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package test.object.misc;
import java.io.File;
import java.lang.management.ManagementFactory;
import java.lang.management.MemoryUsage;
import java.text.DecimalFormat;
import java.util.Vector;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.object.Attribute;
import ncsa.hdf.object.Dataset;
import ncsa.hdf.object.Datatype;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.Group;
import ncsa.hdf.object.ScalarDS;
import ncsa.hdf.object.h5.H5Datatype;
import ncsa.hdf.object.h5.H5File;
public class TestH5MemoryLeak
{
/** Name of test file */
private final static String NAME_FILE_H5="TestH5MemoryLeak.h5";
private final static boolean DEBUG = true;
private final static int NLOOPS = 10000;
private final static int NPRINT = 100;
private final static int NSTART = 2000;
/** Name of test groups */
private final static String NAME_GROUP = "/g0";
private final static String NAME_GROUP_ATTR = "/g0_attr";
private final static String NAME_GROUP_SUB = NAME_GROUP+"/g00";
/** Name of test datasets */
private final static String DNAMES[] = {
"/dataset_byte", "/dataset_int",
"/dataset_float", "/dataset_str",
"/dataset_enum", "/dataset_image",
"/dataset_comp", NAME_GROUP + "/dataset_int",
NAME_GROUP_SUB+ "/dataset_float", NAME_GROUP + "/dataset_comp", "/dataset_str_vlen"};
private final static String NAME_DATASET_CHAR = DNAMES[0];
private final static String NAME_DATASET_INT = DNAMES[1];
private final static String NAME_DATASET_FLOAT = DNAMES[2];
private final static String NAME_DATASET_STR = DNAMES[3];
private final static String NAME_DATASET_ENUM = DNAMES[4];
private final static String NAME_DATASET_IMAGE = DNAMES[5];
private final static String NAME_DATASET_COMPOUND = DNAMES[6];
private final static String NAME_DATASET_SUB = DNAMES[7];
private final static String NAME_DATASET_SUB_SUB = DNAMES[8];
private final static String NAME_DATASET_COMPOUND_SUB = DNAMES[9];
private final static String NAME_DATASET_STR_VLEN = DNAMES[10];
/** Name of test dataype */
private final static String NAME_DATATYPE_INT = NAME_GROUP + "/datatype_int";
private final static String NAME_DATATYPE_FLOAT = NAME_GROUP + "/datatype_float";
private final static String NAME_DATATYPE_STR = NAME_GROUP + "/datatype_str";
// data space information
private final static int DATATYPE_SIZE = 4;
private final static int RANK = 2;
private final static long DIM1 = 10;
private final static long DIM2 = 5;
private final static long[] DIMs = {DIM1, DIM2};
private final static long[] CHUNKs = {DIM1/2, DIM2/2};
private final static int STR_LEN = 20;
private final static int DIM_SIZE = (int)(DIM1*DIM2);;
/* testing data */
private final static int[] DATA_INT = new int[DIM_SIZE];
private final static long[] DATA_LONG = new long[DIM_SIZE];
private final static float[] DATA_FLOAT = new float[DIM_SIZE];
private final static byte[] DATA_BYTE = new byte[DIM_SIZE];
private final static String[] DATA_STR = new String[DIM_SIZE];
private final static int[] DATA_ENUM = new int[DIM_SIZE];
