Re: [Rdkit-discuss] Problem building recent revisions on Windows

[James Davidson]

Thanks Greg

I have now tried using boost 1.56 (the cmake configuration once BOOST_ROOT is 
set is a little different vs. 1.55…).  Either way I can’t seem to build with 
threadsafe/multithreaded support – but perhaps we should draw a line under it 
for now / follow-up ‘off-line’(?).

The good news is that (with the thread settings OFF) the changes you checked-in 
(rev5616) have indeed sorted the MolHash piece, and all tests pass – thanks!

Kind regards

James

From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 14 April 2015 05:35
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Problem building recent revisions on Windows

Hi James

Thanks for your patience here. I will invest the time in trying to get 
automated builds happening on this Windows side so that this stops happening.

I just pushed some changes that should clear up the MolHash-related build 
problems. I had forgotten that that bit of code still needed to be tested on 
Windows. I haven't tested building the cartridge on Windows (I'm not set up to 
do that), but the python wrappers definitely do build for me now with both 
RDK_BUILD_THREADSAFE_SSS and RDK_TEST_MULTITHREADED set to ON. I don't think it 
should make a difference, but just in case: I am doing this using boost 1.56.

Best,
-greg




On Mon, Apr 13, 2015 at 11:30 AM, James Davidson 
mailto:j.david...@vernalis.com>> wrote:
Here’s an update:

Tried building rev5211, but saw similar linking errors (to do with Boost 
threading libraries).  The most recent build that I have successfully managed 
without the errors is rev5016.

It occurred to me that a couple of my cmake options relate to threading 
(RDK_BUILD_THREADSAFE=ON; RDK_TEST_MULTITHREADED=ON) – and perhaps other people 
(Greg, Paolo) with successful Windows builds had these set OFF (default)(?).  
Indeed, if I set both of these to OFF, I can successfully build rev5211, and 
all of the tests pass.
So this is good – but I still don’t understand what has changed (in relation to 
Boost threading) that means that later versions don’t build…

Threading aside, I was now feeling pretty confident that I would be ok to build 
the latest revision (rev5611).  Unfortunately this was not the case – I 
initially hit a problem with MolHash.cpp, which I thought was down to MSVC 
being stupid about snprintf() (line 265).  After a little stack-overflowing, I 
thought changing this to _snprintf() would solve the problem – which it appears 
to (at least MolHash.cpp now compiles), but then I get a couple of further 
errors down-stream (probably related to the change I made?):


Error  1  error LNK2019: unresolved external symbol "class 
std::basic_string,class std::allocator 
> __cdecl RDKit::Descriptors::calcMolFormula(class RDKit::ROMol const 
&,bool,bool)" 
(?calcMolFormula@Descriptors@RDKit@@YA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@AEBVROMol@2@_N1@Z)
 referenced in function "void __cdecl 
RDKit::MolHash::generateMoleculeHashSet(class RDKit::ROMol const &,struct 
RDKit::MolHash::HashSet &,class std::vector > const *,class std::vector > const *)" 
(?generateMoleculeHashSet@MolHash@RDKit@@YAXAEBVROMol@2@AEAUHashSet@12@PEBV?$vector@IV?$allocator@I@std@@@std@@2@Z)
 C:\RDKit\build\Code\GraphMol\MolHash\Wrap\MolHash.lib(MolHash.obj) 
   rdMolHash

Error  2  error LNK1120: 1 unresolved externals   
C:\RDKit\build\rdkit\Chem\Release\rdMolHash.pyd  rdMolHash


So I guess it would still be good to understand the threading issue (or at 
least for someone else to be able to reproduce it); and perhaps the observed 
MolHash issue is an easier one to sort(?)

Kind regards

James

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Re: [Rdkit-discuss] Problem building recent revisions on Windows

[Greg Landrum]

Glad to hear that James.

And, yes, I agree that we should take the threading discussion offline...

-greg

On Tue, Apr 14, 2015 at 4:49 PM, James Davidson 
wrote:

