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Use Intel hardware-accelerated Deflater for writing BAM files where a…
…ppropriate. This is only supported on unix systems. net.sf.samtools.util.zip.IntelDeflater is used instead of java.util.zip.Deflater. In order to use IntelDeflater, a shared library libIntelDeflater.so must be dynamically loaded. This library is included in the picard-tools zipfile. The shared library is found via one of the following methods: If -Dsamjdk.intel_deflater_so_path is set and points to the shared library, it is loaded from that location. Else if the shared library is in the same directory as the Picard jar that is executing, it is loaded from that location. We presume that this will be the typical way in which the shared library will be found. Else if the shared library is found on LD_LIBRARY_PATH, it is loaded from there. Else java.util.zip.Deflater is used. Use of IntelDeflater may be suppressed with -Dsamjdk.try_use_intel_deflater=false. In the header line written by Picard command-line programs, at the end of the line will appear either IntelDeflater or JdkDeflater to indicate which has been loaded. We have seen compression time reduced by 13% to 33% depending on the hardware.
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| Original file line number | Diff line number | Diff line change |
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| /* | ||
| * Copyright (c) 1997, 2010, Oracle and/or its affiliates. All rights reserved. | ||
| * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER. | ||
| * | ||
| * This code is free software; you can redistribute it and/or modify it | ||
| * under the terms of the GNU General Public License version 2 only, as | ||
| * published by the Free Software Foundation. Oracle designates this | ||
| * particular file as subject to the "Classpath" exception as provided | ||
| * by Oracle in the LICENSE file that accompanied this code. | ||
| * | ||
| * This code is distributed in the hope that it will be useful, but WITHOUT | ||
| * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or | ||
| * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License | ||
| * version 2 for more details (a copy is included in the LICENSE file that | ||
| * accompanied this code). | ||
| * | ||
| * You should have received a copy of the GNU General Public License version | ||
| * 2 along with this work; if not, write to the Free Software Foundation, | ||
| * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. | ||
| * | ||
| * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA | ||
| * or visit www.oracle.com if you need additional information or have any | ||
| * questions. | ||
| */ | ||
|
|
||
| /* | ||
| * Native method support for net.sf.samtools.util.zip.IntelDeflater. | ||
| * This is copied from OpenJDK native support for java.util.zip.Deflater, with only package and class name changed. | ||
| */ | ||
|
|
||
| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include "jlong.h" | ||
| #include "jni.h" | ||
| #include "jni_util.h" | ||
| #include "zlib.h" | ||
|
|
||
| #include "net_sf_samtools_util_zip_IntelDeflater.h" | ||
|
|
||
| #define DEF_MEM_LEVEL 8 | ||
|
|
||
| static jfieldID levelID; | ||
| static jfieldID strategyID; | ||
| static jfieldID setParamsID; | ||
| static jfieldID finishID; | ||
| static jfieldID finishedID; | ||
| static jfieldID bufID, offID, lenID; | ||
|
|
||
| JNIEXPORT void JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_initIDs(JNIEnv *env, jclass cls) | ||
| { | ||
| levelID = (*env)->GetFieldID(env, cls, "level", "I"); | ||