private final static Vector DATA_COMP = new Vector(3);
// compound names and datatypes
private final static String[] COMPOUND_MEMBER_NAMES = {"int32", "float32", "string", "uint32"};
private final static H5Datatype[] COMPOUND_MEMBER_DATATYPES = {
new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, -1),
new H5Datatype(Datatype.CLASS_FLOAT, DATATYPE_SIZE, -1, -1),
new H5Datatype(Datatype.CLASS_STRING, STR_LEN, -1, -1),
new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, Datatype.SIGN_NONE),
new H5Datatype(Datatype.CLASS_STRING, -1, -1, -1)};
// attributes
private final static Attribute ATTRIBUTE_STR = new Attribute(
"attrName",
new H5Datatype(Datatype.CLASS_STRING, STR_LEN, -1, -1),
new long[] {1},
new String[] {"attrValue"});
private final static Attribute ATTRIBUTE_INT_ARRAY = new Attribute(
"arrayInt",
new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, -1),
new long[] {10},
new int[] {1, 2, 3, 4, 5, 6, 7, 8, 9, 10});
/**
* Test memory leak by create file, open dataset, read/write data in an infinite loop
* <p>
* @param args
*/
public static void main(final String[] args)
{
boolean is_userfile = false;
long retValue = 0;
if (args.length > 0)
{
File tmpFile = new File(args[0]);
is_userfile = (tmpFile.exists() && tmpFile.isFile());
}
try { H5.H5Eclear();} catch (Exception ex) {}
System.out.flush();
System.out.println("\nCheck memory leak (may take 5 to 10 mintues) ...");
try {
if (is_userfile)
retValue = test_user_file(args[0]);
else
retValue = test_default_file();
} catch (Throwable err) { retValue=1; }
if (retValue <= 0)
System.out.println("PASSED:\tcheck memory leak.\n");
else
System.out.println("FAILED***:\tcheck memory leak.\n");
}
private static final long test_user_file(String fname) throws Exception
{
H5File testFile = null;
MemoryUsage memuse = null;
DecimalFormat df = new DecimalFormat("000.00#E0#");
int count = 0;
String sumStr="-----";
long KB = 1024, mem0=0, mem1=0, sum=0;
if (DEBUG) {
System.out.flush();
System.out.println("\n\nNo. of loops\tIncrease\tUsed(KB)\tTotal(KB)\tNo. of open IDs\n"+
"_______________________________________________________________________________\n");
}
while(count<NLOOPS)
{
count ++;
if (count % NPRINT == 0) {
memuse = (java.lang.management.MemoryUsage) ManagementFactory.getMemoryMXBean().getHeapMemoryUsage();
mem1 = memuse.getCommitted()/KB;
if (count>NSTART) {
sum += (mem1-mem0);
sumStr = df.format(sum);
}
if (DEBUG) {
System.out.println(
df.format(count) + " \t" +
sumStr + " \t" +
df.format((mem1)) + " \t" +
df.format(memuse.getMax() / KB) + " \t" +
H5.getOpenIDCount());
}
if (sum > 0)
break;
mem0 = mem1;
}
testFile = new H5File(fname, FileFormat.READ);
testFile.open();
testFile.getRootNode();
try { Thread.sleep(10); } catch (Exception ex) {;}
testFile.close();
}
return sum;
}
private static final long test_default_file()
{
int nObjs = 0; // number of object left open
Dataset dset =null;
File tmpFile = null;
MemoryUsage memuse = null;
DecimalFormat df = new DecimalFormat("000.00#E0#");
