{"action":"created","issue":{"url":"https://api.github.com/repos/BVLC/caffe/issues/2123","repository_url":"https://api.github.com/repos/BVLC/caffe","labels_url":"https://api.github.com/repos/BVLC/caffe/issues/2123/labels{/name}","comments_url":"https://api.github.com/repos/BVLC/caffe/issues/2123/comments","events_url":"https://api.github.com/repos/BVLC/caffe/issues/2123/events","html_url":"https://github.com/BVLC/caffe/issues/2123","id":61305161,"number":2123,"title":"make runtest error with HDF5 1.8.14","user":{"login":"pblach","id":6686778,"avatar_url":"https://avatars0.githubusercontent.com/u/6686778?v=3","gravatar_id":"","url":"https://api.github.com/users/pblach","html_url":"https://github.com/pblach","followers_url":"https://api.github.com/users/pblach/followers","following_url":"https://api.github.com/users/pblach/following{/other_user}","gists_url":"https://api.github.com/users/pblach/gists{/gist_id}","starred_url":"https://api.github.com/users/pblach/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pblach/subscriptions","organizations_url":"https://api.github.com/users/pblach/orgs","repos_url":"https://api.github.com/users/pblach/repos","events_url":"https://api.github.com/users/pblach/events{/privacy}","received_events_url":"https://api.github.com/users/pblach/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2015-03-14T00:08:45Z","updated_at":"2017-03-29T01:43:50Z","closed_at":"2015-03-15T22:41:01Z","body":"A lot of the tests pass until this:\n[----------] 1 test from HDF5DataLayerTest/0, where TypeParam = caffe::FloatCPU\n[ RUN      ] HDF5DataLayerTest/0.TestRead\nHDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:\n  #000: H5Dio.c line 173 in H5Dread(): can't read data\n    major: Dataset\n    minor: Read failed\n\nThe complete output is below (and HDF5 config at the bottom):\n\nroot@overo:/home/gumstix/caffe/native_caffe/caffe# make runtest\n.build_release/tools/caffe\ncaffe: command line brew\nusage: caffe <command> <args>\n\ncommands:\n  train           train or finetune a model\n  test            score a model\n  device_query    show GPU diagnostic information\n  time            benchmark model execution time\n\n  Flags from tools/caffe.cpp:\n    -gpu (Run in GPU mode on given device ID.) type: int32 default: -1\n    -iterations (The number of iterations to run.) type: int32 default: 50\n    -model (The model definition protocol buffer text file..) type: string\n      default: \"\"\n    -snapshot (Optional; the snapshot solver state to resume training.)\n      type: string default: \"\"\n    -solver (The solver definition protocol buffer text file.) type: string\n      default: \"\"\n    -weights (Optional; the pretrained weights to initialize finetuning. Cannot\n      be set simultaneously with snapshot.) type: string default: \"\"\n.build_release/test/test_all.testbin 0 --gtest_shuffle --gtest_filter=\"-_GPU_\"\nNote: Google Test filter = -_GPU_\nNote: Randomizing tests' orders with a seed of 98246 .\n[==========] Running 593 tests from 111 test cases.\n[----------] Global test environment set-up.\n[----------] 3 tests from MaxPoolingDropoutTest/1, where TypeParam = caffe::DoubleCPU\n[ RUN      ] MaxPoolingDropoutTest/1.TestForward\n[       OK ] MaxPoolingDropoutTest/1.TestForward (3 ms)\n[ RUN      ] MaxPoolingDropoutTest/1.TestBackward\n[       OK ] MaxPoolingDropoutTest/1.TestBackward (1 ms)\n[ RUN      ] MaxPoolingDropoutTest/1.TestSetup\n[       OK ] MaxPoolingDropoutTest/1.TestSetup (0 ms)\n[----------] 3 tests from MaxPoolingDropoutTest/1 (16 ms total)\n\n[----------] 6 tests from NesterovSolverTest/1, where TypeParam = caffe::DoubleCPU\n[ RUN      ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithMomentum\n[       OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithMomentum (355 ms)\n[ RUN      ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithEverything\n[       OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithEverything (778 ms)\n[ RUN      ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateLROneTenth\n[       OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateLROneTenth (148 ms)\n[ RUN      ] NesterovSolverTest/1.TestLeastSquaresUpdateWithMomentumMultiIter\n[       OK ] NesterovSolverTest/1.TestLeastSquaresUpdateWithMomentumMultiIter (778 ms)\n[ RUN      ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithWeightDecay\n[       OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithWeightDecay (149 ms)\n[ RUN      ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdate\n[       OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdate (149 ms)\n[----------] 6 tests from NesterovSolverTest/1 (2415 ms total)\n\n[----------] 6 tests from MVNLayerTest/1, where TypeParam = caffe::DoubleCPU\n[ RUN      ] MVNLayerTest/1.TestGradientMeanOnly\n[       OK ] MVNLayerTest/1.TestGradientMeanOnly (6477 ms)\n[ RUN      ] MVNLayerTest/1.TestGradient\n[       OK ] MVNLayerTest/1.TestGradient (6476 ms)\n[ RUN      ] MVNLayerTest/1.TestForwardAcrossChannels\n[       OK ] MVNLayerTest/1.TestForwardAcrossChannels (1 ms)\n[ RUN      ] MVNLayerTest/1.TestGradientAcrossChannels\n[       OK ] MVNLayerTest/1.TestGradientAcrossChannels (6445 ms)\n[ RUN      ] MVNLayerTest/1.TestForwardMeanOnly\n[       OK ] MVNLayerTest/1.TestForwardMeanOnly (1 ms)\n[ RUN      ] MVNLayerTest/1.TestForward\n[       OK ] MVNLayerTest/1.TestForward (1 ms)\n[----------] 6 tests from MVNLayerTest/1 (19446 ms total)\n\n[----------] 6 tests from SGDSolverTest/0, where TypeParam = caffe::FloatCPU\n[ RUN      ] SGDSolverTest/0.TestLeastSquaresUpdate\n[       OK ] SGDSolverTest/0.TestLeastSquaresUpdate (161 ms)\n[ RUN      ] SGDSolverTest/0.TestLeastSquaresUpdateWithWeightDecay\n[       OK ] SGDSolverTest/0.TestLeastSquaresUpdateWithWeightDecay (143 ms)\n[ RUN      ] SGDSolverTest/0.TestLeastSquaresUpdateWithMomentum\n[       OK ] SGDSolverTest/0.TestLeastSquaresUpdateWithMomentum (274 ms)\n[ RUN      ] SGDSolverTest/0.TestLeastSquaresUpdateWithMomentumMultiIter\n[       OK ] SGDSolverTest/0.TestLeastSquaresUpdateWithMomentumMultiIter (704 ms)\n[ RUN      ] SGDSolverTest/0.TestLeastSquaresUpdateWithEverything\n[       OK ] SGDSolverTest/0.TestLeastSquaresUpdateWithEverything (707 ms)\n[ RUN      ] SGDSolverTest/0.TestLeastSquaresUpdateLROneTenth\n[       OK ] SGDSolverTest/0.TestLeastSquaresUpdateLROneTenth (141 ms)\n[----------] 6 tests from SGDSolverTest/0 (2186 ms total)\n\n[----------] 1 test from StochasticPoolingLayerTest/1, where TypeParam = double\n[ RUN      ] StochasticPoolingLayerTest/1.TestSetup\n[       OK ] StochasticPoolingLayerTest/1.TestSetup (1 ms)\n[----------] 1 test from StochasticPoolingLayerTest/1 (4 ms total)\n\n[----------] 1 test from InfogainLossLayerTest/0, where TypeParam = caffe::FloatCPU\n[ RUN      ] InfogainLossLayerTest/0.TestGradient\n[       OK ] InfogainLossLayerTest/0.TestGradient (30 ms)\n[----------] 1 test from InfogainLossLayerTest/0 (40 ms total)\n\n[----------] 6 tests from SliceLayerTest/1, where TypeParam = caffe::DoubleCPU\n[ RUN      ] SliceLayerTest/1.TestSliceAcrossChannels\n[       OK ] SliceLayerTest/1.TestSliceAcrossChannels (4 ms)\n[ RUN      ] SliceLayerTest/1.TestGradientAcrossChannels\n[       OK ] SliceLayerTest/1.TestGradientAcrossChannels (464 ms)\n[ RUN      ] SliceLayerTest/1.TestSetupChannels\n[       OK ] SliceLayerTest/1.TestSetupChannels (2 ms)\n[ RUN      ] SliceLayerTest/1.TestSliceAcrossNum\n[       OK ] SliceLayerTest/1.TestSliceAcrossNum (2 ms)\n[ RUN      ] SliceLayerTest/1.TestSetupNum\n[       OK ] SliceLayerTest/1.TestSetupNum (2 ms)\n[ RUN      ] SliceLayerTest/1.TestGradientAcrossNum\n[       OK ] SliceLayerTest/1.TestGradientAcrossNum (452 ms)\n[----------] 6 tests from SliceLayerTest/1 (966 ms total)\n\n[----------] 6 tests from AccuracyLayerTest/0, where TypeParam = float\n[ RUN      ] AccuracyLayerTest/0.TestForwardIgnoreLabel\n[       OK ] AccuracyLayerTest/0.TestForwardIgnoreLabel (5 ms)\n[ RUN      ] AccuracyLayerTest/0.TestForwardCPUTopK\n[       OK ] AccuracyLayerTest/0.TestForwardCPUTopK (22 ms)\n[ RUN      ] AccuracyLayerTest/0.TestForwardCPU\n[       OK ] AccuracyLayerTest/0.TestForwardCPU (4 ms)\n[ RUN      ] AccuracyLayerTest/0.TestSetupTopK\n[       OK ] AccuracyLayerTest/0.TestSetupTopK (2 ms)\n[ RUN      ] AccuracyLayerTest/0.TestSetup\n[       OK ] AccuracyLayerTest/0.TestSetup (2 ms)\n[ RUN      ] AccuracyLayerTest/0.TestForwardWithSpatialAxes\n[       OK ] AccuracyLayerTest/0.TestForwardWithSpatialAxes (4 ms)\n[----------] 6 tests from AccuracyLayerTest/0 (76 ms total)\n\n[----------] 1 test from UniformFillerTest/0, where TypeParam = float\n[ RUN      ] UniformFillerTest/0.TestFill\n[       OK ] UniformFillerTest/0.TestFill (0 ms)\n[----------] 1 test from UniformFillerTest/0 (9 ms total)\n\n[----------] 1 test from StochasticPoolingLayerTest/0, where TypeParam = float\n[ RUN      ] StochasticPoolingLayerTest/0.TestSetup\n[       OK ] StochasticPoolingLayerTest/0.TestSetup (1 ms)\n[----------] 1 test from StochasticPoolingLayerTest/0 (1 ms total)\n\n[----------] 1 test from HDF5DataLayerTest/0, where TypeParam = caffe::FloatCPU\n[ RUN      ] HDF5DataLayerTest/0.TestRead\nHDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:\n  #000: H5Dio.c line 173 in H5Dread(): can't read data\n    major: Dataset\n    minor: Read failed\n  #001: H5Dio.c line 550 in H5D__read(): can't read data\n    major: Dataset\n    minor: Read failed\n  #002: H5Dchunk.c line 1872 in H5D__chunk_read(): unable to read raw data chunk\n    major: Low-level I/O\n    minor: Read failed\n  #003: H5Dchunk.c line 2902 in H5D__chunk_lock(): data pipeline read failed\n    major: Data filters\n    minor: Filter operation failed\n  #004: H5Z.c line 1357 in H5Z_pipeline(): required filter 'deflate' is not registered\n    major: Data filters\n    minor: Read failed\n  #005: H5PL.c line 298 in H5PL_load(): search in paths failed\n    major: Plugin for dynamically loaded library\n    minor: Can't get value\n  #006: H5PL.c line 402 in H5PL__find(): can't open directory\n    major: Plugin for dynamically loaded library\n    minor: Can't open directory or file\nF0313 20:19:22.347337  5736 io.cpp:268] Check failed: status >= 0 (-1 vs. 0) Failed to read float dataset data\n**\\* Check failure stack trace: ***\n    @ 0x401948f6  google::LogMessage::Fail()\n    @ 0x4019612a  google::LogMessage::SendToLog()\n    @ 0x401945da  google::LogMessage::Flush()\n    @ 0x4019677c  google::LogMessageFatal::~LogMessageFatal()\n    @ 0x40a32956  caffe::hdf5_load_nd_dataset<>()\n    @ 0x40a3fc80  caffe::HDF5DataLayer<>::LoadHDF5FileData()\n    @ 0x40a3f9a0  caffe::HDF5DataLayer<>::Forward_cpu()\n    @    0xb05a0  caffe::HDF5DataLayerTest_TestRead_Test<>::TestBody()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\n    @   0x18421c  testing::internal::HandleExceptionsInMethodIfSupported<>()\nAborted (core dumped)\nmake: **\\* [runtest] Error 134\nroot@overo:/home/gumstix/caffe/native_caffe/caffe# \n\nAlso I don't have a GPU, this should be CPU only.