/*
* Translate scanned MS options to Watcom options.
*/
void OptionsTranslate( OPT_STORAGE *cmdOpts, CmdLine *compCmdLine,
CmdLine *linkCmdLine )
/****************************************************************/
{
/*** Parse the /nologo switch now so we can print the banner ***/
init_status( &status );
if( cmdOpts->nologo ) {
QuietModeMessage();
} else {
BannerMessage();
}
/*** Parse everything ***/
unsupported_opts( cmdOpts );
default_opts( &status, cmdOpts, compCmdLine, linkCmdLine );
compiler_opts( &status, cmdOpts, compCmdLine );
linker_opts( &status, cmdOpts, linkCmdLine );
merge_opts( &status, cmdOpts, compCmdLine, linkCmdLine );
}
void test_parse_cmdline_inner_loop_are_basic_variables_correctly_set()
{
// --COLOUR_LIST
char* argv1[] = {"cortex", "--colour_list=../data/test/pop_graph/cmd_line/colour_list_1"};
//set up a default cmdline
CmdLine test1;
default_opts(&test1);
char error_string1[LEN_ERROR_STRING];
int err = parse_cmdline_inner_loop(2, argv1, sizeof(Element), &test1, error_string1);
CU_ASSERT(err==0);
CU_ASSERT_STRING_EQUAL(test1.colour_list, "../data/test/pop_graph/cmd_line/colour_list_1");
CU_ASSERT(test1.input_colours==true);
//--MULTICOLOUR_BIN
char* argv2[] = {"cortex", "--multicolour_bin=../data/test/pop_graph/cmd_line/multicolour_bin_1.ctx"};
//set up a default cmdline
CmdLine test2;
default_opts(&test2);
char error_string2[LEN_ERROR_STRING];
int err2 = parse_cmdline_inner_loop(2, argv2, sizeof(Element), &test2, error_string2);
CU_ASSERT(err2==0);
CU_ASSERT_STRING_EQUAL(test2.multicolour_bin, "../data/test/pop_graph/cmd_line/multicolour_bin_1.ctx");
CU_ASSERT(test2.input_multicol_bin==true);
// SE LIST
char* argv3[] = {"cortex", "--se_list=../data/test/pop_graph/cmd_line/se_list1"};
//set up a default cmdline
CmdLine test3;
default_opts(&test3);
char error_string3[LEN_ERROR_STRING];
int err3 = parse_cmdline_inner_loop(2, argv3, sizeof(Element), &test3, error_string3);
CU_ASSERT_STRING_EQUAL(test3.se_list, "../data/test/pop_graph/cmd_line/se_list1");
CU_ASSERT(test3.input_seq==true);
//PE_LIST
char* argv4[] = {"cortex", "--pe_list=../data/test/pop_graph/cmd_line/pe_list1,../data/test/pop_graph/cmd_line/pe_list2"};
//set up a default cmdline
CmdLine test4;
default_opts(&test4);
char error_string4[LEN_ERROR_STRING];
int err4 = parse_cmdline_inner_loop(2, argv4, sizeof(Element), &test4, error_string4);
CU_ASSERT_STRING_EQUAL(test4.pe_list_lh_mates, "../data/test/pop_graph/cmd_line/pe_list1");
CU_ASSERT_STRING_EQUAL(test4.pe_list_rh_mates, "../data/test/pop_graph/cmd_line/pe_list2");
CU_ASSERT(test4.input_seq==true);
// KMER SIZE
char* argv5[] = {"cortex", "--kmer_size=17"};
//set up a default cmdline
CmdLine test5;
default_opts(&test5);
char error_string5[LEN_ERROR_STRING];
int err5 = parse_cmdline_inner_loop(2, argv5, sizeof(Element), &test5, error_string5);
CU_ASSERT(test5.kmer_size==17);
// HASH TABLE NUMBER OF BUCKETS
char* argv6[] = {"cortex", "--mem_height=20"};
//set up a default cmdline
CmdLine test6;
default_opts(&test6);
char error_string6[LEN_ERROR_STRING];
int err6 = parse_cmdline_inner_loop(2, argv6, sizeof(Element), &test6, error_string6);
CU_ASSERT(test6.number_of_buckets_bits==20);
// DEPTH OF HASH TABLE BUCKETS
char* argv7[] = {"cortex", "--mem_height=100"};
//set up a default cmdline
CmdLine test7;
default_opts(&test7);
char error_string7[LEN_ERROR_STRING];
int err7 = parse_cmdline_inner_loop(2, argv7, sizeof(Element), &test7, error_string7);
CU_ASSERT(test7.bucket_size==100);
// REF COLOUR
char* argv8[] = {"cortex", "--ref_colour=0"};
//set up a default cmdline
CmdLine test8;
default_opts(&test8);
