Feat 108 planned retirement

[Ethan-Russell]

@sallyrobson this is ready for review when you are!

[codecov]

Codecov Report

Patch coverage: 92.50% and project coverage change: +0.02 🎉

Comparison is base (31b7e85) 87.17% compared to head (9561ab9) 87.19%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #116      +/-   ##
==========================================
+ Coverage   87.17%   87.19%   +0.02%     
==========================================
  Files          36       36              
  Lines        2627     2655      +28     
==========================================
+ Hits         2290     2315      +25     
- Misses        337      340       +3     

Impacted Files	Coverage Δ
src/E4ST.jl	87.65% <ø> (ø)
src/io/data.jl	88.36% <ø> (ø)
src/io/util.jl	70.80% <71.42%> (+0.18%)	⬆️
src/types/modifications/Storage.jl	95.03% <80.00%> (-0.62%)	⬇️
src/io/config.jl	93.40% <100.00%> (-0.52%)	⬇️
src/model/newgens.jl	87.50% <100.00%> (+0.54%)	⬆️
src/model/util.jl	100.00% <100.00%> (ø)
src/results/parse.jl	96.33% <100.00%> (+0.37%)	⬆️

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[github-actions]

Benchmark result

Judge result

Benchmark Report for /home/runner/work/E4ST.jl/E4ST.jl

Job Properties

• Time of benchmarks:
  • Target: 19 Apr 2023 - 20:35
  • Baseline: 19 Apr 2023 - 20:37
• Package commits:
  • Target: 4a81a9
  • Baseline: 31b7e8
• Julia commits:
  • Target: 17cfb8
  • Baseline: 17cfb8
• Julia command flags:
  • Target: None
  • Baseline: None
• Environment variables:
  • Target: None
  • Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID	time ratio	memory ratio

Benchmark Group List

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

• []

Julia versioninfo

Target

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.2 LTS
  uname: Linux 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64
  CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: 
              speed         user         nice          sys         idle          irq
       #1  2593 MHz       1799 s          0 s        175 s       4888 s          0 s
       #2  2593 MHz       2591 s          0 s        246 s       4037 s          0 s
  Memory: 6.781211853027344 GB (4557.3828125 MB free)
  Uptime: 691.86 sec
  Load Avg:  1.08  0.97  0.54
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  Threads: 1 on 2 virtual cores

Baseline

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.2 LTS
  uname: Linux 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64
  CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: 
              speed         user         nice          sys         idle          irq
       #1  2593 MHz       1954 s          0 s        187 s       6030 s          0 s
       #2  2593 MHz       3716 s          0 s        276 s       4196 s          0 s
  Memory: 6.781211853027344 GB (4642.69921875 MB free)
  Uptime: 823.25 sec
  Load Avg:  1.15  1.03  0.62
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  Threads: 1 on 2 virtual cores

---

Target result

Benchmark Report for /home/runner/work/E4ST.jl/E4ST.jl

Job Properties

• Time of benchmark: 19 Apr 2023 - 20:35
• Package commit: 4a81a9
• Julia commit: 17cfb8
• Julia command flags: None
• Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID	time	GC time	memory	allocations
["get_af"]	103.304 ns (5%)		32 bytes (1%)	2
["get_generator"]	56.140 ns (5%)		48 bytes (1%)	1
["get_plnom"]	107.543 ns (5%)		48 bytes (1%)	3
["read_data"]	35.161 ms (5%)		9.52 MiB (1%)	323307
["setup_model"]	2.870 s (5%)	1.062 s	1.80 GiB (1%)	16746223

Benchmark Group List

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

• []

Julia versioninfo

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.2 LTS
  uname: Linux 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64
  CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: 
              speed         user         nice          sys         idle          irq
       #1  2593 MHz       1799 s          0 s        175 s       4888 s          0 s
       #2  2593 MHz       2591 s          0 s        246 s       4037 s          0 s
  Memory: 6.781211853027344 GB (4557.3828125 MB free)
  Uptime: 691.86 sec
  Load Avg:  1.08  0.97  0.54
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  Threads: 1 on 2 virtual cores

