Installing graph-tool in sagemath

Hello,

I am trying to install graph-tool in sagemath ( check
http://www.sagemath.org/ ), under Ubuntu 12.04.

Basically, sagemath is python with many good modules helpful for
mathematics, and why not physics.

sagemath has its own built version of python, which is standard by using a
virtual environment. The idea is, I guess, not to mess up with your system
python.

By typing in a terminal

$ sage -sh

you enter into sagemath virtual environment, which looks like:

(sage -sh) $

therefore, if you try to run a python console by typing

(sage -sh)$ python

then, it will run the python built in sage's virtual environment.

From the virtual environment I have installed CGAL, and then, I tried to

configure graph-tool typing:

(sage -sh) graph-tool-2.2.29$ ./configure
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... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for library containing strerror... none required
checking how to run the C preprocessor... cpp
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 g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gcc option to accept ISO C99... unsupported
checking for gcc option to accept ISO C89... (cached) none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking how to run the C++ preprocessor... g++ -E
checking for ANSI C header files... (cached) yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
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 gcc... ld
checking if the linker (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 whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
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 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 archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (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... g++ -E
checking for ld used by g++... ld -m elf_x86_64
checking if the linker (ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (ld -m elf_x86_64) supports shared
libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (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 target system type... x86_64-unknown-linux-gnu
checking whether to enable debug info...... no
checking whether C++ compiler supports -std=gnu++11... yes
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 graph filtering...... yes
checking whether to enable parallel algorithms with openmp...... no
checking whether to enable cairo drawing...... yes
checking whether to enable sparsehash...... yes
checking for main in -lm... yes
checking for main in -lbz2... yes
checking for main in -lexpat... yes

Where did you install CGAL? If you installed it in a non-standard
directory, this needs to be passed to the configure script via the
CPPFLAGS and LDFLAGS variables.

Check the output in the config.log file, which includes the reason why
CGAL was not found. You can post the contents of this file to the list,
if you are unable to find the problem.

Best,
Tiago

Hi,

Thanks for the recommendation Tiago. I went further this time and
successfully went though the ./configure and make stage. However, when I
run make install something goes wrong. Below I post the relevant part of
the procedure according to my judgement. First I go into sage's virtual
environment by typing

$ sage -sh

Then I run:

(sage-sh) juan(a)mostro:graph-tool-2.2.29.1$ ./configure
CPPFLAGS="-I/home/juan/usr/local/include/boost"
LDFLAGS="-L/home/juan/usr/local/lib"
SPARSEHASH_CFLAGS="-I/usr/include/google/sparsehash"

some bla bla bla

(sage-sh) juan(a)mostro:graph-tool-2.2.29.1$ make

after many hours...it seems to success. Finally I try to install

(sage-sh) juan(a)mostro:graph-tool-2.2.29.1$ sudo make install

Making install in src
make[1]: Entering directory `/home/juan/Downloads/graph-tool-2.2.29.1/src'
Making install in graph
make[2]: Entering directory
`/home/juan/Downloads/graph-tool-2.2.29.1/src/graph'
Making install in centrality
make[3]: Entering directory
`/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/centrality'
make[4]: Entering directory
`/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/centrality'
make[4]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p
'/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality'
/bin/bash ../../../libtool --mode=install /usr/bin/install -c
libgraph_tool_centrality.la'/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality'
libtool: install: /usr/bin/install -c .libs/libgraph_tool_centrality.so
/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality/libgraph_tool_centrality.so
libtool: install: /usr/bin/install -c .libs/libgraph_tool_centrality.lai
/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality/
libgraph_tool_centrality.la
libtool: finish:
PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
ldconfig -n
/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality

attachment.html (60.2 KB)

Hi,

Thanks for the recommendation Tiago. I went further this time and
successfully went though the ./configure and make stage. However, when I
run make install something goes wrong. Below I post the relevant part of
the procedure according to my judgement. First I go into sage's virtual
environment by typing

$ sage -sh

Then I run:

(sage-sh) juan(a)mostro:graph-tool-2.2.29.1$ ./configure
CPPFLAGS="-I/home/juan/usr/local/include/boost"
LDFLAGS="-L/home/juan/usr/local/lib"
SPARSEHASH_CFLAGS="-I/usr/include/google/sparsehash"

some bla bla bla

(sage-sh) juan(a)mostro:graph-tool-2.2.29.1$ make

after many hours...it seems to success. Finally I try to install

(sage-sh) juan(a)mostro:graph-tool-2.2.29.1$ sudo make install

Making install in src
make[1]: Entering directory `/home/juan/Downloads/graph-tool-2.2.29.1/src'
Making install in graph
make[2]: Entering directory
`/home/juan/Downloads/graph-tool-2.2.29.1/src/graph'
Making install in centrality
make[3]: Entering directory
`/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/centrality'
make[4]: Entering directory
`/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/centrality'
make[4]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p
'/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality'
/bin/bash ../../../libtool --mode=install /usr/bin/install -c
libgraph_tool_centrality.la'/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality'
libtool: install: /usr/bin/install -c .libs/libgraph_tool_centrality.so
/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality/libgraph_tool_centrality.so
libtool: install: /usr/bin/install -c .libs/libgraph_tool_centrality.lai
/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality/
libgraph_tool_centrality.la
libtool: finish:
PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
ldconfig -n
/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality

attachment.html (60.2 KB)

Hi all,

The following seems to fix that problem

http://thinkingcan.blogspot.fi/2013/09/fixed-importerror-cannot-import-name.html

I will summarize here:

attachment.html (69.9 KB)

Hi all,

This seems to solve the problem:

juan(a)mostro:~/Downloads/sage-6.1.1$ export
LD_LIBRARY_PATH=/home/juan/usr/local/lib/
juan(a)mostro:~/Downloads/sage-6.1.1$ ./sage -python
Python 2.7.5 (default, Feb 11 2014, 07:30:05)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import graph_tool
g = graph_tool.Graph()

Wow! That was a though one. I still need to check that it works
properly. After this I will try to summarize the installation process
of graph_tool into sage so others can follow similar steps.

Best Regards,
Juan

attachment.html (76.1 KB)

Hi all,

Below is my summary. It is a bit messy. In fact, it is the "manual
log" that I have followed through the process. I hope that it is
helpful for you.

Best Regards,
Juan

attachment.html (96 KB)