bool Tree::ParseFromHdfString(const std::string &serialized)
{
Clear();
if (serialized.empty()) {
return true;
}
HDF *hdf;
NEOERR *err = hdf_init(&hdf);
if (err != STATUS_OK) {
nerr_ignore(&err);
return false;
}
err = hdf_read_string(hdf, serialized.c_str());
if (err != STATUS_OK) {
nerr_ignore(&err);
hdf_destroy(&hdf);
return false;
}
HDF *child = hdf_obj_child(hdf);
if (!child) {
hdf_destroy(&hdf);
return false;
}
if (!ParseFromHdfInternal(child)) {
hdf_destroy(&hdf);
return false;
}
hdf_destroy(&hdf);
return true;
}
JNIEXPORT jboolean JNICALL Java_org_clearsilver_HDF__1readString(
JNIEnv *env, jobject objClass, jint hdf_obj_ptr, jstring j_data) {
HDF *hdf = (HDF *)hdf_obj_ptr;
NEOERR *err;
const char *data;
jboolean retval;
data = (*env)->GetStringUTFChars(env, j_data, 0);
err = hdf_read_string(hdf, data);
(*env)->ReleaseStringUTFChars(env, j_data, data);
if (err != STATUS_OK) {
jNeoErr(env, err);
}
retval = (err == STATUS_OK);
return retval;
}
void Hdf::fromString(const char *input) {
CheckNeoError(hdf_read_string(getRaw(), (char*)input));
}
int main(int argc, char** argv)
{
char *bugname, *rname_init, *rname_data;
int nupdate, nburnin,niteration;
int thin=1;
int nchain=1;
int nmonitor=0;
char* monitor_list[100];
CHAIN chain;
int i,j;
int ret;
int n;
//SAMPLERLIST* slist = c->model->samplers;
NODE* node;
NODE* monitor_nodes[100];
FILE* fp;
#if __VC
_fullpath(bin_path, argv[0], PATH_MAX);
#endif
strcpy(bin_path, argv[0]);
for( i = strlen(bin_path)-1 ; i >= 0 ; i-- )
{
#ifdef __VC
if( bin_path[i] == '\\' ){
#else
if( bin_path[i] == '/' ){
#endif
bin_path[i] = '\0';
break;
}
}
printf(bin_path);
getcwd(boot_path, PATH_MAX);
if( argc <= 3 )
{
printf("usage: magro [bugs_file] [iteration] [burin-in] <options>\n");
printf("options: -init=[R-init-file]\n");
printf(" -data=[R-data-file]\n");
printf(" -c=[number of chains]\n");
printf(" -m=[monitoring variable]\n");
printf(" -thin=[thinning interval]\n");
printf(" -codegen\n");
printf(" -st\n");
printf(" -v\n");
printf("bugs_file ... the model definition file.\n");
printf("iteration ... the number of MCMC iterations.\n");
printf("burn-in ... the number of MCMC burn-in periods.\n");
printf("-init ... set the initialize parameters file. \n");
printf("-data ... set the data file.\n");
printf("-c ... set the number of chains. if you set more than ONE, you SHOULD NOT set -st option.\n");
printf("-st ... disable multi threading support.\n");
printf("-codegen ... generate human readable code set.\n");
printf("-m ... set the monitoring values. (donot set array values)\n");
printf("-v ... set verbose mode. \n");
exit(1);
}
bugname = argv[1];
if( sscanf(argv[2], "%d", &niteration) != 1 )
{
printf("iteration count must be integer.\n");
exit(2);
}
if( sscanf(argv[3], "%d", &nburnin) != 1 )
{
printf("burn-in count must be integer.\n");
exit(3);
}
if( niteration < nburnin )
{
printf("itertaion[%d] muse be more than burn-in[%d]\n", niteration, nburnin);
exit(4);
}
nupdate = niteration - nburnin;
rname_data = NULL;
