Fabien Campagne fac2003
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| final String inputFilename = "input.compact-reads"; | |
| final MutableString sequence = new MutableString(); | |
| final ReadsReader reader = new ReadsReader(new FileInputStream(inputFilename)); | |
| for (final Reads.ReadEntry readEntry : reader) { | |
| ReadsReader.decodeSequence(readEntry, sequence); | |
| System.out.printf("read-index: %d read-id: %s sequence: %s %n", | |
| readEntry.getReadIndex(), | |
| readEntry.hasReadIdentifier() ? readEntry.getReadIdentifier() : "", |
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| # | |
| # A fatal error has been detected by the Java Runtime Environment: | |
| # | |
| # SIGSEGV (0xb) at pc=0x00007facf76ad324, pid=24368, tid=140382809954048 | |
| # | |
| # JRE version: Java(TM) SE Runtime Environment (8.0_45-b14) (build 1.8.0_45-b14) | |
| # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.45-b02 mixed mode linux-amd64 compressed oops) | |
| # Problematic frame: | |
| # C [libnd4j.so+0x94324] functions::reduce::ReduceFunction<float>::exec(float*, int*, float*, float*, int*, int*, int)+0xc24 | |
| # |
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| # | |
| # A fatal error has been detected by the Java Runtime Environment: | |
| # | |
| # SIGSEGV (0xb) at pc=0x00007f836c387324, pid=28729, tid=140203395344128 | |
| # | |
| # JRE version: Java(TM) SE Runtime Environment (8.0_45-b14) (build 1.8.0_45-b14) | |
| # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.45-b02 mixed mode linux-amd64 compressed oops) | |
| # Problematic frame: | |
| # C [libnd4j.so+0x94324] functions::reduce::ReduceFunction<float>::exec(float*, int*, float*, float*, int*, int*, int)+0xc24 | |
| # |
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| # | |
| # A fatal error has been detected by the Java Runtime Environment: | |
| # | |
| # SIGSEGV (0xb) at pc=0x00007f9eface7353, pid=26247, tid=140320751580928 | |
| # | |
| # JRE version: Java(TM) SE Runtime Environment (8.0_45-b14) (build 1.8.0_45-b14) | |
| # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.45-b02 mixed mode linux-amd64 compressed oops) | |
| # Problematic frame: | |
| # C [libnd4j.so+0x65353] _ZN9functions6reduce14ReduceFunctionIfE4execEPfPiS3_S3_S4_S4_i._omp_fn.56+0x233 | |
| # |
fac2003
/ nvidia-smi.out
Created
June 21, 2016 16:28
typical nvidia-smi result while running DL4J spark Graves example
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| Tue Jun 21 12:27:19 2016 | |
| +------------------------------------------------------+ | |
| | NVIDIA-SMI 352.79 Driver Version: 352.79 | | |
| |-------------------------------+----------------------+----------------------+ | |
| | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | |
| | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | |
| |===============================+======================+======================| | |
| | 0 Tesla K80 Off | 0000:04:00.0 Off | Off | | |
| | N/A 46C P0 61W / 149W | 2442MiB / 12287MiB | 10% Default | |
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| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [127] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [128] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [126] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [121] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [116] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [123] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [119] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [129] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [115] | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [124] |
fac2003
/ gist:44d17565a7f95691c8097d964a440beb
Created
June 21, 2016 17:30
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| o.n.n.NativeOps - Number of threads used for linear algebra 32 | |
| Using existing text file at /tmp/Shakespeare.txt | |
| o.n.j.h.i.CudaZeroHandler - Mapping device [0] to thread [1] | |
| o.n.j.a.c.i.BasicContextPool - Creating new context... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for device [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new cuBLAS handle for device [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for device [0]... | |
| o.n.j.h.i.CudaZeroHandler - Creating bucketID: 0 | |
| o.n.j.h.i.CudaZeroHandler - Creating bucketID: 1 | |
| o.n.j.h.i.CudaZeroHandler - Creating bucketID: 4 |
fac2003
/ gist:7d948f7687194e03a3f066bf0965ef99
Created
July 11, 2016 14:06
running out of memory with dl4j multi-GPU
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| [mas2182@node007 dl4j-spark-cdh5-examples]$ java -Xmx10g -cp target/dl4j-spark-cdh5-examples-1.0-SNAPSHOT.jar org.deeplearning4j.examples.rnn.GravesLSTMCharModellingExample |tee GPU-benchmark-0.4.0-1.txt | |
| o.n.n.NativeOps - Number of threads used for linear algebra 32 | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... |
fac2003
/ gist:b21556e327f66cd03ec2675de4341a12
Created
July 11, 2016 14:18
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| head -1000 GPU-benchmark-0.4.0-2.txt | |
| o.n.n.NativeOps - Number of threads used for linear algebra 32 | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... |
fac2003
/ gist:1f89e21862d6c8e46ee5564fc52a7f37
Created
July 11, 2016 14:26
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| java -Xmx10g -cp target/dl4j-spark-cdh5-examples-1.0-SNAPSHOT.jar org.deeplearning4j.examples.rnn.GravesLSTMCharModellingExample 2>&1 |tee GPU-benchmark-0.4.0-3.txt | |
| o.n.n.NativeOps - Number of threads used for linear algebra 32 | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... | |
| o.n.j.a.c.i.BasicContextPool - Creating new stream for thread: [1], device: [0]... |
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