Dev

.github/workflows/go.yml

@@ -19,7 +19,7 @@ jobs:
     - name: Set up Go
       uses: actions/setup-go@v4
       with:
-        go-version: '1.20'
+        go-version: '1.22'
 
     - name: Test and Coverage
       run: go test -v -race -cover ./...

Dockerfile

@@ -1,6 +1,6 @@
 # syntax=docker/dockerfile:1
 
-FROM golang:1.20 AS build-stage
+FROM golang:1.22 AS build-stage
 
 WORKDIR /app
 
@@ -15,4 +15,4 @@ RUN CGO_ENABLED=0 GOOS=linux go install
 
 # Run the tests in the container
 FROM build-stage AS run-test-stage
-RUN go test -v ./...
+RUN go test -v ./...

TestInputs/DistanceMatrix/Random_2_input.txt

@@ -0,0 +1,2 @@
+0	399	294	169	166	763	263	522	179	205	234	404	484	855	948	754	117	562	88	48	264	149	316	118	217	399	606	522	498	187	554	5	571	433	182	563	360	443	581	379	209	229	445	848	173	531	352	284	910	60	742	116	841	946	987	663	991	788	211	923	133	27	24	643	991	690	975	730	608	912	883	286	84	475	758	522	665	887	772	54	227	994	260	417	511	444	578	975	527	650	809	967	287	985	562	457	734	425	964	768	877	932	311	749	355	363	869	408	875	638	520	281	876	251	733	751	432	553	880	2	557	178	583	398	422	261	307	819	831	532	386	714	783	587	620	576	509	863	885	784	796	670	240	599	827	87	68	904	883	243	729	458	322	6	371	398	924	778	196	845	307	288	186	671	877	555	992	899	532	98	399	355	979	499	584	791	597	181	851	648	686	671	281	467	767	361	909	805	416	949	203	618	200	105	406	854	304	274	629	530	476	192	898	315	799	282	589	68	334	909	988	611	719	947	596	800	91	785	491	634	397	185	376	792	813	338	36	915	264	378	451	182	760	675	700	989	582	680	337	652	550	961	90	925	476	701	811	906	178	983	167	450	734	65	381	733	987	777	486	712	279	41	912	489	819	494	433	190	25	27	848	240	638	993	278	930	205	564	741	160	231	862	626	751	115	469	788	735	622	687	463	24	434	148	840	562	511	176	273	321	347	925	796	623	610	428	235	263	592	554	497	238	502	272	87	876	258	742	302	773	858	886	219	342	744	87	946	66	698	988	106	806	258	910	471	907	827	363	979	731	462	892	360	635	152	41	815	693	720	970	903	993	237	289	618	883	173	394	706	418	705	153	917	821	355	141	890	51	357	95	711	929	169	533	518	600	208	45	486	964	463	805	96	511	474	181	426	263	463	24	622	103	687	19	604	818	0	122	117	64	84	996	148	368	896	253	540	442	904	792	277	242	325	115	279	750	247	127	973	722	756	457	868	900	842	76	134	491	975	285	148	455	65	989	5	343	146	112	984	821	46	481	810	227	885	334	300	682	141	7	377	174	644	185	905	903	156	326	136	520	553	591	642	746	872	214	927	824	394	938	137	363	678	759	330	413	974	388	379	425	766	382	311	416	73	603	591	987	599	119	999	14	549	597	886	824	322	269	982	985	222	575	264	728	827	931	344	914	494	809	299	53	640	441	336	595	578	731	202	676	355	475	388	268	54	584	674	445	944	823	636	495	522	925	405	370	304	616	699	298	298	686	959	554	456	713	975	948	924	885	348	599	633	821	413	619	288	544	356	340	543	361	159	913	330	828	110	565	700	967	689	531	878	266	942	820	918	883	527	918	927	411	200	35	388	288	761	510	97	884	484	789	391	85	16	448	318	826	88	834	391	484	833	995	740	503	783	150	932	938	735	15	647	902	685	152	604	145	808	529	101	766	449	113	750	600	770	746	559	477	91	774	919	523	316	231	583	714	957	875	662	636	593	412	463	185	444	281	127	575	294	773	723	159	797	722	47	394	566	70	735	502	836	138	210	750	913	29	18	28	743	273	656	126	288	370	487	811	137	261	82	270	154	394	607	426	751	605	431	825	585	402	435	318	851	704	708	520	967	979	309	414	284	392	272	242	128	562	12	469	398	652	132	457	689	922	417	259	271	119	560	453	14	869	942	845	181	646	199	496	990	418	600	24	652	621	889	627	321	201	242	314	23	496	9	885	486	587	542	28	724	927	159	1	181	53	977	926	805	209	453	373	746	75	279	813	391	679	445	12	310	728	96	577	414	729	591	914	630	845	668	424	919	352	52	356	108	933	6	95	540	549	501	716	420	773	292	984	550	947	493	308	759	143	871	785	139	676	533	917	413	789	364	485	558	228	309	285	483	104	411	294	155	331	184	730	473	337	476	304	58	633	783	220	190	206	848	796	165	575	996	539	863	626	596	354	322	444	614	978	300	846	642	444	407	892	970	686	926	88	305	201	82	39	282	907	687	15	605	47	616	979	143	55	117	532	907	252	210	715	539	89	624	223	757	314	291	346	734	639	984	705	909	130	235	658	596	3	385	54	325	898	641	571	5	767	289	842	964	500	705	634	606	952	932	376	622	370	526	476	700	419	9	342	73	20	835	266	965	339	420	653	448	427	979	999	496	24	445	922	902	660	491	4	365	5	537	163	567	976	2	850	175	686	853	566	211	127	20	529	401	753	700	483	470	713	346	428	91	2	223	224	613	388	246	60	304	641	278	372	631	750	114	172	54	223	789	674	612	506	180	795	735	929	971	681	20	717	451	389	763
+1	409	645	664	609	522	814	849	716	290	465	520	856	328	560	340	604	438	611	953	731	957	856	620	708	410	703	108	247	936	712	779	272	26	710	738	135	390	221	377	653	701	963	739	323	666	309	662	723	833	999	759	366	41	522	989	633	302	199	524	727	836	119	184	567	389	475	233	866	720	839	674	336	902	684	590	647	990	487	675	725	942	464	490	318	741	968	709	940	83	698	728	820	611	828	684	540	127	125	237	181	521	898	259	908	577	874	197	858	947	858	917	549	221	566	111	689	301	816	763	950	298	283	58	178	255	425	802	562	919	921	62	683	24	910	552	879	568	852	917	918	259	296	947	775	384	73	930	583	488	583	358	34	481	418	879	987	674	359	496	83	101	471	905	285	146	832	803	643	732	571	280	861	191	478	432	824	317	27	269	8	225	611	402	965	632	529	65	120	146	261	60	31	137	611	365	227	511	117	726	484	14	212	490	644	986	627	717	969	146	325	712	643	943	321	952	416	590	59	376	940	310	268	394	929	535	955	125	621	187	108	567	910	120	807	49	781	176	989	318	213	425	130	996	86	690	594	615	623	473	511	610	314	217	841	375	409	635	449	100	838	131	264	230	241	617	794	928	465	866	547	410	712	850	169	358	358	888	396	677	975	61	210	758	63	397	541	513	338	439	945	67	415	437	253	446	303	838	583	996	92	391	72	269	525	376	934	43	681	57	195	760	964	105	234	63	622	207	488	396	870	977	826	102	758	567	310	680	273	327	231	121	528	434	703	636	952	643	972	80	962	124	303	686	690	565	105	916	869	640	562	627	707	422	42	881	736	746	337	663	278	772	528	518	792	236	376	558	845	304	106	863	382	149	12	646	849	728	511	104	213	437	425	832	194	550	468	107	763	369	403	659	379	884	181	856	671	62	849	623	68	509	151	724	982	805	560	721	956	280	978	163	438	162	22	576	404	905	459	189	917	160	559	25	848	432	466	869	474	596	137	41	429	721	564	274	443	974	314	485	272	273	487	963	883	864	228	743	512	75	150	476	720	126	930	122	293	523	187	289	339	12	594	948	346	788	723	881	711	532	475	715	760	882	270	755	861	597	924	869	46	138	839	634	600	592	478	117	859	387	396	829	137	343	862	594	382	74	306	84	286	562	176	193	688	497	715	353	309	644	770	329	285	204	777	121	762	393	983	853	264	5	668	434	515	459	938	223	705	741	151	669	269	136	961	132	697	4	500	463	800	705	997	507	936	334	465	501	523	871	749	515	203	19	888	487	357	598	533	336	640	969	737	535	430	401	821	864	290	98	643	849	987	983	986	53	111	951	917	642	599	230	715	910	599	988	470	263	461	869	271	603	604	332	104	193	283	658	918	687	101	540	745	830	520	831	603	805	201	746	659	287	413	76	914	12	221	199	677	144	271	836	494	566	921	530	301	872	363	87	882	545	663	18	725	940	578	253	77	534	805	864	939	510	697	525	917	911	852	931	26	357	246	347	590	664	544	440	224	687	638	889	707	612	28	663	39	491	527	815	708	598	124	991	119	203	550	307	893	919	66	820	877	423	745	440	336	368	823	146	127	18	289	780	656	144	748	81	14	167	319	359	829	382	233	166	383	742	194	821	852	478	854	579	475	756	497	246	51	45	170	682	458	139	624	150	621	783	196	54	280	556	376	438	76	968	803	724	766	185	742	134	401	401	836	255	80	7	96	506	751	417	312	251	53	724	670	0	875	398	657	578	827	739	997	927	748	629	398	669	157	317	846	577	799	697	858	970	927	536	319	233	966	336	621	847	693	466	847	4	441	794	645	617	249	276	257	876	701	191	735	769	100	177	698	590	372	485	322	258	317	898	339	542	295	44	636	962	506	589	182	622	762	127	686	982	708	281	846	983	950	696	656	643	630	456	890	353	146	762	773	306	965	196	248	890	572	872	623	528	785	66	806	965	764	504	667	475	95	685	291	305	530	209	106	798	509	681	150	379	901	666	211	794	965	286	920	656	364	903	934	844	26	694	891	703	390	2	385	312	366	61	616	965	853	393	980	316	881	156	142	639	976	399	8	793	424	10	293	139	814	827	260	485	943	686	452	27	556	445	5	831	636	392	901	959	679	275	120	381	864	130	3	830	413	919	291	319	873	275	185	130	244	927	65	272	161	228	637	224	753	24	746	190	516	935	998	502	852	106	52	985	660	109	370	184	394	378	668	540	230	315	950	774	736	927	283	429	184	290	649	316	136	987	662	918	171	57	810	639	161	243	588	61	522	396	60	127	568	748	244

