Better getting started with julia documentation #301

SamuelBrand1 · 2024-06-25T15:48:44Z

This PR adds a "Getting Started with using Julia in Projects" page to the documentation which gives an (opinionated) guide to setting up Julia for project development.

Closes #277 .

This PR doesn't change the README.md file for EpiAware, although I'm happy to do another quick PR to update that and give a link to the page if this PR is accepted.

@damonbayer I'd be interested in your thoughts/preferences here.

…contributing.md

github-actions · 2024-06-25T15:56:50Z

Benchmark result

Judge result

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

Job Properties

Time of benchmarks:
- Target: 25 Jun 2024 - 15:56
- Baseline: 25 Jun 2024 - 15:56
Package commits:
- Target: 6a875d
- Baseline: 816622
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  2789 MHz       2542 s          0 s        267 s       2624 s          0 s
       #2  2568 MHz       2498 s          0 s        252 s       2692 s          0 s
       #3  3243 MHz       2480 s          0 s        265 s       2681 s          0 s
       #4  2445 MHz       2503 s          0 s        290 s       2650 s          0 s
  Memory: 15.606487274169922 GB (14058.99609375 MB free)
  Uptime: 546.71 sec
  Load Avg:  2.62  2.68  1.28
  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  3243 MHz       2557 s          0 s        269 s       2746 s          0 s
       #2  2445 MHz       2500 s          0 s        254 s       2827 s          0 s
       #3  2587 MHz       2481 s          0 s        268 s       2816 s          0 s
       #4  3160 MHz       2619 s          0 s        296 s       2667 s          0 s
  Memory: 15.606487274169922 GB (14004.41015625 MB free)
  Uptime: 560.64 sec
  Load Avg:  2.37  2.62  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)

Target result

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

Job Properties

Time of benchmark: 25 Jun 2024 - 15:56
Package commit: 6a875d
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"]`	1.111 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  2789 MHz       2542 s          0 s        267 s       2624 s          0 s
       #2  2568 MHz       2498 s          0 s        252 s       2692 s          0 s
       #3  3243 MHz       2480 s          0 s        265 s       2681 s          0 s
       #4  2445 MHz       2503 s          0 s        290 s       2650 s          0 s
  Memory: 15.606487274169922 GB (14058.99609375 MB free)
  Uptime: 546.71 sec
  Load Avg:  2.62  2.68  1.28
  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: 25 Jun 2024 - 15:56
Package commit: 816622
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  3243 MHz       2557 s          0 s        269 s       2746 s          0 s
       #2  2445 MHz       2500 s          0 s        254 s       2827 s          0 s
       #3  2587 MHz       2481 s          0 s        268 s       2816 s          0 s
       #4  3160 MHz       2619 s          0 s        296 s       2667 s          0 s
  Memory: 15.606487274169922 GB (14004.41015625 MB free)
  Uptime: 560.64 sec
  Load Avg:  2.37  2.62  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)

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

codecov-commenter · 2024-06-25T15:59:41Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.85%. Comparing base (c392db1) to head (ff95a7a).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #301   +/-   ##
=======================================
  Coverage   92.85%   92.85%           
=======================================
  Files          47       47           
  Lines         490      490           
=======================================
  Hits          455      455           
  Misses         35       35

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

damonbayer · 2024-06-25T16:03:03Z

Really really nice, @SamuelBrand1! No changes immediately come to mind. Pinging @thanasibakis for his thoughts.

