installation: make fails at graph_blockmodel_overlap.hh

graph-tool
1

Hi,

I have been trying to install graph-tool on a Debian server which I don't
have root access for for a day now, and after some of trouble I was able to
run configure but now make fails with the following:

  CXX graph_blockmodel.lo
In file included from graph_blockmodel.cc:39:0:
graph_blockmodel_overlap.hh: In lambda function:
graph_blockmodel_overlap.hh:900:50: error: no match for ‘operator’ in
‘((graph_tool::overlap_partition_stats_t*)this)->graph_tool::overlap_partition_stats_t::_embhist[bv_i]’
graph_blockmodel_overlap.hh:900:50: note: candidates are:
In file included from /usr/include/c++/4.7/bits/hashtable.h:36:0,
                 from /usr/include/c++/4.7/unordered_set:45,
                 from ./../graph_properties.hh:24,
                 from ./../graph.hh:35,
                 from ./../graph_filtering.hh:21,
                 from graph_blockmodel.cc:28:
/usr/include/c++/4.7/bits/hashtable_policy.h:435:5: note:
std::__detail::_Map_base<_Key, _Pair, std::_Select1st<_Pair>, true,
_Hashtable>::mapped_type& std::__detail::_Map_base<_Key, _Pair,
std::_Select1st<_Pair>, true, _Hashtable>::operator(const _Key&) [with
_Key = std::vector<int>; _Pair = std::pair<const std::vector<int>,
std::vector<long unsigned int> >; _Hashtable =
std::_Hashtable<std::vector<int>, std::pair<const std::vector<int>,
std::vector<long unsigned int> >, std::allocator<std::pair<const
std::vector<int>, std::vector<long unsigned int> > >,
std::_Select1st<std::pair<const std::vector<int>, std::vector<long unsigned

> >, std::equal_to<std::vector<int> >, std::hash<std::vector<int> >,

std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash,
std::__detail::_Prime_rehash_policy, true, false, true>;
std::__detail::_Map_base<_Key, _Pair, std::_Select1st<_Pair>, true,
_Hashtable>::mapped_type = std::vector<long unsigned int>] <near match>
/usr/include/c++/4.7/bits/hashtable_policy.h:435:5: note: no known
conversion for implicit ‘this’ parameter from ‘const ebhist_t* {aka const
std::unordered_map<std::vector<int>, std::vector<long unsigned int> >*}’ to
‘std::__detail::_Map_base<std::vector<int>, std::pair<const
std::vector<int>, std::vector<long unsigned int> >,
std::_Select1st<std::pair<const std::vector<int>, std::vector<long unsigned

> >, true, std::_Hashtable<std::vector<int>, std::pair<const

std::vector<int>, std::vector<long unsigned int> >,
std::allocator<std::pair<const std::vector<int>, std::vector<long unsigned

> >, std::_Select1st<std::pair<const std::vector<int>,

std::vector<long unsigned int> > >, std::equal_to<std::vector<int> >,
std::hash<std::vector<int> >, std::__detail::_Mod_range_hashing,
std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy,
true, false, true> >*’

This goes on for several lines. Am I using the wrong compiler? My gcc
version is 4.7.2.
I read the INSTALL file and I can't find the solution.

I disabled cairo and sparsehash.

Do you have any idea why I'm getting these errors?

Thanks,
Judit Ács

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2

I cannot reproduce this on any Debian system I have access to, but the
oldest GCC I'm using is version 4.8. I suspect this issue is due to an
old compiler, since graph-tool requires good C++11
support. Unfortunately, without the rest of the error message I cannot
evaluate whether or not this is really a problem with the compiler.

Best,
Tiago

3

I put the full output of configure and make here.
Configure stdout: http://pastebin.com/AMJYwkxB
make stdout: http://pastebin.com/m2wt4F5q
make stderr: http://pastebin.com/nh2nvneQ

I hope this helps. Meanwhile I'll ask around why we have such an old
version of gcc.

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4

Taking a look at the full error message, and inspecting the portion of
the code which causes it, it seems indeed that the compiler is getting
confused with rvalue references and move semantics (a c++11
feature). This is triggered internally in the STL, so it is not even
something that I can work around in the code (which seems perfectly
valid, and compiles just fine in newer GCC and Clang compilers).

