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Merge pull request #85 from Intel-HLS/gp_jni_fix_test_updates
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JNI fixes and test updates
George Powley authored Nov 20, 2017
2 parents 8635d08 + e55eda9 commit c174e37
Showing 8 changed files with 28 additions and 17 deletions.
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -11,6 +11,7 @@ build/
.idea/dictionaries
.idea/vcs.xml
.idea/jsLibraryMappings.xml
.idea/misc.xml

# Sensitive or high-churn files:
.idea/dataSources.ids
12 changes: 11 additions & 1 deletion build.gradle
Original file line number Diff line number Diff line change
@@ -13,7 +13,6 @@ compileTestJava {
}

repositories {
// maven { url uri('/home/gspowley/.m2/repository/')}
mavenLocal()
mavenCentral()
maven { url "https://artifactory.broadinstitute.org/artifactory/libs-snapshot/" }
@@ -85,6 +84,13 @@ test {
// propagate system properties to test JVM
systemProperties = System.getProperties()

if (project.hasProperty('debug')) {
jvmArgs '-verbose:jni', '-Xcheck:jni', '-XX:+RestoreMXCSROnJNICalls'
}
else {
jvmArgs '-Xcheck:jni', '-XX:+RestoreMXCSROnJNICalls'
}

testLogging {
if (!System.env.CI.toString().toBoolean()) {
events "passed", "skipped", "failed", "standardOut", "standardError"
@@ -193,6 +199,10 @@ uploadArchives {
name = "Priya Vaidya"
email = "[email protected]"
}
developer {
name = "Ernesto Brau"
email = "[email protected]"
}
}
}
}
5 changes: 3 additions & 2 deletions src/main/native/compression/IntelDeflater.cc
Original file line number Diff line number Diff line change
@@ -256,7 +256,7 @@ JNIEXPORT jint JNICALL Java_com_intel_gkl_compression_IntelDeflater_deflateNativ

// set finished if endOfStream was set and all input processed
if (endOfStream && lz_stream->avail_in == 0) {
env->SetLongField(obj, FID_finished, true);
env->SetBooleanField(obj, FID_finished, true);
}

// return number of bytes written to output buffer
@@ -299,7 +299,7 @@ JNIEXPORT jint JNICALL Java_com_intel_gkl_compression_IntelDeflater_deflateNativ
env->ReleasePrimitiveArrayCritical(outputBuffer, next_out, 0);

if (ret == Z_STREAM_END && lz_stream->avail_in == 0) {
env->SetLongField(obj, FID_finished, true);
env->SetBooleanField(obj, FID_finished, true);
}

return bytes_out;
@@ -317,6 +317,7 @@ Java_com_intel_gkl_compression_IntelDeflater_endNative(JNIEnv *env, jobject obj)
if (level != 1) {
z_stream* lz_stream = (z_stream*)env->GetLongField(obj, FID_lz_stream);
deflateEnd(lz_stream);
free(lz_stream);
}
else {
isal_zstream* lz_stream = (isal_zstream*)env->GetLongField(obj, FID_lz_stream);
4 changes: 2 additions & 2 deletions src/main/native/compression/IntelInflater.cc
Original file line number Diff line number Diff line change
@@ -151,7 +151,7 @@ JNIEXPORT jint JNICALL Java_com_intel_gkl_compression_IntelInflater_inflateNativ
env->ReleasePrimitiveArrayCritical(outputBuffer, next_out, 0);

if (ret == ISAL_END_INPUT && lz_stream->avail_in == 0) {
env->SetLongField(obj, FID_inf_finished, true);
env->SetBooleanField(obj, FID_inf_finished, true);
}

return bytes_out;
@@ -169,4 +169,4 @@ Java_com_intel_gkl_compression_IntelInflater_endNative(JNIEnv *env, jobject obj)
inflate_state* lz_stream = (inflate_state*)env->GetLongField(obj, FID_inf_lz_stream);
free(lz_stream);