github-actions · 2024-06-25T16:03:42Z

Benchmark result

Judge result

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

Job Properties

Time of benchmarks:
- Target: 25 Jun 2024 - 16:03
- Baseline: 25 Jun 2024 - 16:03
Package commits:
- Target: b53f29
- Baseline: 816622
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  3249 MHz        194 s          0 s         67 s       1174 s          0 s
       #2  3244 MHz        200 s          0 s         61 s       1185 s          0 s
       #3  2445 MHz        172 s          0 s         83 s       1186 s          0 s
       #4  2445 MHz        183 s          0 s         75 s       1170 s          0 s
  Memory: 15.606491088867188 GB (14077.49609375 MB free)
  Uptime: 147.19 sec
  Load Avg:  0.89  0.32  0.12
  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        194 s          0 s         69 s       1324 s          0 s
       #2  3243 MHz        230 s          0 s         62 s       1304 s          0 s
       #3  2762 MHz        189 s          0 s         87 s       1317 s          0 s
       #4  3083 MHz        282 s          0 s         79 s       1219 s          0 s
  Memory: 15.606491088867188 GB (14127.72265625 MB free)
  Uptime: 162.4 sec
  Load Avg:  0.91  0.35  0.13
  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: 25 Jun 2024 - 16:3
Package commit: b53f29
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"]`	1.106 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  3249 MHz        194 s          0 s         67 s       1174 s          0 s
       #2  3244 MHz        200 s          0 s         61 s       1185 s          0 s
       #3  2445 MHz        172 s          0 s         83 s       1186 s          0 s
       #4  2445 MHz        183 s          0 s         75 s       1170 s          0 s
  Memory: 15.606491088867188 GB (14077.49609375 MB free)
  Uptime: 147.19 sec
  Load Avg:  0.89  0.32  0.12
  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: 25 Jun 2024 - 16:3
Package commit: 816622
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  2445 MHz        194 s          0 s         69 s       1324 s          0 s
       #2  3243 MHz        230 s          0 s         62 s       1304 s          0 s
       #3  2762 MHz        189 s          0 s         87 s       1317 s          0 s
       #4  3083 MHz        282 s          0 s         79 s       1219 s          0 s
  Memory: 15.606491088867188 GB (14127.72265625 MB free)
  Uptime: 162.4 sec
  Load Avg:  0.91  0.35  0.13
  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 · 2024-06-25T16:30:40Z

Benchmark result

Judge result

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

Job Properties

Time of benchmarks:
- Target: 25 Jun 2024 - 16:30
- Baseline: 25 Jun 2024 - 16:30
Package commits:
- Target: 3494dc
- Baseline: 816622
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  3244 MHz        131 s          0 s         59 s       2100 s          0 s
       #2  3254 MHz        186 s          0 s         68 s       2054 s          0 s
       #3  3056 MHz        115 s          0 s         64 s       2122 s          0 s
       #4  3220 MHz        244 s          0 s         74 s       1977 s          0 s
  Memory: 15.606491088867188 GB (14130.640625 MB free)
  Uptime: 233.7 sec
  Load Avg:  0.99  0.33  0.12
  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        193 s          0 s         62 s       2166 s          0 s
       #2  2445 MHz        229 s          0 s         72 s       2136 s          0 s
       #3  3192 MHz        118 s          0 s         66 s       2248 s          0 s
       #4  3243 MHz        262 s          0 s         75 s       2088 s          0 s
  Memory: 15.606491088867188 GB (14093.71484375 MB free)
  Uptime: 246.8 sec
  Load Avg:  1.06  0.38  0.14
  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: 25 Jun 2024 - 16:30
Package commit: 3494dc
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  3244 MHz        131 s          0 s         59 s       2100 s          0 s
       #2  3254 MHz        186 s          0 s         68 s       2054 s          0 s
       #3  3056 MHz        115 s          0 s         64 s       2122 s          0 s
       #4  3220 MHz        244 s          0 s         74 s       1977 s          0 s
  Memory: 15.606491088867188 GB (14130.640625 MB free)
  Uptime: 233.7 sec
  Load Avg:  0.99  0.33  0.12
  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: 25 Jun 2024 - 16:30
Package commit: 816622
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  2445 MHz        193 s          0 s         62 s       2166 s          0 s
       #2  2445 MHz        229 s          0 s         72 s       2136 s          0 s
       #3  3192 MHz        118 s          0 s         66 s       2248 s          0 s
       #4  3243 MHz        262 s          0 s         75 s       2088 s          0 s
  Memory: 15.606491088867188 GB (14093.71484375 MB free)
  Uptime: 246.8 sec
  Load Avg:  1.06  0.38  0.14
  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 · 2024-06-25T17:01:58Z

