Re: [Rdkit-discuss] ImportError: No module named rdkit
Greg Landrum writes: > On Fri, Sep 15, 2017 at 1:37 PM, Loris Bennett > wrote: > > When I did > > make test > > some of the tests failed: > > 61% tests passed, 46 tests failed out of 117 > > but most of the failures seemed to have been caused by > > ImportError: No module named rdkit > > Yeah, this is because you'd need to also setup the RDBASE, PYTHONPATH, > and LD_LIBRARY_PATH variables for the account that's running ctest. I think that is already correctly set up. If I look at the first error: Command: "/opt/rh/python27/root/usr/bin/python" "/home/BUILD/rdkit/rdkit-Release_2017_03_3/Code/DataStructs/Wrap/testBV.py" Directory: /home/BUILD/rdkit/rdkit-Release_2017_03_3/build/Code/DataStructs/Wrap "pyBV" start time: Sep 15 12:55 CEST Output: -- Traceback (most recent call last): File "/home/BUILD/rdkit/rdkit-Release_2017_03_3/Code/DataStructs/Wrap/testBV.py", line 1, in from rdkit import DataStructs ImportError: No module named rdkit I can run this test directly and it succeeds: $ /opt/rh/python27/root/usr/bin/python /home/BUILD/rdkit/rdkit-Release_2017_03_3/Code/DataStructs/Wrap/testBV.py . -- Ran 13 tests in 0.545s OK So, strangely, it sort of looks as if part of the environment is being overwritten when I run 'make test'. However, I may have to leave this for the time-being. I'm sure the users will let me know if something is still broken. [snip (7 lines)] > If you have some time next Wed./Thurs. you should swing by the UGM > during one of the breaks and say hi. :-) Thanks, will do. Cheers, Loris -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On Fri, Sep 15, 2017 at 1:37 PM, Loris Bennett wrote: > > When I did > > make test > > some of the tests failed: > > 61% tests passed, 46 tests failed out of 117 > > but most of the failures seemed to have been caused by > > ImportError: No module named rdkit > Yeah, this is because you'd need to also setup the RDBASE, PYTHONPATH, and LD_LIBRARY_PATH variables for the account that's running ctest. > However, if I set up the user environment (we use modules: > http://modules.sourceforge.net/), I can import 'rdkit' without any > problem, so there must just be something I need to tweak before running > the tests. Thus, apart from the outstanding 46 tests, I think I'm done. > > Excellent. I'm glad to hear it. I hope things end up working now for your users. If you have some time next Wed./Thurs. you should swing by the UGM during one of the breaks and say hi. :-) -greg -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
Hi Greg, Greg Landrum writes: > One thing that may help is this (somewhat older, but I believe still > accurate) post from Riccardo: > https://sourceforge.net/p/rdkit/mailman/message/30074971/ > > It's been a while since I looked at this (since I mainly use conda these > days), but I just did a quick experiment with: > > mkdir build > cd build > cmake -DCMAKE_INSTALL_PREFIX=/opt/rdkit_test -DRDK_INSTALL_INTREE=OFF .. > > followed by > > make install > > and that seems to have worked. > > This type of install behaves somewhat differently from what the > documentation describes. It arranges the files in the PREFIX directory > like "normal" software is arranged. So as a user I need to set my > PYTHONPATH like this: > > export PYTHONPATH=/opt/rdkit_test/lib/python3.5/site-packages > and modify LD_LIBRARY_PATH to include: /opt/rdkit_test/lib > RDBASE is: > export RDBASE=/opt/rdkit_test/share/RDKit > > This is not documented in any useful way, which is something that we > ought to change. OK, I think I have got things mostly working. The -DRDK_INSTALL_INTREE=OFF seems to have been the main thing I was missing. Additionally I had to add some environment variables by hand that cmake didn't pickup on, presumably because due to my having multiple versions of Python installed. This is what I did: export VERSION=2017_03_3 export RDBASE=/home/BUILD/rdkit/rdkit-Release_${VERSION} export LD_LIBRARY_PATH=${RDBASE}:${LD_LIBRARY_PATH} source /cm/shared/apps/python27/enable export PYTHON_ROOT=/opt/rh/python27/root export CMAKE_INSTALL_PREFIX=/cm/shared/apps/rdkit/${VERSION} export PYTHON_INCLUDE_DIR=${PYTHON_ROOT}/usr/include/python2.7 export PYTHON_LIBRARY=${PYTHON_ROOT}/usr/lib64/libpython2.7.so export PYTHON_NUMPY_INCLUDE_PATH=${PYTHON_ROOT}/usr/lib64/python2.7/site-packages/numpy/core/include cmake -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} \ -DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIR} \ -DPYTHON_LIBRARY=${PYTHON_LIBRARY} \ -DPYTHON_NUMPY_INCLUDE_PATH=${PYTHON_NUMPY_INCLUDE_PATH} \ -DRDK_INSTALL_INTREE=OFF \ .. make make install When I did make test some of the tests failed: 61% tests passed, 46 tests failed out of 117 but most of the failures seemed to have been caused by ImportError: No module named rdkit However, if I set up the user environment (we use modules: http://modules.sourceforge.net/), I can import 'rdkit' without any problem, so there must just be something I need to tweak before running the tests. Thus, apart from the outstanding 46 tests, I think I'm done. Thanks for the help, Loris -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