for (int i=0; i<DIM_SIZE; i++) {
DATA_INT[i] = i;
DATA_LONG[i] = i;
DATA_FLOAT[i] = i+i/100.0f;
DATA_BYTE[i] = (byte)Math.IEEEremainder(i, 127);
DATA_STR[i] = "str"+i;
DATA_ENUM[i] = (int)Math.IEEEremainder(i, 2);
}
DATA_COMP.add(0, DATA_INT);
DATA_COMP.add(1, DATA_FLOAT);
DATA_COMP.add(2, DATA_STR);
DATA_COMP.add(3, DATA_LONG);
int count = 0;
String sumStr="-----";
long KB = 1024, mem0=0, mem1=0, sum=0, diff=0;
if (DEBUG) {
System.out.flush();
System.out.println("\n\nNo. of loops\tIncrease\tUsed(KB)\tTotal(KB)\tNo. of open IDs\n"+
"_______________________________________________________________________________\n");
}
int nhigh = 0;
while(count<NLOOPS)
{
count ++;
if (count % NPRINT == 0) {
memuse = (java.lang.management.MemoryUsage) ManagementFactory.getMemoryMXBean().getHeapMemoryUsage();
mem1 = memuse.getCommitted()/KB;
if (count>NSTART) {
diff = mem1-mem0;
sum += diff;
if (diff>0)
nhigh++;
else
nhigh=0;
sumStr = df.format(sum);
}
if (DEBUG) {
System.out.println(
df.format(count) + " \t" +
sumStr + " \t" +
df.format((mem1)) + " \t" +
df.format(memuse.getMax() / KB) + " \t" +
H5.getOpenIDCount());
}
if ((sum/KB) > 0 || nhigh > 3)
break;
mem0 = mem1;
}
tmpFile = null;
try {
try {
tmpFile = createTestFile();
} catch (Exception ex) {
sum = 1;
tmpFile = null;
break;
}
// test two open options: open full tree or open individual object only
for (int openOption=0; openOption<2; openOption++)
{
nObjs = 0;
H5File file = new H5File(NAME_FILE_H5, FileFormat.WRITE);
if (openOption == 0) {
try {
file.open(); // open the full tree
} catch (Exception ex) {
System.err.println("file.open(). "+ ex);
}
}
try {
Group rootGrp = (Group) file.get("/");
// datasets
for (int j=0; j<DNAMES.length; j++) {
dset = (Dataset)file.get(DNAMES[j]);
dset.init();
Object data = dset.getData();
try { dset.write(data); } catch (Exception ex) {}
dset.getMetadata();
// copy data into a new datast
if (dset instanceof ScalarDS) {
try {
dset = dset.copy(rootGrp, DNAMES[j]+"_copy"+openOption, DIMs, data);
} catch (Exception ex) {}
}
}
// groups
file.get(NAME_GROUP);
file.get(NAME_GROUP_ATTR);
file.get(NAME_GROUP_SUB);
// datatypes
file.get(NAME_DATATYPE_INT);
file.get(NAME_DATATYPE_FLOAT);
file.get(NAME_DATATYPE_STR);
} catch (Exception ex) {
System.err.println("file.get(). "+ ex);
}
nObjs = 0;
try { nObjs = H5.H5Fget_obj_count(file.getFID(), HDF5Constants.H5F_OBJ_ALL); }
catch (Exception ex) { ; }
if (nObjs > 1) {
System.err.println("Possible memory leak. Some objects are still open.");
}
try {
file.close();
} catch (Exception ex) {
System.err.println("file.close() failed. "+ ex);
}
} // for (int openOption=0; openOption<2; openOption++)
} finally {
// delete the testing file
if (tmpFile != null) {
tmpFile.delete();
}
}
} // while (true)
return sum;
}
/**
* Calls garbage collector
*/
private static void collectGarbage() {
try {
System.gc();
Thread.sleep(100);
System.runFinalization();
Thread.sleep(100);
}
catch (final Exception ex){
ex.printStackTrace();
}
}
/**
* Creates an HDF5 test file.