}
}
8 changes: 3 additions & 5 deletions src/main/native/smithwaterman/IntelSmithWaterman.cc
Original file line number Diff line number Diff line change
@@ -49,6 +49,9 @@ if(is_avx512_supported())
JNIEXPORT jint JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_alignNative
(JNIEnv * env, jclass obj, jbyteArray ref, jbyteArray alt, jbyteArray cigar, jint match, jint mismatch, jint open, jint extend, jint strategy)
{
jint refLength = env->GetArrayLength(ref);
jint altLength = env->GetArrayLength(alt);

jbyte* reference = (jbyte*)env->GetPrimitiveArrayCritical(ref, 0);
jbyte* alternate = (jbyte*)env->GetPrimitiveArrayCritical(alt, 0);
jbyte* cigarArray = (jbyte*)env->GetPrimitiveArrayCritical(cigar, 0);
@@ -57,18 +60,13 @@ JNIEXPORT jint JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_align
jint offset = 0;

// call the low level routine
jint refLength = env->GetArrayLength(ref);
jint altLength = env->GetArrayLength(alt);


offset = g_runSWOnePairBT(match, mismatch, open, extend,(uint8_t*) reference, (uint8_t*) alternate,refLength, altLength, strategy, (char *) cigarArray, (int16_t*) &count);

// release buffers
env->ReleasePrimitiveArrayCritical(ref, reference, 0);
env->ReleasePrimitiveArrayCritical(alt, alternate, 0);
env->ReleasePrimitiveArrayCritical(cigar, cigarArray, 0);


return offset;
}

6 changes: 4 additions & 2 deletions src/test/java/com/intel/gkl/IntelGKLUtilsUnitTest.java
Original file line number Diff line number Diff line change
@@ -9,7 +9,8 @@
public class IntelGKLUtilsUnitTest {
private final static Logger log = LogManager.getLogger(IntelGKLUtilsUnitTest.class);

@Test(enabled = true)
// disable this test because it fails with jvmArg '-XX:+RestoreMXCSROnJNICalls'
@Test(enabled = false)
public void simpleTest() {

IntelGKLUtils utils = new IntelGKLUtils();
@@ -43,7 +44,8 @@ public void run() {
}
}

@Test(enabled = true)
// disable this test because it fails with jvmArg '-XX:+RestoreMXCSROnJNICalls'
@Test(enabled = false)
public void childThreadTest() {

log.info("Parent setting FTZ = true");
6 changes: 4 additions & 2 deletions src/test/java/com/intel/gkl/compression/DeflaterProfile.java
Original file line number Diff line number Diff line change
@@ -28,7 +28,9 @@ public void profileTest() throws IOException {
final String filename = System.getProperty("input", INPUT_FILE);
final File inputFile = new File(filename);
final File outputFile = File.createTempFile("output", ".bam");
//outputFile.deleteOnExit();
outputFile.deleteOnExit();
final File profileFile = File.createTempFile("profile", ".csv");
profileFile.deleteOnExit();

SamReaderFactory readerFactory =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
@@ -50,7 +52,7 @@ public Deflater makeDeflater(final int compressionLevel, final boolean nowrap) {
deflaterFactories.add(javaDeflaterFactory);

// create profile log file
final FileWriter fileWriter = new FileWriter("profile.csv");
final FileWriter fileWriter = new FileWriter(profileFile);

fileWriter.write("level, time(sec), filesize\n");

Original file line number Diff line number Diff line change
@@ -18,7 +18,6 @@ public class SmithWatermanUnitTest {
private final static Logger logger = LogManager.getLogger(SmithWatermanUnitTest.class);

static final String smithwatermanData = IntelGKLUtils.pathToTestResource("smith-waterman.SOFTCLIP.in");
static final String smithwatermanOutput = IntelGKLUtils.pathToTestResource("smith-waterman.SOFTCLIP.out");
int MAX_SEQ_LEN = 1024;

@Test(enabled = true)
@@ -38,10 +37,8 @@ public void simpleTest() {
try {

final File inputFile = new File(smithwatermanData);
final File outputFile = new File(smithwatermanOutput);
long inputBytes = inputFile.length();
final FileReader input = new FileReader(inputFile);
final FileWriter output = new FileWriter(outputFile);
final BufferedReader in = new BufferedReader(input);

byte[] ref;

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