Thread: [Rdkit-devel] Compiling RDKit on CentOS 5.3 x64
Open-Source Cheminformatics and Machine Learning
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From: Adrian S. <am...@ca...> - 2009-10-15 18:40:03
Attachments:
rdkit.out
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Hi Greg, I tried to compile RDKit on CentOS 5.3 64 bit but for one target I get a cryptic error. The bjam output is attached. Any suggestions? Adrian ---- gcc -v Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) |
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From: Greg L. <gre...@gm...> - 2009-10-16 04:23:38
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Hi Adrian, The problem below should be solvable by adding a compile flag. Please try adding: <toolset>gcc:<cflags>-DBOOST_PYTHON_NO_PY_SIGNATURES to $RDBASE/Code/Jamroot There's some information here: https://sourceforge.net/mailarchive/message.php?msg_name=60825b0f0901152045i20eff2p427119822d8c2518%40mail.gmail.com Best regards, -greg On Thu, Oct 15, 2009 at 8:39 PM, Adrian Schreyer <am...@ca...> wrote: > Hi Greg, > > I tried to compile RDKit on CentOS 5.3 64 bit but for one target I get > a cryptic error. The bjam output is attached. Any suggestions? > > Adrian > > ---- > gcc -v > Using built-in specs. > Target: x86_64-redhat-linux > Configured with: ../configure --prefix=/usr --mandir=/usr/share/man > --infodir=/usr/share/info --enable-shared --enable-threads=posix > --enable-checking=release --with-system-zlib --enable-__cxa_atexit > --disable-libunwind-exceptions --enable-libgcj-multifile > --enable-languages=c,c++,objc,obj-c++,java,fortran,ada > --enable-java-awt=gtk --disable-dssi --enable-plugin > --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre > --with-cpu=generic --host=x86_64-redhat-linux > Thread model: posix > gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) > |
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From: Adrian S. <am...@ca...> - 2009-10-16 08:15:57
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Thanks, that worked. Maybe you can add this to the WorkingBuild wiki page. Here are the results from the benchmark on my machine (Intel i7 920 / CentOS 5.3 x64 (on vmware with 2 cores and 2gb memory) / g++ 4.1.2-44)) : times: 1.3 || 0.8 || 0.4 || 1.9 || 2.1 || 0.0 || 5.9 || 6.0 || 0.4 || 0.6 || 15.4 || 0.5 || 7.5 Adrian On Fri, Oct 16, 2009 at 05:23, Greg Landrum <gre...@gm...> wrote: > Hi Adrian, > > The problem below should be solvable by adding a compile flag. > Please try adding: > <toolset>gcc:<cflags>-DBOOST_PYTHON_NO_PY_SIGNATURES > to $RDBASE/Code/Jamroot > > There's some information here: > https://sourceforge.net/mailarchive/message.php?msg_name=60825b0f0901152045i20eff2p427119822d8c2518%40mail.gmail.com > > Best regards, > -greg > > On Thu, Oct 15, 2009 at 8:39 PM, Adrian Schreyer <am...@ca...> wrote: >> Hi Greg, >> >> I tried to compile RDKit on CentOS 5.3 64 bit but for one target I get >> a cryptic error. The bjam output is attached. Any suggestions? >> >> Adrian >> >> ---- >> gcc -v >> Using built-in specs. >> Target: x86_64-redhat-linux >> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man >> --infodir=/usr/share/info --enable-shared --enable-threads=posix >> --enable-checking=release --with-system-zlib --enable-__cxa_atexit >> --disable-libunwind-exceptions --enable-libgcj-multifile >> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada >> --enable-java-awt=gtk --disable-dssi --enable-plugin >> --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre >> --with-cpu=generic --host=x86_64-redhat-linux >> Thread model: posix >> gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) >> > |
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From: Greg L. <gre...@gm...> - 2009-10-16 09:02:44
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Hi Adrian, Thanks for the update. I saw the comment on the benchmarks page and updated that already, I'll put the information in the working build page as well. Thanks again, -greg On Fri, Oct 16, 2009 at 10:15 AM, Adrian Schreyer <am...@ca...> wrote: > Thanks, that worked. Maybe you can add this to the WorkingBuild wiki page. > > Here are the results from the benchmark on my machine (Intel i7 920 / > CentOS 5.3 x64 (on vmware with 2 cores and 2gb memory) / g++ > 4.1.2-44)) : > > times: 1.3 || 0.8 || 0.4 || 1.9 || 2.1 || 0.0 || 5.9 || 6.0 || 0.4 || > 0.6 || 15.4 || 0.5 || 7.5 > |
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From: Adrian S. <am...@ca...> - 2009-10-16 09:19:37
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I should have mentioned that I used boost_1_39_0, not the latest version. In addition, boost.jam is not available through yum and has to be compiled manually. On Fri, Oct 16, 2009 at 10:02, Greg Landrum <gre...@gm...> wrote: > Hi Adrian, > > Thanks for the update. I saw the comment on the benchmarks page and > updated that already, I'll put the information in the working build > page as well. > > Thanks again, > -greg > > On Fri, Oct 16, 2009 at 10:15 AM, Adrian Schreyer <am...@ca...> wrote: >> Thanks, that worked. Maybe you can add this to the WorkingBuild wiki page. >> >> Here are the results from the benchmark on my machine (Intel i7 920 / >> CentOS 5.3 x64 (on vmware with 2 cores and 2gb memory) / g++ >> 4.1.2-44)) : >> >> times: 1.3 || 0.8 || 0.4 || 1.9 || 2.1 || 0.0 || 5.9 || 6.0 || 0.4 || >> 0.6 || 15.4 || 0.5 || 7.5 >> > |