Hi, I'm trying to install graph-tool under Ubuntu 14. I didn't found gcc5 in the list of synaptic packages but I did installed clang3.4. But when I run ./configure, it doesn't find clang3.4 (and probably detects pre-installed gcc 4.8.2 instead). How can I tell ./configure to use clang3.4 rather than gcc4.8.2 ? Thanks in advance Yannis -- ------------------------------------------------------- Yannis Haralambous Professor Institut Mines-Télécom, Télécom Bretagne Computer Science Department UMR CNRS 6285 Lab-STICC Technopôle Brest Iroise CS 83818, 29238 Brest Cedex 3, France Email: yannis.haralambous@telecom-bretagne.eu Internet: http://perso.telecom-bretagne.eu/yannisharalambous/ ICBM address: 48°21'31.57"N 4°34'16.76"W Twitter: y_haralambous ------------------------------------------------------- ...the ball I threw while playing in the park has not yet reached the ground (Dylan Thomas) Es gab eine Zeit, wo ich nur ungern über Schubert sprechen, nur Nächtens den Bäumen und Sternen von ihm vorerzählen mögen. (Robert Schumann)
On 13.04.2016 17:13, Yannis Haralambous wrote:
I'm trying to install graph-tool under Ubuntu 14. I didn't found gcc5 in the list of synaptic packages but I did installed clang3.4.
Clang 3.4 is too old to compile graph-tool. Please read the installation instructions carefully, in particular the note about Ubuntu 14: https://graph-tool.skewed.de/download#debian which says: When using Ubuntu 14.04 LTS (Trusty Tahr) or 15.04 (Vivid Vervet), it is necessary need to install the following PPA repository, which contains a newer GCC version and associated libraries: add-apt-repository ppa:ubuntu-toolchain-r/test This will give you GCC 5. Also, please use the pre-compiled packages for Ubuntu, instead of trying compiling it yourself.
But when I run ./configure, it doesn't find clang3.4 (and probably detects pre-installed gcc 4.8.2 instead). How can I tell ./configure to use clang3.4 rather than gcc4.8.2 ?
To select a particular compiler, e.g. GCC 5, you have to call ./configure CXX="gcc-5" But please try to install the pre-compiled packages first, since it is far easier. Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Thanks for the advice. I added the repository and installed gcc-5 via Synaptics. I asked for ./configure CXX="gcc-5" as you said, but I still get the error message checking whether gcc-5 supports C++14 features by default... no checking whether gcc-5 supports C++14 features with -std=gnu++14... no checking whether gcc-5 supports C++14 features with -std=gnu++0x... no configure: error: *** A compiler with support for C++14 language features is required. My version of gcc-5 is gcc version 5.3.0 20151204 (Ubuntu 5.3.0-3ubuntu1~14.04) What am I doing wrong? 2016-04-13 18:08 GMT+02:00 Tiago de Paula Peixoto <tiago@skewed.de>:
On 13.04.2016 17:13, Yannis Haralambous wrote:
I'm trying to install graph-tool under Ubuntu 14. I didn't found gcc5 in the list of synaptic packages but I did installed clang3.4.
Clang 3.4 is too old to compile graph-tool.
Please read the installation instructions carefully, in particular the note about Ubuntu 14:
https://graph-tool.skewed.de/download#debian
which says:
When using Ubuntu 14.04 LTS (Trusty Tahr) or 15.04 (Vivid Vervet), it is necessary need to install the following PPA repository, which contains a newer GCC version and associated libraries:
add-apt-repository ppa:ubuntu-toolchain-r/test
This will give you GCC 5.
Also, please use the pre-compiled packages for Ubuntu, instead of trying compiling it yourself.
But when I run ./configure, it doesn't find clang3.4 (and probably detects pre-installed gcc 4.8.2 instead). How can I tell ./configure to use clang3.4 rather than gcc4.8.2 ?
To select a particular compiler, e.g. GCC 5, you have to call
./configure CXX="gcc-5"
But please try to install the pre-compiled packages first, since it is far easier.
Best, Tiago
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
On 13.04.2016 18:24, Yannis Haralambous wrote:
Thanks for the advice. I added the repository and installed gcc-5 via Synaptics. I asked for ./configure CXX="gcc-5" as you said, but I still get the error message
checking whether gcc-5 supports C++14 features by default... no checking whether gcc-5 supports C++14 features with -std=gnu++14... no checking whether gcc-5 supports C++14 features with -std=gnu++0x... no configure: error: *** A compiler with support for C++14 language features is required.
My version of gcc-5 is gcc version 5.3.0 20151204 (Ubuntu 5.3.0-3ubuntu1~14.04)
What am I doing wrong?