One thing that may help is this (somewhat older, but I believe still accurate) post from Riccardo: https://sourceforge.net/p/rdkit/mailman/message/30074971/ It's been a while since I looked at this (since I mainly use conda these days), but I just did a quick experiment with: mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX=/opt/rdkit_test -DRDK_INSTALL_INTREE=OFF .. followed by make install and that seems to have worked. This type of install behaves somewhat differently from what the documentation describes. It arranges the files in the PREFIX directory like "normal" software is arranged. So as a user I need to set my PYTHONPATH like this: export PYTHONPATH=/opt/rdkit_test/lib/python3.5/site-packages and modify LD_LIBRARY_PATH to include: /opt/rdkit_test/lib RDBASE is: export RDBASE=/opt/rdkit_test/share/RDKit This is not documented in any useful way, which is something that we ought to change. -greg On Fri, Sep 15, 2017 at 8:19 AM, Loris Bennett wrote: > > > import rdkit > > > > I get > > > > ImportError: No module named rdkit > > > > I am not a Python person and my naive expectation was that there should > > be a file called > > > > rdkit.py > > > > Based on the info provided so far, there should be a directory called > > rdkit in the directory: /cm/shared/apps/rdkit/rdkit_2017_03_3 > > This directory exists. > > > That directory should contain a number of sub dirs, other files, and a > > file called __init__.py (this is the one that tells Python that it can > > import the directory as a package). What do you see there? > > The directory just contains > > lib > rdkit > > an nothing else, in particular, no __init__.py. I have plenty of > __init__.pys in the build directory, so I assume I must have done some > thing wrong when running cmake and/or make install. > I must admit that I found the installation instructions somewhat unclear > on that point. I would find it clearer if things were couched in terms > of 'source' and 'destination'. For me, as a make-guy rather than a > cmake-guy, it would also be helpful if it were made clearer at which > point the destination directory should be specified. I ended up with > RDKit being installed under a very long path with included both my > intended path and the original build path, so I had to move things > around and may have goofed up at that point. > > > which has to be on my PYTHONPATH. However, since the unpacked sources > > together with the build don't seem to contain such a file, either > > something is broken or the rdkit module should be found by some other > > mechanism. > > > > Again, based on the info above, I would expect that you want "make > > install" to copy the "rdkit" and "lib" directories (as well as a > > couple others) to /cm/shared/apps/rdkit/rdkit_2017_03_3. Once we > > figure out what actually happened I can maybe help you figure out how > > to fix it. > > This is what I did: > > module add boost # this just sets the boost stuff up > > export VERSION=2017_03_3 > export RDBASE=/home/BUILD/rdkit/rdkit-rdkit-Release_${VERSION} > export LD_LIBRARY_PATH=${RDBASE}:${LD_LIBRARY_PATH} > export DESTDIR=/cm/shared/apps/rdkit/${VERSION} > > and then probably > > cmake -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/rdkit/${VERSION} > > so I may have over-egged my install-path-cake. I started all the > fiddling with DESTDIR and CMAKE_INSTALL_PREFIX, because my initial > attempt resulted in the destination directory being the same as the > build directory, which didn't work so well. > > Thanks for the help - I'll have another go Python 3.5 and try to keep my > eye on __init__.py. > > Cheers, > > Loris > > -- > Dr. Loris Bennett (Mr.) > ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On Fri, Sep 15, 2017 at 9:12 AM, Loris Bennett wrote: > > Greg Landrum writes: > > > I'll provide a more detailed answer in a bit, but since you aren't > > using the system python anyway, is there any chance that you could > > switch to anaconda python on your machines? Anaconda is a great python > > distribution for scientific applications and it makes many things > > (including system administration) a ton easier. > > Anaconda might be a possibility. On