char error_string8[LEN_ERROR_STRING];
int err8 = parse_cmdline_inner_loop(2, argv8, sizeof(Element), &test8, error_string8);
CU_ASSERT(test8.ref_colour==0);
CU_ASSERT(test8.using_ref==true);
// REMV PCR DUPS
char* argv9[] = {"cortex", "--remove_pcr_duplicates"};
//set up a default cmdline
CmdLine test9;
default_opts(&test9);
char error_string9[LEN_ERROR_STRING];
int err9 = parse_cmdline_inner_loop(2, argv9, sizeof(Element), &test9, error_string9);
CU_ASSERT(test9.remove_pcr_dups==true);
// CUT HOMOPOLYMERS
char* argv10[] = {"cortex", "--cut_homopolymers=4"};
//set up a default cmdline
CmdLine test10;
default_opts(&test10);
char error_string10[LEN_ERROR_STRING];
int err10 = parse_cmdline_inner_loop(2, argv10, sizeof(Element), &test10, error_string10);
CU_ASSERT(test10.cut_homopolymers==true);
CU_ASSERT(test10.homopolymer_limit==4);
// QUALITY SCORE THRESHOLD
char* argv12[] = {"cortex", "--quality_score_threshold=47"};
//set up a default cmdline
CmdLine test12;
default_opts(&test12);
char error_string12[LEN_ERROR_STRING];
int err12 = parse_cmdline_inner_loop(2, argv12, sizeof(Element), &test12, error_string12);
CU_ASSERT(test12.quality_score_threshold==47);
// REMOVE SEQ ERRORS USING COVG AND TOPOLOGY OF GRAPH
char* argv14[] = {"cortex", "--remove_seq_errors"};
//set up a default cmdline
CmdLine test14;
default_opts(&test14);
char error_string14[LEN_ERROR_STRING];
int err14 = parse_cmdline_inner_loop(2, argv14, sizeof(Element), &test14, error_string14);
CU_ASSERT(test14.remove_seq_errors==true);
// DUMP BINARY
char* argv15[] = {"cortex", "--dump_binary=/path/to/nonexistent/file"};
//set up a default cmdline
CmdLine test15;
default_opts(&test15);
char error_string15[LEN_ERROR_STRING];
int err15 = parse_cmdline_inner_loop(2, argv15, sizeof(Element), &test15, error_string15);
CU_ASSERT(test15.dump_binary==true);
CU_ASSERT_STRING_EQUAL(test15.output_binary_filename, "/path/to/nonexistent/file");
// DETECT_BUBBLES_1
char* argv17[] = {"cortex", "--detect_bubbles1=1,4,9/2,4"};
//set up a default cmdline
CmdLine test17;
default_opts(&test17);
char error_string17[LEN_ERROR_STRING];
int err17 = parse_cmdline_inner_loop(2, argv17, sizeof(Element), &test17, error_string17);
CU_ASSERT(test17.detect_bubbles1==true);
CU_ASSERT(test17.num_colours_in_detect_bubbles1_first_colour_list==3);
CU_ASSERT(test17.detect_bubbles1_first_colour_list[0]==1);
CU_ASSERT(test17.detect_bubbles1_first_colour_list[1]==4);
CU_ASSERT(test17.detect_bubbles1_first_colour_list[2]==9);
CU_ASSERT(test17.num_colours_in_detect_bubbles1_second_colour_list==2);
CU_ASSERT(test17.detect_bubbles1_second_colour_list[0]==2 );
CU_ASSERT(test17.detect_bubbles1_second_colour_list[1]==4 );
// DETECT_BUBBLES_2
char* argv18[] = {"cortex", "--detect_bubbles2=1,4,9/2,4"};
//set up a default cmdline
CmdLine test18;
default_opts(&test18);
char error_string18[LEN_ERROR_STRING];
int err18 = parse_cmdline_inner_loop(2, argv18, sizeof(Element), &test18, error_string18);
CU_ASSERT(test18.detect_bubbles2==true);
CU_ASSERT(test18.num_colours_in_detect_bubbles2_first_colour_list==3);
CU_ASSERT(test18.detect_bubbles2_first_colour_list[0]==1);
CU_ASSERT(test18.detect_bubbles2_first_colour_list[1]==4);
CU_ASSERT(test18.detect_bubbles2_first_colour_list[2]==9);
CU_ASSERT(test18.num_colours_in_detect_bubbles2_second_colour_list==2);
CU_ASSERT(test18.detect_bubbles2_second_colour_list[0]==2 );
CU_ASSERT(test18.detect_bubbles2_second_colour_list[1]==4 );
// OUTPUT DETECT_BUBBLES1
char* argv19[] = {"cortex", "--output_bubbles1=/nonexistent_file_zamzam"};
//set up a default cmdline
CmdLine test19;