Please post the _entire_ output of the ./configure script, together with the config.log file. -- Tiago de Paula Peixoto <tiago@skewed.de>
I solved the problem by also installing g++-5 and setting CC variable to gcc-5 and CXX variable to g++-5. But now I have a new problem: although I have installed packages sparsehash 1.10-1ubuntu1 and libsparsehash-dev 1.10-1ubuntu1, the configure script does not see them Here is the output, I attach the config.log file root@ubuntu:/home/user/Téléchargements/graph-tool-2.14# ./configurechecking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking target system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking for style of include used by make... GNU checking for gcc... /usr/bin/gcc-5 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /usr/bin/gcc-5 accepts -g... yes checking for /usr/bin/gcc-5 option to accept ISO C89... none needed checking whether /usr/bin/gcc-5 understands -c and -o together... yes checking dependency style of /usr/bin/gcc-5... gcc3 checking for library containing strerror... none required checking how to run the C preprocessor... /usr/bin/gcc-5 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether we are using the GNU C++ compiler... yes checking whether /usr/bin/g++-5 accepts -g... yes checking dependency style of /usr/bin/g++-5... gcc3 checking for /usr/bin/gcc-5 option to accept ISO C99... unsupported checking for /usr/bin/gcc-5 option to accept ISO C89... (cached) none needed checking for /usr/bin/gcc-5 option to accept ISO Standard C... (cached) none needed checking how to run the C++ preprocessor... /usr/bin/g++-5 -E checking for ANSI C header files... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by /usr/bin/gcc-5... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from /usr/bin/gcc-5 object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if /usr/bin/gcc-5 supports -fno-rtti -fno-exceptions... no checking for /usr/bin/gcc-5 option to produce PIC... -fPIC -DPIC checking if /usr/bin/gcc-5 PIC flag -fPIC -DPIC works... yes checking if /usr/bin/gcc-5 static flag -static works... yes checking if /usr/bin/gcc-5 supports -c -o file.o... yes checking if /usr/bin/gcc-5 supports -c -o file.o... (cached) yes checking whether the /usr/bin/gcc-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... /usr/bin/g++-5 -E checking for ld used by /usr/bin/g++-5... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the /usr/bin/g++-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for /usr/bin/g++-5 option to produce PIC... -fPIC -DPIC checking if /usr/bin/g++-5 PIC flag -fPIC -DPIC works... yes checking if /usr/bin/g++-5 static flag -static works... yes checking if /usr/bin/g++-5 supports -c -o file.o... yes checking if /usr/bin/g++-5 supports -c -o file.o... (cached) yes checking whether the /usr/bin/g++-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking whether /usr/bin/g++-5 supports C++14 features by default... no checking whether /usr/bin/g++-5 supports C++14 features with -std=gnu++14... yes checking whether to enable debug info... no checking whether to enable function inlining...... yes checking whether to enable optimizations... yes checking whether to enable symbol visibility manipulation... yes checking whether to enable parallel algorithms with openmp... no checking whether to enable cairo drawing... yes checking for main in -lm... yes checking for main in -lbz2... no checking for main in -lexpat... yes ================ Detecting python ================ checking for a Python interpreter with version >= 2.6... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for python2.7... (cached) /usr/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.6'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/dist-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes graph-tool will be installed at: /usr/lib/python2.7/dist-packages =========================== Using python version: 2.7.6 =========================== checking for boostlib >= 1.54.0... yes checking whether the Boost::Python library is available... yes checking whether boost_python is the correct library... yes checking whether the Boost::Iostreams library is available... yes checking for exit in -lboost_iostreams... yes checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes checking whether the Boost::Coroutine library is available... no configure: WARNING: No usable boost::coroutine found! Some functionality will be disabled in the library. checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph... yes checking for main in -lCGAL... yes checking whether to enable cgal debbuging with valgrind... no checking python module: numpy... yes checking for /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h... yes checking python module: scipy... yes checking expat.h usability... yes checking expat.h presence... yes checking for expat.h... yes checking CGAL/version.h usability... yes checking CGAL/version.h presence... yes checking for CGAL/version.h... yes checking for CAIROMM... yes checking python module: cairo... yes checking pycairo/pycairo.h usability... yes checking pycairo/pycairo.h presence... yes checking for pycairo/pycairo.h... yes checking whether to enable sparsehash... yes checking for SPARSEHASH... no not found by pkgconfig, trying default... checking sparsehash/dense_hash_set usability... no checking sparsehash/dense_hash_set presence... no checking for sparsehash/dense_hash_set... no configure: error: sparsehash headers not found 2016-04-13 18:26 GMT+02:00 Tiago de Paula Peixoto <tiago@skewed.de>:
On 13.04.2016 18:24, Yannis Haralambous wrote:
Thanks for the advice. I added the repository and installed gcc-5 via Synaptics. I asked for ./configure CXX="gcc-5" as you said, but I still get the error message
checking whether gcc-5 supports C++14 features by default... no checking whether gcc-5 supports C++14 features with -std=gnu++14... no checking whether gcc-5 supports C++14 features with -std=gnu++0x... no configure: error: *** A compiler with support for C++14 language features is required.
