make runtest error with HDF5 1.8.14

[pblach]

A lot of the tests pass until this:
[----------] 1 test from HDF5DataLayerTest/0, where TypeParam = caffe::FloatCPU
[ RUN ] HDF5DataLayerTest/0.TestRead
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
#000: H5Dio.c line 173 in H5Dread(): can't read data
major: Dataset
minor: Read failed

The complete output is below (and HDF5 config at the bottom):

root@overo:/home/gumstix/caffe/native_caffe/caffe# make runtest
.build_release/tools/caffe
caffe: command line brew
usage: caffe

commands:
train train or finetune a model
test score a model
device_query show GPU diagnostic information
time benchmark model execution time

Flags from tools/caffe.cpp:
-gpu (Run in GPU mode on given device ID.) type: int32 default: -1
-iterations (The number of iterations to run.) type: int32 default: 50
-model (The model definition protocol buffer text file..) type: string
default: ""
-snapshot (Optional; the snapshot solver state to resume training.)
type: string default: ""
-solver (The solver definition protocol buffer text file.) type: string
default: ""
-weights (Optional; the pretrained weights to initialize finetuning. Cannot
be set simultaneously with snapshot.) type: string default: ""
.build_release/test/test_all.testbin 0 --gtest_shuffle --gtest_filter="-GPU"
Note: Google Test filter = -GPU
Note: Randomizing tests' orders with a seed of 98246 .
[==========] Running 593 tests from 111 test cases.
[----------] Global test environment set-up.
[----------] 3 tests from MaxPoolingDropoutTest/1, where TypeParam = caffe::DoubleCPU
[ RUN ] MaxPoolingDropoutTest/1.TestForward
[ OK ] MaxPoolingDropoutTest/1.TestForward (3 ms)
[ RUN ] MaxPoolingDropoutTest/1.TestBackward
[ OK ] MaxPoolingDropoutTest/1.TestBackward (1 ms)
[ RUN ] MaxPoolingDropoutTest/1.TestSetup
[ OK ] MaxPoolingDropoutTest/1.TestSetup (0 ms)
[----------] 3 tests from MaxPoolingDropoutTest/1 (16 ms total)

[----------] 6 tests from NesterovSolverTest/1, where TypeParam = caffe::DoubleCPU
[ RUN ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithMomentum
[ OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithMomentum (355 ms)
[ RUN ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithEverything
[ OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithEverything (778 ms)
[ RUN ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateLROneTenth
[ OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateLROneTenth (148 ms)
[ RUN ] NesterovSolverTest/1.TestLeastSquaresUpdateWithMomentumMultiIter
[ OK ] NesterovSolverTest/1.TestLeastSquaresUpdateWithMomentumMultiIter (778 ms)
[ RUN ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithWeightDecay
[ OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdateWithWeightDecay (149 ms)
[ RUN ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdate
[ OK ] NesterovSolverTest/1.TestNesterovLeastSquaresUpdate (149 ms)
[----------] 6 tests from NesterovSolverTest/1 (2415 ms total)

[----------] 6 tests from MVNLayerTest/1, where TypeParam = caffe::DoubleCPU
[ RUN ] MVNLayerTest/1.TestGradientMeanOnly
[ OK ] MVNLayerTest/1.TestGradientMeanOnly (6477 ms)
[ RUN ] MVNLayerTest/1.TestGradient
[ OK ] MVNLayerTest/1.TestGradient (6476 ms)
[ RUN ] MVNLayerTest/1.TestForwardAcrossChannels
[ OK ] MVNLayerTest/1.TestForwardAcrossChannels (1 ms)
[ RUN ] MVNLayerTest/1.TestGradientAcrossChannels
[ OK ] MVNLayerTest/1.TestGradientAcrossChannels (6445 ms)
[ RUN ] MVNLayerTest/1.TestForwardMeanOnly
[ OK ] MVNLayerTest/1.TestForwardMeanOnly (1 ms)
[ RUN ] MVNLayerTest/1.TestForward
[ OK ] MVNLayerTest/1.TestForward (1 ms)
[----------] 6 tests from MVNLayerTest/1 (19446 ms total)

[----------] 6 tests from SGDSolverTest/0, where TypeParam = caffe::FloatCPU
[ RUN ] SGDSolverTest/0.TestLeastSquaresUpdate
[ OK ] SGDSolverTest/0.TestLeastSquaresUpdate (161 ms)
[ RUN ] SGDSolverTest/0.TestLeastSquaresUpdateWithWeightDecay
[ OK ] SGDSolverTest/0.TestLeastSquaresUpdateWithWeightDecay (143 ms)
[ RUN ] SGDSolverTest/0.TestLeastSquaresUpdateWithMomentum
[ OK ] SGDSolverTest/0.TestLeastSquaresUpdateWithMomentum (274 ms)
[ RUN ] SGDSolverTest/0.TestLeastSquaresUpdateWithMomentumMultiIter
[ OK ] SGDSolverTest/0.TestLeastSquaresUpdateWithMomentumMultiIter (704 ms)
[ RUN ] SGDSolverTest/0.TestLeastSquaresUpdateWithEverything
[ OK ] SGDSolverTest/0.TestLeastSquaresUpdateWithEverything (707 ms)
[ RUN ] SGDSolverTest/0.TestLeastSquaresUpdateLROneTenth
[ OK ] SGDSolverTest/0.TestLeastSquaresUpdateLROneTenth (141 ms)
[----------] 6 tests from SGDSolverTest/0 (2186 ms total)

