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Rui Carvalho | 17 Dec 2007 21:31
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Parallel algorithms in graph-tool

Hi,

I'm trying to compile graph-tool with parallel algorithms enabled, but I
must be missing something from the instructions on:
http://projects.forked.de/graph-tool/wiki/ParallelAlgorithms

Basically, the problem is where it says:
$ cd gcc-4.2.0
$ patch -E -p1 < ../gcc-shared-openmp.patch

I don't have a folder gcc-4.2.0 on my Ubuntu 64 bit system, although I have
gcc-4.2.0 installed. I've tried to save the patch to this directory instead:
$cd /usr/lib/gcc/x86_64-linux-gnu/4.2 
But when I issue the command I get:
Patch: **** Only garbage was found in the patch input.

Any help would be much appreciated :)

Thanks,
Rui
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Tiago de Paula Peixoto | 17 Dec 2007 23:33
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Re: Parallel algorithms in graph-tool

On 12/17/2007 06:31 PM, Rui Carvalho wrote:
> Hi,
> 
> I'm trying to compile graph-tool with parallel algorithms enabled, but I
> must be missing something from the instructions on:
> http://projects.forked.de/graph-tool/wiki/ParallelAlgorithms
> 
> Basically, the problem is where it says:
> $ cd gcc-4.2.0
> $ patch -E -p1 < ../gcc-shared-openmp.patch
> 
> I don't have a folder gcc-4.2.0 on my Ubuntu 64 bit system, although I have
> gcc-4.2.0 installed. I've tried to save the patch to this directory instead:
> $cd /usr/lib/gcc/x86_64-linux-gnu/4.2 
> But when I issue the command I get:
> Patch: **** Only garbage was found in the patch input.
> 
> Any help would be much appreciated :)

Hi Rui.

How did you download the patch? Did you get it from the link below?

http://projects.forked.de/graph-tool/attachment/wiki/ParallelAlgorithms/gcc-shared-openmp.patch?format=raw

Be careful not do download html...

But notice also that you should try the patch in the _source_ directory
of GCC, which is not installed by default on any system (I know of). You
have to download the code from the GCC website, unpack it, apply the
(Continue reading)

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Rui Carvalho | 18 Dec 2007 00:56
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Re: Parallel algorithms in graph-tool

Hi Tiago,

Hummm... building gcc sounds like too much work.
I had a look at the bug and at the planned changes in gcc-4.3 and there's no mention of correcting the bug. What
a shame!

Anyway, many thanks for getting back on this.

Rui

-----Original Message-----
From: graph-tool-bounces <at> forked.de [mailto:graph-tool-bounces <at> forked.de] On Behalf Of Tiago de
Paula Peixoto
Sent: 17 December 2007 22:34
To: Main discussion list for the graph-tool project
Subject: Re: [graph-tool] Parallel algorithms in graph-tool

On 12/17/2007 06:31 PM, Rui Carvalho wrote:
> Hi,
> 
> I'm trying to compile graph-tool with parallel algorithms enabled, but 
> I must be missing something from the instructions on:
> http://projects.forked.de/graph-tool/wiki/ParallelAlgorithms
> 
> Basically, the problem is where it says:
> $ cd gcc-4.2.0
> $ patch -E -p1 < ../gcc-shared-openmp.patch
> 
> I don't have a folder gcc-4.2.0 on my Ubuntu 64 bit system, although I 
> have gcc-4.2.0 installed. I've tried to save the patch to this directory instead:
(Continue reading)

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Rui Carvalho | 18 Dec 2007 02:34
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libgraph_tool

Sorry to post again :)

I'm trying to compile graph-tool on my new desktop. I've downloaded the
development source code and I think (or thought!) I have everything needed
for the install. 

Here's what I do logged in as root:
$./autogen.sh
$./configure --disable-visibility
$make
$make install

All seems to work with no visible errors. However, here's what I get when I
type
$graph-tool --help

Traceback (most recent call last):
  File "/usr/local/bin/graph-tool", line 19, in <module>
    from graph_tool import *
  File "/usr/local/lib/python2.5/site-packages/graph_tool.py", line 26, in
<module>
    import libgraph_tool
ImportError: No module named libgraph_tool

I must be making a basic mistake somewhere? I've got python 2.5.1 on an
ubuntu 7.10.

Many thanks again,
Rui
(Continue reading)

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Tiago de Paula Peixoto | 18 Dec 2007 03:18
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Re: libgraph_tool

On 12/17/2007 11:34 PM, Rui Carvalho wrote:
> Sorry to post again :)

Post as many times as you want! :)

> I'm trying to compile graph-tool on my new desktop. I've downloaded the
> development source code and I think (or thought!) I have everything needed
> for the install. 
> 
> Here's what I do logged in as root:
> $./autogen.sh
> $./configure --disable-visibility
> $make
> $make install
> 
> All seems to work with no visible errors. However, here's what I get when I
> type
> $graph-tool --help
> 
> Traceback (most recent call last):
>   File "/usr/local/bin/graph-tool", line 19, in <module>
>     from graph_tool import *
>   File "/usr/local/lib/python2.5/site-packages/graph_tool.py", line 26, in
> <module>
>     import libgraph_tool
> ImportError: No module named libgraph_tool
> 
> 
> I must be making a basic mistake somewhere? I've got python 2.5.1 on an
> ubuntu 7.10.
(Continue reading)

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Rui Carvalho | 21 Dec 2007 21:57
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Re: libgraph_tool

Hi Tiago,

Sorry for my late reply, but I only got the chance to try it now and it works :)

One more stupid question: can one use the pre-compiled binaries to bypass the problem with gcc and have
multi-threaded parallel algorithm support on graph-tool?

Many thanks,
Rui

-----Original Message-----
From: graph-tool-bounces <at> forked.de [mailto:graph-tool-bounces <at> forked.de] On Behalf Of Tiago de
Paula Peixoto
Sent: 18 December 2007 02:19
To: Main discussion list for the graph-tool project
Subject: Re: [graph-tool] libgraph_tool

On 12/17/2007 11:34 PM, Rui Carvalho wrote:
> Sorry to post again :)

Post as many times as you want! :)

> I'm trying to compile graph-tool on my new desktop. I've downloaded 
> the development source code and I think (or thought!) I have 
> everything needed for the install.
> 
> Here's what I do logged in as root:
> $./autogen.sh
> $./configure --disable-visibility
> $make
(Continue reading)

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Tiago de Paula Peixoto | 21 Dec 2007 23:04
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Re: libgraph_tool

On 12/21/2007 06:57 PM, Rui Carvalho wrote:
> Hi Tiago,
> 
> Sorry for my late reply, but I only got the chance to try it now and
> it works :)

Great. ;-)

> One more stupid question: can one use the pre-compiled binaries to
> bypass the problem with gcc and have multi-threaded parallel algorithm
> support on graph-tool?

In principle yes, if one links to a static version of libgomp (GCC's
implementation of openmp) that works. But note that there's yet a much
more severe problem with openmp and GCC:
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=33361

This bug actually causes GCC to crash when compiling graph-tool... I
guess openmp is still a quite young addition to GCC and it needs to
stabilize a bit.

Cheers,
Tiago

--

-- 
Tiago de Paula Peixoto <tiago <at> forked.de>
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