Add Doctest infra and add doctests to EpiAwareUtils #332

seabbs · 2024-07-04T16:34:32Z

As the title this PR makes a start on resolving #48 by adding doctests to @testitem and adding some to code base for EpiAwareUtils

After looking into it it doesn't look like there is a way to make sure example code is being run in docstrings unless we use doctests and definitely not if we want the output in Documenter (which I think we do to guide our users).

github-actions · 2024-07-04T16:41:20Z

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmarks:
- Target: 4 Jul 2024 - 16:40
- Baseline: 4 Jul 2024 - 16:41
Package commits:
- Target: e2623d
- Baseline: 849b70
Julia commits:
- Target: 48d4fd
- Baseline: 48d4fd
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

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Target

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2594 MHz       2429 s          0 s        244 s       2421 s          0 s
       #2  2445 MHz       2453 s          0 s        237 s       2403 s          0 s
       #3  3241 MHz       2390 s          0 s        248 s       2421 s          0 s
       #4  2445 MHz       2507 s          0 s        242 s       2340 s          0 s
  Memory: 15.606491088867188 GB (14037.6953125 MB free)
  Uptime: 512.21 sec
  Load Avg:  2.43  2.61  1.27
  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 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3071 MHz       2502 s          0 s        252 s       2614 s          0 s
       #2  3199 MHz       2546 s          0 s        241 s       2579 s          0 s
       #3  2445 MHz       2451 s          0 s        252 s       2630 s          0 s
       #4  3242 MHz       2543 s          0 s        247 s       2574 s          0 s
  Memory: 15.606491088867188 GB (14023.87109375 MB free)
  Uptime: 539.64 sec
  Load Avg:  2.01  2.5  1.26
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 4 Jul 2024 - 16:40
Package commit: e2623d
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.095 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2594 MHz       2429 s          0 s        244 s       2421 s          0 s
       #2  2445 MHz       2453 s          0 s        237 s       2403 s          0 s
       #3  3241 MHz       2390 s          0 s        248 s       2421 s          0 s
       #4  2445 MHz       2507 s          0 s        242 s       2340 s          0 s
  Memory: 15.606491088867188 GB (14037.6953125 MB free)
  Uptime: 512.21 sec
  Load Avg:  2.43  2.61  1.27
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 4 Jul 2024 - 16:41
Package commit: 849b70
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.101 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3071 MHz       2502 s          0 s        252 s       2614 s          0 s
       #2  3199 MHz       2546 s          0 s        241 s       2579 s          0 s
       #3  2445 MHz       2451 s          0 s        252 s       2630 s          0 s
       #4  3242 MHz       2543 s          0 s        247 s       2574 s          0 s
  Memory: 15.606491088867188 GB (14023.87109375 MB free)
  Uptime: 539.64 sec
  Load Avg:  2.01  2.5  1.26
  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:                           4890.85
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 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; 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

github-actions · 2024-07-04T17:00:17Z

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmarks:
- Target: 4 Jul 2024 - 16:59
- Baseline: 4 Jul 2024 - 17:00
Package commits:
- Target: ca9e11
- Baseline: 849b70
Julia commits:
- Target: 48d4fd
- Baseline: 48d4fd
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

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Target

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz        350 s          0 s         66 s       2200 s          0 s
       #2  2445 MHz        418 s          0 s         70 s       2125 s          0 s
       #3  3273 MHz        349 s          0 s         88 s       2165 s          0 s
       #4  3243 MHz        311 s          0 s         76 s       2207 s          0 s
  Memory: 15.606491088867188 GB (14114.94140625 MB free)
  Uptime: 264.82 sec
  Load Avg:  1.32  0.51  0.2
  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 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3244 MHz        398 s          0 s         72 s       2423 s          0 s
       #2  3280 MHz        439 s          0 s         73 s       2377 s          0 s
       #3  3053 MHz        445 s          0 s         93 s       2340 s          0 s
       #4  3173 MHz        411 s          0 s         84 s       2377 s          0 s
  Memory: 15.606491088867188 GB (14049.9375 MB free)
  Uptime: 292.48 sec
  Load Avg:  1.19  0.56  0.22
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 4 Jul 2024 - 16:59
Package commit: ca9e11
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.099 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz        350 s          0 s         66 s       2200 s          0 s
       #2  2445 MHz        418 s          0 s         70 s       2125 s          0 s
       #3  3273 MHz        349 s          0 s         88 s       2165 s          0 s
       #4  3243 MHz        311 s          0 s         76 s       2207 s          0 s
  Memory: 15.606491088867188 GB (14114.94140625 MB free)
  Uptime: 264.82 sec
  Load Avg:  1.32  0.51  0.2
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 4 Jul 2024 - 17:0
Package commit: 849b70
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.098 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3244 MHz        398 s          0 s         72 s       2423 s          0 s
       #2  3280 MHz        439 s          0 s         73 s       2377 s          0 s
       #3  3053 MHz        445 s          0 s         93 s       2340 s          0 s
       #4  3173 MHz        411 s          0 s         84 s       2377 s          0 s
  Memory: 15.606491088867188 GB (14049.9375 MB free)
  Uptime: 292.48 sec
  Load Avg:  1.19  0.56  0.22
  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; 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

github-actions · 2024-07-04T17:23:56Z

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmarks:
- Target: 4 Jul 2024 - 17:23
- Baseline: 4 Jul 2024 - 17:23
Package commits:
- Target: 4e0add
- Baseline: 849b70
Julia commits:
- Target: 48d4fd
- Baseline: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	0.93 (5%) ✅	1.00 (1%)

