JP and George - Excellent! I'm glad to hear my CentOS install walk-through is going to good use. 8^)
Greg - I'm reasonably sure that when I tried to build NumPy in the absence of the linear algebra libraries, I received an error and the build failed. Unfortunately, I didn't bother to try them one at a time to verify which was needed. I'll leave that as an exercise for the reader. 8^) I edited the Wiki stating that the libraries may or may not be necessary. Regarding repos necessary, I see that all but atlas can be found in the "base" repo, which I assume is the CentOS default. I'm puzzled as to why blas* and atlas* aren't there. I did put in a link to the epel repository RPM, which should cure the yum install problem for all linear algebra libraries. -Kirk On Wed, Feb 23, 2011 at 6:04 AM, George Papadatos <gpapada...@gmail.com>wrote: > Fair enough, I did not know that! However, according to the same > documentation, these packages are highly recommended for NumPy and required > for SciPy: > http://scipy.org/Installing_SciPy/Linux#head-9cf6f4b7fe9ba63fc228203c4f28554a74970847 > > > <http://scipy.org/Installing_SciPy/Linux#head-9cf6f4b7fe9ba63fc228203c4f28554a74970847>In > any case, here is a repository for CentOS 5/RHEL 5 with the necessary rpms > (for those who can't access yum): > http://download.opensuse.org/repositories/home:/ashigabou/ > <http://download.opensuse.org/repositories/home:/ashigabou/>After that, > Kirk's walk though has been most helpful. > > George > > > On 23 February 2011 11:12, Greg Landrum <greg.land...@gmail.com> wrote: > >> Let me elaborate on that... from the numpy installation page >> (http://docs.scipy.org/doc/numpy/user/install.html: >> "NumPy does not require any external linear algebra libraries to be >> installed. However, if these are available, NumPy’s setup script can >> detect them and use them for building. A number of different LAPACK >> library setups can be used, including optimized LAPACK libraries such >> as ATLAS, MKL or the Accelerate/vecLib framework on OS X." >> >> Best, >> -greg >> >> >> >> >> On Wed, Feb 23, 2011 at 12:10 PM, Greg Landrum <greg.land...@gmail.com> >> wrote: >> > I'm not convinced of that. I'm pretty sure that I have built numpy on >> > redhat and ubuntu systems without ever installing lapack. >> > >> > -greg >> > >> > >> > On Wed, Feb 23, 2011 at 12:06 PM, George Papadatos < >> gpapada...@gmail.com> wrote: >> >> ...yet you need them to build Numpy... >> >> George >> >> >> >> On 23 February 2011 11:03, Greg Landrum <greg.land...@gmail.com> >> wrote: >> >>> >> >>> To be very clear: you do not need *any* of these packages to install >> the >> >>> RDKit. >> >>> >> >>> -greg >> >>> >> >>> >> >>> On Wed, Feb 23, 2011 at 10:53 AM, JP <jeanpaul.ebe...@inhibox.com> >> wrote: >> >>> > Great wiki - I wonder how I missed that. >> >>> > But the first instruction >> >>> > sudo yum install atlas, atlas-devel, blas blas-devel lapack >> lapack-devel >> >>> > >> >>> > Gives me the following error: >> >>> > No package atlas, available. >> >>> > No package atlas-devel, available. >> >>> > No package blas available. >> >>> > No package lapack available. >> >>> > Is there a repos I have to add to /etc/yum.repos.d/ ? >> >>> > >> >>> > >> >>> > On 22 February 2011 18:41, Robert DeLisle <rkdeli...