upd. benchmarks

benchmark/benchmark_systems.jl

@@ -23,6 +23,8 @@ function get_benchmark_suite(id)
         benchmark_set_6()
     elseif id == 7
         benchmark_set_7()
+    elseif id == 8
+        benchmark_set_8()
     end
 end
 
@@ -71,7 +73,11 @@ function benchmark_set_1()
         ("reimer 6", Groebner.reimern(6, k=ground_field)),
         ("reimer 7", Groebner.reimern(7, k=ground_field)),
         ("reimer 8", Groebner.reimern(8, k=ground_field)),
-        ("reimer 9", Groebner.reimern(9, k=ground_field))
+        ("reimer 9", Groebner.reimern(9, k=ground_field)),
+        ("chandra 11", Groebner.chandran(11, k=ground_field)),
+        ("chandra 12", Groebner.chandran(12, k=ground_field)),
+        ("chandra 13", Groebner.chandran(13, k=ground_field)),
+        ("chandra 14", Groebner.chandran(14, k=ground_field))
     ]
 
     (name="Integers modulo 2^30 + 3", field=ground_field, systems=systems)
@@ -98,13 +104,19 @@ function benchmark_set_2()
         ("noon 8", Groebner.noonn(8, k=ground_field)),
         ("noon 9", Groebner.noonn(9, k=ground_field)),
         ("noon 10", Groebner.noonn(10, k=ground_field)),
+        ("noon 11", Groebner.noonn(11, k=ground_field)),
         ("henrion 5", Groebner.henrion5(k=ground_field)),
         ("henrion 6", Groebner.henrion6(k=ground_field)),
         ("henrion 7", Groebner.henrion7(k=ground_field)),
+        ("henrion 8", Groebner.henrion8(k=ground_field)),
         ("reimer 6", Groebner.reimern(6, k=ground_field)),
         ("reimer 7", Groebner.reimern(7, k=ground_field)),
         ("reimer 8", Groebner.reimern(8, k=ground_field)),
-        ("reimer 9", Groebner.reimern(9, k=ground_field))
+        ("reimer 9", Groebner.reimern(9, k=ground_field)),
+        ("chandra 11", Groebner.chandran(11, k=ground_field)),
+        ("chandra 12", Groebner.chandran(12, k=ground_field)),
+        ("chandra 13", Groebner.chandran(13, k=ground_field)),
+        ("chandra 14", Groebner.chandran(14, k=ground_field))
     ]
 
     (name="Integers modulo 1031", field=ground_field, systems=systems)
@@ -129,9 +141,11 @@ function benchmark_set_3()
         ("reimer 6", Groebner.reimern(6, k=ground_field)),
         ("reimer 7", Groebner.reimern(7, k=ground_field)),
         ("reimer 8", Groebner.reimern(8, k=ground_field)),
-        ("chandra 4", Groebner.chandran(4, k=ground_field, ordering=:degrevlex)),
-        ("chandra 5", Groebner.chandran(5, k=ground_field, ordering=:degrevlex)),
-        ("chandra 6", Groebner.chandran(6, k=ground_field, ordering=:degrevlex)),
+        ("chandra 9", Groebner.chandran(9, k=ground_field, ordering=:degrevlex)),
+        ("chandra 10", Groebner.chandran(10, k=ground_field, ordering=:degrevlex)),
+        ("chandra 11", Groebner.chandran(11, k=ground_field, ordering=:degrevlex)),
+        ("chandra 12", Groebner.chandran(12, k=ground_field, ordering=:degrevlex)),
+        ("chandra 13", Groebner.chandran(13, k=ground_field, ordering=:degrevlex)),
         ("reimer 7", Groebner.reimern(7, k=ground_field)),
         ("reimer 8", Groebner.reimern(8, k=ground_field)),
         ("ipp", Groebner.ipp(k=ground_field, tol=0.0, ordering=:degrevlex))
@@ -175,14 +189,36 @@ end
 function benchmark_set_7()
     ground_field = AbstractAlgebra.QQ
     systems = [
+        ("chandra 5", Groebner.chandran(5, ordering=:degrevlex, k=ground_field)),
+        ("chandra 6", Groebner.chandran(6, ordering=:degrevlex, k=ground_field)),
+        ("chandra 7", Groebner.chandran(7, ordering=:degrevlex, k=ground_field)),
+        ("chandra 8", Groebner.chandran(8, ordering=:degrevlex, k=ground_field)),
+        ("chandra 9", Groebner.chandran(9, ordering=:degrevlex, k=ground_field)),
+        ("chandra 10", Groebner.chandran(10, ordering=:degrevlex, k=ground_field)),
         ("chandra 11", Groebner.chandran(11, ordering=:degrevlex, k=ground_field)),
         ("chandra 12", Groebner.chandran(12, ordering=:degrevlex, k=ground_field)),
-        ("chandra 13", Groebner.chandran(13, ordering=:degrevlex, k=ground_field)),
-        ("chandra 14", Groebner.chandran(14, ordering=:degrevlex, k=ground_field)),
         ("boon", Groebner.boon(ordering=:degrevlex, k=ground_field)),
         ("rps10", Groebner.rps10(ordering=:degrevlex, k=ground_field)),
         ("ipp", Groebner.ipp(ordering=:degrevlex, k=ground_field))
     ]
 