default_opts(&test19);
char error_string19[LEN_ERROR_STRING];
int err19 = parse_cmdline_inner_loop(2, argv19, sizeof(Element), &test19, error_string19);
CU_ASSERT_STRING_EQUAL(test19.output_detect_bubbles1, "/nonexistent_file_zamzam");
// OUTPUT DETECT_BUBBLES2
char* argv20[] = {"cortex", "--output_bubbles2=/nonexistent_file_zim"};
//set up a default cmdline
CmdLine test20;
default_opts(&test20);
char error_string20[LEN_ERROR_STRING];
int err20 = parse_cmdline_inner_loop(2, argv20, sizeof(Element), &test20, error_string20);
CU_ASSERT_STRING_EQUAL(test20.output_detect_bubbles2, "/nonexistent_file_zim");
// INPUT FORMAT
char* argv21[] = {"cortex", "--format=CTX"};
//set up a default cmdline
CmdLine test21;
default_opts(&test21);
char error_string21[LEN_ERROR_STRING];
int err21 = parse_cmdline_inner_loop(2, argv21, sizeof(Element), &test21, error_string21);
CU_ASSERT(test21.format_of_input_seq==CTX);
//MAX READ LENGTH
char* argv22[] = {"cortex", "--max_read_len=1047"};
//set up a default cmdline
CmdLine test22;
default_opts(&test22);
char error_string22[LEN_ERROR_STRING];
int err22 = parse_cmdline_inner_loop(2, argv22, sizeof(Element), &test22, error_string22);
CU_ASSERT(test22.max_read_length==1047);
// PRINT COLOUR COVERAGES
char* argv23[] = {"cortex", "--print_colour_coverages"};
//set up a default cmdline
CmdLine test23;
default_opts(&test23);
char error_string23[LEN_ERROR_STRING];
int err23 = parse_cmdline_inner_loop(2, argv23, sizeof(Element), &test23, error_string23);
CU_ASSERT(err23==0);
CU_ASSERT(test23.print_colour_coverages==true);
}
void build_kernels(void) noexcept
{
std::string default_opts("-Isrc/opencl/cl "
"-cl-fast-relaxed-math "
#ifdef OPENCL_DP
"-DOPENCL_DP "
#endif
#ifdef OPENCL_USE_NATIVE_FUNCTIONS
"-DOPENCL_USE_NATIVE_FUNCTIONS "
#endif
#ifdef OPENCL_USE_VECTOR_TYPE
"-DOPENCL_USE_VECTOR_TYPE "
#endif
);
std::ostringstream params;
params << "-DNUM_ATOMS=" << ::atoms::num_atoms << ' ';
params << "-DNUM_CELLS=" << ::cells::num_cells << ' ';
params << "-DDT=" << ::mp::dt << ' ';
default_opts.append(params.str());
// dipole calculations enabled?
if (::sim::hamiltonian_simulation_flags[4])
{
// build dipolar kernels
vcl::update_dip = vcl::build_kernel_from_file("src/opencl/cl/dipole.cl",
"update_dipole_fields",
default_opts);
vcl::update_atm_dip = vcl::build_kernel_from_file("src/opencl/cl/dipole.cl",
"update_atm_dipole_fields",
default_opts);
vcl::update_cell_mag = vcl::build_kernel_from_file("src/opencl/cl/dipole.cl",
"update_cell_magnetization",
default_opts);
}
// external field kernel
vcl::update_ext = vcl::build_kernel_from_file("src/opencl/cl/external_fields.cl",
"update_external_fields",
default_opts);
// matrix multiplication for exchange
std::ostringstream exch_opts;
exch_opts << default_opts << "-DEXCH_TYPE=" << ::atoms::exchange_type;
vcl::exchange::calculate_exchange = vcl::build_kernel_from_file("src/opencl/cl/csrmatmul.cl",
"matmul",
exch_opts.str());
// non exchange spin fields
vcl::update_nexch_spin_fields = vcl::build_kernel_from_file("src/opencl/cl/spin_fields.cl",
"update_nexch_spin_fields",
default_opts);
// gaussian prng
vcl::rng::grng = vcl::build_kernel_from_file("src/opencl/cl/random.cl",
"gen_grands",
default_opts
#ifdef ENABLE_MULTIPLE_DEVICES
,
vcl::extra_device,
vcl::context_other
#endif // ENABLE_MULTIPLE_DEVICES
);
// llg heun steps
vcl::llg::predictor_step = vcl::build_kernel_from_file("src/opencl/cl/llg_heun.cl",
"llg_heun_predictor_step",
default_opts);
vcl::llg::corrector_step = vcl::build_kernel_from_file("src/opencl/cl/llg_heun.cl",
"llg_heun_corrector_step",
default_opts);
}