the other hand we already have 3 > versions of Python in use: 2.6 from the OS, and 2.7 and 3.5 from the > Software Collections. In addition, the current cluster is nearing its > end-of-life, probably before the end of the year and so I am somewhat > loathe to install yet another one and add to my can of worms (or pit of > snakes). > Got it. I figured I'd ask anyway. As you're thinking about/planning the new cluster, it's really worth taking a look at using the anaconda distribution to provide Python. > However, now I have a slight handle on the problem and know that there > is a responsive and helpful mailing list to back me up, I'm happy to > invest a little more time in trying another source build. A glutton for punishment! ;-) -greg -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
Well, if you have python 2.7 and 3.5 already running ,you can use (mini)conda for the RDKit installation (conda is anaconda but instead of one huge package you can install the packages you want including RDKit) On Fri, Sep 15, 2017 at 9:12 AM, Loris Bennett wrote: > Hi Greg, > > Greg Landrum writes: > > > I'll provide a more detailed answer in a bit, but since you aren't > > using the system python anyway, is there any chance that you could > > switch to anaconda python on your machines? Anaconda is a great python > > distribution for scientific applications and it makes many things > > (including system administration) a ton easier. > > Anaconda might be a possibility. On the other hand we already have 3 > versions of Python in use: 2.6 from the OS, and 2.7 and 3.5 from the > Software Collections. In addition, the current cluster is nearing its > end-of-life, probably before the end of the year and so I am somewhat > loathe to install yet another one and add to my can of worms (or pit of > snakes). > > However, now I have a slight handle on the problem and know that there > is a responsive and helpful mailing list to back me up, I'm happy to > invest a little more time in trying another source build. > > Cheers, > > Loris > > -- > Dr. Loris Bennett (Mr.) > ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
Hi Greg, Greg Landrum writes: > I'll provide a more detailed answer in a bit, but since you aren't > using the system python anyway, is there any chance that you could > switch to anaconda python on your machines? Anaconda is a great python > distribution for scientific applications and it makes many things > (including system administration) a ton easier. Anaconda might be a possibility. On the other hand we already have 3 versions of Python in use: 2.6 from the OS, and 2.7 and 3.5 from the Software Collections. In addition, the current cluster is nearing its end-of-life, probably before the end of the year and so I am somewhat loathe to install yet another one and add to my can of worms (or pit of snakes). However, now I have a slight handle on the problem and know that there is a responsive and helpful mailing list to back me up, I'm happy to invest a little more time in trying another source build. Cheers, Loris -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
BTW, python 3.6 is out since last Christmas ;-) (and made it to sub-release .2) On Fri, Sep 15, 2017 at 8:36 AM, Greg Landrum wrote: > I'll provide a more detailed answer in a bit, but since you aren't using > the system python anyway, is there any chance that you could switch to > anaconda python on your machines? Anaconda is a great python distribution > for scientific applications and it makes many things (including system > administration) a ton easier. > > -greg > > > On Fri, Sep 15, 2017 at 8:19 AM, Loris Bennett > wrote: > >> Hi Greg, >> >> Greg Landrum writes: >> >> > Hi Loris, >> > >> > On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett < >> loris.benn...@fu-berlin.de> wrote: >> > >> > I am trying to install RDKit on a university cluster running Linux from >> > source. The build seem to go OK and 'make install' copied the >> > directories >> > >> > lib >> > rdkit >> > >> > to the NFS share where the software should reside. I then do >> > >> > export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3 >> > export PYTHONPATH=$PYTHONPATH:$RDBASE >> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib >> > >> > However when I then run Python (2.6.6) and try >> > >> > Just to do some expectation management: python 2.6 is pretty ancient >> > and there's no guarantee that all of the RDKit code will work with >> > it. Python 2.7 is the minimum version that we "officially" >> > support. It's a very good idea to update. >> >> OK. I didn't notice that 2.6 was deprecated - maybe this could be >> explicitly mentioned in the install