HDF5 versions conflict

[Dmitry Yutkin]

I use anaconda2 and when I do

make runtest

I get this:

Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.15, library is 1.8.16
    SUMMARY OF THE HDF5 CONFIGURATION
    =================================


General Information:
-------------------
   HDF5 Version: 1.8.16
  Configured on: Sun Dec  6 13:09:34 PST 2015
  Configured by: brew@elcapitanvm.local
 Configure mode: production
    Host system: i386-apple-darwin15.0.0
      Uname information: Darwin elcapitanvm.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64
       Byte sex: little-endian
      Libraries: static, shared
     Installation point: /usr/local/Cellar/hdf5/1.8.16_1
make: *** [runtest] Abort trap: 6
...

How can I fix it?

[jiqing wu]

[Jan C Peters]

By exactly doing what the error message tells you. Setting the HDF5_DISABLE_VERSION_CHECK is dangerous, I would not recommend it, although in this case it will probably do no harm, as there is only a very minor version difference. The better option is - as the message says - compiling with the same version of the library that is used during runtime. Probably you have these two versions since you installed one somehow (I have no idea how that is usually done on MacOS, I have read about something called homebrew somewhere...) and the other one is provided by Anaconda.

Actually I have never seen such a verbose and explanatory version mismatch error message. Well done HDF5 guys!

Jan

[Tongxin Wang]

I have the same problem! How did you fix it eventually?

在 2016年2月6日星期六 UTC+8下午9:49:49，Dmitry Yutkin写道：

[Cristian Balint]

It's HDF's fault not caffe.

a) Upgrade HDF to latest 1.8.16 (not 1.8.15-partch1)

b) Do in CLI 'export HDF5_DISABLE_VERSION_CHECK=2'

--
You received this message because you are subscribed to the Google Groups "Caffe Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to caffe-users...@googlegroups.com.
To post to this group, send email to caffe...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/caffe-users/a7840856-4b1d-4c28-9803-ec3eaf5b0a0f%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Balint Cristian
e-mail: cristia...@gmail.com

[Tongxin Wang]

My situation is strange. I am using anaconda. And hdf5 should be contained in it. However, if I don't install hdf5 via brew, I cannot make caffe properly. It says that 'ibhdf5_hl.10.dylib is not loaded'. '(I have adjusted the .config file to anaconda correctly). So I am if it still hdf5's fault or I am making some kind of mistakes. Thanks!

在 2016年2月22日星期一 UTC+8下午5:46:59，Cristian Balint写道：

[摩羯小虾]

Can you tell me how to config?

在 2016年2月22日星期一 UTC+8下午5:56:28，Tongxin Wang写道：