Benchmark result

Judge result

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

Job Properties

Time of benchmarks:
- Target: 25 Jun 2024 - 17:01
- Baseline: 25 Jun 2024 - 17:01
Package commits:
- Target: 64d157
- Baseline: 816622
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        159 s          0 s         59 s       1922 s          0 s
       #2  2596 MHz        175 s          0 s         61 s       1904 s          0 s
       #3  3243 MHz        146 s          0 s         74 s       1912 s          0 s
       #4  2445 MHz        198 s          0 s         75 s       1873 s          0 s
  Memory: 15.606491088867188 GB (14128.00390625 MB free)
  Uptime: 217.83 sec
  Load Avg:  0.75  0.25  0.09
  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  3241 MHz        176 s          0 s         60 s       2037 s          0 s
       #2  3215 MHz        179 s          0 s         64 s       2031 s          0 s
       #3  3167 MHz        221 s          0 s         79 s       1966 s          0 s
       #4  2445 MHz        230 s          0 s         78 s       1971 s          0 s
  Memory: 15.606491088867188 GB (14080.296875 MB free)
  Uptime: 231.16 sec
  Load Avg:  0.81  0.29  0.1
  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: 25 Jun 2024 - 17:1
Package commit: 64d157
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        159 s          0 s         59 s       1922 s          0 s
       #2  2596 MHz        175 s          0 s         61 s       1904 s          0 s
       #3  3243 MHz        146 s          0 s         74 s       1912 s          0 s
       #4  2445 MHz        198 s          0 s         75 s       1873 s          0 s
  Memory: 15.606491088867188 GB (14128.00390625 MB free)
  Uptime: 217.83 sec
  Load Avg:  0.75  0.25  0.09
  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: 25 Jun 2024 - 17:1
Package commit: 816622
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"]`	1.103 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  3241 MHz        176 s          0 s         60 s       2037 s          0 s
       #2  3215 MHz        179 s          0 s         64 s       2031 s          0 s
       #3  3167 MHz        221 s          0 s         79 s       1966 s          0 s
       #4  2445 MHz        230 s          0 s         78 s       1971 s          0 s
  Memory: 15.606491088867188 GB (14080.296875 MB free)
  Uptime: 231.16 sec
  Load Avg:  0.81  0.29  0.1
  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

thanasibakis · 2024-06-25T17:39:38Z

I think this reads really well!

zsusswein

Looks pretty good. Put on my @seabbs hat and left some nitpicky stuff inline.

EpiAware/docs/src/examples/getting_started.jl

EpiAware/docs/src/man/getting-started-julia.md

SamuelBrand1 · 2024-06-26T12:47:40Z

Made some changes:

Hopefully clarified and rejigged it in response to @zsusswein comments.
Clarified/corrected the order of primacy in stacked environments bit.

github-actions · 2024-06-26T12:48:11Z

Benchmark result

Judge result

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

Job Properties

Time of benchmarks:
- Target: 26 Jun 2024 - 12:47
- Baseline: 26 Jun 2024 - 12:48
Package commits:
- Target: c424d8
- Baseline: c392db
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  3044 MHz        148 s          0 s         66 s       1764 s          0 s
       #2  3243 MHz        105 s          0 s         50 s       1839 s          0 s
       #3  2445 MHz        254 s          0 s         72 s       1664 s          0 s
       #4  2599 MHz        177 s          0 s         77 s       1739 s          0 s
  Memory: 15.606491088867188 GB (14113.61328125 MB free)
  Uptime: 203.11 sec
  Load Avg:  1.01  0.4  0.14
  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        175 s          0 s         68 s       1866 s          0 s
       #2  2593 MHz        133 s          0 s         53 s       1940 s          0 s
       #3  2445 MHz        322 s          0 s         76 s       1724 s          0 s
       #4  3241 MHz        181 s          0 s         80 s       1864 s          0 s
  Memory: 15.606491088867188 GB (14075.9921875 MB free)
  Uptime: 216.31 sec
  Load Avg:  1.01  0.43  0.16
  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: 26 Jun 2024 - 12:47
Package commit: c424d8
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"]`	1.103 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  3044 MHz        148 s          0 s         66 s       1764 s          0 s
       #2  3243 MHz        105 s          0 s         50 s       1839 s          0 s
       #3  2445 MHz        254 s          0 s         72 s       1664 s          0 s
       #4  2599 MHz        177 s          0 s         77 s       1739 s          0 s
  Memory: 15.606491088867188 GB (14113.61328125 MB free)
  Uptime: 203.11 sec
  Load Avg:  1.01  0.4  0.14
  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: 26 Jun 2024 - 12:48
Package commit: c392db
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        175 s          0 s         68 s       1866 s          0 s
       #2  2593 MHz        133 s          0 s         53 s       1940 s          0 s
       #3  2445 MHz        322 s          0 s         76 s       1724 s          0 s
       #4  3241 MHz        181 s          0 s         80 s       1864 s          0 s
  Memory: 15.606491088867188 GB (14075.9921875 MB free)
  Uptime: 216.31 sec
  Load Avg:  1.01  0.43  0.16
  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

zsusswein

Looks good!