instructions. I'm running the >> RedHat clone Scientific Linux 6, so everything in this thread on >> RH/Python applies. So I can use either Python 2.7 or Python 3.5. I can >> ask the users what they prefer - although, as you seem know my users >> here in Berlin, maybe you know too ;-) >> >> > import rdkit >> > >> > I get >> > >> > ImportError: No module named rdkit >> > >> > I am not a Python person and my naive expectation was that there should >> > be a file called >> > >> > rdkit.py >> > >> > Based on the info provided so far, there should be a directory called >> > rdkit in the directory: /cm/shared/apps/rdkit/rdkit_2017_03_3 >> >> This directory exists. >> >> > That directory should contain a number of sub dirs, other files, and a >> > file called __init__.py (this is the one that tells Python that it can >> > import the directory as a package). What do you see there? >> >> The directory just contains >> >> lib >> rdkit >> >> an nothing else, in particular, no __init__.py. I have plenty of >> __init__.pys in the build directory, so I assume I must have done some >> thing wrong when running cmake and/or make install. >> >> I must admit that I found the installation instructions somewhat unclear >> on that point. I would find it clearer if things were couched in terms >> of 'source' and 'destination'. For me, as a make-guy rather than a >> cmake-guy, it would also be helpful if it were made clearer at which >> point the destination directory should be specified. I ended up with >> RDKit being installed under a very long path with included both my >> intended path and the original build path, so I had to move things >> around and may have goofed up at that point. >> >> > which has to be on my PYTHONPATH. However, since the unpacked sources >> > together with the build don't seem to contain such a file, either >> > something is broken or the rdkit module should be found by some other >> > mechanism. >> > >> > Again, based on the info above, I would expect that you want "make >> > install" to copy the "rdkit" and "lib" directories (as well as a >> > couple others) to /cm/shared/apps/rdkit/rdkit_2017_03_3. Once we >> > figure out what actually happened I can maybe help you figure out how >> > to fix it. >> >> This is what I did: >> >> module add boost # this just sets the boost stuff up >> >> export VERSION=2017_03_3 >> export RDBASE=/home/BUILD/rdkit/rdkit-rdkit-Release_${VERSION} >> export LD_LIBRARY_PATH=${RDBASE}:${LD_LIBRARY_PATH} >> export DESTDIR=/cm/shared/apps/rdkit/${VERSION} >> >> and then probably >> >> cmake -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/rdkit/${VERSION} >> >> so I may have over-egged my install-path-cake. I started all the >> fiddling with DESTDIR and CMAKE_INSTALL_PREFIX, because my initial >> attempt resulted in the destination directory being the same as the >> build directory, which didn't work so well. >> >> Thanks for the help - I'll have another go Python 3.5 and try to keep my >> eye on __init__.py. >> >> Cheers, >> >> Loris >> >> -- >> Dr. Loris Bennett (Mr.) >> ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de >> > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-disc
Re: [Rdkit-discuss] ImportError: No module named rdkit
I'll provide a more detailed answer in a bit, but since you aren't using the system python anyway, is there any chance that you could switch to anaconda python on your machines? Anaconda is a great python distribution for scientific applications and it makes many things (including system administration) a ton easier. -greg On Fri, Sep 15, 2017 at 8:19 AM, Loris Bennett wrote: > Hi Greg, > > Greg Landrum writes: > > > Hi Loris, > > > > On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett < > loris.benn...@fu-berlin.de> wrote: > > > > I am trying to install RDKit on a university cluster running Linux from > > source. The build seem to go OK and 'make install' copied the > > directories > > > > lib > > rdkit > > > > to the NFS share where the software should reside. I then do > > > > export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3 > > export PYTHONPATH=$PYTHONPATH:$RDBASE > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib > > > > However when I then run Python (2.6.6) and try > > > > Just to do some expectation management: python 2.6 is pretty ancient > > and there's no guarantee that all of the RDKit code will work with > > it. Python 2.7 is the minimum version that we "officially" > > support. It's a very good idea to update. > > OK. I didn't notice that 2.6 was deprecated - maybe this could be > explicitly mentioned in the install instructions. I'm running the > RedHat clone Scientific Linux 6, so