cluster_test.go

@@ -2,7 +2,7 @@ package main
 
 import (
 	"bytes"
-	"io/ioutil"
+	"os"
 	"path"
 	"testing"
 )
@@ -24,8 +24,8 @@ func TestCluster(t *testing.T) {
 	output_buffer.Flush()
 	out_file.Close()
 
-	f1, _ := ioutil.ReadFile(output_tree)
-	f2, _ := ioutil.ReadFile(expected_output_tree)
+	f1, _ := os.ReadFile(output_tree)
+	f2, _ := os.ReadFile(expected_output_tree)
 	if !bytes.Equal(f1, f2) {
 		t.Fatal("Input and output files to not match.")
 	}
@@ -37,13 +37,13 @@ type LinkageMethodTest struct {
 }
 
 var LinkageMethodTests = []LinkageMethodTest{
-	LinkageMethodTest{0, "average"},
-	LinkageMethodTest{1, "centroid"},
-	LinkageMethodTest{2, "complete"},
-	LinkageMethodTest{3, "mcquitty"},
-	LinkageMethodTest{4, "median"},
-	LinkageMethodTest{5, "single"},
-	LinkageMethodTest{6, "ward"},
+	{0, "average"},
+	{1, "centroid"},
+	{2, "complete"},
+	{3, "mcquitty"},
+	{4, "median"},
+	{5, "single"},
+	{6, "ward"},
 }
 