@gmail.com> >> wrote: >> >>> >> >> >>> >> What are your environment settings? You should have at minimum, >> these: >> >>> >> >> >>> >> $RDBASE = <the directory where you have installed the RDKit code> >> >>> >> >> >>> >> >> >>> >> $LD_LIBRARY_PATH = /usr/local/lib:/$RDBASE/lib >> >>> >> >> >>> >> $PYTHONPATH = $RDBASE >> >>> >> >> >>> >> >> >>> >> At least this worked for me for a CentOS installation, detailed >> here - >> >>> >> http://code.google.com/p/rdkit/wiki/BuildingOnCentOS >> >>> >> >> >>> >> >> >>> >> >> >>> >> Another possibility is your PATH variable. Make sure that >> /usr/local >> >>> >> pathnames precede any /usr options. >> >>> >> This will ensure looking into /usr/local first. >> >>> >> >> >>> >> There also may be options for cmake that will force it into the >> correct >> >>> >> directory. I've found in the past that even though >> >>> >> >> >>> >> >> >>> >> it says in the initial output that is looking in the correct >> location >> >>> >> for >> >>> >> boost and python, it doesn't necessarily follow its >> >>> >> own advice. >> >>> >> >> >>> >> -Kirk >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> On Tue, Feb 22, 2011 at 9:44 AM, JP <jeanpaul.ebe...@inhibox.com> >> >>> >> wrote: >> >>> >>> >> >>> >>> I ended up not using yum to install Numpy - I installed it from >> >>> >>> source, >> >>> >>> which was only slightly painful. >> >>> >>> >>> import platform; print platform.python_version() >> >>> >>> # /usr/local/lib/python2.7/platform.pyc matches >> >>> >>> /usr/local/lib/python2.7/platform.py >> >>> >>> import platform # precompiled from >> >>> >>> /usr/local/lib/python2.7/platform.pyc >> >>> >>> 2.7.0 >> >>> >>> >>> import numpy as N >> >>> >>> >>> a=N.random.randn(10, 10) >> >>> >>> >>> >> >>> >>> In /usr/lib64/ I can find some libpython2.4.so >> , libpython2.4.so.1.0 >> >>> >>> What should I do? >> >>> >>> >> >>> >>> On 22 February 2011 16:23, <rkdeli...@gmail.com> wrote: >> >>> >>>> >> >>> >>>> Are you sure that your NumPy installation is going to the correct >> >>> >>>> Python >> >>> >>>> instance? I see from the logs that you have Python 2.7 installed, >> or >> >>> >>>> at >> >>> >>>> least that is what cmake is finding at /usr/local/lib. You use >> yum to >> >>> >>>> install NumPy, but the standard installation of Python on CentOS >> 5.x >> >>> >>>> is 2.4 >> >>> >>>> and it is located in /usr/lib. Which version of Python has NumPy? >> >>> >>>> >> >>> >>>> >> >>> >>>> -Kirk >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> On Feb 22, 2011 9:14am, JP <jeanpaul.ebe...@inhibox.com> wrote: >> >>> >>>> > I've installed Atlas, Numpy, Boostand everything works fine >> until I >> >>> >>>> > try: >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > cmake .. -DBOOST_ROOT=/share/apps/boost_1_45_0/ >> >>> >>>> > sudo make VERBOSE=1 >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > At which point everything fails as follows:: >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > [ 3%] Building CXX object >> >>> >>>> > Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o >> >>> >>>> > >> >>> >>>> > cd /share/apps/RDKit_2010_12_1/build/Code/RDBoost && >> /usr/bin/c++ >> >>> >>>> > -DRDBoost_EXPORTS -O3 -DNDEBUG -fPIC >> -I/usr/local/include/python2.7 >> >>> >>>> > -I/usr/local/lib/python2.7/site-packages/numpy/core/include >> >>> >>>> > -I/share/apps/boost_1_45_0/include >> >>> >>>> > -I/share/apps/RDKit_2010_12_1/Code >> >>> >>>> > -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC >> -o >> >>> >>>> > CMakeFiles/RDBoost.dir/Wrap.cpp.o -c >> >>> >>>> > /share/apps/RDKit_2010_12_1/Code/RDBoost/Wrap.cpp >> >>> >>>> > >> >>> >>>> > Linking CXX shared library ../../lib/libRDBoost.so >> >>> >>>> > cd /share/apps/RDKit_2010_12_1/build/Code/RDBoost && >> >>> >>>> > /usr/local/bin/cmake -E cmake_link_script >> >>> >>>> > CMakeFiles/RDBoost.dir/link.txt >> >>> >>>> > --verbose=1 >> >>> >>>> > >> >>> >>>> > /usr/bin/c++ -fPIC -O3 -DNDEBUG -shared >> >>> >>>> > -Wl,-soname,libRDBoost.so.1 >> >>> >>>> > -o ../../lib/libRDBoost.so.1.2010.12.1 >> >>> >>>> > CMakeFiles/RDBoost.dir/Wrap.cpp.o >> >>> >>>> > -L/usr/local/lib/libpython2.7.a -L/share/apps/boost_1_45_0/lib >> >>> >>>> > /usr/local/lib/libpython2.7.a >> >>> >>>> > /share/apps/boost_1_45_0/lib/libboost_python.so >> >>> >>>> > >> >>> >>>> > >> -Wl,-rpath,/usr/local/lib/libpython2.7.a:/share/apps/boost_1_45_0/lib: >> >>> >>>> > >> >>> >>>> > /usr/bin/ld: /usr/local/lib/libpython2.7.a(exceptions.o): >> >>> >>>> > relocation >> >>> >>>> > R_X86_64_32 against `_Py_NoneStruct' can not be used when >> making a >> >>> >>>> > shared >> >>> >>>> > object; recompile with -fPIC >> >>> >>>> > >> >>> >>>> > /usr/local/lib/libpython2.7.a: could not read symbols: Bad >> value >> >>> >>>> > collect2: ld returned 1 exit status >> >>> >>>> > >> >>> >>>> > make[2]: *** [lib/libRDBoost.so.1.2010.12.1] Error 1 >> >>> >>>> > make[2]: Leaving directory `/share/apps/RDKit_2010_12_1/build' >> >>> >>>> > >> >>> >>>> > make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2 >> >>> >>>> > make[1]: Leaving directory `/share/apps/RDKit_2010_12_1/build' >> >>> >>>> > >> >>> >>>> > make: *** [all] Error 2 >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > Note that all env variables have been set: >> >>> >>>> > >> >>> >>>> > [jpebe@caio build]$ echo $LD_LIBRARY_PATH >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> /share/apps/boost_1_45_0/lib:/share/apps/openbabel-2.3.0/lib:/usr/lib64/atlas/sse2:/share/apps/RDKit_2010_12_1/lib:/opt/gridengine/lib/lx26-amd64 >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > Any ideas? I spent the whole day on this... >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > And its freaking me out... >> >>> >>>> > >> >>> >>> >> >>> >>> >> >>> >>> -- >> >>> >>> >> >>> >>> Jean-Paul Ebejer >> >>> >>> Early Stage Researcher >> >>> >>> InhibOx Ltd >> >>> >>> Pembroke House >> >>> >>> 36-37 Pembroke Street >> >>> >>> Oxford >> >>> >>> OX1 1BP >> >>> >>> UK >> >>> >>> (+44 / 0) 1865 262 034 >> >>> >>> >> >>> >>> >> >>> >>> This email and any files transmitted with it are confidential and >> >>> >>> intended solely for the use of the individual or entity to whom >> they >> >>> >>> are >> >>> >>> addressed. Any unauthorised dissemination or copying of this email >> or >> >>> >>> its >> >>> >>> attachments, and any use or disclosure of any information >> contained in >> >>> >>> them, >> >>> >>> is strictly prohibited and may be illegal. If you have received >> this >> >>> >>> email >> >>> >>> in error please notify the sender and delete all copies from your >> >>> >>> system. >> >>> >>> >> >>> >>> We and our group companies accept no liability or responsibility >> for >> >>> >>> personal emails or emails unconnected with our business. >> >>> >>> >> >>> >>> Internet communications including emails and access and use of web >> >>> >>> sites >> >>> >>> cannot be guaranteed to be secure or error free as information can >> be >> >>> >>> intercepted, corrupted, lost or arrive late. Furthermore, while we >> >>> >>> have >> >>> >>> taken steps to control the spread of viruses on our systems, we >> cannot >> >>> >>> guarantee that this email and any files transmitted with it are >> virus >> >>> >>> free. >> >>> >>> No liability is accepted for any