everything in this thread on > RH/Python applies. So I can use either Python 2.7 or Python 3.5. I can > ask the users what they prefer - although, as you seem know my users > here in Berlin, maybe you know too ;-) > > > import rdkit > > > > I get > > > > ImportError: No module named rdkit > > > > I am not a Python person and my naive expectation was that there should > > be a file called > > > > rdkit.py > > > > Based on the info provided so far, there should be a directory called > > rdkit in the directory: /cm/shared/apps/rdkit/rdkit_2017_03_3 > > This directory exists. > > > That directory should contain a number of sub dirs, other files, and a > > file called __init__.py (this is the one that tells Python that it can > > import the directory as a package). What do you see there? > > The directory just contains > > lib > rdkit > > an nothing else, in particular, no __init__.py. I have plenty of > __init__.pys in the build directory, so I assume I must have done some > thing wrong when running cmake and/or make install. > > I must admit that I found the installation instructions somewhat unclear > on that point. I would find it clearer if things were couched in terms > of 'source' and 'destination'. For me, as a make-guy rather than a > cmake-guy, it would also be helpful if it were made clearer at which > point the destination directory should be specified. I ended up with > RDKit being installed under a very long path with included both my > intended path and the original build path, so I had to move things > around and may have goofed up at that point. > > > which has to be on my PYTHONPATH. However, since the unpacked sources > > together with the build don't seem to contain such a file, either > > something is broken or the rdkit module should be found by some other > > mechanism. > > > > Again, based on the info above, I would expect that you want "make > > install" to copy the "rdkit" and "lib" directories (as well as a > > couple others) to /cm/shared/apps/rdkit/rdkit_2017_03_3. Once we > > figure out what actually happened I can maybe help you figure out how > > to fix it. > > This is what I did: > > module add boost # this just sets the boost stuff up > > export VERSION=2017_03_3 > export RDBASE=/home/BUILD/rdkit/rdkit-rdkit-Release_${VERSION} > export LD_LIBRARY_PATH=${RDBASE}:${LD_LIBRARY_PATH} > export DESTDIR=/cm/shared/apps/rdkit/${VERSION} > > and then probably > > cmake -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/rdkit/${VERSION} > > so I may have over-egged my install-path-cake. I started all the > fiddling with DESTDIR and CMAKE_INSTALL_PREFIX, because my initial > attempt resulted in the destination directory being the same as the > build directory, which didn't work so well. > > Thanks for the help - I'll have another go Python 3.5 and try to keep my > eye on __init__.py. > > Cheers, > > Loris > > -- > Dr. Loris Bennett (Mr.) > ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
Hi Greg, Greg Landrum writes: > Hi Loris, > > On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett > wrote: > > I am trying to install RDKit on a university cluster running Linux from > source. The build seem to go OK and 'make install' copied the > directories > > lib > rdkit > > to the NFS share where the software should reside. I then do > > export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3 > export PYTHONPATH=$PYTHONPATH:$RDBASE > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib > > However when I then run Python (2.6.6) and try > > Just to do some expectation management: python 2.6 is pretty ancient > and there's no guarantee that all of the RDKit code will work with > it. Python 2.7 is the minimum version that we "officially" > support. It's a very good idea to update. OK. I didn't notice that 2.6 was deprecated - maybe this could be explicitly mentioned in the install instructions. I'm running the RedHat clone Scientific Linux 6, so everything in this thread on RH/Python applies. So I can use either Python 2.7 or Python 3.5. I can ask the users what they prefer - although, as you seem know my users here in Berlin, maybe you know too ;-) > import rdkit > > I get > > ImportError: No module named rdkit > > I am not a Python person and my naive expectation was that there should > be a file called > > rdkit.py > > Based on the info provided so far, there should be a directory called > rdkit in the directory: /cm/shared/apps/rdkit/rdkit_2017_03_3 This directory exists. > That directory should contain a number of sub dirs, other files, and a > file called __init__.py (this is the one that tells Python that it can > import the directory as a package). What do you