Re: [Rdkit-discuss] Developing on Visual C++
Hi,
Thanks for trying with gcc.
When I compile and link with bjam and toolset=msvc it works for me too, but it
is when I try to complie using the build process integrated with Visual C++
Express that I get the runtime error.
It would be very kind if you could let me have your command line for compiling
and linking with gcc, this might help me turn the right options on on Visual
C++.
Thanks a lot.
George.
Subject: Re: [Rdkit-discuss] Developing on Visual C++
From: ig...@helix.nih.gov
To: oakm...@hotmail.com
CC: rdkit-discuss@lists.sourceforge.net
Date: Fri, 20 Feb 2009 12:07:17 -0500
George,
I compiled your example with gcc, everything works fine there.
Igor
On Fri, 2009-02-20 at 16:25 +, George Oakman wrote:
Hi all,
I am trying to write a piece of C++ code with the RDKit C++ library
(I'm using Visual C++ Express edition as the development environment).
Thank you very much for the GettingStarted example in C++, that works
fine. I can compile the GettingStarted example using bjam very well,
so I guess this is good news.
I am now trying to create a proper Visual C++ project (WIN32 console
app) and compile via the Build process on Visual C++. So far so good,
I have a mini program that compiles and outputs a Hello RDKit using
BOOST_LOG:
#include stdio.h
#include GraphMol/RDKitBase.h
#include RDGeneral/RDLog.h
using namespace RDKit;
int main(int argc, char *argv[])
{
RDLog::InitLogs();
BOOST_LOG(rdInfoLog) Hello RDKit std::endl;
return 0;
}
This is a Win32 Console Application, that I link with libRDGeneral.lib
libGraphMol.lib libRDGeometry.lib
The piece of code above executes fine (although I receive the
following warning at link time: warning LNK4098: defaultlib 'MSVCRT'
conflicts with use of other libs; use /NODEFAULTLIB:library).
Things start breaking when I try to create a molecule object with
RWMol *mol=new RWMol();
#include stdio.h
#include GraphMol/RDKitBase.h
#include RDGeneral/RDLog.h
using namespace RDKit;
int main(int argc, char *argv[])
{
RDLog::InitLogs();
RWMol *mol=new RWMol();
BOOST_LOG(rdInfoLog) Hello RDKit std::endl;
return 0;
}
This piece of code compiles and links well (same warning as before)
but, at runtime, I receive a 'buffer overflow' on line 28 in RWMol.h:
RWMol() { d_partialBonds.clear(); }
Am I missing something obvious?
Sorry, I know you are not really supporting VC++ and prefer the
boost.build/bjam framework, but maybe someone else is developing using
Visual C++ projects and could help me.
Thanks for your help,
George.
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Re: [Rdkit-discuss] Optimizing SSS in the RDKit
On Feb 17, 2009, at 8:30 PM, Andrew Dalke wrote: Thanks for the link. I've read [Andrew Smellie's] paper now. It's very nicely written, clear, with good background, description, and results, ... Andrew Smellie didn't take what I thought would be the obvious next step and use a trie (probably a Patricia trie) to store things. ... Now I want to try it out! :) I made a first pass implementation of my trie idea using Python. It's attached. My quick summary is: fingerprint size of time for size of time for time for size bits bits trie trie trie (no hits) === === === 9883714 MB 0.05s59 MB0.6s 0.04s 19881928 MB 0.09s 105 MB0.7s 0.07s Based on the paper, it seems his C code requires about 160 MB for 200,000 compounds so there's a clear savings due to at least one of the two memory savings techniques I tried. I expect faster performance for the regular based screens if I were to do the test directly in C. I'm guessing a factor of 3. I expect an even better performance increase and reduced memory use were I to rewrite the trie in C. There I expect about 10x-30x performance, which brings them to the same times. But that's a scientific wild-ass guess. There's no real conclusion you can draw from these numbers other than that I've managed to save a lot of memory and that this is an avenue worth considering. Andrew da...@dalkescientific.com
Re: [Rdkit-discuss] Developing on Visual C++
George,
Sure, here it is (I named your file t.cpp):
g++ -c -I ../rdkit-svn/Code -I ../rdkit-svn/External/vflib-2.0/include/
-I ../boost_1_37_0 t.cpp
export LD_LIBRARY_PATH=../rdkit-svn/bin/
g++ -o t t.o -L ../rdkit-svn/bin/ -lRDGeneral -lGraphMol -lRDGeometry
./t
[12:37:07] Hello RDKit
Hope this helps,
Igor
On Sat, 2009-02-21 at 09:13 +, George Oakman wrote:
Hi,
Thanks for trying with gcc.