rname_init = NULL;
for( i = 1 ; i < argc ; i++ )
{
if( argv[i][0] == '-' )
{
if( strncmp(argv[i], "-init=", 6) == 0 )
{
rname_init = &argv[i][6];
}
else if( strncmp(argv[i], "-data=", 6) == 0 )
{
rname_data = &argv[i][6];
}
else if( strcmp(argv[i], "-st") == 0 )
{
mode_thread = 0;
}
else if( strcmp(argv[i], "-codegen") == 0 )
{
mode_codegen = 1;
}
else if( strcmp(argv[i], "-v") == 0 )
{
mode_verbose = 1;
}
else if( strncmp(argv[i], "-thin=", 6) == 0 )
{
if( sscanf(&argv[i][6], "%d", &thin) != 1 )
{
printf("option '-thin': value must be integer.\n");
exit(11);
}
if( thin < 1 )
{
printf("option '-thin': value must be greater than one.\n");
exit(12);
}
}
else if( strncmp(argv[i], "-c=", 3) == 0 )
{
if( sscanf(&argv[i][3], "%d", &nchain) != 1 )
{
printf("option '-c': value must be integer.\n");
exit(13);
}
if( nchain < 1 || nchain>=CHAIN_MAX)
{
printf("option '-c': value must be greater than 0 and less than %d.\n", CHAIN_MAX-1);
exit(14);
}
}
else if( strncmp(argv[i], "-v=", 3) == 0 )
{
if( sscanf(&argv[i][3], "%d", &mode_verbose) != 1 )
{
printf("option '-v': value must be integer.\n");
exit(13);
}
if( mode_verbose < 1 )
{
printf("option '-v': value must be greater than one.");
exit(14);
}
}
else if( strncmp(argv[i], "-m=", 3) == 0 )
{
char* p = &argv[i][3];
int l = strlen(p);
char* buff = p;//GC_MALLOC(sizeof(char) * l);
int j,k,n;
n = 0;
for( j = 0 ; j < l ; j++ )
{
if( p[j] == ',' ) n++;
}
nmonitor = n+1;
n = 0;
k = 0;
monitor_list[n++] = p;
for( j = 0 ; j < l ; j++ )
{
if( buff[j] == ',' )
{
buff[j] = '\0';
monitor_list[n++] = buff+j+1;
}
}
buff[l] = '\0';
}
}
}
GC_INIT();
chain_init(&chain, nchain);
printf("reading model in %s ... ", bugname);
ret = chain_loadmodel(&chain, bugname);
if( ret == -1 )
{
printf("fail to open the file.\n");
exit(1);
}
if( ret > 0 )
{
printf("%d errors found.\n", ret);
exit(-1);
}
if( rname_data != NULL )
{
printf("reading data in %s ... ", rname_data);
ret = chain_loaddata(&chain, rname_data);
if( ret != -1 )
{
if( ret > 0 )
{
printf("%d errors found.\n", ret);
return -1;
}
printf("success\n");
}
else
{
printf("fail to open the file.\n");
exit(1);
}
}
printf("compiling ... ");
chain_compile(&chain);
printf("success\n");
if( mode_verbose > 1 )
{
for( i = 0 ; i < nchain ; i++ )
{
printf("chain #%d\n", i+1);
printf(" number of samplers = %d\n", chain.core[i].compiler->model->samplers->count);
printf(" number of nodes of the graph = %d\n", chain.core[i].compiler->graph->count);
}
}
if( rname_init != NULL )
{
printf("reading parameter file in %s ... ", rname_init);
ret = chain_loadinit(&chain, rname_init);
if( ret == -1 )
{
printf("faile to open the file\n");
exit(1);
}
if( ret > 0 )
{
printf("%d errors found.\n", ret);
return -1;
}
printf("success\n");
}
chain_initialize(&chain);
for ( j = 0 ; j < nchain ; j++ )
{
chain.core[j].nmonitor = nmonitor;
for( i = 0 ; i < nmonitor ; i++ )
{
CHAINCORE* core = &chain.core[j];
node = nodedic_findnode_byliteral(core->compiler->model->relations, monitor_list[i]);