| strategyID = (*env)->GetFieldID(env, cls, "strategy", "I"); | ||
| setParamsID = (*env)->GetFieldID(env, cls, "setParams", "Z"); | ||
| finishID = (*env)->GetFieldID(env, cls, "finish", "Z"); | ||
| finishedID = (*env)->GetFieldID(env, cls, "finished", "Z"); | ||
| bufID = (*env)->GetFieldID(env, cls, "buf", "[B"); | ||
| offID = (*env)->GetFieldID(env, cls, "off", "I"); | ||
| lenID = (*env)->GetFieldID(env, cls, "len", "I"); | ||
| } | ||
|
|
||
| JNIEXPORT jlong JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_init(JNIEnv *env, jclass cls, jint level, | ||
| jint strategy, jboolean nowrap) | ||
| { | ||
| z_stream *strm = calloc(1, sizeof(z_stream)); | ||
|
|
||
| if (strm == 0) { | ||
| JNU_ThrowOutOfMemoryError(env, 0); | ||
| return jlong_zero; | ||
| } else { | ||
| char *msg; | ||
| switch (deflateInit2(strm, level, Z_DEFLATED, | ||
| nowrap ? -MAX_WBITS : MAX_WBITS, | ||
| DEF_MEM_LEVEL, strategy)) { | ||
| case Z_OK: | ||
| return ptr_to_jlong(strm); | ||
| case Z_MEM_ERROR: | ||
| free(strm); | ||
| JNU_ThrowOutOfMemoryError(env, 0); | ||
| return jlong_zero; | ||
| case Z_STREAM_ERROR: | ||
| free(strm); | ||
| JNU_ThrowIllegalArgumentException(env, 0); | ||
| return jlong_zero; | ||
| default: | ||
| msg = strm->msg; | ||
| free(strm); | ||
| JNU_ThrowInternalError(env, msg); | ||
| return jlong_zero; | ||
| } | ||
| } | ||
| } | ||
|
|
||
| JNIEXPORT void JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_setDictionary(JNIEnv *env, jclass cls, jlong addr, | ||
| jarray b, jint off, jint len) | ||
| { | ||
| Bytef *buf = (*env)->GetPrimitiveArrayCritical(env, b, 0); | ||
| int res; | ||
| if (buf == 0) {/* out of memory */ | ||
| return; | ||
| } | ||
| res = deflateSetDictionary((z_stream *)jlong_to_ptr(addr), buf + off, len); | ||
| (*env)->ReleasePrimitiveArrayCritical(env, b, buf, 0); | ||
| switch (res) { | ||
| case Z_OK: | ||
| break; | ||
| case Z_STREAM_ERROR: | ||
| JNU_ThrowIllegalArgumentException(env, 0); | ||
| break; | ||
| default: | ||
| JNU_ThrowInternalError(env, ((z_stream *)jlong_to_ptr(addr))->msg); | ||
| break; | ||
| } | ||
| } | ||
|
|
||
| JNIEXPORT jint JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_deflateBytes(JNIEnv *env, jobject this, jlong addr, | ||
| jarray b, jint off, jint len, jint flush) | ||
| { | ||
| z_stream *strm = jlong_to_ptr(addr); | ||
|
|
||
| jarray this_buf = (*env)->GetObjectField(env, this, bufID); | ||
| jint this_off = (*env)->GetIntField(env, this, offID); | ||
| jint this_len = (*env)->GetIntField(env, this, lenID); | ||
| jbyte *in_buf; | ||
| jbyte *out_buf; | ||
| int res; | ||
| if ((*env)->GetBooleanField(env, this, setParamsID)) { | ||
| int level = (*env)->GetIntField(env, this, levelID); | ||
| int strategy = (*env)->GetIntField(env, this, strategyID); | ||
| in_buf = (*env)->GetPrimitiveArrayCritical(env, this_buf, 0); | ||
| if (in_buf == NULL) { | ||
| // Throw OOME only when length is not zero | ||
| if (this_len != 0) | ||
| JNU_ThrowOutOfMemoryError(env, 0); | ||
| return 0; | ||
| } | ||
| out_buf = (*env)->GetPrimitiveArrayCritical(env, b, 0); | ||
| if (out_buf == NULL) { | ||
| (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0); | ||
| if (len != 0) | ||
| JNU_ThrowOutOfMemoryError(env, 0); | ||
| return 0; | ||
| } | ||
|
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||
| strm->next_in = (Bytef *) (in_buf + this_off); | ||
| strm->next_out = (Bytef *) (out_buf + off); | ||
| strm->avail_in = this_len; | ||
| strm->avail_out = len; | ||
| res = deflateParams(strm, level, strategy); | ||
