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|
#include "gov_ornl_ccs_Adios.h"
#include <adios.h>
#include <iostream>
#include <string.h>
#include <stdlib.h>
#define STR(A) #A
#define CONCAT2(A, B) A ## B
#define CONCAT3(A, B, C) CONCAT2(CONCAT2(A, B), C)
#define GET_ARRAY_ELEMENT(TYPE) CONCAT3(Get, TYPE, ArrayElements)
#define WRITE_ONE(JTYPE) \
/* std::cout << __FUNCTION__ << "..." << std::endl; */ \
int result; \
const char *str_var_name; \
str_var_name = env->GetStringUTFChars(var_name, NULL); \
if (str_var_name == NULL) return -1; \
result = adios_write ((int64_t) fh, str_var_name, &val); \
env->ReleaseStringUTFChars(var_name, str_var_name); \
return result;
#define WRITE_ARRAY(JTYPE, CTYPE) \
/* std::cout << __FUNCTION__ << " ..." << std::endl;*/ \
int result; \
const char *str_var_name; \
JTYPE *valarr = env->Get ##CTYPE ##ArrayElements(val, NULL); \
str_var_name = env->GetStringUTFChars(var_name, NULL); \
if (str_var_name == NULL) return -1; \
result = adios_write ((int64_t) fh, str_var_name, (void *) valarr); \
env->ReleaseStringUTFChars(var_name, str_var_name); \
env->Release ##CTYPE ##ArrayElements(val, valarr, 0); \
return result;
#define FUNC_WRITE_ONE(FNAME, JTYPE) \
JNIEXPORT jint JNICALL FNAME \
(JNIEnv * env, jclass cls, jlong fh, jstring var_name, JTYPE val) \
{ \
WRITE_ONE(JTYPE); \
}
#define FUNC_WRITE_ARRAY(FNAME, JTYPE, CTYPE) \
JNIEXPORT jint JNICALL FNAME \
(JNIEnv * env, jclass cls, jlong fh, jstring var_name, JTYPE ##Array val) \
{ \
WRITE_ARRAY(JTYPE, CTYPE); \
}
#define STR_ALLOC(var) \
const char *str_##var = env->GetStringUTFChars(var, NULL); \
if (str_##var == NULL) return -1;
#define STR_ALLOC2(var) \
const char *str_##var = env->GetStringUTFChars(var, NULL); \
if (str_##var == NULL) goto end;
#define STR_FREE(var) \
env->ReleaseStringUTFChars(var, str_##var);
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_init
* Signature: (Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_gov_ornl_ccs_Adios_adios_1init
(JNIEnv *env, jclass cls, jstring xml_fname, jlong comm)
{
//std::cout << __FUNCTION__ << "..." << std::endl;
int result;
jboolean isCopy;
STR_ALLOC(xml_fname);
result = adios_init(str_xml_fname, (MPI_Comm) comm);
//std::cout << "result = " << result << std::endl;
STR_FREE(xml_fname);
return result;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_open
* Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;J)J
*/
JNIEXPORT jlong JNICALL Java_gov_ornl_ccs_Adios_adios_1open
(JNIEnv * env, jclass cls, jstring group_name, jstring file_name, jstring mode, jlong comm)
{
//std::cout << __FUNCTION__ << "..." << std::endl;
int result;
int64_t fd_p = 0;
STR_ALLOC(group_name);
STR_ALLOC(file_name);
STR_ALLOC(mode);
//std::cout << "[IN] fd_p = " << (int64_t) fd_p << std::endl;
//std::cout << "[IN] str_group_name = " << str_group_name << std::endl;
//std::cout << "[IN] str_file_name = " << str_file_name << std::endl;
//std::cout << "[IN] str_mode = " << str_mode << std::endl;
//std::cout << "[IN] comm = " << (long) comm << std::endl;
result = adios_open(&fd_p, str_group_name, str_file_name, str_mode, (MPI_Comm) comm);
//std::cout << "[OUT] fd_p = " << fd_p << std::endl;
//std::cout << "[OUT] result = " << result << std::endl;
STR_FREE(group_name);
STR_FREE(file_name);
STR_FREE(mode);
return (jlong) fd_p;
}
JNIEXPORT jlong JNICALL Java_gov_ornl_ccs_Adios_adios_1group_1size
(JNIEnv * env, jclass cls, jlong fh, jlong group_size)
{
//std::cout << __FUNCTION__ << "..." << std::endl;
uint64_t total_size = 0;
int result;
//std::cout << "[IN] fh = " << (int64_t) fh << std::endl;
//std::cout << "[IN] group_size = " << (uint64_t) group_size << std::endl;