My version of gcc-5 is gcc version 5.3.0 20151204 (Ubuntu 5.3.0-3ubuntu1~14.04)
What am I doing wrong?
Please post the _entire_ output of the ./configure script, together with the config.log file.
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
On 13.04.2016 18:38, Yannis Haralambous wrote:
I solved the problem by also installing g++-5 and setting CC variable to gcc-5 and CXX variable to g++-5. But now I have a new problem: although I have installed packages sparsehash 1.10-1ubuntu1 and libsparsehash-dev 1.10-1ubuntu1, the configure script does not see them
In Ubuntu, you have also to pass the option: --with-sparsehash-prefix=google to ./configure. -- Tiago de Paula Peixoto <tiago@skewed.de>
OK, I passed the configure stage, but now I can't pass the make stage: root@ubuntu:/home/user/Téléchargements/graph-tool-2.14# make make all-recursive make[1]: entrant dans le répertoire « /home/user/Téléchargements/graph-tool-2.14 » Making all in src make[2]: entrant dans le répertoire « /home/user/Téléchargements/graph-tool-2.14/src » Making all in graph make[3]: entrant dans le répertoire « /home/user/Téléchargements/graph-tool-2.14/src/graph » Making all in centrality make[4]: entrant dans le répertoire « /home/user/Téléchargements/graph-tool-2.14/src/graph/centrality » CXX graph_closeness.lo *g++-5: internal compiler error: Processus arrêté (program cc1plus)*Please submit a full bug report, with preprocessed source if appropriate. See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions. make[4]: *** [graph_closeness.lo] Erreur 1 make[4]: quittant le répertoire « /home/user/Téléchargements/graph-tool-2.14/src/graph/centrality » make[3]: *** [all-recursive] Erreur 1 make[3]: quittant le répertoire « /home/user/Téléchargements/graph-tool-2.14/src/graph » make[2]: *** [all-recursive] Erreur 1 make[2]: quittant le répertoire « /home/user/Téléchargements/graph-tool-2.14/src » make[1]: *** [all-recursive] Erreur 1 make[1]: quittant le répertoire « /home/user/Téléchargements/graph-tool-2.14 » make: *** [all] Erreur 2 2016-04-13 18:45 GMT+02:00 Tiago de Paula Peixoto <tiago@skewed.de>:
On 13.04.2016 18:38, Yannis Haralambous wrote:
I solved the problem by also installing g++-5 and setting CC variable to gcc-5 and CXX variable to g++-5. But now I have a new problem: although I have installed packages sparsehash 1.10-1ubuntu1 and libsparsehash-dev 1.10-1ubuntu1, the configure script does not see them
In Ubuntu, you have also to pass the option:
--with-sparsehash-prefix=google
to ./configure.
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
On 13.04.2016 18:51, Yannis Haralambous wrote:
make[4]: entrant dans le répertoire « /home/user/Téléchargements/graph-tool-2.14/src/graph/centrality » CXX graph_closeness.lo *g++-5: internal compiler error: Processus arrêté (program cc1plus) *Please submit a full bug report,
An internal compiler error is always a compiler bug, it is not graph-tool's fault. I haven't observed a compiler error with Ubuntu 14 using GCC 5; and I managed to compile graph-tool just fine. So I don't know why you are encountering this. As I said before, I recommend you simply install the available binary package for Ubuntu 14. Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
I was able to compile graph-tool using conda on Ubuntu 14.04 ( https://anaconda.org/ostrokach/graph-tool), but it was hacky in that I had to use system gcc-5 to compile and libgcc-5 from salford_systems as a runtime dependency. If you don't have admin rights on your computer, you can try installing from my conda channel (or compiling the conda recipes yourself). On Wed, Apr 13, 2016 at 12:59 PM, Tiago de Paula Peixoto <tiago@skewed.de> wrote:
On 13.04.2016 18:51, Yannis Haralambous wrote:
make[4]: entrant dans le répertoire « /home/user/Téléchargements/graph-tool-2.14/src/graph/centrality » CXX graph_closeness.lo *g++-5: internal compiler error: Processus arrêté (program cc1plus) *Please submit a full bug report,
An internal compiler error is always a compiler bug, it is not graph-tool's fault.