 func TestGetLinkageMethod(t *testing.T) {

data_scheduler.go

@@ -22,61 +22,81 @@ Determine how many bins of the input dataset should be processed when running th
 The bucket size means the x Profiles will be processed by a thread, which will directly
 relate to how many go routines are run at a time.
 */
-func CalculateBucketSize(data_length int, runtime_cpus int, cpu_modifier int) int {
-	if cpu_modifier <= 0 {
-		log.Fatal("CPU modifier must be greater than 0")
+func CalculateBucketSize(data_length int, minimum_bins int, bucket_increase int) (int, int) {
+
+	if minimum_bins == 0 {
+		log.Fatal("You must have a CPU modifier value greater than 0")
+	}
+
+	bucket_size := (data_length / minimum_bins)
+	if bucket_size == 0 {
+		bucket_size++
+	}
+
+	remainder := data_length % minimum_bins
+
+	if remainder == 0 {
+		/*
+			when the remainder is 0 there is now spill over resulting in a
+			temporary reduction in the number of "bins used". As there is no
+			spill over bin.
+		*/
+		bucket_size--
 	}
-	bucket_size := data_length / (runtime_cpus * cpu_modifier)
-	return bucket_size
+
+	if data_length < bucket_size {
+		return data_length, 1
+	}
+
+	if bucket_size < minimum_bins {
+		bucket_size *= bucket_increase
+		minimum_bins = data_length / bucket_size
+	}
+
+	return bucket_size, minimum_bins
 }
 
 // A pair containing the start and end values for a given range of data to be processed.
 type Bucket struct {
 	start, end int
 }
 
+// Get the difference in indices between the two bucket fields
+func (t *Bucket) Diff() int {
+	return t.end - t.start
+}
+
 // The distance metric for a given comparison
 type ComparedProfile struct {
 	compared, reference *string
 	distance            float64
 }
 
-/*
-For a given data set determine the the start and end range of each of the bins to be used.
-e.g. if a dataset has 1000 profiles, and our bucket size is 500 we will create bins with
-an of [0, 500], [500, 1000]
-*/
-func BucketsIndices(data_length int, bucket_size int) []Bucket {
-	var bucks []Bucket
-	cpu_load_factor := CPU_LOAD_FACTOR // Need to add description to global options
-	window := bucket_size
-
-	cpu_load_string := fmt.Sprintf("CPU load factor x%d", cpu_load_factor)
-	log.Println(cpu_load_string)
-
-	if window > data_length {
-		bucks = append(bucks, Bucket{0, data_length})
-		log.Println("Running single threaded as there are too few entries to justify multithreading.")
-		return bucks
-	}
+// Calculate the initial bin sizes to use for running profiles in parallel
+func CreateBucketIndices(data_length int, bucket_size int, modifier int) []Bucket {
+	var buckets []Bucket
 
-	if data_length < (runtime.NumCPU() * cpu_load_factor) {
-		bucks = append(bucks, Bucket{0, data_length})
-		log.Println("Running single threaded as there are too few entries to justify multithreading.")
-		return bucks
+	if (data_length-modifier) < bucket_size || bucket_size > data_length {
+		// Just return the one set of indices the values are small enough
+		buckets = append(buckets, Bucket{modifier, data_length})
+		return buckets
 	}
 
-	for i := window; i < data_length; i = i + window {
-		bucks = append(bucks, Bucket{i - window, i})
+	for i := (bucket_size + modifier); i < data_length; i = i + bucket_size {
+		new_bucket := Bucket{i - bucket_size, i}
+		buckets = append(buckets, new_bucket)
 	}
 
-	bucks = append(bucks, Bucket{bucks[len(bucks)-1].end, data_length})
+	final_start := buckets[len(buckets)-1].end
+	final_end := data_length
 
-	threads_running := fmt.Sprintf("Using %d threads for running.", len(bucks)-1)
-	log.Println(threads_running)
-	profiles_to_thread := fmt.Sprintf("Allocating ~%d profiles per a thread.", window)
-	log.Println(profiles_to_thread)
-	return bucks
+	if final_end-final_start < bucket_size {
+		// Extend the last index if required if it is very small
+		buckets[len(buckets)-1].end = data_length
+	} else {
+		buckets = append(buckets, Bucket{final_start, final_end})
+	}
+	return buckets
 }
 