     (name="HC", field=ground_field, systems=systems)
 end
+
+function benchmark_set_8()
+    ground_field = AbstractAlgebra.GF(2^30 + 3)
+    systems = [
+        ("chandra 5", Groebner.chandran(5, ordering=:degrevlex, k=ground_field)),
+        ("chandra 6", Groebner.chandran(6, ordering=:degrevlex, k=ground_field)),
+        ("chandra 7", Groebner.chandran(7, ordering=:degrevlex, k=ground_field)),
+        ("chandra 8", Groebner.chandran(8, ordering=:degrevlex, k=ground_field)),
+        ("chandra 9", Groebner.chandran(9, ordering=:degrevlex, k=ground_field)),
+        ("chandra 10", Groebner.chandran(10, ordering=:degrevlex, k=ground_field)),
+        ("chandra 11", Groebner.chandran(11, ordering=:degrevlex, k=ground_field)),
+        ("chandra 12", Groebner.chandran(12, ordering=:degrevlex, k=ground_field)),
+        ("chandra 13", Groebner.chandran(13, ordering=:degrevlex, k=ground_field)),
+        ("chandra 14", Groebner.chandran(14, ordering=:degrevlex, k=ground_field))
+    ]
+
+    (name="HC modulo 2^30 + 3", field=ground_field, systems=systems)
+end

benchmark/generate/benchmark_generators.jl

@@ -66,7 +66,7 @@ function generate_benchmark_source_for_maple(
     println(buf, "with(Groebner):")
     println(buf, "with(PolynomialIdeals):")
     println(buf, "kernelopts(numcpus=1);")
-    system_repr = join(map(s -> "\t\t" * s, map(repr, system)), ",\n")
+    system_repr = replace(join(map(s -> "\t\t" * s, map(repr, system)), ",\n"), "//" => "/")
     vars_repr = join(map(string, gens(ring)), ", ")
     println(buf, "")
     println(buf, "runtime := 2^1000:")

benchmark/one_script_to_run_them_all.jl

@@ -877,15 +877,15 @@ end
 function check_args(args)
     backend = args["backend"]
     @assert backend in ("groebner", "singular", "maple", "openf4", "msolve", "ALL")
-    if backend == "openf4" && args["suite"] in [3]
+    if backend == "openf4" && args["suite"] in [3, 7]
         throw("Running benchmarks over the rationals is not possible for openf4")
     end
-    if backend == "msolve" && args["suite"] in [3] && args["validate"] != "no"
+    if backend == "msolve" && args["suite"] in [3, 7] && args["validate"] != "no"
         throw(
             "Validating results for msolve over the rationals is not possible. Use command line option --validate=no"
         )
     end
-    if backend == "learn_apply" && args in [3]
+    if backend == "learn_apply" && args in [3, 7]
         throw("Cannot learn & apply over the rationals")
     end
 end

