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Ubuntu 15.04 compilation failure due to "hdf5.h" instead of "hdf5/serial/hdf5.h" and similarly "hdf5_hl.h" #2690

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Ubuntu 15.04 compilation failure due to "hdf5.h" instead of "hdf5/serial/hdf5.h" and similarly "hdf5_hl.h"#2690
@robertsdionne

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@robertsdionne
robertsdionne
opened on Jul 4, 2015
No description provided.

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robertsdionne
changed the title [-]Ubuntu 15.05 compilation failure due to "hdf5.h" instead of "hdf5/serial/hdf5.h" and similarly "hdf5_hl.h"[/-] [+]Ubuntu 15.04 compilation failure due to "hdf5.h" instead of "hdf5/serial/hdf5.h" and similarly "hdf5_hl.h"[/+] on Jul 4, 2015
robertsdionne

robertsdionne commented on Jul 4, 2015

@robertsdionne
robertsdionne
on Jul 4, 2015
Author

Similarly, unable to find libhdf5 or libhdf5_hl, which are located at /usr/lib/x86_64-linux-gnu/hdf5/serial/

robertsdionne

robertsdionne commented on Jul 4, 2015

@robertsdionne
robertsdionne
on Jul 4, 2015
Author
diff --git a/Makefile.config.example b/Makefile.config.example
index a873502..33441b3 100644
--- a/Makefile.config.example
+++ b/Makefile.config.example
@@ -70,7 +70,7 @@ PYTHON_LIB := /usr/lib

 # Whatever else you find you need goes here.
 INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include
-LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib
+LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu/hdf5/serial

 # If Homebrew is installed at a non standard location (for example your home directory) and you use it for general dependencies
 # INCLUDE_DIRS += $(shell brew --prefix)/include
diff --git a/include/caffe/data_layers.hpp b/include/caffe/data_layers.hpp
index 3958cb7..2ccbaec 100644
--- a/include/caffe/data_layers.hpp
+++ b/include/caffe/data_layers.hpp
@@ -6,7 +6,7 @@
 #include <vector>

 #include "boost/scoped_ptr.hpp"
-#include "hdf5.h"
+#include "hdf5/serial/hdf5.h"

 #include "caffe/blob.hpp"
 #include "caffe/common.hpp"
diff --git a/include/caffe/util/io.hpp b/include/caffe/util/io.hpp
index 3a62c3c..f4363f0 100644
--- a/include/caffe/util/io.hpp
+++ b/include/caffe/util/io.hpp
@@ -5,8 +5,8 @@
 #include <string>

 #include "google/protobuf/message.h"
-#include "hdf5.h"
-#include "hdf5_hl.h"
+#include "hdf5/serial/hdf5.h"
+#include "hdf5/serial/hdf5_hl.h"

 #include "caffe/blob.hpp"
 #include "caffe/common.hpp"
diff --git a/src/caffe/layers/hdf5_data_layer.cpp b/src/caffe/layers/hdf5_data_layer.cpp
index 8a782f7..42890be 100644
--- a/src/caffe/layers/hdf5_data_layer.cpp
+++ b/src/caffe/layers/hdf5_data_layer.cpp
@@ -10,8 +10,8 @@ TODO:
 #include <string>
 #include <vector>

-#include "hdf5.h"
-#include "hdf5_hl.h"
+#include "hdf5/serial/hdf5.h"
+#include "hdf5/serial/hdf5_hl.h"
 #include "stdint.h"

 #include "caffe/data_layers.hpp"
diff --git a/src/caffe/layers/hdf5_data_layer.cu b/src/caffe/layers/hdf5_data_layer.cu
index 5e3e4ce..23bc02a 100644
--- a/src/caffe/layers/hdf5_data_layer.cu
+++ b/src/caffe/layers/hdf5_data_layer.cu
@@ -7,8 +7,8 @@ TODO:
 #include <string>
 #include <vector>

-#include "hdf5.h"
-#include "hdf5_hl.h"
+#include "hdf5/serial/hdf5.h"
+#include "hdf5/serial/hdf5_hl.h"

 #include "caffe/data_layers.hpp"
 #include "caffe/layer.hpp"
diff --git a/src/caffe/layers/hdf5_output_layer.cpp b/src/caffe/layers/hdf5_output_layer.cpp
index f63375c..0b57eb9 100644
--- a/src/caffe/layers/hdf5_output_layer.cpp
+++ b/src/caffe/layers/hdf5_output_layer.cpp
@@ -1,7 +1,7 @@
 #include <vector>

-#include "hdf5.h"
-#include "hdf5_hl.h"
+#include "hdf5/serial/hdf5.h"
+#include "hdf5/serial/hdf5_hl.h"

 #include "caffe/blob.hpp"
 #include "caffe/common.hpp"
diff --git a/src/caffe/layers/hdf5_output_layer.cu b/src/caffe/layers/hdf5_output_layer.cu
index ae497c3..ada682f 100644
--- a/src/caffe/layers/hdf5_output_layer.cu
+++ b/src/caffe/layers/hdf5_output_layer.cu
@@ -1,7 +1,7 @@
 #include <vector>