I haven't observed a compiler error with Ubuntu 14 using GCC 5; and I managed to compile graph-tool just fine. So I don't know why you are encountering this.
As I said before, I recommend you simply install the available binary package for Ubuntu 14.
Best, Tiago
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
An internal compiler error is always a compiler bug, it is not graph-tool's fault.
It was a memory problem, by allowing 2 GB of RAM I had much more *.lo files compiled, but still got the internal error. With 3072 MB I got the ones in centrality, clustering, community_old, correlations, draw, flow, generation, inference but not any further (and it took hours!) Is there some way to compile those .lo file groups separately?
Le 13 avr. 2016 à 18:59, Tiago de Paula Peixoto <tiago@skewed.de> a écrit :
As I said before, I recommend you simply install the available binary package for Ubuntu 14.
Do you have an Ubuntu graph-tool binary package? Synaptic couldn't locate it. Can you give me the name and repository? -- ------------------------------------------------------- Yannis Haralambous Professor Institut Mines-Télécom, Télécom Bretagne Computer Science Department UMR CNRS 6285 Lab-STICC Technopôle Brest Iroise CS 83818, 29238 Brest Cedex 3, France Email: yannis.haralambous@telecom-bretagne.eu Internet: http://perso.telecom-bretagne.eu/yannisharalambous/ ICBM address: 48°21'31.57"N 4°34'16.76"W Twitter: y_haralambous ------------------------------------------------------- ...the ball I threw while playing in the park has not yet reached the ground (Dylan Thomas) Es gab eine Zeit, wo ich nur ungern über Schubert sprechen, nur Nächtens den Bäumen und Sternen von ihm vorerzählen mögen. (Robert Schumann)
https://graph-tool.skewed.de/download#debian On Wed, Apr 13, 2016 at 7:43 PM, Yannis Haralambous <yannis1962@gmail.com> wrote:
An internal compiler error is always a compiler bug, it is not graph-tool's fault.
It was a memory problem, by allowing 2 GB of RAM I had much more *.lo files compiled, but still got the internal error. With 3072 MB I got the ones in centrality, clustering, community_old, correlations, draw, flow, generation, inference but not any further (and it took hours!) Is there some way to compile those .lo file groups separately?
Le 13 avr. 2016 à 18:59, Tiago de Paula Peixoto <tiago@skewed.de> a écrit :
As I said before, I recommend you simply install the available binary package for Ubuntu 14.
Do you have an Ubuntu graph-tool binary package? Synaptic couldn't locate it. Can you give me the name and repository?
-- ------------------------------------------------------- Yannis Haralambous Professor Institut Mines-Télécom, Télécom Bretagne Computer Science Department UMR CNRS 6285 Lab-STICC Technopôle Brest Iroise CS 83818, 29238 Brest Cedex 3, France Email: yannis.haralambous@telecom-bretagne.eu Internet: http://perso.telecom-bretagne.eu/yannisharalambous/ ICBM address: 48°21'31.57"N 4°34'16.76"W Twitter: y_haralambous ------------------------------------------------------- ...the ball I threw while playing in the park has not yet reached the ground (Dylan Thomas)
Es gab eine Zeit, wo ich nur ungern über Schubert sprechen, nur Nächtens den Bäumen und Sternen von ihm vorerzählen mögen. (Robert Schumann)
_______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
You have the habit of asking questions which are plainly answered in the documentation. If you read https://graph-tool.skewed.de/download you will see that you need at least 4GB of RAM to compile graph-tool (there is even a plot showing memory usage over time). In that same page you find the instructions on how to install the Ubuntu packages. On 13.04.2016 19:43, Yannis Haralambous wrote:
An internal compiler error is always a compiler bug, it is not graph-tool's fault.
It was a memory problem, by allowing 2 GB of RAM I had much more *.lo files compiled, but still got the internal error. With 3072 MB I got the ones in centrality, clustering, community_old, correlations, draw, flow, generation, inference but not any further (and it took hours!) Is there some way to compile those .lo file groups separately?
Le 13 avr. 2016 à 18:59, Tiago de Paula Peixoto <tiago@skewed.de> a écrit :
As I said before, I recommend you simply install the available binary package for Ubuntu 14.
Do you have an Ubuntu graph-tool binary package? Synaptic couldn't locate it. Can you give me the name and repository?
-- Tiago de Paula Peixoto <tiago@skewed.de>
participants (5)
-
Alexandre Hannud Abdo -
Alexey Strokach -
Tiago de Paula Peixoto -
Yannis Haralambous -
Yannis Haralambous