…ntation

github-actions · 2024-06-26T12:59:22Z

Benchmark result

Judge result

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

Job Properties

Time of benchmarks:
- Target: 26 Jun 2024 - 12:59
- Baseline: 26 Jun 2024 - 12:59
Package commits:
- Target: 53fd86
- Baseline: c392db
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       2533 s          0 s        281 s       2911 s          0 s
       #2  2673 MHz       2640 s          0 s        246 s       2844 s          0 s
       #3  3240 MHz       2447 s          0 s        276 s       3001 s          0 s
       #4  3259 MHz       2511 s          0 s        266 s       2961 s          0 s
  Memory: 15.606491088867188 GB (14041.28515625 MB free)
  Uptime: 576.37 sec
  Load Avg:  2.78  2.75  1.3
  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       2544 s          0 s        283 s       3033 s          0 s
       #2  2445 MHz       2729 s          0 s        251 s       2886 s          0 s
       #3  3241 MHz       2448 s          0 s        278 s       3135 s          0 s
       #4  3220 MHz       2542 s          0 s        268 s       3065 s          0 s
  Memory: 15.606491088867188 GB (14005.97265625 MB free)
  Uptime: 590.08 sec
  Load Avg:  2.51  2.69  1.3
  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: 26 Jun 2024 - 12:59
Package commit: 53fd86
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  2445 MHz       2533 s          0 s        281 s       2911 s          0 s
       #2  2673 MHz       2640 s          0 s        246 s       2844 s          0 s
       #3  3240 MHz       2447 s          0 s        276 s       3001 s          0 s
       #4  3259 MHz       2511 s          0 s        266 s       2961 s          0 s
  Memory: 15.606491088867188 GB (14041.28515625 MB free)
  Uptime: 576.37 sec
  Load Avg:  2.78  2.75  1.3
  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: 26 Jun 2024 - 12:59
Package commit: c392db
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  2445 MHz       2544 s          0 s        283 s       3033 s          0 s
       #2  2445 MHz       2729 s          0 s        251 s       2886 s          0 s
       #3  3241 MHz       2448 s          0 s        278 s       3135 s          0 s
       #4  3220 MHz       2542 s          0 s        268 s       3065 s          0 s
  Memory: 15.606491088867188 GB (14005.97265625 MB free)
  Uptime: 590.08 sec
  Load Avg:  2.51  2.69  1.3
  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; 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

SamuelBrand1 added 3 commits June 25, 2024 16:41

Create getting-started-julia.md

d48937f

update pages.jl to include new getting started with julia and move …

aaa2334

…contributing.md

Update pages.jl

cb9570c

SamuelBrand1 requested a review from seabbs June 25, 2024 15:48

SamuelBrand1 linked an issue Jun 25, 2024 that may be closed by this pull request

Better getting started with Julia documentation #277

Closed

pre-commit fix

43107cd

fill TOC

d82dbe9

pin ADTypes to 1.3.0 to fix getting started example

78bd10a

fix to new usage of AutoReverseDiff

bcfafe9

SamuelBrand1 mentioned this pull request Jun 25, 2024

New version of ADTypes causing breaking changes in documentation #302

Closed

SamuelBrand1 requested a review from zsusswein June 25, 2024 19:47

zsusswein reviewed Jun 26, 2024

View reviewed changes

Update getting-started-julia.md

56e0eda

SamuelBrand1 requested a review from zsusswein June 26, 2024 12:46

pre-commit fix

0372a63

zsusswein approved these changes Jun 26, 2024

View reviewed changes

Merge branch 'main' into 277-better-getting-started-with-julia-docume…

ff95a7a

…ntation

zsusswein added this pull request to the merge queue Jun 26, 2024

Merged via the queue into main with commit 20298b2 Jun 26, 2024
11 checks passed

zsusswein deleted the 277-better-getting-started-with-julia-documentation branch June 26, 2024 14:19

seabbs mentioned this pull request Jun 28, 2024

"Hints and tips" documentation #276

Closed

Better getting started with julia documentation #301

Better getting started with julia documentation #301

Conversation

SamuelBrand1 commented Jun 25, 2024

github-actions bot commented Jun 25, 2024

Judge result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Target

Baseline

Target result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Baseline result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Runtime information

codecov-commenter commented Jun 25, 2024 • edited Loading

Codecov Report

damonbayer commented Jun 25, 2024

github-actions bot commented Jun 25, 2024

Judge result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Target

Baseline

Target result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Baseline result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Runtime information

github-actions bot commented Jun 25, 2024

Judge result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Target

Baseline

Target result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Baseline result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

Runtime information

github-actions bot commented Jun 25, 2024

Judge result

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

Job Properties

Results

Benchmark Group List

Julia versioninfo

codecov-commenter commented Jun 25, 2024 •

edited

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