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* Fix benchmark values * Add custom benchmark tool for rsidvar
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| Original file line number | Diff line number | Diff line change |
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| @@ -1 +1 @@ | ||
| 2.7.0 | ||
| 2.7.1 |
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| @@ -0,0 +1,11 @@ | ||
| set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib) | ||
| set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib) | ||
| set(RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/cmd) | ||
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| # Add the binary tree directory to the search path for linking and include files | ||
| link_directories(${PROJECT_BINARY_DIR}/src) | ||
| include_directories(${CMAKE_CURRENT_BINARY_DIR} ${PROJECT_BINARY_DIR}/src) | ||
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| file(COPY DESTINATION ${CMAKE_CURRENT_BINARY_DIR}) | ||
| add_executable(rsidvar_bench rsidvar_bench.c) | ||
| target_link_libraries(rsidvar_bench variantkey) |
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| // Benchmark tool for rsidvar | ||
| // | ||
| // rsidvar_bench.c | ||
| // | ||
| // @category Tools | ||
| // @author Nicola Asuni <nicola.asuni@genomicsplc.com> | ||
| // @copyright 2017-2018 GENOMICS plc | ||
| // @license MIT (see LICENSE) | ||
| // @link https://github.com/genomicsplc/variantkey | ||
| // | ||
| // LICENSE | ||
| // | ||
| // Copyright (c) 2017-2018 GENOMICS plc | ||
| // | ||
| // Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| // of this software and associated documentation files (the "Software"), to deal | ||
| // in the Software without restriction, including without limitation the rights | ||
| // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| // copies of the Software, and to permit persons to whom the Software is | ||
| // furnished to do so, subject to the following conditions: | ||
| // | ||
| // The above copyright notice and this permission notice shall be included in | ||
| // all copies or substantial portions of the Software. | ||
| // | ||
| // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| // THE SOFTWARE. | ||
| // | ||
| // VariantKey by Nicola Asuni | ||
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| // NOTE: This test is slow because it generates the test files from scratch. | ||
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| #if __STDC_VERSION__ >= 199901L | ||
| #define _XOPEN_SOURCE 600 | ||
| #else | ||
| #define _XOPEN_SOURCE 500 | ||
| #endif | ||
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| #include <inttypes.h> | ||
| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include <string.h> | ||
| #include <time.h> | ||
| #include <sys/mman.h> | ||
| #include "../../src/rsidvar.h" | ||
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| #define TEST_DATA_SIZE 400000000UL | ||
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| // returns current time in nanoseconds | ||
| uint64_t get_time() | ||
| { | ||
| struct timespec t; | ||
| clock_gettime(CLOCK_PROCESS_CPUTIME_ID, &t); | ||
| return (((uint64_t)t.tv_sec * 1000000000) + (uint64_t)t.tv_nsec); | ||
| } | ||
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| int benchmark_find_rv_variantkey_by_rsid() | ||
| { | ||
| const char *filename = "rsvk_test_400M.bin"; | ||
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| uint32_t i; | ||
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| FILE *f = fopen(filename, "w"); | ||
| if (f == NULL) | ||
| { | ||
| fprintf(stderr, " * %s Unable to open %s file in writing mode.\n", __func__, filename); | ||
| return 1; | ||
| } | ||
| unsigned char b0, b1, b2, b3, z = 0; | ||
| for (i=0 ; i < TEST_DATA_SIZE; i++) | ||
| { | ||
| b0 = i & 0xFF; | ||
| b1 = (i >> 8) & 0xFF; | ||
| b2 = (i >> 16) & 0xFF; | ||
| b3 = (i >> 24) & 0xFF; | ||
| fprintf(f, "%c%c%c%c%c%c%c%c%c%c%c%c", b3, b2, b1, b0, z, z, z, z, b3, b2, b1, b0); | ||
| } | ||
| fclose(f); | ||
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| mmfile_t rv = {0}; | ||
| mmap_binfile(filename, &rv); | ||
| uint64_t nitems = (uint64_t)(rv.size / BINBLKLEN); | ||
| if (nitems != TEST_DATA_SIZE) | ||
