Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-12 Thread Gianluca Sforna 
On Tue, Apr 12, 2016 at 11:51 AM, Gianluca Sforna  wrote:
> On Mon, Apr 11, 2016 at 1:20 PM, Greg Landrum  wrote:
>> This could be the issue fixed by this PR from Matt Swain:
>> https://github.com/rdkit/rdkit/pull/856
>
> Yeah, that's it. Thanks!

But no joy still


[ 36%] Building CXX object
Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o
cd 
/builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse
&& /usr/bin/c++   -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHR
EADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS
-I/usr/include/python2.7
-I/builddir/build/BUILD/rdkit-Release_2016_03_1b1/pyt
hon2/Code  -O2 -g -pipe -Wall -Werror=format-security
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong
--param=ssp-buffer-size=
4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
-m64 -mtune=generic  -mpopcnt -Wno-deprecated -Wno-unused-function -f
no-strict-aliasing -fPIC -Wall -Wextra -O2 -g -DNDEBUG -fPIC
-DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o
CMakeFiles/SmilesParse.dir/lex.yys
marts.cpp.o -c 
/builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmarts.cpp
smiles.ll:40:52: error: 'yyscan_t' has not been declared
 size_t setup_smiles_string(const std::string ,yyscan_t yyscanner){
^
smiles.ll: In function 'size_t setup_smiles_string(const string&, int)':
smiles.ll:49:46: error: too many arguments to function 'void*
yysmiles_alloc(yy_size_t)'
   buf = (char *) yysmiles_alloc(n ,yyscanner );
  ^
/builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmiles.cpp:326:7:
note: declared here
 void *yysmiles_alloc (yy_size_t  );
   ^
smiles.ll:69:45: error: too many arguments to function
'yy_buffer_state* yysmiles__scan_buffer(char*, yy_size_t)'
   b = yysmiles__scan_buffer(buf,n ,yyscanner);
 ^
/builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmiles.cpp:322:17:
note: declared here
 YY_BUFFER_STATE yysmiles__scan_buffer (char *base,yy_size_t size  );




-- 
Gianluca Sforna

http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
Tinker Garage - http://tinkergarage.it

--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-12 Thread Gianluca Sforna 
On Mon, Apr 11, 2016 at 1:20 PM, Greg Landrum  wrote:
> This could be the issue fixed by this PR from Matt Swain:
> https://github.com/rdkit/rdkit/pull/856

Yeah, that's it. Thanks!



-- 
Gianluca Sforna

http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
Tinker Garage - http://tinkergarage.it

--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-11 Thread Guillaume GODIN 
Dear All,


Thanks Greg!


Using your command compilation line (see bellow), It's the first time I can 
really test mutlithread rdkit on my mac.


"cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG 
-DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG 
-DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON 
-DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include 
-DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc 
-DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 
-DBUILD_SHARED_LIBS:BOOL=ON -DRDK_INSTALL_INTREE=OFF 
-DCMAKE_BUILD_TYPE=RelWithDebInfo -DRDK_BUILD_INCHI_SUPPORT:BOOL=ON 
-DRDK_BUILD_THREADSAFE_SSS:BOOL=ON -DRDK_BUILD_CAIRO_SUPPORT:BOOL=ON 
-DRDK_INSTALL_STATIC_LIBS:BOOL=OFF -DRDK_USE_FLEXBISON:BOOL=ON 
-DRDK_TEST_MULTITHREADED:BOOL=ON 
-DPYTHON_EXECUTABLE:FILEPATH=/Library/Frameworks/Python.framework/Versions/2.7/bin/python"


MacBook-Pro-de-MBP:Book mbp$ time python genconformersmutiltherads.py 
numthread=1


real 0m10.941s

user 0m10.869s

sys 0m0.059s

MacBook-Pro-de-MBP:Book mbp$ time python genconformersmutiltherads.py 
numthread=4


real 0m3.979s

user 0m11.638s

sys 0m0.106s



I will try to include this now into javascript version of RDKit and build 
WebAssembly instead of simple js file. Now emscripten / binaryen project should 
allows to compile C++ into webassembly which will be the standard of Chrome/ 
Firefox / Edge in the near future if you want to have faster time execution 
compare to current javascript codes.


best regards,

Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE   +41 (0)79 536 1039

Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8



De : Greg Landrum <greg.land...@gmail.com>
Envoyé : lundi 11 avril 2016 13:20
À : Gianluca Sforna
Cc : RDKit Discuss; RDKit Developers List
Objet : Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

Gianluca,

This could be the issue fixed by this PR from Matt Swain: 
https://github.com/rdkit/rdkit/pull/856

-greg


On Mon, Apr 11, 2016 at 12:32 PM, Gianluca Sforna 
<gia...@gmail.com<mailto:gia...@gmail.com>> wrote:
On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum 
<greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote:
> I have tagged a beta of the next RDKit release here:
> https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1


Tried to rebuild the RPMs but got this right on cmake:

-- Found INCHI: /usr/lib64/libinchi.so
CMake Error at External/INCHI-API/CMakeLists.txt:64 (install):
  install TARGETS given target "Inchi" which does not exist in this
  directory.


cmake invocation as follow:

/usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr
-DINCLUDE_INSTALL_DIR:PATH=/usr/include
-DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc
-DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64
-DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D
CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D
RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D
RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=ON -D
RDK_TEST_MULTITHREADED:BOOL=ON -D
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2 .

I'll dig in it later, in the meanwhile if you have ideas they will be
very welcome.
**  
DISCLAIMER  
This email and any files transmitted with it, including replies and forwarded 
copies (which may contain alterations) subsequently transmitted from Firmenich, 
are confidential and solely for the use of the intended recipient. The contents 
do not represent the opinion of Firmenich except to the extent that it relates 
to their official business.  
**--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-11 Thread Greg Landrum 
Gianluca,

This could be the issue fixed by this PR from Matt Swain:
https://github.com/rdkit/rdkit/pull/856

-greg


On Mon, Apr 11, 2016 at 12:32 PM, Gianluca Sforna  wrote:

> On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum 
> wrote:
> > I have tagged a beta of the next RDKit release here:
> > https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1
>
>
> Tried to rebuild the RPMs but got this right on cmake:
>
> -- Found INCHI: /usr/lib64/libinchi.so
> CMake Error at External/INCHI-API/CMakeLists.txt:64 (install):
>   install TARGETS given target "Inchi" which does not exist in this
>   directory.
>
>
> cmake invocation as follow:
>
> /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr
> -DINCLUDE_INSTALL_DIR:PATH=/usr/include
> -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc
> -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64
> -DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D
> CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D
> RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D
> RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=ON -D
> RDK_TEST_MULTITHREADED:BOOL=ON -D
> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2 .
>
> I'll dig in it later, in the meanwhile if you have ideas they will be
> very welcome.
>
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-11 Thread Gianluca Sforna 
On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum  wrote:
> I have tagged a beta of the next RDKit release here:
> https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1


Tried to rebuild the RPMs but got this right on cmake:

-- Found INCHI: /usr/lib64/libinchi.so
CMake Error at External/INCHI-API/CMakeLists.txt:64 (install):
  install TARGETS given target "Inchi" which does not exist in this
  directory.


cmake invocation as follow:

/usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr
-DINCLUDE_INSTALL_DIR:PATH=/usr/include
-DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc
-DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64
-DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D
CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D
RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D
RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=ON -D
RDK_TEST_MULTITHREADED:BOOL=ON -D
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2 .

I'll dig in it later, in the meanwhile if you have ideas they will be
very welcome.

--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss