diff --git a/hail/build.gradle b/hail/build.gradle index 36e378998c4..bc8ca4c101c 100644 --- a/hail/build.gradle +++ b/hail/build.gradle @@ -204,7 +204,7 @@ dependencies { bundled 'com.kohlschutter.junixsocket:junixsocket-core:2.6.1' - bundled 'com.github.luben:zstd-jni:1.5.5-2' + bundled 'com.github.luben:zstd-jni:1.5.2-1' bundled project(path: ':shadedazure', configuration: 'shadow') } diff --git a/hail/python/hail/matrixtable.py b/hail/python/hail/matrixtable.py index 6baceae5d33..fd17c2a9b36 100644 --- a/hail/python/hail/matrixtable.py +++ b/hail/python/hail/matrixtable.py @@ -2662,6 +2662,22 @@ def checkpoint(self, output: str, overwrite: bool = False, stage_locally: bool = -------- >>> dataset = dataset.checkpoint('output/dataset_checkpoint.mt') """ + if _codec_spec is None: + _codec_spec = """{ + "name": "LEB128BufferSpec", + "child": { + "name": "BlockingBufferSpec", + "blockSize": 32768, + "child": { + "name": "LZ4FastBlockBufferSpec", + "blockSize": 32768, + "child": { + "name": "StreamBlockBufferSpec" + } + } + } +}""" + hl.current_backend().validate_file_scheme(output) if not _read_if_exists or not hl.hadoop_exists(f'{output}/_SUCCESS'): diff --git a/hail/python/hail/table.py b/hail/python/hail/table.py index b778e38ab4f..9febea65b9f 100644 --- a/hail/python/hail/table.py +++ b/hail/python/hail/table.py @@ -1327,6 +1327,22 @@ def checkpoint(self, output: str, overwrite: bool = False, stage_locally: bool = """ hl.current_backend().validate_file_scheme(output) + if _codec_spec is None: + _codec_spec = """{ + "name": "LEB128BufferSpec", + "child": { + "name": "BlockingBufferSpec", + "blockSize": 32768, + "child": { + "name": "LZ4FastBlockBufferSpec", + "blockSize": 32768, + "child": { + "name": "StreamBlockBufferSpec" + } + } + } +}""" + if not _read_if_exists or not hl.hadoop_exists(f'{output}/_SUCCESS'): self.write(output=output, overwrite=overwrite, stage_locally=stage_locally, _codec_spec=_codec_spec) _assert_type = self._type diff --git a/hail/python/hail/vds/combiner/variant_dataset_combiner.py b/hail/python/hail/vds/combiner/variant_dataset_combiner.py index f47e465bfb3..02a1bcb4d4d 100644 --- a/hail/python/hail/vds/combiner/variant_dataset_combiner.py +++ b/hail/python/hail/vds/combiner/variant_dataset_combiner.py @@ -43,10 +43,10 @@ class CombinerOutType(NamedTuple): "name": "LEB128BufferSpec", "child": { "name": "BlockingBufferSpec", - "blockSize": 65536, + "blockSize": 32768, "child": { - "name": "ZstdBlockBufferSpec", - "blockSize": 65536, + "name": "LZ4FastBlockBufferSpec", + "blockSize": 32768, "child": { "name": "StreamBlockBufferSpec" } diff --git a/hail/python/test/hail/backend/test_service_backend.py b/hail/python/test/hail/backend/test_service_backend.py index 1a0e0fa50b5..12da7814688 100644 --- a/hail/python/test/hail/backend/test_service_backend.py +++ b/hail/python/test/hail/backend/test_service_backend.py @@ -9,9 +9,13 @@ @skip_unless_service_backend() def test_tiny_driver_has_tiny_memory(): try: - hl.eval(hl.range(1024 * 1024).map(lambda x: hl.range(1024 * 1024))) - except hl.utils.FatalError as exc: - assert "HailException: Hail off-heap memory exceeded maximum threshold: limit " in exc.args[0] + hl.utils.range_table(100_000_000, 50).to_pandas() + except Exception as exc: + # Sometimes the JVM properly OOMs, sometimes it just dies. + assert ( + 'java.lang.OutOfMemoryError: Java heap space' in exc.args[0] or + 'batch.worker.jvm_entryway_protocol.EndOfStream' in exc.args[0] + ) else: assert False diff --git a/hail/python/test/hail/matrixtable/test_file_formats.py b/hail/python/test/hail/matrixtable/test_file_formats.py index d4a098f72fe..5d158ae8a4b 100644 --- a/hail/python/test/hail/matrixtable/test_file_formats.py +++ b/hail/python/test/hail/matrixtable/test_file_formats.py @@ -73,7 +73,7 @@ def all_values_table_fixture(init_hail): @pytest.mark.parametrize("path", mt_paths) def test_backward_compatability_mt(path, all_values_matrix_table_fixture): - assert len(mt_paths) == 56, str((resource_dir, ht_paths)) + assert len(mt_paths) == 46, str((resource_dir, ht_paths)) old = hl.read_matrix_table(path) @@ -88,7 +88,7 @@ def test_backward_compatability_mt(path, all_values_matrix_table_fixture): @pytest.mark.parametrize("path", ht_paths) def test_backward_compatability_ht(path, all_values_table_fixture): - assert len(ht_paths) == 52, str((resource_dir, ht_paths)) + assert len(ht_paths) == 42, str((resource_dir, ht_paths)) old = hl.read_table(path) diff --git a/hail/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala b/hail/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala index 0b23745d117..ff854ce4b06 100644 --- a/hail/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala +++ b/hail/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala @@ -198,5 +198,5 @@ class MatrixTableSpec( } object FileFormat { - val version: SemanticVersion = SemanticVersion(1, 7, 0) + val version: SemanticVersion = SemanticVersion(1, 6, 0) } diff --git a/hail/src/main/scala/is/hail/expr/ir/Emit.scala b/hail/src/main/scala/is/hail/expr/ir/Emit.scala index 304d39343af..d45be5c44e9 100644 --- a/hail/src/main/scala/is/hail/expr/ir/Emit.scala +++ b/hail/src/main/scala/is/hail/expr/ir/Emit.scala @@ -740,7 +740,7 @@ class Emit[C]( val ns = sigs.length val deserializers = sc.states.states .slice(start, start + ns) - .map(sc => sc.deserialize(spec)) + .map(sc => sc.deserialize(BufferSpec.defaultUncompressed)) Array.range(start, start + ns).foreach(i => sc.newState(cb, i)) @@ -2374,7 +2374,7 @@ class Emit[C]( PCanonicalTuple(true, et.emitType.storageType).constructFromFields(cb, region, FastIndexedSeq(et), deepCopy = false) } - val bufferSpec: BufferSpec = BufferSpec.blockedUncompressed + val bufferSpec: BufferSpec = BufferSpec.defaultUncompressed val emitGlobals = EmitCode.fromI(mb)(cb => emitInNewBuilder(cb, globals)) diff --git a/hail/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala b/hail/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala index bbb8c5e9d34..3c8a58dc5c9 100644 --- a/hail/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala +++ b/hail/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala @@ -333,7 +333,7 @@ class EmitClassBuilder[C]( private[this] def encodeLiterals(): Array[AnyRef] = { val (literals, preEncodedLiterals) = emodb.literalsResult() val litType = PCanonicalTuple(true, literals.map(_._1.canonicalPType.setRequired(true)): _*) - val spec = TypedCodecSpec(litType, BufferSpec.wireSpec) + val spec = TypedCodecSpec(litType, BufferSpec.defaultUncompressed) cb.addInterface(typeInfo[FunctionWithLiterals].iname) val mb2 = newEmitMethod("addAndDecodeLiterals", FastIndexedSeq[ParamType](typeInfo[Array[AnyRef]]), typeInfo[Unit]) diff --git a/hail/src/main/scala/is/hail/expr/ir/IR.scala b/hail/src/main/scala/is/hail/expr/ir/IR.scala index 0caae00a07f..0a33bec0672 100644 --- a/hail/src/main/scala/is/hail/expr/ir/IR.scala +++ b/hail/src/main/scala/is/hail/expr/ir/IR.scala @@ -111,7 +111,7 @@ object EncodedLiteral { case ts: PString => Str(ts.loadString(addr)) case _ => val etype = EType.defaultFromPType(pt) - val codec = TypedCodecSpec(etype, pt.virtualType, BufferSpec.wireSpec) + val codec = TypedCodecSpec(etype, pt.virtualType, BufferSpec.defaultUncompressed) val bytes = codec.encodeArrays(ctx, pt, addr) EncodedLiteral(codec, bytes) } diff --git a/hail/src/main/scala/is/hail/expr/ir/Interpret.scala b/hail/src/main/scala/is/hail/expr/ir/Interpret.scala index bb90e50f064..fa7521c9e95 100644 --- a/hail/src/main/scala/is/hail/expr/ir/Interpret.scala +++ b/hail/src/main/scala/is/hail/expr/ir/Interpret.scala @@ -897,7 +897,7 @@ object Interpret { // TODO Is this right? where does wrapped run? ctx.scopedExecution((hcl, fs, htc, r) => SafeRow(rt, f(hcl, fs, htc, r).apply(r, globalsOffset))) } else { - val spec = BufferSpec.blockedUncompressed + val spec = BufferSpec.defaultUncompressed val (_, initOp) = CompileWithAggregators[AsmFunction2RegionLongUnit](ctx, extracted.states, diff --git a/hail/src/main/scala/is/hail/expr/ir/TableIR.scala b/hail/src/main/scala/is/hail/expr/ir/TableIR.scala index 34bf23d0011..46c0ebac13e 100644 --- a/hail/src/main/scala/is/hail/expr/ir/TableIR.scala +++ b/hail/src/main/scala/is/hail/expr/ir/TableIR.scala @@ -2562,7 +2562,7 @@ case class TableMapRows(child: TableIR, newRow: IR) extends TableIR { else null - val spec = BufferSpec.blockedUncompressed + val spec = BufferSpec.defaultUncompressed // Order of operations: // 1. init op on all aggs and serialize to byte array. @@ -3059,7 +3059,7 @@ case class TableKeyByAndAggregate( val globalsBc = prev.globals.broadcast(ctx.theHailClassLoader) - val spec = BufferSpec.blockedUncompressed + val spec = BufferSpec.defaultUncompressed val res = genUID() val extracted = agg.Extract(expr, res, Requiredness(this, ctx)) diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala b/hail/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala index 6873c365ec4..5c12541defe 100644 --- a/hail/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala +++ b/hail/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala @@ -39,7 +39,7 @@ trait AggregatorState { val lazyBuffer = kb.getOrDefineLazyField[MemoryBufferWrapper](Code.newInstance[MemoryBufferWrapper](), ("AggregatorStateBufferWrapper")) cb += lazyBuffer.invoke[Array[Byte], Unit]("set", bytes.loadBytes(cb)) val ib = cb.memoize(lazyBuffer.invoke[InputBuffer]("buffer")) - deserialize(BufferSpec.blockedUncompressed)(cb, ib) + deserialize(BufferSpec.defaultUncompressed)(cb, ib) cb += lazyBuffer.invoke[Unit]("invalidate") } @@ -48,7 +48,7 @@ trait AggregatorState { val addr = kb.genFieldThisRef[Long]("addr") cb += lazyBuffer.invoke[Unit]("clear") val ob = cb.memoize(lazyBuffer.invoke[OutputBuffer]("buffer")) - serialize(BufferSpec.blockedUncompressed)(cb, ob) + serialize(BufferSpec.defaultUncompressed)(cb, ob) cb.assign(addr, t.allocate(r, lazyBuffer.invoke[Int]("length"))) t.storeLength(cb, addr, lazyBuffer.invoke[Int]("length")) cb += lazyBuffer.invoke[Long, Unit]("copyToAddress", t.bytesAddress(addr)) diff --git a/hail/src/main/scala/is/hail/io/BufferSpecs.scala b/hail/src/main/scala/is/hail/io/BufferSpecs.scala index 2ca8876fc89..b98fca3aa4a 100644 --- a/hail/src/main/scala/is/hail/io/BufferSpecs.scala +++ b/hail/src/main/scala/is/hail/io/BufferSpecs.scala @@ -12,30 +12,24 @@ import org.json4s.jackson.JsonMethods import org.json4s.{Extraction, JValue} object BufferSpec { - val zstdCompressionLEB: BufferSpec = LEB128BufferSpec( - BlockingBufferSpec(64 * 1024, - ZstdBlockBufferSpec(64 * 1024, + val default: BufferSpec = LEB128BufferSpec( + BlockingBufferSpec(32 * 1024, + LZ4HCBlockBufferSpec(32 * 1024, new StreamBlockBufferSpec))) - val default: BufferSpec = zstdCompressionLEB - - val blockedUncompressed: BufferSpec = BlockingBufferSpec(32 * 1024, + val defaultUncompressed: BufferSpec = BlockingBufferSpec(32 * 1024, new StreamBlockBufferSpec) + val unblockedUncompressed: BufferSpec = new StreamBufferSpec val wireSpec: BufferSpec = LEB128BufferSpec( - BlockingBufferSpec(64 * 1024, - ZstdSizedBasedBlockBufferSpec(64 * 1024, - /*minCompressionSize=*/256, - new StreamBlockBufferSpec))) - val memorySpec: BufferSpec = wireSpec - - // longtime default spec - val lz4HCCompressionLEB: BufferSpec = LEB128BufferSpec( BlockingBufferSpec(32 * 1024, - LZ4HCBlockBufferSpec(32 * 1024, + LZ4SizeBasedBlockBufferSpec("fast", 32 * 1024, + 256, new StreamBlockBufferSpec))) + val memorySpec: BufferSpec = wireSpec + val blockSpecs: Array[BufferSpec] = Array( BlockingBufferSpec(64 * 1024, new StreamBlockBufferSpec), @@ -45,9 +39,6 @@ object BufferSpec { BlockingBufferSpec(32 * 1024, LZ4FastBlockBufferSpec(32 * 1024, new StreamBlockBufferSpec)), - BlockingBufferSpec(64 * 1024, - ZstdBlockBufferSpec(64 * 1024, - new StreamBlockBufferSpec)), new StreamBufferSpec) val specs: Array[BufferSpec] = blockSpecs.flatMap { blockSpec => @@ -70,7 +61,6 @@ object BufferSpec { classOf[LZ4HCBlockBufferSpec], classOf[LZ4FastBlockBufferSpec], classOf[LZ4SizeBasedBlockBufferSpec], - classOf[ZstdBlockBufferSpec], classOf[StreamBlockBufferSpec], classOf[BufferSpec], classOf[LEB128BufferSpec], @@ -184,34 +174,6 @@ final case class LZ4SizeBasedBlockBufferSpec(compressorType: String, blockSize: Code.newInstance[LZ4SizeBasedCompressingOutputBlockBuffer, LZ4, Int, Int, OutputBlockBuffer](stagedlz4, blockSize, minCompressionSize, child.buildCodeOutputBuffer(out)) } -final case class ZstdBlockBufferSpec(blockSize: Int, child: BlockBufferSpec) extends BlockBufferSpec { - require(blockSize <= (1 << 16)) - - def buildInputBuffer(in: InputStream): InputBlockBuffer = new ZstdInputBlockBuffer(blockSize, child.buildInputBuffer(in)) - - def buildOutputBuffer(out: OutputStream): OutputBlockBuffer = new ZstdOutputBlockBuffer(blockSize, child.buildOutputBuffer(out)) - - def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] = - Code.newInstance[ZstdInputBlockBuffer, Int, InputBlockBuffer](blockSize, child.buildCodeInputBuffer(in)) - - def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] = - Code.newInstance[ZstdOutputBlockBuffer, Int, OutputBlockBuffer](blockSize, child.buildCodeOutputBuffer(out)) -} - -final case class ZstdSizedBasedBlockBufferSpec(blockSize: Int, minCompressionSize: Int, child: BlockBufferSpec) extends BlockBufferSpec { - require(blockSize <= (1 << 16)) - - def buildInputBuffer(in: InputStream): InputBlockBuffer = new ZstdSizedBasedInputBlockBuffer(blockSize, child.buildInputBuffer(in)) - - def buildOutputBuffer(out: OutputStream): OutputBlockBuffer = new ZstdSizedBasedOutputBlockBuffer(blockSize, minCompressionSize, child.buildOutputBuffer(out)) - - def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] = - Code.newInstance[ZstdSizedBasedInputBlockBuffer, Int, InputBlockBuffer](blockSize, child.buildCodeInputBuffer(in)) - - def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] = - Code.newInstance[ZstdSizedBasedOutputBlockBuffer, Int, Int, OutputBlockBuffer](blockSize, minCompressionSize, child.buildCodeOutputBuffer(out)) -} - object StreamBlockBufferSpec { def extract(jv: JValue): StreamBlockBufferSpec = new StreamBlockBufferSpec } diff --git a/hail/src/main/scala/is/hail/io/InputBuffers.scala b/hail/src/main/scala/is/hail/io/InputBuffers.scala index dd22a159112..60a899d850d 100644 --- a/hail/src/main/scala/is/hail/io/InputBuffers.scala +++ b/hail/src/main/scala/is/hail/io/InputBuffers.scala @@ -8,8 +8,6 @@ import is.hail.annotations.{Memory, Region} import is.hail.io.compress.LZ4 import is.hail.utils._ -import com.github.luben.zstd.Zstd - trait InputBuffer extends Closeable { def close(): Unit @@ -629,57 +627,3 @@ final class LZ4SizeBasedCompressingInputBlockBuffer(lz4: LZ4, blockSize: Int, in result } } - -final class ZstdInputBlockBuffer(blockSize: Int, in: InputBlockBuffer) extends InputBlockBuffer { - private val comp = new Array[Byte](4 + Zstd.compressBound(blockSize).toInt) - - def close(): Unit = { - in.close() - } - - def seek(offset: Long): Unit = in.seek(offset) - - def readBlock(buf: Array[Byte]): Int = { - val blockLen = in.readBlock(comp) - if (blockLen == -1) { - blockLen - } else { - val compLen = blockLen - 4 - val decompLen = Memory.loadInt(comp, 0) - val ret = Zstd.decompressByteArray(buf, 0, decompLen, comp, 4, compLen) - if (Zstd.isError(ret)) - throw new com.github.luben.zstd.ZstdException(ret) - decompLen - } - } -} - -final class ZstdSizedBasedInputBlockBuffer(blockSize: Int, in: InputBlockBuffer) extends InputBlockBuffer { - private val comp = new Array[Byte](4 + Zstd.compressBound(blockSize).toInt) - - def close(): Unit = { - in.close() - } - - def seek(offset: Long): Unit = in.seek(offset) - - def readBlock(buf: Array[Byte]): Int = { - val blockLen = in.readBlock(comp) - if (blockLen == -1) { - blockLen - } else { - val compLen = blockLen - 4 - val decomp = Memory.loadInt(comp, 0) - if (decomp % 2 == 0) { - System.arraycopy(comp, 4, buf, 0, compLen) - compLen - } else { - val decompLen = decomp >>> 1 - val ret = Zstd.decompressByteArray(buf, 0, decompLen, comp, 4, compLen) - if (Zstd.isError(ret)) - throw new com.github.luben.zstd.ZstdException(ret) - decompLen - } - } - } -} diff --git a/hail/src/main/scala/is/hail/io/OutputBuffers.scala b/hail/src/main/scala/is/hail/io/OutputBuffers.scala index cc942ccb871..065665c5a03 100644 --- a/hail/src/main/scala/is/hail/io/OutputBuffers.scala +++ b/hail/src/main/scala/is/hail/io/OutputBuffers.scala @@ -8,8 +8,6 @@ import is.hail.io.compress.LZ4 import is.hail.utils._ import is.hail.utils.richUtils.ByteTrackingOutputStream -import com.github.luben.zstd.Zstd - trait OutputBuffer extends Closeable { def flush(): Unit @@ -343,48 +341,4 @@ final class LZ4SizeBasedCompressingOutputBlockBuffer(lz4: LZ4, blockSize: Int, m } def getPos(): Long = out.getPos() -} - -final class ZstdOutputBlockBuffer(blockSize: Int, out: OutputBlockBuffer) extends OutputBlockBuffer { - private val comp = new Array[Byte](4 + Zstd.compressBound(blockSize).toInt) - - def flush(): Unit = out.flush() - - def close(): Unit = out.close() - - def writeBlock(buf: Array[Byte], decompLen: Int): Unit = { - val compLen = Zstd.compressByteArray(comp, 4, comp.length - 4, buf, 0, decompLen, Zstd.defaultCompressionLevel()) - if (Zstd.isError(compLen)) - throw new com.github.luben.zstd.ZstdException(compLen) - Memory.storeInt(comp, 0, decompLen.toInt) - out.writeBlock(comp, compLen.toInt + 4) - } - - def getPos(): Long = out.getPos() -} - -final class ZstdSizedBasedOutputBlockBuffer(blockSize: Int, minCompressionSize: Int, out: OutputBlockBuffer) extends OutputBlockBuffer { - private val comp = new Array[Byte](4 + Zstd.compressBound(blockSize).toInt) - - def flush(): Unit = out.flush() - - def close(): Unit = out.close() - - def writeBlock(buf: Array[Byte], decompLen: Int): Unit = { - val compLen = if (decompLen < minCompressionSize) { - System.arraycopy(buf, 0, comp, 4, decompLen) - Memory.storeInt(comp, 0, 0) - decompLen - } else { - val compLen = Zstd.compressByteArray(comp, 4, comp.length - 4, buf, 0, decompLen, Zstd.defaultCompressionLevel()) - if (Zstd.isError(compLen)) - throw new com.github.luben.zstd.ZstdException(compLen) - Memory.storeInt(comp, 0, (decompLen << 1) + 1) - compLen.toInt - } - - out.writeBlock(comp, compLen + 4) - } - - def getPos(): Long = out.getPos() -} +} \ No newline at end of file diff --git a/hail/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala b/hail/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala index 514af6b9e12..4365bf64d4f 100644 --- a/hail/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala +++ b/hail/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala @@ -84,7 +84,7 @@ object BgenRDDPartitions extends Logging { val nonEmptyFilesAfterFilter = sortedFiles.filter(_.nVariants > 0) - val (leafSpec, intSpec) = BgenSettings.indexCodecSpecs(files.head.indexVersion, rg) + val (leafSpec, intSpec) = BgenSettings.indexCodecSpecs(rg) val getKeysFromFile = StagedBGENReader.queryIndexByPosition(ctx, leafSpec, intSpec) nonEmptyFilesAfterFilter.zipWithIndex.map { case (file, fileIndex) => diff --git a/hail/src/main/scala/is/hail/io/bgen/BgenSettings.scala b/hail/src/main/scala/is/hail/io/bgen/BgenSettings.scala index e833a06365e..b433837e172 100644 --- a/hail/src/main/scala/is/hail/io/bgen/BgenSettings.scala +++ b/hail/src/main/scala/is/hail/io/bgen/BgenSettings.scala @@ -7,7 +7,7 @@ import is.hail.types.encoded._ import is.hail.types.physical._ import is.hail.types.virtual._ import is.hail.types.{MatrixType, TableType} -import is.hail.utils._ +import is.hail.utils.FastIndexedSeq import is.hail.variant.ReferenceGenome @@ -22,16 +22,11 @@ object BgenSettings { val indexAnnotationType: Type = TStruct.empty - private def specFromVersion(indexVersion: SemanticVersion): BufferSpec = - if (indexVersion >= SemanticVersion(1, 2, 0)) { - BufferSpec.zstdCompressionLEB - } else { - BufferSpec.lz4HCCompressionLEB - } - - - def indexCodecSpecs(indexVersion: SemanticVersion, rg: Option[String]): (AbstractTypedCodecSpec, AbstractTypedCodecSpec) = { - val bufferSpec = specFromVersion(indexVersion) + def indexCodecSpecs(rg: Option[String]): (AbstractTypedCodecSpec, AbstractTypedCodecSpec) = { + val bufferSpec = LEB128BufferSpec( + BlockingBufferSpec(32 * 1024, + LZ4HCBlockBufferSpec(32 * 1024, + new StreamBlockBufferSpec))) val keyVType = indexKeyType(rg) val keyEType = EBaseStruct(FastIndexedSeq( diff --git a/hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala b/hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala index dc7e4dba05c..994a34fe1d5 100644 --- a/hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala +++ b/hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala @@ -39,7 +39,6 @@ case class BgenHeader( case class BgenFileMetadata( indexPath: String, - indexVersion: SemanticVersion, header: BgenHeader, rg: Option[String], contigRecoding: Map[String, String], @@ -196,8 +195,7 @@ object LoadBgen { case _ => None } val metadata = IndexReader.readMetadata(fs, indexFile, keyType, annotationType) - val indexVersion = SemanticVersion(metadata.fileVersion) - val (leafSpec, internalSpec) = BgenSettings.indexCodecSpecs(indexVersion, rg) + val (leafSpec, internalSpec) = BgenSettings.indexCodecSpecs(rg) val getKeys = cacheByRG.getOrElseUpdate(rg, StagedBGENReader.queryIndexByPosition(ctx, leafSpec, internalSpec)) @@ -213,7 +211,6 @@ object LoadBgen { BgenFileMetadata( indexFile, - indexVersion, h, rg, contigRecoding, @@ -343,9 +340,6 @@ object MatrixBGENReader { val indexFiles = LoadBgen.getIndexFiles(fs, allFiles, params.indexFileMap) val fileMetadata = LoadBgen.getBgenFileMetadata(ctx, allFiles, indexFiles) assert(fileMetadata.nonEmpty) - if (fileMetadata.exists(md => md.indexVersion != fileMetadata.head.indexVersion)) { - fatal("BGEN index version mismatch. The index versions of all files must be the same, use 'index_bgen' to reindex all files to ensure that all index versions match before calling 'import_bgen' again") - } val sampleIds = params.sampleFile.map(file => LoadBgen.readSampleFile(fs, file)) .getOrElse(LoadBgen.readSamples(fs, fileMetadata.head.path)) @@ -613,7 +607,7 @@ case class BgenPartitionReaderWithVariantFilter(fileMetadata: Array[BgenFileMeta val contigRecoding = mb.genFieldThisRef[Map[String, String]]("bgen_contig_recoding") val indexNKeys = mb.genFieldThisRef[Long]("index_nkeys") - val (leafCodec, intCodec) = BgenSettings.indexCodecSpecs(fileMetadata.head.indexVersion, rg) + val (leafCodec, intCodec) = BgenSettings.indexCodecSpecs(rg) val index = new StagedIndexReader(mb, leafCodec, intCodec) val currVariantIndex = mb.genFieldThisRef[Long]("currVariantIndex") @@ -751,7 +745,7 @@ case class BgenPartitionReader(fileMetadata: Array[BgenFileMetadata], rg: Option val currVariantIndex = mb.genFieldThisRef[Long]("bgen_currIdx") val endVariantIndex = mb.genFieldThisRef[Long]("bgen_endIdx") - val (leafCodec, intCodec) = BgenSettings.indexCodecSpecs(fileMetadata.head.indexVersion, rg) + val (leafCodec, intCodec) = BgenSettings.indexCodecSpecs(rg) val index = new StagedIndexReader(mb, leafCodec, intCodec) var out: EmitSettable = null // filled in later @@ -827,4 +821,4 @@ case class BgenPartitionReader(fileMetadata: Array[BgenFileMetadata], rg: Option } def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats) -} +} \ No newline at end of file diff --git a/hail/src/main/scala/is/hail/io/index/IndexWriter.scala b/hail/src/main/scala/is/hail/io/index/IndexWriter.scala index f89ddb44517..be777688fe0 100644 --- a/hail/src/main/scala/is/hail/io/index/IndexWriter.scala +++ b/hail/src/main/scala/is/hail/io/index/IndexWriter.scala @@ -73,7 +73,7 @@ case class IndexMetadata( ) extends AbstractIndexMetadata object IndexWriter { - val version: SemanticVersion = SemanticVersion(1, 2, 0) + val version: SemanticVersion = SemanticVersion(1, 1, 0) val spec: BufferSpec = BufferSpec.default def builder( diff --git a/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/README.txt b/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/README.txt deleted file mode 100644 index 27ac7850704..00000000000 --- a/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/README.txt +++ /dev/null @@ -1,3 +0,0 @@ -This folder comprises a Hail (www.hail.is) native Table or MatrixTable. - Written with version 0.2.115-cdba2731749a - Created at 2023/05/08 11:07:11 \ No newline at end of file diff --git a/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/_SUCCESS b/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/_SUCCESS deleted file mode 100644 index e69de29bb2d..00000000000 diff --git a/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/cols/README.txt b/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/cols/README.txt deleted file mode 100644 index 27ac7850704..00000000000 --- a/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/cols/README.txt +++ /dev/null @@ -1,3 +0,0 @@ -This folder comprises a Hail (www.hail.is) native Table or MatrixTable. - Written with version 0.2.115-cdba2731749a - Created at 2023/05/08 11:07:11 \ No newline at end of file diff --git a/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/cols/_SUCCESS b/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/cols/_SUCCESS deleted file mode 100644 index e69de29bb2d..00000000000 diff --git a/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/cols/metadata.json.gz b/hail/src/test/resources/backward_compatability/1.7.0/matrix_table/0.hmt/cols/metadata.json.gz deleted file 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a/hail/src/test/resources/backward_compatability/1.7.0/table/9.ht/rows/parts/part-2-20e4b7f5-0c77-4482-8dc6-8ca428297f79 b/hail/src/test/resources/backward_compatability/1.7.0/table/9.ht/rows/parts/part-2-20e4b7f5-0c77-4482-8dc6-8ca428297f79 deleted file mode 100644 index 0f945857900..00000000000 Binary files a/hail/src/test/resources/backward_compatability/1.7.0/table/9.ht/rows/parts/part-2-20e4b7f5-0c77-4482-8dc6-8ca428297f79 and /dev/null differ diff --git a/hail/src/test/scala/is/hail/expr/ir/Aggregators2Suite.scala b/hail/src/test/scala/is/hail/expr/ir/Aggregators2Suite.scala index a5638983080..3f107b33217 100644 --- a/hail/src/test/scala/is/hail/expr/ir/Aggregators2Suite.scala +++ b/hail/src/test/scala/is/hail/expr/ir/Aggregators2Suite.scala @@ -33,7 +33,7 @@ class Aggregators2Suite extends HailSuite { val argT = PType.canonical(TStruct(args.map { case (n, (typ, _)) => n -> typ }: _*)).setRequired(true).asInstanceOf[PStruct] val argVs = Row.fromSeq(args.map { case (_, (_, v)) => v }) val argRef = Ref(genUID(), argT.virtualType) - val spec = BufferSpec.wireSpec + val spec = BufferSpec.defaultUncompressed val (_, combAndDuplicate) = CompileWithAggregators[AsmFunction1RegionUnit](ctx, Array.fill(nPartitions)(aggSig.state), diff --git a/hail/src/test/scala/is/hail/expr/ir/IRSuite.scala b/hail/src/test/scala/is/hail/expr/ir/IRSuite.scala index b5b2de2250b..989a075917f 100644 --- a/hail/src/test/scala/is/hail/expr/ir/IRSuite.scala +++ b/hail/src/test/scala/is/hail/expr/ir/IRSuite.scala @@ -3411,7 +3411,7 @@ class IRSuite extends HailSuite { def testReadWriteValues(pt: SingleCodeType, value: Any): Unit = { implicit val execStrats = ExecStrategy.compileOnly val node = In(0, SingleCodeEmitParamType(true, pt)) - val spec = TypedCodecSpec(PType.canonical(node.typ), BufferSpec.blockedUncompressed) + val spec = TypedCodecSpec(PType.canonical(node.typ), BufferSpec.defaultUncompressed) val writer = ETypeValueWriter(spec) val reader = ETypeValueReader(spec) val prefix = ctx.createTmpPath("test-read-write-values") @@ -3425,7 +3425,7 @@ class IRSuite extends HailSuite { def testReadWriteValueDistributed(pt: SingleCodeType, value: Any): Unit = { implicit val execStrats = ExecStrategy.compileOnly val node = In(0, SingleCodeEmitParamType(true, pt)) - val spec = TypedCodecSpec(PType.canonical(node.typ), BufferSpec.blockedUncompressed) + val spec = TypedCodecSpec(PType.canonical(node.typ), BufferSpec.defaultUncompressed) val writer = ETypeValueWriter(spec) val reader = ETypeValueReader(spec) val prefix = ctx.createTmpPath("test-read-write-value-dist")