result = adios_group_size ((int64_t) fh, (uint64_t) group_size, (uint64_t *) &total_size);
//std::cout << "[OUT] fh = " << (int64_t) fh << std::endl;
//std::cout << "[OUT] total size = " << total_size << std::endl;
//std::cout << "[OUT] result = " << result << std::endl;
return total_size;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_write
* Signature: (JLjava/lang/String;B)I
* Signature: (JLjava/lang/String;I)I
* Signature: (JLjava/lang/String;J)I
* Signature: (JLjava/lang/String;F)I
* Signature: (JLjava/lang/String;D)I
*/
FUNC_WRITE_ONE (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2B,
jbyte)
FUNC_WRITE_ONE (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2I,
jint)
FUNC_WRITE_ONE (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2J,
jlong)
FUNC_WRITE_ONE (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2F,
jfloat)
FUNC_WRITE_ONE (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2D,
jdouble)
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_write
* Signature: (JLjava/lang/String;[B)I
* Signature: (JLjava/lang/String;[I)I
* Signature: (JLjava/lang/String;[J)I
* Signature: (JLjava/lang/String;[F)I
* Signature: (JLjava/lang/String;[D)I
*/
FUNC_WRITE_ARRAY (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2_3B,
jbyte,
Byte)
FUNC_WRITE_ARRAY (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2_3I,
jint,
Int)
FUNC_WRITE_ARRAY (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2_3J,
jlong,
Long)
FUNC_WRITE_ARRAY (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2_3F,
jfloat,
Float)
FUNC_WRITE_ARRAY (
Java_gov_ornl_ccs_Adios_adios_1write__JLjava_lang_String_2_3D,
jdouble,
Double)
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_close
* Signature: (J)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1close
(JNIEnv * env, jclass cls, jlong fh)
{
//std::cout << __FUNCTION__ << "..." << std::endl;
//std::cout << "[IN] fh = " << fh << std::endl;
return adios_close ((int64_t) fh);
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_finalize
* Signature: (I)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1finalize
(JNIEnv * env, jclass cls, jint id)
{
//std::cout << __FUNCTION__ << "..." << std::endl;
return adios_finalize (id);
}
#ifdef ADIOS_USE_MPI
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_mpi_init
* Signature: ([Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1init
(JNIEnv * env, jclass cls, jobjectArray args)
{
int argc = env->GetArrayLength(args);
char **argv;
int result;
for (int i = 0; i < argc; i )
{
jstring jstr = (jstring) env->GetObjectArrayElement(args, i);
const char *chr = env->GetStringUTFChars(jstr, 0);
//argv[i] = (char *) malloc(env->GetStringLength(jstr) 1);
argv[i] = new char[env->GetStringLength(jstr) 1];
strcpy(argv[i], chr);
env->ReleaseStringUTFChars(jstr, chr);
}
result = MPI_Init(&argc, &argv);
for (int i = 0; i < argc; i )
{
//free(argv[i]);
delete[] argv[i];
}
return result;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_mpi_comm_rank
* Signature: (I)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1comm_1rank
(JNIEnv * env, jclass cls, jlong comm)
{
int rank;
MPI_Comm_rank((MPI_Comm) comm, &rank);
return rank;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_mpi_comm_size
* Signature: (I)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1comm_1size
(JNIEnv * env, jclass cls, jlong comm)
{
int size;
MPI_Comm_size((MPI_Comm) comm, &size);
return size;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_mpi_finalize
* Signature: ()I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1finalize
(JNIEnv * env, jclass cls)
{
return MPI_Finalize();
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_mpi_comm_world