-#include "hdf5.h"
-#include "hdf5_hl.h"
+#include "hdf5/serial/hdf5.h"
+#include "hdf5/serial/hdf5_hl.h"

 #include "caffe/blob.hpp"
 #include "caffe/common.hpp"
TheOpenSourceNinja

TheOpenSourceNinja commented on Jul 4, 2015

@TheOpenSourceNinja
TheOpenSourceNinja
on Jul 4, 2015

A slightly simpler solution:

diff --git a/Makefile.config.example b/Makefile.config.example
index a873502..88828cc 100644
--- a/Makefile.config.example
+++ b/Makefile.config.example
@@ -69,8 +69,8 @@ PYTHON_LIB := /usr/lib
 # WITH_PYTHON_LAYER := 1

 # Whatever else you find you need goes here.
-INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include
-LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib
+INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/
+LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu/hdf5/serial/

 # If Homebrew is installed at a non standard location (for example your home directory) and you use it for general dependencies
 # INCLUDE_DIRS += $(shell brew --prefix)/include
robertsdionne

robertsdionne commented on Jul 5, 2015

@robertsdionne
robertsdionne
on Jul 5, 2015
Author

Ah, thanks! As this goes in Makefile.config and is platform-specific, I'll close this report.

robertsdionne
closed this as completedon Jul 5, 2015
seanbell
mentioned this on Sep 15, 2015
byshen

byshen commented on Nov 2, 2015

@byshen
byshen
on Nov 2, 2015

just modify the Makefile.config works for me !
Thanks a lot 😄

+INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/
+LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu/hdf5/serial/

datahack-ru

datahack-ru commented on Nov 26, 2015

@datahack-ru
datahack-ru
on Nov 26, 2015

It works!

ml-and-ml
mentioned this on Jan 7, 2016
dgorissen
mentioned this on Jan 14, 2016
sid-kap
mentioned this on Jan 25, 2016
cuongduc

cuongduc commented on Feb 4, 2016

@cuongduc
cuongduc
on Feb 4, 2016

Thanks! It works for me

minarc

minarc commented on Feb 5, 2016

@minarc
minarc
on Feb 5, 2016

I am on ubuntu 16.04 and it Works!

hustc12

hustc12 commented on Feb 28, 2016

@hustc12
hustc12
on Feb 28, 2016

@byshen, it works for me, thanks!

vatsal12117

vatsal12117 commented on Apr 27, 2016

@vatsal12117
vatsal12117
on Apr 27, 2016

how to solve this issue on ubuntu 16.04?

machisuke

machisuke commented on Jun 10, 2016

@machisuke
machisuke
on Jun 10, 2016

It works for me too. Thanks.
Version is ubuntu 15.10

han-qiu

han-qiu commented on Jun 28, 2016

@han-qiu
han-qiu
on Jun 28, 2016

Thank you!
It works for me.
Ubuntu 16.04

ghost
oggata

oggata commented on Dec 7, 2016

@oggata
oggata
on Dec 7, 2016

Thank you, it worked! Ubuntu 15.04

dweekly

dweekly commented on Dec 20, 2016

@dweekly
dweekly
on Dec 20, 2016

Can I suggest we add a commented out version of the above with a note "uncomment these to install on Ubuntu"?

olypros

olypros commented on Feb 3, 2017

@olypros
olypros
on Feb 3, 2017

Its WORKS !!!!!

manpowre

manpowre commented on Jun 11, 2017

@manpowre
manpowre
on Jun 11, 2017

adding these in ubuntu 16.04 works:
+INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/
+LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu/hdf5/serial/

I first verified the path exists before adding it.

GonzaBCCC

GonzaBCCC commented on Jun 14, 2017

@GonzaBCCC
GonzaBCCC
on Jun 14, 2017

did not work for me (Ubuntu 16.04)

LD -o .build_release/lib/libcaffe.so.1.0.0
/usr/bin/ld: cannot find -lhdf5_serial_h
collect2: error: ld returned 1 exit status
Makefile:573: fallo en las instrucciones para el objetivo '.build_release/lib/libcaffe.so.1.0.0'
make: *** [.build_release/lib/libcaffe.so.1.0.0] Error 1

ysangkok

ysangkok commented on Jul 14, 2017

@ysangkok
ysangkok
on Jul 14, 2017

@GonzaBCCC did you install the libhdf5-dev package? on Ubuntu 17.04, this actually contains hdf5-serial and development headers even though there is a package named libhdf5-serial-dev (it contains just copyright info and such)

yangyanglisjtu

yangyanglisjtu commented on Dec 26, 2017

@yangyanglisjtu
yangyanglisjtu
on Dec 26, 2017

@byshen it works

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          Ubuntu 15.04 compilation failure due to "hdf5.h" instead of "hdf5/serial/hdf5.h" and similarly "hdf5_hl.h" · Issue #2690 · BVLC/caffe