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Target

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3151 MHz        303 s          0 s         77 s       2916 s          0 s
       #2  2608 MHz        339 s          0 s         67 s       2869 s          0 s
       #3  3241 MHz        371 s          0 s         76 s       2856 s          0 s
       #4  2445 MHz        348 s          0 s         71 s       2887 s          0 s
  Memory: 15.606491088867188 GB (14092.24609375 MB free)
  Uptime: 333.0 sec
  Load Avg:  1.3  0.5  0.2
  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 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3160 MHz        387 s          0 s         79 s       3097 s          0 s
       #2  2607 MHz        394 s          0 s         71 s       3076 s          0 s
       #3  3242 MHz        420 s          0 s         83 s       3067 s          0 s
       #4  2445 MHz        416 s          0 s         76 s       3081 s          0 s
  Memory: 15.606491088867188 GB (14045.95703125 MB free)
  Uptime: 359.74 sec
  Load Avg:  1.2  0.54  0.22
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 4 Jul 2024 - 17:23
Package commit: 4e0add
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.015 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3151 MHz        303 s          0 s         77 s       2916 s          0 s
       #2  2608 MHz        339 s          0 s         67 s       2869 s          0 s
       #3  3241 MHz        371 s          0 s         76 s       2856 s          0 s
       #4  2445 MHz        348 s          0 s         71 s       2887 s          0 s
  Memory: 15.606491088867188 GB (14092.24609375 MB free)
  Uptime: 333.0 sec
  Load Avg:  1.3  0.5  0.2
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 4 Jul 2024 - 17:23
Package commit: 849b70
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.096 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3160 MHz        387 s          0 s         79 s       3097 s          0 s
       #2  2607 MHz        394 s          0 s         71 s       3076 s          0 s
       #3  3242 MHz        420 s          0 s         83 s       3067 s          0 s
       #4  2445 MHz        416 s          0 s         76 s       3081 s          0 s
  Memory: 15.606491088867188 GB (14045.95703125 MB free)
  Uptime: 359.74 sec
  Load Avg:  1.2  0.54  0.22
  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; 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

github-actions · 2024-07-05T09:52:54Z

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmarks:
- Target: 5 Jul 2024 - 09:52
- Baseline: 5 Jul 2024 - 09:52
Package commits:
- Target: 97dca0
- Baseline: 849b70
Julia commits:
- Target: 48d4fd
- Baseline: 48d4fd
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

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Target

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3253 MHz       2438 s          0 s        216 s       2621 s          0 s
       #2  3242 MHz       2493 s          0 s        250 s       2550 s          0 s
       #3  3244 MHz       2401 s          0 s        235 s       2640 s          0 s
       #4  2445 MHz       2359 s          0 s        241 s       2690 s          0 s
  Memory: 15.606491088867188 GB (14068.265625 MB free)
  Uptime: 531.54 sec
  Load Avg:  2.45  2.58  1.25
  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 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       2477 s          0 s        220 s       2849 s          0 s
       #2  2591 MHz       2597 s          0 s        252 s       2716 s          0 s
       #3  2445 MHz       2496 s          0 s        243 s       2810 s          0 s
       #4  3243 MHz       2381 s          0 s        244 s       2937 s          0 s
  Memory: 15.606491088867188 GB (14083.8203125 MB free)
  Uptime: 558.84 sec
  Load Avg:  1.95  2.46  1.24
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 5 Jul 2024 - 9:52
Package commit: 97dca0
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.096 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3253 MHz       2438 s          0 s        216 s       2621 s          0 s
       #2  3242 MHz       2493 s          0 s        250 s       2550 s          0 s
       #3  3244 MHz       2401 s          0 s        235 s       2640 s          0 s
       #4  2445 MHz       2359 s          0 s        241 s       2690 s          0 s
  Memory: 15.606491088867188 GB (14068.265625 MB free)
  Uptime: 531.54 sec
  Load Avg:  2.45  2.58  1.25
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 5 Jul 2024 - 9:52
Package commit: 849b70
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.097 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       2477 s          0 s        220 s       2849 s          0 s
       #2  2591 MHz       2597 s          0 s        252 s       2716 s          0 s
       #3  2445 MHz       2496 s          0 s        243 s       2810 s          0 s
       #4  3243 MHz       2381 s          0 s        244 s       2937 s          0 s
  Memory: 15.606491088867188 GB (14083.8203125 MB free)
  Uptime: 558.84 sec
  Load Avg:  1.95  2.46  1.24
  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:                           4890.87
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; 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

github-actions · 2024-07-05T10:27:02Z

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmarks:
- Target: 5 Jul 2024 - 10:26
- Baseline: 5 Jul 2024 - 10:26
Package commits:
- Target: b66230
- Baseline: 849b70
Julia commits:
- Target: 48d4fd
- Baseline: 48d4fd
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