 // Compute profile differences in a given go routine.
@@ -103,7 +123,8 @@ them directly to the passed in bufio.Writer.
 func RunData(profile_data *[]*Profile, f *bufio.Writer) {
 	/* Schedule and arrange the calculation of the data in parallel
 	This function is quite large and likely has room for optimization.
-	TODO redistribute data across threads at run time
+
+	Once day an incredible optimization here would be to go lockless, or re-use threads
 	*/
 
 	start := time.Now()
@@ -113,49 +134,52 @@ func RunData(profile_data *[]*Profile, f *bufio.Writer) {
 
 	bucket_index := 0
 	empty_name := ""
-	const cpu_modifier = 2
-	bucket_size := CalculateBucketSize(len(data), runtime.NumCPU(), cpu_modifier)
-	buckets := BucketsIndices(len(data), bucket_size)
-	arr_pos := 1
+	const cpu_modifier = 3
+	data_size := len(data)
+	minimum_buckets := runtime.NumCPU() * cpu_modifier
+	bucket_size, _ := CalculateBucketSize(data_size, minimum_buckets, cpu_modifier)
+	buckets := CreateBucketIndices(data_size, bucket_size, 0)
 	format_expression := GetFormatString()
-
-	// TODO can create a pool of go routines and pass the profile to compare to each channel
+	initial_bucket_location := buckets[0].start
 	var wg sync.WaitGroup
-	for g := range data[0:] {
-		profile_comp := data[g] // copy struct for each thread
+
+	for idx := range data {
+		profile_comp := data[idx] // copy struct for each thread
 		values_write := make([]*[]*ComparedProfile, len(buckets)-bucket_index)
-		// TODO an incredible optimization here would be to go lockless, or re-use threads
-		for i := bucket_index; i < len(buckets); i++ {
-			array_writes := make([]*ComparedProfile, buckets[i].end-buckets[i].start)
-			values_write[i-bucket_index] = &array_writes
+		for b_idx, b := range buckets {
+			array_writes := make([]*ComparedProfile, b.Diff())
+			values_write[b_idx] = &array_writes
 			wg.Add(1)
 			go func(output_array *[]*ComparedProfile, bucket_compute Bucket, profile_compare *Profile) {
 				ThreadExecution(&data, profile_compare, bucket_compute, dist, output_array)
 				wg.Done()
-			}(&array_writes, buckets[i], profile_comp)
+			}(&array_writes, b, profile_comp)
 		}
-		wg.Wait()                     // Wait for everyone to catch up
-		buckets[bucket_index].start++ // update the current buckets tracker
+
+		wg.Wait()          // Wait for everyone to catch up
+		buckets[0].start++ // update the current buckets tracker
 
 		for _, i := range values_write {
 			for _, value := range *i {
 				fmt.Fprintf(f, format_expression, *(*value).compared, *(*value).reference, (*value).distance)
 			}
 		}
 
-		if len(buckets) > 1 && arr_pos%bucket_size == 0 {
-			for f := buckets[bucket_index].end - bucket_size; f < buckets[bucket_index].end; f++ {
-				data[f].profile = nil
-				data[f].name = empty_name
-
+		if len(buckets) != 1 && buckets[0].Diff() < minimum_buckets {
+			bucket_size, minimum_buckets = CalculateBucketSize(data_size-idx, minimum_buckets, cpu_modifier)
+			buckets = CreateBucketIndices(data_size, bucket_size, idx)
+			for index := initial_bucket_location; index < buckets[0].start; index++ {
+				data[index].profile = nil
+				data[index].name = empty_name
 			}
-			bucket_index++
-			end := time.Now().Sub(start)
-			thread_depletion_time := fmt.Sprintf("One thread depleted in: %fs", end.Seconds())
+			initial_bucket_location = buckets[0].start
+			buckets[0].start++ // start index is reserved so needs to be incremented
+			end := time.Since(start)
+			thread_depletion_time := fmt.Sprintf("Redistributing data across threads. %fs", end.Seconds())
 			log.Println(thread_depletion_time)
 			start = time.Now()
 		}
-		arr_pos++
+
 	}
 	wg.Wait()
 	f.Flush()

data_scheduler_test.go

@@ -2,7 +2,7 @@ package main
 
 import (
 	"bytes"
-	"io/ioutil"
+	"os"
 	"path"
 	"testing"
 )
@@ -12,13 +12,13 @@ type bucket_tests struct {
 }
 