\nBelow is the config from HDF5 (when I run ./configure before I run make):\n\nPost process src/libhdf5.settings\nconfig.status: executing depfiles commands\nconfig.status: executing libtool commands\n            SUMMARY OF THE HDF5 CONFIGURATION\n            =================================\n## General Information:\n\n```\n               HDF5 Version: 1.8.14\n              Configured on: Sat Mar 14 00:03:56 UTC 2015\n              Configured by: gumstix@overo\n             Configure mode: production\n                Host system: armv7l-unknown-linux-gnueabi\n          Uname information: Linux overo 3.2.1-linaro-omap #3 PREEMPT Thu Jul 26 17:05:26 PDT 2012 armv7l armv7l armv7l GNU/Linux\n                   Byte sex: little-endian\n                  Libraries: static, shared\n         Installation point: /home/gumstix/caffe/hdf5/hdf5-1.8.14/hdf5\n```\n## Compiling Options:\n\n```\n           Compilation Mode: production\n                 C Compiler: /usr/bin/gcc\n                     CFLAGS: \n                  H5_CFLAGS:  \n                  AM_CFLAGS: \n                   CPPFLAGS: \n                H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L   -DNDEBUG -UH5_DEBUG_API\n                AM_CPPFLAGS: -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE \n           Shared C Library: yes\n           Static C Library: yes\n```\n\n  Statically Linked Executables: no\n                        LDFLAGS: \n                     H5_LDFLAGS: \n                     AM_LDFLAGS:  -L/home/gumstix/caffe/hdf5/hdf5-1.8.14/hdf5/lib\n                Extra libraries:  -lz -lrt -ldl -lm \n                       Archiver: ar\n                         Ranlib: ranlib\n              Debugged Packages: \n                    API Tracing: no\n## Languages:\n\n```\n                    Fortran: no\n\n                        C++: no\n```\n## Features:\n\n```\n              Parallel HDF5: no\n         High Level library: yes\n               Threadsafety: no\n        Default API Mapping: v18\n```\n\n With Deprecated Public Symbols: yes\n         I/O filters (external): deflate(zlib)\n         I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset\n                            MPE: no\n                     Direct VFD: no\n                        dmalloc: no\nClear file buffers before write: yes\n           Using memory checker: no\n         Function Stack Tracing: no\n      Strict File Format Checks: no\n   Optimization Instrumentation: no\n       Large File Support (LFS): yes\ngumstix@overo:~/caffe/hdf5/hdf5-1.8.14$ \n\nAnything I can try or look up?\n"},"comment":{"url":"https://api.github.com/repos/BVLC/caffe/issues/comments/289956768","html_url":"https://github.com/BVLC/caffe/issues/2123#issuecomment-289956768","issue_url":"https://api.github.com/repos/BVLC/caffe/issues/2123","id":289956768,"user":{"login":"tianoak","id":13596177,"avatar_url":"https://avatars1.githubusercontent.com/u/13596177?v=3","gravatar_id":"","url":"https://api.github.com/users/tianoak","html_url":"https://github.com/tianoak","followers_url":"https://api.github.com/users/tianoak/followers","following_url":"https://api.github.com/users/tianoak/following{/other_user}","gists_url":"https://api.github.com/users/tianoak/gists{/gist_id}","starred_url":"https://api.github.com/users/tianoak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tianoak/subscriptions","organizations_url":"https://api.github.com/users/tianoak/orgs","repos_url":"https://api.github.com/users/tianoak/repos","events_url":"https://api.github.com/users/tianoak/events{/privacy}","received_events_url":"https://api.github.com/users/tianoak/received_events","type":"User","site_admin":false},"created_at":"2017-03-29T01:43:50Z","updated_at":"2017-03-29T01:43:50Z","body":"I have to use  --enable-fortran90, so it can ignore fortran2003"}}
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