[----------] 1 test from StochasticPoolingLayerTest/1, where TypeParam = double
[ RUN ] StochasticPoolingLayerTest/1.TestSetup
[ OK ] StochasticPoolingLayerTest/1.TestSetup (1 ms)
[----------] 1 test from StochasticPoolingLayerTest/1 (4 ms total)

[----------] 1 test from InfogainLossLayerTest/0, where TypeParam = caffe::FloatCPU
[ RUN ] InfogainLossLayerTest/0.TestGradient
[ OK ] InfogainLossLayerTest/0.TestGradient (30 ms)
[----------] 1 test from InfogainLossLayerTest/0 (40 ms total)

[----------] 6 tests from SliceLayerTest/1, where TypeParam = caffe::DoubleCPU
[ RUN ] SliceLayerTest/1.TestSliceAcrossChannels
[ OK ] SliceLayerTest/1.TestSliceAcrossChannels (4 ms)
[ RUN ] SliceLayerTest/1.TestGradientAcrossChannels
[ OK ] SliceLayerTest/1.TestGradientAcrossChannels (464 ms)
[ RUN ] SliceLayerTest/1.TestSetupChannels
[ OK ] SliceLayerTest/1.TestSetupChannels (2 ms)
[ RUN ] SliceLayerTest/1.TestSliceAcrossNum
[ OK ] SliceLayerTest/1.TestSliceAcrossNum (2 ms)
[ RUN ] SliceLayerTest/1.TestSetupNum
[ OK ] SliceLayerTest/1.TestSetupNum (2 ms)
[ RUN ] SliceLayerTest/1.TestGradientAcrossNum
[ OK ] SliceLayerTest/1.TestGradientAcrossNum (452 ms)
[----------] 6 tests from SliceLayerTest/1 (966 ms total)

[----------] 6 tests from AccuracyLayerTest/0, where TypeParam = float
[ RUN ] AccuracyLayerTest/0.TestForwardIgnoreLabel
[ OK ] AccuracyLayerTest/0.TestForwardIgnoreLabel (5 ms)
[ RUN ] AccuracyLayerTest/0.TestForwardCPUTopK
[ OK ] AccuracyLayerTest/0.TestForwardCPUTopK (22 ms)
[ RUN ] AccuracyLayerTest/0.TestForwardCPU
[ OK ] AccuracyLayerTest/0.TestForwardCPU (4 ms)
[ RUN ] AccuracyLayerTest/0.TestSetupTopK
[ OK ] AccuracyLayerTest/0.TestSetupTopK (2 ms)
[ RUN ] AccuracyLayerTest/0.TestSetup
[ OK ] AccuracyLayerTest/0.TestSetup (2 ms)
[ RUN ] AccuracyLayerTest/0.TestForwardWithSpatialAxes
[ OK ] AccuracyLayerTest/0.TestForwardWithSpatialAxes (4 ms)
[----------] 6 tests from AccuracyLayerTest/0 (76 ms total)

[----------] 1 test from UniformFillerTest/0, where TypeParam = float
[ RUN ] UniformFillerTest/0.TestFill
[ OK ] UniformFillerTest/0.TestFill (0 ms)
[----------] 1 test from UniformFillerTest/0 (9 ms total)

[----------] 1 test from StochasticPoolingLayerTest/0, where TypeParam = float
[ RUN ] StochasticPoolingLayerTest/0.TestSetup
[ OK ] StochasticPoolingLayerTest/0.TestSetup (1 ms)
[----------] 1 test from StochasticPoolingLayerTest/0 (1 ms total)

[----------] 1 test from HDF5DataLayerTest/0, where TypeParam = caffe::FloatCPU
[ RUN ] HDF5DataLayerTest/0.TestRead
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
#000: H5Dio.c line 173 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#1: H5Dio.c line 550 in H5D__read(): can't read data
major: Dataset
minor: Read failed
#2: H5Dchunk.c line 1872 in H5D__chunk_read(): unable to read raw data chunk
major: Low-level I/O
minor: Read failed
#3: H5Dchunk.c line 2902 in H5D__chunk_lock(): data pipeline read failed
major: Data filters
minor: Filter operation failed
#4: H5Z.c line 1357 in H5Z_pipeline(): required filter 'deflate' is not registered
major: Data filters
minor: Read failed
#5: H5PL.c line 298 in H5PL_load(): search in paths failed
major: Plugin for dynamically loaded library
minor: Can't get value
#6: H5PL.c line 402 in H5PL__find(): can't open directory
major: Plugin for dynamically loaded library
minor: Can't open directory or file
F0313 20:19:22.347337 5736 io.cpp:268] Check failed: status >= 0 (-1 vs. 0) Failed to read float dataset data
*** Check failure stack trace: ***
@ 0x401948f6 google::LogMessage::Fail()
@ 0x4019612a google::LogMessage::SendToLog()
@ 0x401945da google::LogMessage::Flush()
@ 0x4019677c google::LogMessageFatal::~LogMessageFatal()
@ 0x40a32956 caffe::hdf5_load_nd_dataset<>()
@ 0x40a3fc80 caffe::HDF5DataLayer<>::LoadHDF5FileData()
@ 0x40a3f9a0 caffe::HDF5DataLayer<>::Forward_cpu()
@ 0xb05a0 caffe::HDF5DataLayerTest_TestRead_Test<>::TestBody()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0x18421c testing::internal::HandleExceptionsInMethodIfSupported<>()
Aborted (core dumped)
make: *** [runtest] Error 134
root@overo:/home/gumstix/caffe/native_caffe/caffe#

