void pairalign_init (char *filename)
{
int i;
if (!filename || !filename[0]) {
bots_error(0, "Please specify an input file with the -f option\n");
}
init_matrix();
nseqs = readseqs(1,filename);
bots_message("Multiple Pairwise Alignment (%d sequences)\n",nseqs);
for (i = 1; i <= nseqs; i++)
bots_debug("Sequence %d: %s %6.d aa\n", i, names[i], seqlen_array[i]);
ktup = 1;
window = 5;
signif = 5;
gap_open = 10.0;
gap_extend = 0.2;
pw_go_penalty = 10.0;
pw_ge_penalty = 0.1;
}
void bots_print_results()
{
char str_name[BOTS_TMP_STR_SZ];
char str_parameters[BOTS_TMP_STR_SZ];
char str_model[BOTS_TMP_STR_SZ];
char str_resources[BOTS_TMP_STR_SZ];
char str_result[15];
char str_time_program[15];
char str_time_sequential[15];
char str_speed_up[15];
char str_number_of_tasks[15];
char str_number_of_tasks_per_second[15];
char str_exec_date[BOTS_TMP_STR_SZ];
char str_exec_message[BOTS_TMP_STR_SZ];
char str_architecture[BOTS_TMP_STR_SZ];
char str_load_avg[BOTS_TMP_STR_SZ];
char str_comp_date[BOTS_TMP_STR_SZ];
char str_comp_message[BOTS_TMP_STR_SZ];
char str_cc[BOTS_TMP_STR_SZ];
char str_cflags[BOTS_TMP_STR_SZ];
char str_ld[BOTS_TMP_STR_SZ];
char str_ldflags[BOTS_TMP_STR_SZ];
char str_cutoff[BOTS_TMP_STR_SZ];
/* compute output strings */
sprintf(str_name, "%s", bots_name);
sprintf(str_parameters, "%s", bots_parameters);
sprintf(str_model, "%s", bots_model);
sprintf(str_cutoff, "%s", bots_cutoff);
sprintf(str_resources, "%s", bots_resources);
switch(bots_result)
{
case BOTS_RESULT_NA:
sprintf(str_result, "n/a");
break;
case BOTS_RESULT_SUCCESSFUL:
sprintf(str_result, "successful");
break;
case BOTS_RESULT_UNSUCCESSFUL:
sprintf(str_result, "UNSUCCESSFUL");
break;
case BOTS_RESULT_NOT_REQUESTED:
sprintf(str_result, "Not requested");
break;
default:
sprintf(str_result, "error");
break;
}
sprintf(str_time_program, "%f", bots_time_program);
if (bots_sequential_flag) sprintf(str_time_sequential, "%f", bots_time_sequential);
else sprintf(str_time_sequential, "n/a");
if (bots_sequential_flag)
sprintf(str_speed_up, "%3.2f", bots_time_sequential/bots_time_program);
else sprintf(str_speed_up, "n/a");
sprintf(str_number_of_tasks, "%3.2f", (float) bots_number_of_tasks);
sprintf(str_number_of_tasks_per_second, "%3.2f", (float) bots_number_of_tasks/bots_time_program);
sprintf(str_exec_date, "%s", bots_exec_date);
sprintf(str_exec_message, "%s", bots_exec_message);
bots_get_architecture(str_architecture);
bots_get_load_average(str_load_avg);
sprintf(str_comp_date, "%s", bots_comp_date);
sprintf(str_comp_message, "%s", bots_comp_message);
sprintf(str_cc, "%s", bots_cc);
sprintf(str_cflags, "%s", bots_cflags);
sprintf(str_ld, "%s", bots_ld);
sprintf(str_ldflags, "%s", bots_ldflags);
if(bots_print_header)
{
switch(bots_output_format)
{
case 0:
break;
case 1:
break;
case 2:
fprintf(stdout,
"Benchmark;Parameters;Model;Cutoff;Resources;Result;\
Time;Sequential;Speed-up;\
Nodes;Nodes/Sec;\
Exec Date;Exec Time;Exec Message;\
Architecture;Processors;Load Avg-1;Load Avg-5;Load Avg-15;\
Comp Date;Comp Time;Comp Message;CC;CFLAGS;LD;LDFLAGS\n");
break;
case 3:
break;
case 4:
fprintf(stdout,
"Benchmark;Parameters;Model;Cutoff;Resources;Result;\