>  Thanks Greg
>
>
>
> I have now tried using boost 1.56 (the cmake configuration once BOOST_ROOT
> is set is a little different vs. 1.55…).  Either way I can’t seem to build
> with threadsafe/multithreaded support – but perhaps we should draw a line
> under it for now / follow-up ‘off-line’(?).
>
>
>
> The good news is that (with the thread settings OFF) the changes you
> checked-in (rev5616) have indeed sorted the MolHash piece, and all tests
> pass – thanks!
>
>
>
> Kind regards
>
>
>
> James
>
>
>
> *From:* Greg Landrum [mailto:greg.land...@gmail.com]
> *Sent:* 14 April 2015 05:35
> *To:* James Davidson
> *Cc:* rdkit-discuss@lists.sourceforge.net
> *Subject:* Re: [Rdkit-discuss] Problem building recent revisions on
> Windows
>
>
>
> Hi James
>
>
>
> Thanks for your patience here. I will invest the time in trying to get
> automated builds happening on this Windows side so that this stops
> happening.
>
>
>
> I just pushed some changes that should clear up the MolHash-related build
> problems. I had forgotten that that bit of code still needed to be tested
> on Windows. I haven't tested building the cartridge on Windows (I'm not set
> up to do that), but the python wrappers definitely do build for me now with
> both RDK_BUILD_THREADSAFE_SSS and RDK_TEST_MULTITHREADED set to ON. I don't
> think it should make a difference, but just in case: I am doing this using
> boost 1.56.
>
>
>
> Best,
>
> -greg
>
>
>
>
>
>
>
>
>
> On Mon, Apr 13, 2015 at 11:30 AM, James Davidson 
> wrote:
>
> Here’s an update:
>
>
>
> Tried building rev5211, but saw similar linking errors (to do with Boost
> threading libraries).  The most recent build that I have successfully
> managed without the errors is rev5016.
>
>
>
> It occurred to me that a couple of my cmake options relate to threading
> (RDK_BUILD_THREADSAFE=ON; RDK_TEST_MULTITHREADED=ON) – and perhaps other
> people (Greg, Paolo) with successful Windows builds had these set OFF
> (default)(?).  Indeed, if I set both of these to OFF, I can successfully
> build rev5211, and all of the tests pass.
>
> So this is good – but I still don’t understand what has changed (in
> relation to Boost threading) that means that later versions don’t build…
>
>
>
> Threading aside, I was now feeling pretty confident that I would be ok to
> build the latest revision (rev5611).  Unfortunately this was not the case –
> I initially hit a problem with MolHash.cpp, which I thought was down to
> MSVC being stupid about snprintf() (line 265).  After a little
> stack-overflowing, I thought changing this to _snprintf() would solve the
> problem – which it appears to (at least MolHash.cpp now compiles), but then
> I get a couple of further errors down-stream (probably related to the
> change I made?):
>
>
>
>
>
> Error  1  error LNK2019: unresolved external symbol "class
> std::basic_string,class
> std::allocator > __cdecl RDKit::Descriptors::calcMolFormula(class
> RDKit::ROMol const &,bool,bool)" (?calcMolFormula@Descriptors@RDKit@
> @YA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@
> @AEBVROMol@2@_N1@Z) referenced in function "void __cdecl
> RDKit::MolHash::generateMoleculeHashSet(class RDKit::ROMol const &,struct
> RDKit::MolHash::HashSet &,class std::vector std::allocator > const *,class std::vector std::allocator > const *)" (?generateMoleculeHashSet@MolHash
> @RDKit@@YAXAEBVROMol@2@AEAUHashSet@12@PEBV?$vector@IV?$allocator@I@std@
> @@std@@2@Z)
> C:\RDKit\build\Code\GraphMol\MolHash\Wrap\MolHash.lib(MolHash.obj)
> rdMolHash
>
>
>
> Error  2  error LNK1120: 1 unresolved externals
> C:\RDKit\build\rdkit\Chem\Release\rdMolHash.pyd  rdMolHash
>
>
>
>
>
> So I guess it would still be good to understand the threading issue (or at
> least for someone else to be able to reproduce it); and perhaps the
> observed MolHash issue is an easier one to sort(?)
>
>
>
> Kind regards
>
>
>
> James
>
>
> __
> PLEASE READ: This email is confidential and may be privileged. It is
> intended for the named addressee(s) only and access to it by anyone else is
> unauthorised. If you are not an addressee, any disclosure or copying of the
> contents of this email or any action taken (or not taken) in reliance on it
> is unauthorised and may be unlawful. If you have received this email in
> error, please notify the sender or postmas...@vernalis.com. Email is not
> a secure method of communication and the Company cannot accept
> responsibility for the accuracy or completeness of this message or any
> attachment(s). Please check this email for virus infection for which the
> Company accepts no responsibility. If verification of this email is sought
> then please request a hard copy. Unless otherwise stated, any views or
> opinions presented are so

Re: [Rdkit-discuss] Clustering in RDKit (take 2 - missing wiki link)

[JP]

This is now at:
https://github.com/rdkit/rdkit/blob/master/Docs/Book/Cookbook.rst

-
Jean-Paul Ebejer
Early Stage Researcher

On 11 April 2015 at 10:46, JP  wrote:

> Hi RDKitters!
>
> I have a bit of python RDKit clustering code using Butina which is
> commented with:
> # Ripped off from https://code.google.com/p/rdkit/wiki/ClusteringMolecules
>
> Sadly, and as it happens I need to refer back to this.
>
> This was written by Greg, I think as a result of this "nudge":
>
> https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02449.html
>
> This page doesn't seem to exist anymore in the WIki.  Is this because of a
> technical / administrative glitch?  Or has this been removed purposefully
> (perhaps the functionality is not supported anymore) ?
>
> Thanks!
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
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