 var bucket_size_tests = []bucket_tests{
-	bucket_tests{10, 1, 1, 10},
-	bucket_tests{10, 2, 1, 5},
+	{10, 1, 1, 9},
+	{10, 2, 1, 4},
 }
 
 func TestCalculateBucketSize(t *testing.T) {
 	for _, test := range bucket_size_tests {
-		if output := CalculateBucketSize(test.data_length, test.bucket_size, test.cpu_modifier); output != test.expected {
+		if output, _ := CalculateBucketSize(test.data_length, test.bucket_size, test.cpu_modifier); output != test.expected {
 			t.Errorf("Output %d not equal to expected %d", output, test.expected)
 			t.Errorf("Output %+v", output)
 		}
@@ -47,10 +47,86 @@ func TestRunData(t *testing.T) {
 	out_file.Close()
 
 	// Compare outputs line by line
-	f1, _ := ioutil.ReadFile(test_expected_output)
-	f2, _ := ioutil.ReadFile(test_output_file)
-
+	f1, _ := os.ReadFile(test_expected_output)
+	f2, _ := os.ReadFile(test_output_file)
 	if !bytes.Equal(f1, f2) {
 		t.Fatal("Input and output files to not match.")
 	}
 }
+
+func TestRunDataSmall(t *testing.T) {
+	tempdir := t.TempDir()
+
+	t.Log("Starting end to end test for distance calculations.")
+	test_input := "TestInputs/DistanceMatrix/Random_2_input.txt"
+	test_output_file := path.Join(tempdir, "output.txt")
+
+	t.Logf("Test Input: %s", test_input)
+	t.Logf("Test Output Temp File: %s", test_output_file)
+	t.Log("Creating output buffer.")
+	out_buffer, out_file := CreateOutputBuffer(test_output_file)
+
+	t.Log("Loading test allele profiles.")
+	test_data := LoadProfile(test_input)
+	RunData(test_data, out_buffer)
+	out_buffer.Flush()
+	out_file.Close()
+
+	// Compare outputs line by line
+	f2, _ := os.ReadFile(test_output_file)
+	output := string(f2)
+	if output != "1 1 0\n" {
+		t.Fatal("Input does not equal output.")
+	}
+}
+
+// Testing the redistribution of bucket indices at runtime
+func TestRedistributeBuckets(t *testing.T) {
+	var profile_size int = 100
+	var cpus int = 6
+	BUCKET_SCALE = 2
+	minimum_bucket_size := cpus * BUCKET_SCALE
+	var buckets int
+	buckets, minimum_bucket_size = CalculateBucketSize(profile_size, minimum_bucket_size, BUCKET_SCALE)
+	bucket_indices := CreateBucketIndices(profile_size, buckets, 0)
+
+	comparisons := make([][]int, profile_size)
+	for idx := range comparisons {
+		comparisons[idx] = make([]int, 0)
+	}
+
+	corrected_profile_size := profile_size
+	for val := range profile_size {
+		for _, b := range bucket_indices {
+			for i := b.start; i < b.end; i++ {
+				comparisons[val] = append(comparisons[val], i)
+			}
+		}
+
+		if len(bucket_indices) != 1 && bucket_indices[0].Diff() < minimum_bucket_size {
+			buckets, minimum_bucket_size = CalculateBucketSize(profile_size-val, minimum_bucket_size, BUCKET_SCALE)
+			bucket_indices = CreateBucketIndices(profile_size, buckets, val)
+		}
+		bucket_indices[0].start++
+	}
+
+	profile_sizes := 0
+	// Check correct number of values computed
+	for idx := profile_sizes; idx != 0; idx-- {
+		if len(comparisons[idx]) != corrected_profile_size {
+			t.Fatalf("Mismatched number of outputs for entry for index %d: %d != %d", idx, profile_sizes, len(comparisons[idx]))
+		}
+		profile_sizes++
+	}
+
+	// Check content
+	for val := range corrected_profile_size {
+		idx := val
+		for _, i := range comparisons[val] {
+			if i != idx {
+				t.Fatalf("Index: %d, Incorrect outputs: %d != %d", val, i, idx)
+			}
+			idx++
+		}
+	}
+}