Time;Sequential;Speed-up;\
Nodes;Nodes/Sec;\n");
break;
default:
break;
}
}
/* print results */
switch(bots_output_format)
{
case 0:
break;
case 1:
fprintf(stdout, "\n");
fprintf(stdout, "Program = %s\n", str_name); /*fix*/
fprintf(stdout, "Parameters = %s\n", str_parameters); /*fix*/
fprintf(stdout, "Model = %s\n", str_model);
fprintf(stdout, "Embedded cut-off = %s\n", str_cutoff);
// fprintf(stdout, "# of Threads = %s\n", str_resources);
fprintf(stdout, "Verification = %s\n", str_result);
if (bots_print_times) {
fprintf(stdout, "Time Program = %s seconds\n", str_time_program);
if (bots_sequential_flag) {
fprintf(stdout, "Time Sequential = %s seconds\n", str_time_sequential);
fprintf(stdout, "Speed-up = %s\n", str_speed_up);
}
}
if ( bots_number_of_tasks > 0 ) {
fprintf(stdout, "Nodes = %s\n", str_number_of_tasks);
fprintf(stdout, "Nodes/Sec = %s\n", str_number_of_tasks_per_second);
}
// fprintf(stdout, "Execution Date = %s\n", str_exec_date);
fprintf(stdout, "Execution Message = %s\n", str_exec_message);
fprintf(stdout, "Architecture = %s\n", str_architecture);
// fprintf(stdout, "Load Avg [1:5:15] = %s\n", str_load_avg);
fprintf(stdout, "Compilation Date = %s\n", str_comp_date);
fprintf(stdout, "Compilation Message = %s\n", str_comp_message);
fprintf(stdout, "Compiler = %s\n", str_cc);
fprintf(stdout, "Compiler Flags = %s\n", str_cflags);
fprintf(stdout, "Linker = %s\n", str_ld);
fprintf(stdout, "Linker Flags = %s\n", str_ldflags);
fflush(stdout);
break;
case 2:
fprintf(stdout,"%s;%s;%s;%s;%s;%s;",
str_name,
str_parameters,
str_model,
str_cutoff,
str_resources,
str_result
);
fprintf(stdout,"%s;%s;%s;",
str_time_program,
str_time_sequential,
str_speed_up
);
fprintf(stdout,"%s;%s;",
str_number_of_tasks,
str_number_of_tasks_per_second
);
fprintf(stdout,"%s;%s;",
str_exec_date,
str_exec_message
);
fprintf(stdout,"%s;%s;",
str_architecture,
str_load_avg
);
fprintf(stdout,"%s;%s;",
str_comp_date,
str_comp_message
);
fprintf(stdout,"%s;%s;%s;%s;",
str_cc,
str_cflags,
str_ld,
str_ldflags
);
fprintf(stdout,"\n");
break;
case 3:
fprintf(stdout, "\n");
fprintf(stdout, "Program = %s\n", str_name); /*fix*/
fprintf(stdout, "Parameters = %s\n", str_parameters); /*fix*/
fprintf(stdout, "Model = %s\n", str_model);
fprintf(stdout, "Embedded cut-off = %s\n", str_cutoff);
fprintf(stdout, "# of Threads = %s\n", str_resources);
fprintf(stdout, "Verification = %s\n", str_result);
fprintf(stdout, "Time Program = %s seconds\n", str_time_program);
if (bots_sequential_flag) {
fprintf(stdout, "Time Sequential = %s seconds\n", str_time_sequential);
fprintf(stdout, "Speed-up = %s\n", str_speed_up);
}
if ( bots_number_of_tasks > 0 ) {
fprintf(stdout, "Nodes = %s\n", str_number_of_tasks);
fprintf(stdout, "Nodes/Sec = %s\n", str_number_of_tasks_per_second);
}
break;
case 4:
fprintf(stdout,"%s;%s;%s;%s;%s;%s;",
str_name,
str_parameters,
str_model,
str_cutoff,
str_resources,
str_result
);
fprintf(stdout,"%s;%s;%s;",
str_time_program,
str_time_sequential,
str_speed_up
);
fprintf(stdout,"%s;%s;",
str_number_of_tasks,
str_number_of_tasks_per_second
);
fprintf(stdout,"\n");
break;
default:
bots_error(BOTS_ERROR,"No valid output format\n");
break;
}
}