* Signature: ()I
*/
JNIEXPORT jlong JNICALL Java_gov_ornl_ccs_Adios_adios_1mpi_1comm_1world
(JNIEnv * env, jclass cls)
{
return (jlong) MPI_COMM_WORLD;
}
#endif
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_open_and_set_group_size
* Signature: (Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;JJ)J
*/
JNIEXPORT jlong JNICALL Java_gov_ornl_ccs_Adios_adios_1open_1and_1set_1group_1size
(JNIEnv * env, jclass cls, jstring group_name, jstring file_name, jstring mode, jlong group_size, jlong comm)
{
// Doesn't work, either
//jlong fh = Java_gov_ornl_ccs_Adios_adios_1open(env, cls, group_name, file_name, mode, comm);
//Java_gov_ornl_ccs_Adios_adios_1group_1size(env, cls, fh, group_size);
//std::cout << __FUNCTION__ << "..." << std::endl;
int result;
int64_t fd_p = 0;
STR_ALLOC(group_name);
STR_ALLOC(file_name);
STR_ALLOC(mode);
//std::cout << "[IN] fd_p = " << (int64_t) fd_p << std::endl;
//std::cout << "[IN] str_group_name = " << str_group_name << std::endl;
//std::cout << "[IN] str_file_name = " << str_file_name << std::endl;
//std::cout << "[IN] str_mode = " << str_mode << std::endl;
//std::cout << "[IN] comm = " << (long) comm << std::endl;
result = adios_open(&fd_p, str_group_name, str_file_name, str_mode, (MPI_Comm) comm);
//std::cout << "[OUT] fd_p = " << fd_p << std::endl;
//std::cout << "[OUT] result = " << result << std::endl;
STR_FREE(group_name);
STR_FREE(file_name);
STR_FREE(mode);
uint64_t total_size;
//std::cout << "[IN] fd_p = " << (int64_t) fd_p << std::endl;
adios_group_size (fd_p, group_size, (uint64_t *) &total_size);
//std::cout << "[OUT] total size = " << total_size << std::endl;
return (jlong) fd_p;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_init_noxml
* Signature: ()I
*/
JNIEXPORT jint JNICALL
Java_gov_ornl_ccs_Adios_adios_1init_1noxml
(JNIEnv *env, jclass cls, jlong comm)
{
return adios_init_noxml((MPI_Comm) comm);
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_allocate_buffer
* Signature: (IJ)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1allocate_1buffer
(JNIEnv * env, jclass cls, jint when, jlong size)
{
return adios_allocate_buffer((ADIOS_BUFFER_ALLOC_WHEN) when, size);
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_declare_group
* Signature: (Ljava/lang/String;Ljava/lang/String;I)J
*/
JNIEXPORT jlong JNICALL Java_gov_ornl_ccs_Adios_adios_1declare_1group
(JNIEnv * env, jclass cls, jstring name, jstring time_index, jint stats)
{
int64_t id_p;
int result;
STR_ALLOC(name);
STR_ALLOC(time_index);
result = adios_declare_group(&id_p, str_name, str_time_index, (ADIOS_STATISTICS_FLAG) stats);
STR_FREE(name);
STR_FREE(time_index);
return (jlong) id_p;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_define_var
* Signature: (JLjava/lang/String;Ljava/lang/String;ILjava/lang/String;Ljava/lang/String;Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1define_1var
(JNIEnv * env, jclass cls, jlong group_id, jstring name, jstring path, jint type, jstring dimensions, jstring global_dimensions, jstring local_offsets)
{
int result;
STR_ALLOC(name);
STR_ALLOC(path);
STR_ALLOC(dimensions);
STR_ALLOC(global_dimensions);
STR_ALLOC(local_offsets);
result = adios_define_var((int64_t) group_id, str_name, str_path, (ADIOS_DATATYPES) type, str_dimensions, str_global_dimensions, str_local_offsets);
STR_FREE(name);
STR_FREE(path);
STR_FREE(dimensions);
STR_FREE(global_dimensions);
STR_FREE(local_offsets);
return result;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_define_attribute
* Signature: (JLjava/lang/String;Ljava/lang/String;ILjava/lang/String;Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1define_1attribute