When I compile and link with bjam and toolset=msvc it works for me
too, but it is when I try to complie using the build process
integrated with Visual C++ Express that I get the runtime error.
It would be very kind if you could let me have your command line for
compiling and linking with gcc, this might help me turn the right
options on on Visual C++.
Thanks a lot.
George.
Subject: Re: [Rdkit-discuss] Developing on Visual C++
From: ig...@helix.nih.gov
To: oakm...@hotmail.com
CC: rdkit-discuss@lists.sourceforge.net
Date: Fri, 20 Feb 2009 12:07:17 -0500
George,
I compiled your example with gcc, everything works fine there.
Igor
On Fri, 2009-02-20 at 16:25 +, George Oakman wrote:
Hi all,
I am trying to write a piece of C++ code with the RDKit C++
library
(I'm using Visual C++ Express edition as the development
environment).
Thank you very much for the GettingStarted example in C++, that
works
fine. I can compile the GettingStarted example using bjam very
well,
so I guess this is good news.
I am now trying to create a proper Visual C++ project (WIN32
console
app) and compile via the Build process on Visual C++. So far so
good,
I have a mini program that compiles and outputs a Hello RDKit
using
BOOST_LOG:
#include stdio.h
#include GraphMol/RDKitBase.h
#include RDGeneral/RDLog.h
using namespace RDKit;
int main(int argc, char *argv[])
{
RDLog::InitLogs();
BOOST_LOG(rdInfoLog) Hello RDKit std::endl;
return 0;
}
This is a Win32 Console Application, that I link with
libRDGeneral.lib
libGraphMol.lib libRDGeometry.lib
The piece of code above executes fine (although I receive the
following warning at link time: warning LNK4098: defaultlib
'MSVCRT'
conflicts with use of other libs; use /NODEFAULTLIB:library).
Things start breaking when I try to create a molecule object with
RWMol *mol=new RWMol();
#include stdio.h
#include GraphMol/RDKitBase.h
#include RDGeneral/RDLog.h
using namespace RDKit;
int main(int argc, char *argv[])
{
RDLog::InitLogs();
RWMol *mol=new RWMol();
BOOST_LOG(rdInfoLog) Hello RDKit std::endl;
return 0;
}
This piece of code compiles and links well (same warning as
before)
but, at runtime, I receive a 'buffer overflow' on line 28 in
RWMol.h:
RWMol() { d_partialBonds.clear(); }
Am I missing something obvious?
Sorry, I know you are not really supporting VC++ and prefer the
boost.build/bjam framework, but maybe someone else is developing
using
Visual C++ projects and could help me.
Thanks for your help,
George.
__
Beyond Hotmail - see what else you can do with Windows Live Find
out
more!
--
Open Source Business Conference (OSBC), March 24-25, 2009, San
Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the
Enterprise
-Strategies to boost innovation and cut costs with open source
participation
-Receive a $600 discount off the registration fee with the source
code: SFAD
http://p.sf.net/sfu/XcvMzF8H
___ Rdkit-discuss
mailing list Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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Igor Filippov [Contr] ig...@helix.nih.gov