In view of this I'll update the minimum requirements to GCC 4.8 in the
website.

Best,
Tiago

5

Unfortunately the stable Debian version still comes with gcc4.7, see here:
https://packages.debian.org/wheezy/gcc

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6

Yes, but there is very little I can do. Dropping c++11 is not possible.
It is a pity that debian stable is so outdated.

You can also ask your sysadmin to pull gcc 4.8 from testing.

A possible workaround for you is to attempt to use sparsehash, since it
will avoid using the code with unordered_map the compiler is failing on.

Best,
Tiago

7

I wanted to try graph-tool on my laptop before asking the sysadmin to
install a newer gcc. I'm using Linux Mint with gcc4.8.2.

There were two problems:
I installed both libsparsehash-dev and sparsehash from the official ubuntu
repos but configure still can't find it. I could sidestep this by disabling
sparsehash.

The more important problem is that make runs out of memory. I have 4GB RAM
+ 2GB swap in my laptop.
It's killed while compiling this:

Making all in community
make[4]: Entering directory
`/home/judit/bin/graph-tool-2.2.35/src/graph/community'
  CXX graph_community_network_eavg_imp1.lo

Is graph-tool intended for stronger machines?

Thank you,
Judit

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8

I wanted to try graph-tool on my laptop before asking the sysadmin to install a newer gcc. I'm using Linux Mint with gcc4.8.2.

There were two problems:
I installed both libsparsehash-dev and sparsehash from the official
ubuntu repos but configure still can't find it. I could sidestep this
by disabling sparsehash.

Take a look at config.log to see why it is failing. In some versions of
ubuntu/debian, you need to pass the following option to configure:

    --with-sparsehash-prefix=google

The more important problem is that make runs out of memory. I have 4GB
RAM + 2GB swap in my laptop.

You need slightly more than 4GB to compile graph-tool, unfortunately. If
you have around 6GB with swap, make sure there is nothing else consuming
much memory, and that the compilation is not being done in parallel
(i.e. do not use make -j2 or similar).

If you still cannot compile it, you can try using the clang compiler. It
is also available for ubuntu, and it should use only about half as much
ram.

Best,
Tiago

9

> I wanted to try graph-tool on my laptop before asking the sysadmin to
install a newer gcc. I'm using Linux Mint with gcc4.8.2.
>
> There were two problems:
> I installed both libsparsehash-dev and sparsehash from the official
> ubuntu repos but configure still can't find it. I could sidestep this
> by disabling sparsehash.

Take a look at config.log to see why it is failing. In some versions of
ubuntu/debian, you need to pass the following option to configure:

    --with-sparsehash-prefix=google

Thank you, this solve the sparsehash issue. I also tried it on the server
but the old gcc still fails.

> The more important problem is that make runs out of memory. I have 4GB
> RAM + 2GB swap in my laptop.

You need slightly more than 4GB to compile graph-tool, unfortunately. If
you have around 6GB with swap, make sure there is nothing else consuming
much memory, and that the compilation is not being done in parallel
(i.e. do not use make -j2 or similar).

If you still cannot compile it, you can try using the clang compiler. It
is also available for ubuntu, and it should use only about half as much
ram.

I'll try this tonight.

Best,
Judit

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10

You need slightly more than 4GB to compile graph-tool, unfortunately. If

you have around 6GB with swap, make sure there is nothing else consuming

much memory, and that the compilation is not being done in parallel
(i.e. do not use make -j2 or similar).

If you still cannot compile it, you can try using the clang compiler. It
is also available for ubuntu, and it should use only about half as much
ram.

I'll try this tonight.

It worked with nothing else memory-consuming running.

gcc 4.8.2
~3.5GB free memory, 2GB swap

Meanwhile the sysadmin installed the Debian package found in your repo, but
its name was graph-tool, not python-graph-tool.

Thank you again for your help,

Judit

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11

Be careful, this is a *very old* version of graph-tool! All newer
versions are called python-graph-tool.

Best,
Tiago