MHz 1826 s 0 s 131 s 4765 s 0 s
#3 3229 MHz 1124 s 0 s 133 s 5451 s 0 s
#4 3243 MHz 832 s 0 s 144 s 5743 s 0 s
Memory: 15.606498718261719 GB (13597.375 MB free)
Uptime: 674.81 sec
Load Avg: 1.04 1.02 0.58
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (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: 4890.86
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 invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves 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 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
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 |
Pull Request Test Coverage Report for Build 8545078607
Details
- 245 of 250 (98.0%) changed or added relevant lines in 5 files are covered.
- 3 unchanged lines in 3 files lost coverage.
- Overall coverage increased (+0.09%) to 96.51%
| Changes Missing Coverage | Covered Lines | Changed/Added Lines | % |
|---|---|---|---|
| src/computation/homology.jl | 62 | 63 | 98.41% |
| src/filtrations/rips.jl | 2 | 3 | 66.67% |
| src/computation/involuted.jl | 42 | 45 | 93.33% |
| <!-- | Total: | 245 | 250 |
| Files with Coverage Reduction | New Missed Lines | % |
|---|---|---|
| src/filtrations/cubical.jl | 1 | 98.03% |
| src/base/simplexrecipes.jl | 1 | 66.13% |
| src/computation/utils.jl | 1 | 88.89% |
| <!-- | Total: | 3 |
| Totals | |
|---|---|
| Change from base Build 3797140729: | 0.09% |
| Covered Lines: | 1770 |
| Relevant Lines: | 1834 |