errors, omissions, interceptions, >> >>> >>> corrupted >> >>> >>> mail, lost communications or late delivery arising as a result of >> >>> >>> receiving >> >>> >>> this message via the Internet or for any virus that may be >> contained >> >>> >>> in it. >> >>> >>> >> >>> >> >> >>> > >> >>> > >> >>> > >> >>> > -- >> >>> > >> >>> > Jean-Paul Ebejer >> >>> > Early Stage Researcher >> >>> > InhibOx Ltd >> >>> > Pembroke House >> >>> > 36-37 Pembroke Street >> >>> > Oxford >> >>> > OX1 1BP >> >>> > UK >> >>> > (+44 / 0) 1865 262 034 >> >>> > >> >>> > >> >>> > This email and any files transmitted with it are confidential and >> >>> > intended >> >>> > solely for the use of the individual or entity to whom they are >> >>> > addressed. >> >>> > Any unauthorised dissemination or copying of this email or its >> >>> > attachments, >> >>> > and any use or disclosure of any information contained in them, is >> >>> > strictly >> >>> > prohibited and may be illegal. If you have received this email in >> error >> >>> > please notify the sender and delete all copies from your system. >> >>> > >> >>> > We and our group companies accept no liability or responsibility for >> >>> > personal emails or emails unconnected with our business. >> >>> > >> >>> > Internet communications including emails and access and use of web >> sites >> >>> > cannot be guaranteed to be secure or error free as information can >> be >> >>> > intercepted, corrupted, lost or arrive late. Furthermore, while we >> have >> >>> > taken steps to control the spread of viruses on our systems, we >> cannot >> >>> > guarantee that this email and any files transmitted with it are >> virus >> >>> > free. >> >>> > No liability is accepted for any errors, omissions, interceptions, >> >>> > corrupted >> >>> > mail, lost communications or late delivery arising as a result of >> >>> > receiving >> >>> > this message via the Internet or for any virus that may be contained >> in >> >>> > it. >> >>> > >> >>> > >> >>> > >> >>> > >> ------------------------------------------------------------------------------ >> >>> > Free Software Download: Index, Search & Analyze Logs and other IT >> data >> >>> > in >> >>> > Real-Time with Splunk. Collect, index and harness all the fast >> moving IT >> >>> > data >> >>> > generated by your applications, servers and devices whether >> physical, >> >>> > virtual >> >>> > or in the cloud. Deliver compliance at lower cost and gain new >> business >> >>> > insights. http://p.sf.net/sfu/splunk-dev2dev >> >>> > _______________________________________________ >> >>> > Rdkit-discuss mailing list >> >>> > Rdkit-discuss@lists.sourceforge.net >> >>> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >>> > >> >>> > >> >>> >> >>> >> >>> >> ------------------------------------------------------------------------------ >> >>> Free Software Download: Index, Search & Analyze Logs and other IT data >> in >> >>> Real-Time with Splunk. Collect, index and harness all the fast moving >> IT >> >>> data >> >>> generated by your applications, servers and devices whether physical, >> >>> virtual >> >>> or in the cloud. Deliver compliance at lower cost and gain new >> business >> >>> insights. http://p.sf.net/sfu/splunk-dev2dev >> >>> _______________________________________________ >> >>> Rdkit-discuss mailing list >> >>> Rdkit-discuss@lists.sourceforge.net >> >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> >> >> >> >> >> -- >> >> Dr. George Papadatos >> >> >> >> >> > >> > > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