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Target

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2672 MHz        250 s          0 s         74 s       3023 s          0 s
       #2  3106 MHz        394 s          0 s         72 s       2875 s          0 s
       #3  3242 MHz        414 s          0 s         77 s       2863 s          0 s
       #4  3156 MHz        290 s          0 s         75 s       2969 s          0 s
  Memory: 15.606491088867188 GB (14101.4609375 MB free)
  Uptime: 338.4 sec
  Load Avg:  1.3  0.53  0.22
  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 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz        354 s          0 s         82 s       3191 s          0 s
       #2  3242 MHz        477 s          0 s         75 s       3069 s          0 s
       #3  2445 MHz        471 s          0 s         81 s       3081 s          0 s
       #4  2594 MHz        315 s          0 s         79 s       3219 s          0 s
  Memory: 15.606491088867188 GB (14041.26171875 MB free)
  Uptime: 366.45 sec
  Load Avg:  1.18  0.58  0.24
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 5 Jul 2024 - 10:26
Package commit: b66230
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.102 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2672 MHz        250 s          0 s         74 s       3023 s          0 s
       #2  3106 MHz        394 s          0 s         72 s       2875 s          0 s
       #3  3242 MHz        414 s          0 s         77 s       2863 s          0 s
       #4  3156 MHz        290 s          0 s         75 s       2969 s          0 s
  Memory: 15.606491088867188 GB (14101.4609375 MB free)
  Uptime: 338.4 sec
  Load Avg:  1.3  0.53  0.22
  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/Rt-without-renewal/Rt-without-renewal

Job Properties

Time of benchmark: 5 Jul 2024 - 10:26
Package commit: 849b70
Julia commit: 48d4fd
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
`["EpiAwareUtils", "censored_pmf"]`	1.102 μs (5%)		352 bytes (1%)	4

Benchmark Group List

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

["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz        354 s          0 s         82 s       3191 s          0 s
       #2  3242 MHz        477 s          0 s         75 s       3069 s          0 s
       #3  2445 MHz        471 s          0 s         81 s       3081 s          0 s
       #4  2594 MHz        315 s          0 s         79 s       3219 s          0 s
  Memory: 15.606491088867188 GB (14041.26171875 MB free)
  Uptime: 366.45 sec
  Load Avg:  1.18  0.58  0.24
  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; 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

codecov-commenter · 2024-07-05T10:37:48Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.18%. Comparing base (849b707) to head (21e093a).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #332   +/-   ##
=======================================
  Coverage   93.18%   93.18%           
=======================================
  Files          50       50           
  Lines         528      528           
=======================================
  Hits          492      492           
  Misses         36       36

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

SamuelBrand1

This is good stuff. Noting #333 issue, which is very irritating but worth moving forwards here and trying to add more complicated doctests later.

seabbs added 7 commits July 4, 2024 15:55

add doctest infra and add doctests for censored_pmf

d419afe

add the right environment

48dba73

use StableRNGs

78c0969

add doctests for HalfNormal

9df2418

add prefix doctest

3c28a53

add doctest for scan

60437b1

turn doc building back on

c85e60e

seabbs requested a review from SamuelBrand1 July 4, 2024 16:34

seabbs enabled auto-merge July 4, 2024 16:34

move new docstring deps to test as this is the only place they are run

53c8a48

Add mcmcchains

077029c

seabbs added 2 commits July 4, 2024 18:38

don't try and match random numbers instead just make sure itsa number

8884418

use @doc raw

f718cc5

seabbs added 2 commits July 5, 2024 11:12

stop trying to fix the seed in doctests

c0efa1f

remove failing doc test for now

21e093a

SamuelBrand1 approved these changes Jul 5, 2024

View reviewed changes

seabbs added this pull request to the merge queue Jul 5, 2024

Merged via the queue into main with commit df3f7d7 Jul 5, 2024
11 checks passed

seabbs deleted the add-doctests branch July 5, 2024 11:26

Add Doctest infra and add doctests to EpiAwareUtils #332

Add Doctest infra and add doctests to EpiAwareUtils #332

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seabbs commented Jul 4, 2024 • edited Loading

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seabbs commented Jul 4, 2024 •

edited

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