---

Baseline result

Benchmark Report for /home/runner/work/E4ST.jl/E4ST.jl

Job Properties

• Time of benchmark: 19 Apr 2023 - 20:37
• Package commit: 31b7e8
• Julia commit: 17cfb8
• Julia command flags: None
• Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID	time	GC time	memory	allocations
["get_af"]	99.318 ns (5%)		32 bytes (1%)	2
["get_generator"]	56.656 ns (5%)		48 bytes (1%)	1
["get_plnom"]	102.971 ns (5%)		48 bytes (1%)	3
["read_data"]	34.709 ms (5%)		9.50 MiB (1%)	323045
["setup_model"]	2.851 s (5%)	1.052 s	1.80 GiB (1%)	16746023

Benchmark Group List

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

• []

Julia versioninfo

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.2 LTS
  uname: Linux 5.15.0-1035-azure #42-Ubuntu SMP Tue Feb 28 19:41:23 UTC 2023 x86_64 x86_64
  CPU: Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz: 
              speed         user         nice          sys         idle          irq
       #1  2593 MHz       1954 s          0 s        187 s       6030 s          0 s
       #2  2593 MHz       3716 s          0 s        276 s       4196 s          0 s
  Memory: 6.781211853027344 GB (4642.69921875 MB free)
  Uptime: 823.25 sec
  Load Avg:  1.15  1.03  0.62
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
  Threads: 1 on 2 virtual cores

---

Runtime information

Runtime Info
BLAS #threads	1
BLAS.vendor()	openblas64
Sys.CPU_THREADS	2

lscpu output:

Architecture:                    x86_64
CPU op-mode(s):                  32-bit, 64-bit
Address sizes:                   46 bits physical, 48 bits virtual
Byte Order:                      Little Endian
CPU(s):                          2
On-line CPU(s) list:             0,1
Vendor ID:                       GenuineIntel
Model name:                      Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz
CPU family:                      6
Model:                           85
Thread(s) per core:              1
Core(s) per socket:              2
Socket(s):                       1
Stepping:                        7
BogoMIPS:                        5187.80
Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase bmi1 hle avx2 smep bmi2 erms invpcid rtm avx512f avx512dq rdseed adx smap clflushopt avx512cd avx512bw avx512vl xsaveopt xsavec xsaves md_clear
Hypervisor vendor:               Microsoft
Virtualization type:             full
L1d cache:                       64 KiB (2 instances)
L1i cache:                       64 KiB (2 instances)
L2 cache:                        2 MiB (2 instances)
L3 cache:                        35.8 MiB (1 instance)
NUMA node(s):                    1
NUMA node0 CPU(s):               0,1
Vulnerability Itlb multihit:     KVM: Mitigation: VMX unsupported
Vulnerability L1tf:              Mitigation; PTE Inversion
Vulnerability Mds:               Mitigation; Clear CPU buffers; SMT Host state unknown
Vulnerability Meltdown:          Mitigation; PTI
Vulnerability Mmio stale data:   Vulnerable: Clear CPU buffers attempted, no microcode; SMT Host state unknown
Vulnerability Retbleed:          Vulnerable
Vulnerability Spec store bypass: Vulnerable
Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:        Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected
Vulnerability Srbds:             Not affected
Vulnerability Tsx async abort:   Mitigation; Clear CPU buffers; SMT Host state unknown

Cpu Property	Value
Brand	Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz
Vendor	:Intel
Architecture	:Skylake
Model	Family: 0x06, Model: 0x55, Stepping: 0x07, Type: 0x00
Cores	2 physical cores, 2 logical cores (on executing CPU)
	No Hyperthreading hardware capability detected
Clock Frequencies	Not supported by CPU
Data Cache	Level 1:3 : (32, 1024, 36608) kbytes
	64 byte cache line size
Address Size	48 bits virtual, 46 bits physical
SIMD	512 bit = 64 byte max. SIMD vector size
Time Stamp Counter	TSC is accessible via rdtsc
	TSC increased at every clock cycle (non-invariant TSC)
Perf. Monitoring	Performance Monitoring Counters (PMC) are not supported
Hypervisor	Yes, Microsoft

[sallyrobson]

closes #108