see there? The directory just contains lib rdkit an nothing else, in particular, no __init__.py. I have plenty of __init__.pys in the build directory, so I assume I must have done some thing wrong when running cmake and/or make install. I must admit that I found the installation instructions somewhat unclear on that point. I would find it clearer if things were couched in terms of 'source' and 'destination'. For me, as a make-guy rather than a cmake-guy, it would also be helpful if it were made clearer at which point the destination directory should be specified. I ended up with RDKit being installed under a very long path with included both my intended path and the original build path, so I had to move things around and may have goofed up at that point. > which has to be on my PYTHONPATH. However, since the unpacked sources > together with the build don't seem to contain such a file, either > something is broken or the rdkit module should be found by some other > mechanism. > > Again, based on the info above, I would expect that you want "make > install" to copy the "rdkit" and "lib" directories (as well as a > couple others) to /cm/shared/apps/rdkit/rdkit_2017_03_3. Once we > figure out what actually happened I can maybe help you figure out how > to fix it. This is what I did: module add boost # this just sets the boost stuff up export VERSION=2017_03_3 export RDBASE=/home/BUILD/rdkit/rdkit-rdkit-Release_${VERSION} export LD_LIBRARY_PATH=${RDBASE}:${LD_LIBRARY_PATH} export DESTDIR=/cm/shared/apps/rdkit/${VERSION} and then probably cmake -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/rdkit/${VERSION} so I may have over-egged my install-path-cake. I started all the fiddling with DESTDIR and CMAKE_INSTALL_PREFIX, because my initial attempt resulted in the destination directory being the same as the build directory, which didn't work so well. Thanks for the help - I'll have another go Python 3.5 and try to keep my eye on __init__.py. Cheers, Loris -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On Thu, Sep 14, 2017 at 9:58 PM, Andrew Dalke wrote: > On Sep 14, 2017, at 19:26, Dimitri Maziuk wrote: > > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > > linux distros that will be officially with us until June 30, 2024. > > If only Greg got as much money for long term RDKit support as Red Hat > gets for long term RHEL support. :) > I like the way Andrew thinks! :-) -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On 09/14/2017 03:04 PM, Markus Sitzmann wrote: > Not on Centos 6 - Docker requires Centos 7 for the host system. You can't win... :( -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
Not on Centos 6 - Docker requires Centos 7 for the host system. On Thu, Sep 14, 2017 at 10:01 PM, Dimitri Maziuk wrote: > On 09/14/2017 02:58 PM, Andrew Dalke wrote: > > > If only Greg got as much money for long term RDKit support as Red Hat > > gets for long term RHEL support. :) > > Yep. But an rdkit docker container might be feasible. > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On 09/14/2017 02:58 PM, Andrew Dalke wrote: > If only Greg got as much money for long term RDKit support as Red Hat > gets for long term RHEL support. :) Yep. But an rdkit docker container might be feasible. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On Sep 14, 2017, at 19:26, Dimitri Maziuk wrote: > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > linux distros that will be officially with us until June 30, 2024. If only Greg got as much money for long term RDKit support as Red Hat gets for long term RHEL support. :) Andrew da...@dalkescientific.com -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On Thu, Sep 14, 2017 at 9:07 PM, Dimitri Maziuk wrote: > > All great when it's one computer and that one's your own personal laptop. > > > # yum ls \*python27\* > > ... > > python27.x86_642.7.13-2.ius.el6 > @salt-2015.8 > > [...]... > > Any guesses as to how many things will break in my infrastructure > manglement setup (saltstack) if I enable Software Collections and some > of those get updated from SCL and some: from Salt? > sorry, I'm not familiar with saltstack, so I am unable to comment much. as far as I understood, the RH software collection packages are meant to be installed in parallel to the system software without overwriting any RHEL package (it's not just an extension repository, users need to enable the SCL packages to make them available in the runtime environment, similarly to how virtualenvs are activated or environment modules are added), I don't know how the saltstack packages are designed to work, so the discussion would quickly go further off-topic (but I seem to