* <p>
* The test file contains the following objects:
* <pre>
/dataset_byte Dataset {50, 10}
/dataset_comp Dataset {50, 10}
/dataset_enum Dataset {50, 10}
/dataset_float Dataset {50, 10}
/dataset_int Dataset {50, 10}
/dataset_image Dataset {50, 10}
/dataset_str Dataset {50, 10}
/g0 Group
/g0/dataset_int Dataset {50, 10}
/g0/g00 Group
/g0/g00/dataset_float Dataset {50, 10}
/g0_attr Group
* </pre>
* @throws Exception
*/
private static final File createTestFile() throws Exception
{
H5File file=null;
Group g0, g1, g00;
final H5Datatype typeInt = new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, -1);
final H5Datatype typeFloat = new H5Datatype(Datatype.CLASS_FLOAT, DATATYPE_SIZE, -1, -1);
final H5Datatype typeStr = new H5Datatype(Datatype.CLASS_STRING, STR_LEN, -1, -1);
final H5Datatype typeStrVlen = new H5Datatype(Datatype.CLASS_STRING, -1, -1, -1);
final H5Datatype typeChar = new H5Datatype(Datatype.CLASS_CHAR, 1, -1, -1);
final H5Datatype typeEnum = new H5Datatype(Datatype.CLASS_ENUM, DATATYPE_SIZE, -1, -1);
file = new H5File(NAME_FILE_H5, FileFormat.CREATE);
file.open();
g0 = file.createGroup(NAME_GROUP, null);
g1 = file.createGroup(NAME_GROUP_ATTR, null);
g00 = file.createGroup(NAME_GROUP_SUB, null);
g1.writeMetadata(ATTRIBUTE_STR);
g1.writeMetadata(ATTRIBUTE_INT_ARRAY);
final Dataset[] dsets = new Dataset[11];
dsets[0] = file.createScalarDS (NAME_DATASET_INT, null, typeInt, DIMs, null, CHUNKs, 9, DATA_INT);
dsets[1] = file.createScalarDS (NAME_DATASET_FLOAT, null, typeFloat, DIMs, null, CHUNKs, 9, DATA_FLOAT);
dsets[2] = file.createScalarDS (NAME_DATASET_CHAR, null, typeChar, DIMs, null, CHUNKs, 9, DATA_BYTE);
dsets[3] = file.createScalarDS (NAME_DATASET_STR, null, typeStr, DIMs, null, CHUNKs, 9, DATA_STR);
dsets[4] = file.createScalarDS (NAME_DATASET_ENUM, null, typeEnum, DIMs, null, CHUNKs, 9, DATA_ENUM);
dsets[5] = file.createScalarDS (NAME_DATASET_SUB, g0, typeInt, DIMs, null, CHUNKs, 9, DATA_INT);
dsets[6] = file.createScalarDS (NAME_DATASET_SUB_SUB, g00, typeFloat, DIMs, null, CHUNKs, 9, DATA_FLOAT);
dsets[7] = file.createImage (NAME_DATASET_IMAGE, null, typeInt, DIMs, null, CHUNKs, 9, 1, -1, DATA_BYTE);
dsets[8] = file.createCompoundDS(NAME_DATASET_COMPOUND, null, DIMs, null, CHUNKs, 9,
COMPOUND_MEMBER_NAMES, COMPOUND_MEMBER_DATATYPES, null, DATA_COMP);
dsets[9] = file.createCompoundDS(NAME_DATASET_COMPOUND_SUB, null, DIMs, null, CHUNKs, 9,
COMPOUND_MEMBER_NAMES, COMPOUND_MEMBER_DATATYPES, null, DATA_COMP);
dsets[10] = file.createScalarDS (NAME_DATASET_STR_VLEN, null, typeStrVlen, DIMs, null, CHUNKs, 9, DATA_STR);
for (int i=0; i<dsets.length; i++) {
dsets[i].writeMetadata(ATTRIBUTE_STR);
dsets[i].writeMetadata(ATTRIBUTE_INT_ARRAY);
}
file.createDatatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, -1, -1, NAME_DATATYPE_INT);
file.createDatatype(Datatype.CLASS_FLOAT, DATATYPE_SIZE, -1, -1, NAME_DATATYPE_FLOAT);
file.createDatatype(Datatype.CLASS_STRING, STR_LEN, -1, -1, NAME_DATATYPE_STR);
int nObjs = 0;
try { nObjs = H5.H5Fget_obj_count(file.getFID(), HDF5Constants.H5F_OBJ_ALL); }
catch (final Exception ex) { ; }
if (nObjs > 1) {
System.err.println("Possible memory leak. Some objects are still open." +nObjs);
}
try { file.close(); } catch (final Exception ex) {}
return file;
}
}
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