benchmark/results/benchmark_result_8.md

@@ -0,0 +1,44 @@
+## Benchmark results
+
+2024-01-12T09:17:58.879
+
+Benchmarked backends: Any["groebner", "maple", "msolve", "openf4", "singular"]
+
+Benchmark suite: HC modulo 2^30 + 3
+
+- Workers: 4
+- Timeout: 1000 s
+- Aggregated over: 1 runs
+
+**All timings in seconds.**
+
+|Model|groebner|maple|msolve|openf4|singular|
+|:----|---|---|---|---|---|
+|chandra 5|0.00|0.01|0.02|0.01|0.00|
+|chandra 6|0.00|0.01|0.02|0.03|0.00|
+|chandra 7|0.00|0.01|0.03|0.03|0.01|
+|chandra 8|0.01|0.02|0.04|0.08|0.06|
+|chandra 9|0.04|0.05|0.08|0.56|0.40|
+|chandra 10|0.32|0.16|0.20|1.70|2.62|
+|chandra 11|0.87|0.81|0.95|9.92|23.09|
+|chandra 12|4.65|4.55|5.16|71.29|183.02|
+|chandra 13|32.91|26.50|33.15|503.61| - |
+
+*Benchmarking environment:*
+
+* Total RAM (GiB): 188
+* Processor: Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz
+* Julia version: 1.9.2
+
+Versions of the dependencies:
+
+* Primes : 0.5.5
+* TimerOutputs : 0.5.23
+* PrecompileTools : 1.2.0
+* MultivariatePolynomials : 0.5.3
+* Combinatorics : 1.0.2
+* AbstractAlgebra : 0.34.7
+* Nemo : 0.38.3
+* Atomix : 0.1.0
+* ExprTools : 0.1.10
+* PrettyTables : 2.3.1

benchmark/results/groebner/benchmark_result_4.md

@@ -1,13 +1,13 @@
 ## Benchmark results
 
-2024-01-12T06:08:17.235
+2024-01-12T08:37:44.375
 
 Benchmarked backend: groebner
 
 Benchmark suite: SIAN modulo 2^30 + 3
 
 - Workers: 16
-- Timeout: 5000 s
+- Timeout: 1000 s
 - Aggregated over: 1 runs
 
 **All timings in seconds.**
@@ -16,44 +16,50 @@ Benchmark suite: SIAN modulo 2^30 + 3
 |:----|---|
 |Biohydrogenation|0.00|
 |Biohydrogenation_with_weights|0.01|
-|ChemicalReactionNetwork|0.33|
-|ChemicalReactionNetwork_with_weights|0.51|
-|Cholera|65.40|
-|Cholera_with_weights|69.96|
+|COVID_m1|0.65|
+|COVID_m1_with_weights|0.19|
+|ChemicalReactionNetwork|0.38|
+|ChemicalReactionNetwork_with_weights|0.55|
+|Cholera|52.40|
+|Cholera_with_weights|57.69|
 |DAISY_ex3|0.00|
 |DAISY_ex3_with_weights|0.00|
 |DAISY_mamil3|0.00|
 |DAISY_mamil3_with_weights|0.00|
 |DAISY_mamil4|0.32|
-|DAISY_mamil4_with_weights|0.34|
+|DAISY_mamil4_with_weights|0.31|
+|Goodwin| - |
+|Goodwin_with_weights|223.73|
 |HIV|0.01|
-|HIV2|3.35|
-|HIV2_with_weights|2.58|
-|HIV_with_weights|0.01|
+|HIV2|3.14|
+|HIV2_with_weights|2.16|
+|HIV_with_weights|0.03|
 |LV|0.00|
 |LV_with_weights|0.00|
 |Lipolysis|0.00|
 |Lipolysis_with_weights|0.00|
-|NFkB|1629.72|
-|NFkB_with_weights|559.35|
+|NFkB| - |
+|NFkB_with_weights|285.44|
 |OralGlucose|0.00|
 |OralGlucose_with_weights|0.00|
 |Pharm| - |
-|Pharm_with_weights|1922.79|
+|Pharm_with_weights| - |
 |SEIR|0.00|
-|SEIR2|0.01|
-|SEIR2_with_weights|0.05|
-|SEIR_with_weights|0.00|
-|SIRSForced|0.76|
-|SIRSForced_with_weights|0.20|
+|SEIR2| - |
+|SEIR2_with_weights|0.03|
+|SEIRP| - |
+|SEIRP_with_weights|34.90|
+|SEIR_with_weights| - |
+|SIRSForced|0.72|
+|SIRSForced_with_weights|0.27|
 |SIR_R0|0.00|
-|SIR_R0_with_weights|0.00|
-|SlowFast|0.00|
+|SIR_R0_with_weights|0.02|
+|SlowFast| - |
 |SlowFast_with_weights|0.00|
-|Treatment|0.01|
+|Treatment| - |
 |Treatment_with_weights|0.03|
 |Tumor|0.05|
-|Tumor_with_weights|0.21|
+|Tumor_with_weights|0.18|
 