(JNIEnv * env, jclass cls, jlong group_id, jstring name, jstring path, jint type, jstring value, jstring var)
{
int result;
STR_ALLOC(name);
STR_ALLOC(path);
STR_ALLOC(value);
STR_ALLOC(var);
result = adios_define_attribute((int64_t) group_id, str_name, str_path, (ADIOS_DATATYPES) type, str_value, str_var);
STR_FREE(name);
STR_FREE(path);
STR_FREE(value);
STR_FREE(var);
return result;
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_select_method
* Signature: (JLjava/lang/String;Ljava/lang/String;Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL Java_gov_ornl_ccs_Adios_adios_1select_1method
(JNIEnv * env, jclass cls, jlong group_id, jstring method, jstring parameters, jstring base_path)
{
int result;
STR_ALLOC(method);
STR_ALLOC(parameters);
STR_ALLOC(base_path);
result = adios_select_method((int64_t) group_id, str_method, str_parameters, str_base_path);
STR_FREE(method);
STR_FREE(parameters);
STR_FREE(base_path);
return result;
}
#define READ_ONE(JTYPE) \
/* std::cout << __FUNCTION__ << " ..." << std::endl; */ \
int result; \
JTYPE val; \
const char *str_var_name; \
uint64_t read_size = sizeof(JTYPE); \
str_var_name = env->GetStringUTFChars(var_name, NULL); \
if (str_var_name == NULL) return -1; \
result = adios_read ((int64_t) fh, str_var_name, &val, sizeof(JTYPE)); \
env->ReleaseStringUTFChars(var_name, str_var_name); \
return val;
#define FUNC_READ_ONE(FNAME, JTYPE) \
JNIEXPORT JTYPE JNICALL FNAME \
(JNIEnv * env, jclass cls, jlong fh, jstring var_name) \
{ \
READ_ONE(JTYPE); \
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_read_byte_value
* Signature: (JLjava/lang/String;)B
* Signature: (JLjava/lang/String;)I
* Signature: (JLjava/lang/String;)J
* Signature: (JLjava/lang/String;)F
* Signature: (JLjava/lang/String;)D
*/
FUNC_READ_ONE(
Java_gov_ornl_ccs_Adios_adios_1read_1byte_1value,
jbyte);
FUNC_READ_ONE(
Java_gov_ornl_ccs_Adios_adios_1read_1int_1value,
jint);
FUNC_READ_ONE(
Java_gov_ornl_ccs_Adios_adios_1read_1long_1value,
jlong);
FUNC_READ_ONE(
Java_gov_ornl_ccs_Adios_adios_1read_1float_1value,
jfloat);
FUNC_READ_ONE(
Java_gov_ornl_ccs_Adios_adios_1read_1double_1value,
jdouble);
#define READ_ARRAY(JTYPE, CTYPE) \
/* std::cout << __FUNCTION__ << " ..." << std::endl; */ \
int result; \
const char *str_var_name; \
JTYPE *valarr = env->Get ##CTYPE ##ArrayElements(val, NULL); \
uint64_t read_size = env->GetArrayLength(val) * sizeof(JTYPE); \
str_var_name = env->GetStringUTFChars(var_name, NULL); \
if (str_var_name == NULL) return -1; \
result = adios_read ((int64_t) fh, str_var_name, (void *) valarr, read_size); \
env->ReleaseStringUTFChars(var_name, str_var_name); \
env->Release ##CTYPE ##ArrayElements(val, valarr, 0); \
return result;
#define FUNC_READ_ARRAY(FNAME, JTYPE, CTYPE) \
JNIEXPORT jint JNICALL FNAME \
(JNIEnv * env, jclass cls, jlong fh, jstring var_name, JTYPE ##Array val) \
{ \
READ_ARRAY(JTYPE, CTYPE); \
}
/*
* Class: gov_ornl_ccs_Adios
* Method: adios_read
* Signature: (JLjava/lang/String;[B)I
* Signature: (JLjava/lang/String;[I)I
* Signature: (JLjava/lang/String;[J)I
* Signature: (JLjava/lang/String;[F)I
* Signature: (JLjava/lang/String;[D)I
*/
FUNC_READ_ARRAY(
Java_gov_ornl_ccs_Adios_adios_1read__JLjava_lang_String_2_3B,
jbyte,
Byte);
FUNC_READ_ARRAY(
Java_gov_ornl_ccs_Adios_adios_1read__JLjava_lang_String_2_3I,
jint,
Int);
FUNC_READ_ARRAY(
Java_gov_ornl_ccs_Adios_adios_1read__JLjava_lang_String_2_3J,
jlong,
Long);
FUNC_READ_ARRAY(
Java_gov_ornl_ccs_Adios_adios_1read__JLjava_lang_String_2_3F,
jfloat,
Float);
FUNC_READ_ARRAY(
Java_gov_ornl_ccs_Adios_adios_1read__JLjava_lang_String_2_3D,
jdouble,
Double);
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