| (*env)->ReleasePrimitiveArrayCritical(env, b, out_buf, 0); | ||
| (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0); | ||
|
|
||
| switch (res) { | ||
| case Z_OK: | ||
| (*env)->SetBooleanField(env, this, setParamsID, JNI_FALSE); | ||
| this_off += this_len - strm->avail_in; | ||
| (*env)->SetIntField(env, this, offID, this_off); | ||
| (*env)->SetIntField(env, this, lenID, strm->avail_in); | ||
| return len - strm->avail_out; | ||
| case Z_BUF_ERROR: | ||
| (*env)->SetBooleanField(env, this, setParamsID, JNI_FALSE); | ||
| return 0; | ||
| default: | ||
| JNU_ThrowInternalError(env, strm->msg); | ||
| return 0; | ||
| } | ||
| } else { | ||
| jboolean finish = (*env)->GetBooleanField(env, this, finishID); | ||
| in_buf = (*env)->GetPrimitiveArrayCritical(env, this_buf, 0); | ||
| if (in_buf == NULL) { | ||
| if (this_len != 0) | ||
| JNU_ThrowOutOfMemoryError(env, 0); | ||
| return 0; | ||
| } | ||
| out_buf = (*env)->GetPrimitiveArrayCritical(env, b, 0); | ||
| if (out_buf == NULL) { | ||
| (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0); | ||
| if (len != 0) | ||
| JNU_ThrowOutOfMemoryError(env, 0); | ||
|
|
||
| return 0; | ||
| } | ||
|
|
||
| strm->next_in = (Bytef *) (in_buf + this_off); | ||
| strm->next_out = (Bytef *) (out_buf + off); | ||
| strm->avail_in = this_len; | ||
| strm->avail_out = len; | ||
| res = deflate(strm, finish ? Z_FINISH : flush); | ||
| (*env)->ReleasePrimitiveArrayCritical(env, b, out_buf, 0); | ||
| (*env)->ReleasePrimitiveArrayCritical(env, this_buf, in_buf, 0); | ||
|
|
||
| switch (res) { | ||
| case Z_STREAM_END: | ||
| (*env)->SetBooleanField(env, this, finishedID, JNI_TRUE); | ||
| /* fall through */ | ||
| case Z_OK: | ||
| this_off += this_len - strm->avail_in; | ||
| (*env)->SetIntField(env, this, offID, this_off); | ||
| (*env)->SetIntField(env, this, lenID, strm->avail_in); | ||
| return len - strm->avail_out; | ||
| case Z_BUF_ERROR: | ||
| return 0; | ||
| default: | ||
| JNU_ThrowInternalError(env, strm->msg); | ||
| return 0; | ||
| } | ||
| } | ||
| } | ||
|
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||
| JNIEXPORT jint JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_getAdler(JNIEnv *env, jclass cls, jlong addr) | ||
| { | ||
| return ((z_stream *)jlong_to_ptr(addr))->adler; | ||
| } | ||
|
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| JNIEXPORT jlong JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_getBytesRead(JNIEnv *env, jclass cls, jlong addr) | ||
| { | ||
| return ((z_stream *)jlong_to_ptr(addr))->total_in; | ||
| } | ||
|
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| JNIEXPORT jlong JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_getBytesWritten(JNIEnv *env, jclass cls, jlong addr) | ||
| { | ||
| return ((z_stream *)jlong_to_ptr(addr))->total_out; | ||
| } | ||
|
|
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| JNIEXPORT void JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_reset(JNIEnv *env, jclass cls, jlong addr) | ||
| { | ||
| if (deflateReset((z_stream *)jlong_to_ptr(addr)) != Z_OK) { | ||
| JNU_ThrowInternalError(env, 0); | ||
| } | ||
| } | ||
|
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| JNIEXPORT void JNICALL | ||
| Java_net_sf_samtools_util_zip_IntelDeflater_end(JNIEnv *env, jclass cls, jlong addr) | ||
| { | ||
| if (deflateEnd((z_stream *)jlong_to_ptr(addr)) == Z_STREAM_ERROR) { | ||
| JNU_ThrowInternalError(env, 0); | ||
| } else { | ||
| free((z_stream *)jlong_to_ptr(addr)); | ||
| } | ||
| } |
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