core->monitor_nodes[i] = node;
if( node == NULL )
{
printf("cannot find monitoring variable named '%s'\n", monitor_list[i]);
exit(99);
}
}
}
if( mode_codegen == 0 )
{
int ind=0;
for( i = 0 ; i < nchain ; i++ )
{
int monitor_size = (int)((double)nupdate-1 / thin) + 1;
double* monitor_buff = GC_MALLOC(sizeof(double) * monitor_size * nmonitor);
// int monitor_count = 0;
CHAINCORE* core = &chain.core[i];
core->monitor_buff = monitor_buff;
core->monitor_counter = 0;
core->nthin = thin;
}
printf("burn-in\n");
printf("--------------------------------------------------| %d\n", nburnin);
chain_update(&chain, nburnin, 0);
printf("* 100%%\n");
ind = 0;
printf("updates\n");
printf("--------------------------------------------------| %d\n", nupdate);
chain_update(&chain, nupdate, 1);
printf("* 100%%\n");
// printf("*** DUMP MONITORTED VALUES***\n");
saveCODA(&chain, nmonitor, monitor_list);
/*
for( j = 0 ; j < nchain ; j++ )
{
CHAINCORE* core = &chain.core[j];
double* monitor_buff = core->monitor_buff;
int monitor_count = core->monitor_counter;
for( n = 0 ; n < nmonitor; n++ )
{
printf("%s:\n", monitor_list[n]);
for( i = 0 ; i < monitor_count; i++ )
{
printf("%d\t%f\n", thin*i, monitor_buff[i*nmonitor+n]);
}
}
}
*/
}
else if( mode_codegen == 1 )
{
DIR* dir = opendir(CODEGEN_DIRNAME);
if( dir == NULL )
{
#ifndef __VC
if( mkdir(CODEGEN_DIRNAME, S_IRWXU | S_IRWXG | S_IRWXO) != 0 )
#else
if( mkdir(CODEGEN_DIRNAME, 0) != 0 )
#endif
{
printf("failed to make directory named '%s'\n", CODEGEN_DIRNAME);
exit(90);
}
}
else closedir(dir);
chdir("codegen");
printf("writing sampler.hdf ... ");
fp = fopen("sampler.hdf", "w");
if( fp != NULL )
{
chain_savehdf(&chain, fp, monitor_list, nmonitor, nburnin, nupdate, thin);
fclose(fp);
printf("OK\n");
printf("reading sampler.hdf ... ");
fp = fopen("sampler.hdf", "r");
if( fp != NULL )
{
int sz;
char *buf;
char* templatedir;
char cmdbuf[1024];
HDF* hdf;
fseek(fp, 0, SEEK_END);
sz = ftell(fp);
fseek(fp, 0, SEEK_SET);
buf = (char*)GC_MALLOC_ATOMIC(sz);
fread(buf, 1, sz, fp);
fclose(fp);
printf("OK\n");
hdf_init(&hdf);
printf("parsing hdf ... ");
hdf_read_string(hdf, buf);
printf("OK\n");
templatedir = gettemplatedir();
printf("templatedir = %s\n", templatedir);
savesrc(templatedir, "main.c.cs", "main.c", hdf);
savesrc(templatedir, "conf.h.cs", "conf.h", hdf);
savesrc(templatedir, "nmath.h.cs", "nmath.h", hdf);
savesrc(templatedir, "sampler.c.cs", "sampler.c", hdf);
savesrc(templatedir, "sampler.h.cs", "sampler.h", hdf);
savesrc(templatedir, "environment.c.cs", "environment.c", hdf);
savesrc(templatedir, "environment.h.cs", "environment.h", hdf);
hdf_destroy(&hdf);
#ifndef __VC
system("gcc main.c environment.c sampler.c -L/usr/local/lib -lnmath -I/usr/local/include -W -Wall -lm -pthread");
#else
system("cl main.c environment.c sampler.c /FD /EHsc /MD /Gy /c /Zi /TC");
snprintf(cmdbuf, 1024, "link main.obj environment.obj sampler.obj nmath.lib /LIBPATH:\"%s\"", bin_path);
system(cmdbuf);
#endif
}
}
}
chain_free(&chain);
return 0;
}