Also I don't have a GPU, this should be CPU only.
Below is the config from HDF5 (when I run ./configure before I run make):

Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
SUMMARY OF THE HDF5 CONFIGURATION
=================================

General Information:

               HDF5 Version: 1.8.14
              Configured on: Sat Mar 14 00:03:56 UTC 2015
              Configured by: gumstix@overo
             Configure mode: production
                Host system: armv7l-unknown-linux-gnueabi
          Uname information: Linux overo 3.2.1-linaro-omap #3 PREEMPT Thu Jul 26 17:05:26 PDT 2012 armv7l armv7l armv7l GNU/Linux
                   Byte sex: little-endian
                  Libraries: static, shared
         Installation point: /home/gumstix/caffe/hdf5/hdf5-1.8.14/hdf5

Compiling Options:

           Compilation Mode: production
                 C Compiler: /usr/bin/gcc
                     CFLAGS: 
                  H5_CFLAGS:  
                  AM_CFLAGS: 
                   CPPFLAGS: 
                H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS: -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE 
           Shared C Library: yes
           Static C Library: yes

Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS: -L/home/gumstix/caffe/hdf5/hdf5-1.8.14/hdf5/lib
Extra libraries: -lz -lrt -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no

Languages:

                    Fortran: no

                        C++: no

Features:

              Parallel HDF5: no
         High Level library: yes
               Threadsafety: no
        Default API Mapping: v18

With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
gumstix@overo:~/caffe/hdf5/hdf5-1.8.14$

Anything I can try or look up?

[pblach]

i redid HDF5 and now it said 593 tests from 111 test cases ran (370843 ms total)
[ PASSED ] 593 tests.

So apparently I didn't get HDF5 right the first time and now all seems to work.
For the record here is what I did with HDF5:
cd hdf5-1.8.14
./configure --prefix=/usr/local/hdf5 --enable-cxx
make
make check
sudo make install
sudo make check-install

i then copied a bunch of .so libraries to /usr/lib
and that's it.

[gjy3035]

@pblach How to solve it ?
I encountered the same error. Thanks for your help!

[gjy3035]

@pblach I tried to solve it following you. However, the problem still appeared.
can you give me a method to solve it in detial?

[apouschi]

@gjy3035 I just dealt with this issue. It turns out that the hdf5 'deflate' filter mentioned in error 4 requires the zlib package to work properly. I got this error because my hdf5 couldn't find zlib in its default install location. To fix this, I left my zlib unchanged, uninstalled my hdf5 build, and then configured a new hdf5 build by running the following in the hdf5 directory:

./configure --enable-cxx --enable-fortran --with-zlib=/path/to/zlib/include,/path/to/zlib/lib
--prefix=/usr/local/hdf5

(Just as a general note: the --enable flags may be unnecessary. I had them left over from a previous attempt to solve this, and haven't tried configuring hdf5 without them. Also, the --with-zlib part is described in section 4.3.7 of the hdf5 installation instructions, in case more detail is needed.)

From there I finished installing hdf5 with its make commands, then did the same for caffe.

For clarity, all the commands i used are replicated below:

cd hdf5-1.8.14
./configure --enable-cxx --enable-fortran --with-zlib=/path/to/zlib/include,/path/to/zlib/lib
--prefix=/usr/local/hdf5
make
make check
sudo make install
sudo make install-check
cd ../caffe-master
make
make test
make runtest

I'm guessing that pblach's hdf5 was able to find zlib after he installed it, while yours, like mine, was not, but that's just a guess. For anyone else who might find this thread, I'd advise you to try pblach's solution first, and if you still get the same error, try mine.

Hope this helps

[vgprasadh]

@apouschi - Thanks for the zlib info. I was lost until I saw your post. Thanks once again.

[pblach]

what a coincidence, i'm building hdf5 as we speak (with the goal of
building caffe). I will let you know how it goes.

On Tue, Nov 3, 2015 at 5:28 AM, Guha Prasad Venkataraman <
notifications@github.com> wrote:

@apouschi https://github.com/apouschi - Thanks for the zlib info. I was
lost until I saw your post. Thanks once again.

—
Reply to this email directly or view it on GitHub
#2123 (comment).

[tianoak]

I have to use --enable-fortran90, so it can ignore fortran2003