| { | ||
| fprintf(stderr, " * %s Expecting rsvk_test_400M.bin %" PRIu64 " items, got instead: %" PRIu64 "\n", __func__, TEST_DATA_SIZE, nitems); | ||
| return 1; | ||
| } | ||
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| uint64_t tstart, tend, offset; | ||
| volatile uint64_t sum = 0; | ||
| uint64_t first; | ||
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| tstart = get_time(); | ||
| for (i=0 ; i < TEST_DATA_SIZE; i++) | ||
| { | ||
| sum += i; | ||
| } | ||
| tend = get_time(); | ||
| offset = (tend - tstart); | ||
| fprintf(stdout, " * %s sum: %" PRIu64 "\n", __func__, sum); | ||
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| int j; | ||
| for (j=0 ; j < 3; j++) | ||
| { | ||
| sum = 0; | ||
| tstart = get_time(); | ||
| for (i=0 ; i < TEST_DATA_SIZE; i++) | ||
| { | ||
| first = 0; | ||
| sum += find_rv_variantkey_by_rsid(rv.src, &first, TEST_DATA_SIZE, i); | ||
| } | ||
| tend = get_time(); | ||
| fprintf(stdout, " * %s %d. sum: %" PRIu64 " -- time: %" PRIu64 " ns -- %" PRIu64 " ns/op\n", __func__, j, sum, (tend - tstart - offset), (tend - tstart - offset)/TEST_DATA_SIZE); | ||
| } | ||
| return 0; | ||
| } | ||
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| int benchmark_find_vr_rsid_by_variantkey() | ||
| { | ||
| const char *filename = "vkrs_test_400M.bin"; | ||
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| uint64_t i; | ||
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| FILE *f = fopen(filename, "w"); | ||
| if (f == NULL) | ||
| { | ||
| fprintf(stderr, " * %s Unable to open %s file in writing mode.\n", __func__, filename); | ||
| return 1; | ||
| } | ||
| unsigned char b0, b1, b2, b3, z = 0; | ||
| for (i=0 ; i < TEST_DATA_SIZE; i++) | ||
| { | ||
| b0 = i & 0xFF; | ||
| b1 = (i >> 8) & 0xFF; | ||
| b2 = (i >> 16) & 0xFF; | ||
| b3 = (i >> 24) & 0xFF; | ||
| fprintf(f, "%c%c%c%c%c%c%c%c%c%c%c%c", z, z, z, z, b3, b2, b1, b0, b3, b2, b1, b0); | ||
| } | ||
| fclose(f); | ||
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| mmfile_t vr = {0}; | ||
| mmap_binfile(filename, &vr); | ||
| uint64_t nitems = (uint64_t)(vr.size / BINBLKLEN); | ||
| if (nitems != TEST_DATA_SIZE) | ||
| { | ||
| fprintf(stderr, " * %s Expecting vkrs_test_400M.bin %" PRIu64 " items, got instead: %" PRIu64 "\n", __func__, TEST_DATA_SIZE, nitems); | ||
| return 1; | ||
| } | ||
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| uint64_t tstart, tend, offset; | ||
| volatile uint64_t sum = 0; | ||
| uint64_t first; | ||
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| tstart = get_time(); | ||
| for (i=0 ; i < TEST_DATA_SIZE; i++) | ||
| { | ||
| sum += i; | ||
| } | ||
| tend = get_time(); | ||
| offset = (tend - tstart); | ||
| fprintf(stdout, " * %s sum: %" PRIu64 "\n", __func__, sum); | ||
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| int j; | ||
| for (j=0 ; j < 3; j++) | ||
| { | ||
| sum = 0; | ||
| tstart = get_time(); | ||
| for (i=0 ; i < TEST_DATA_SIZE; i++) | ||
| { | ||
| first = 0; | ||
| sum += find_vr_rsid_by_variantkey(vr.src, &first, TEST_DATA_SIZE, i); | ||
| } | ||
| tend = get_time(); | ||
| fprintf(stdout, " * %s %d. sum: %" PRIu64 " -- time: %" PRIu64 " ns -- %" PRIu64 " ns/op\n", __func__, j, sum, (tend - tstart - offset), (tend - tstart - offset)/TEST_DATA_SIZE); | ||
| } | ||
| return 0; | ||
| } | ||
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| int main() | ||
| { | ||
| int ret = 0; | ||
| ret += benchmark_find_rv_variantkey_by_rsid(); | ||
| ret += benchmark_find_vr_rsid_by_variantkey(); | ||
| return ret; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| package: | ||
| name: vk | ||
| version: 2.7.0 | ||
| version: 2.7.1 | ||
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| source: | ||
| path: ../.. | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| package: | ||
| name: variantkey | ||
| version: 2.7.0 | ||
| version: 2.7.1 | ||
|
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||
| source: | ||
| path: ../.. | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| package: | ||
| name: r-variantkey | ||
| version: 2.7.0 | ||
| version: 2.7.1 | ||
|
|
||
| source: | ||
| path: ../.. | ||
|
|
||
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