 *Benchmarking environment:*
 

benchmark/results/groebner/benchmark_result_7.md

@@ -0,0 +1,46 @@
+## Benchmark results
+
+2024-01-12T09:04:15.474
+
+Benchmarked backend: groebner
+
+Benchmark suite: HC
+
+- Workers: 4
+- Timeout: 1200 s
+- Aggregated over: 1 runs
+
+**All timings in seconds.**
+
+|Model|Total, s|
+|:----|---|
+|boon|0.01|
+|chandra 5|0.01|
+|chandra 6|0.04|
+|chandra 7|0.22|
+|chandra 8|0.44|
+|chandra 9|2.52|
+|chandra 10|5.07|
+|chandra 11|17.69|
+|chandra 12|108.19|
+|ipp|185.73|
+|rps10| - |
+
+*Benchmarking environment:*
+
+* Total RAM (GiB): 188
+* Processor: Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz
+* Julia version: 1.9.2
+
+Versions of the dependencies:
+
+* Primes : 0.5.5
+* TimerOutputs : 0.5.23
+* PrecompileTools : 1.2.0
+* MultivariatePolynomials : 0.5.3
+* Combinatorics : 1.0.2
+* AbstractAlgebra : 0.34.7
+* Nemo : 0.38.3
+* Atomix : 0.1.0
+* ExprTools : 0.1.10
+* PrettyTables : 2.3.1

benchmark/results/groebner/benchmark_result_8.md

@@ -0,0 +1,44 @@
+## Benchmark results
+
+2024-01-12T08:50:04.619
+
+Benchmarked backend: groebner
+
+Benchmark suite: HC modulo 2^30 + 3
+
+- Workers: 4
+- Timeout: 1000 s
+- Aggregated over: 1 runs
+
+**All timings in seconds.**
+
+|Model|Total, s|
+|:----|---|
+|chandra 5|0.00|
+|chandra 6|0.00|
+|chandra 7|0.00|
+|chandra 8|0.01|
+|chandra 9|0.04|
+|chandra 10|0.32|
+|chandra 11|0.87|
+|chandra 12|4.65|
+|chandra 13|32.91|
+
+*Benchmarking environment:*
+
+* Total RAM (GiB): 188
+* Processor: Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz
+* Julia version: 1.9.2
+
+Versions of the dependencies:
+
+* Primes : 0.5.5
+* TimerOutputs : 0.5.23
+* PrecompileTools : 1.2.0
+* MultivariatePolynomials : 0.5.3
+* Combinatorics : 1.0.2
+* AbstractAlgebra : 0.34.7
+* Nemo : 0.38.3
+* Atomix : 0.1.0
+* ExprTools : 0.1.10
+* PrettyTables : 2.3.1