understand it provides yet another alternative to the system python, or not?) -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On Thu, Sep 14, 2017 at 7:26 PM, Dimitri Maziuk wrote: > On 09/14/2017 10:43 AM, Greg Landrum wrote: > > > Just to do some expectation management: python 2.6 is pretty ancient and > > there's no guarantee that all of the RDKit code will work with it. Python > > 2.7 is the minimum version that we "officially" support. It's a very good > > idea to update. > > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > linux distros that will be officially with us until June 30, 2024. Yep, but it's not supported by the python community (and hasn't been since 2013). Newer versions of the RDKit no longer require backwards compatibility with python 2.6. If you are stuck with an old version of Python, you may well be stuck with an old version of the RDKit. -greg -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On 09/14/2017 01:41 PM, Riccardo Vianello wrote: > True, but there shouldn't be any strong need for using the system python > for running application software. Python 2.7 (together with python 3) has > been available to RHEL6 subscribers since almost five years, as part of the > Red Hat Software Collections (also available to non-subscribers from the > upstream CentOS/Fedora repositories). A detailed discussion is available > from this post > http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html > > And the anaconda python distribution of course provides another alternative. All great when it's one computer and that one's your own personal laptop. > # yum ls \*python27\* > ... > python27.x86_642.7.13-2.ius.el6 > @salt-2015.8 > python27-babel.noarch 0.9.4-5.2.el6 > @salt-2015.8 > python27-chardet.noarch2.2.1-3.el6 > @salt-2015.8 > python27-crypto.x86_64 2.6.1-4.el6 > @salt-2015.8 > python27-futures.noarch3.0.3-2.el6 > @salt-2015.8 > python27-jinja2.noarch 2.8.1-2.el6 > @salt-2015.8 > python27-libs.x86_64 2.7.13-2.ius.el6 > @salt-2015.8 > python27-markupsafe.x86_64 0.11-11.el6 > @salt-2015.8 > python27-msgpack.x86_640.4.6-2.el6 > @salt-2015.8 > python27-psutil.x86_64 5.2.2-1.ius.el6 > @salt-2015.8 > python27-pycurl.x86_64 7.19.0-10.el6 > @salt-2015.8 > python27-requests.noarch 2.6.0-4.el6 > @salt-2015.8 > python27-six.noarch1.9.0-3.el6 > @salt-2015.8 > python27-tornado.x86_644.2.1-3.el6 > @salt-2015.8 > python27-urllib3.noarch1.10.2-2.el6 > @salt-2015.8 > python27-zmq.x86_6414.5.0-3.el6 > @salt-2015.8 ... > python27-babel.noarch 0.9.6-7.sc1.el6 > centos-sclo-rh > python27-pip.noarch9.0.1-1.ius.el6 > salt-2015.8 ... > python27-python.x86_64 2.7.13-3.el6 > centos-sclo-rh > python27-python-babel.noarch 0.9.6-7.sc1.el6 > centos-sclo-rh > python27-python-jinja2.noarch 2.6-10.sc1.el6 > centos-sclo-rh > python27-python-libs.x86_642.7.13-3.el6 > centos-sclo-rh > python27-python-markupsafe.x86_64 0.11-11.sc1.el6 > centos-sclo-rh > python27-python-pip.noarch 8.1.2-1.el6 > centos-sclo-rh ... Any guesses as to how many things will break in my infrastructure manglement setup (saltstack) if I enable Software Collections and some of those get updated from SCL and some: from Salt? And don't get me started on PIP. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On Thu, Sep 14, 2017 at 7:26 PM, Dimitri Maziuk wrote: > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > linux distros that will be officially with us until June 30, 2024. > True, but there shouldn't be any strong need for using the system python for running application software. Python 2.7 (together with python 3) has been available to RHEL6 subscribers since almost five years, as part of the Red Hat Software Collections (also available to non-subscribers from the upstream CentOS/Fedora repositories). A detailed discussion is available from this post http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html And the anaconda python distribution of course provides another alternative. --Riccardo -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
On 09/14/2017 10:43 AM, Greg Landrum wrote: > Just to do some expectation management: python 2.6 is pretty ancient and > there's no guarantee that all of the RDKit code will work with it. Python > 2.7 is the minimum version that we "officially" support. It's a very good > idea to update. Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of linux distros that will be officially with us until June 30, 2024. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] ImportError: No module named rdkit
Hi Loris, On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett wrote: > > I am trying to install RDKit on a university cluster running Linux from > source. The build seem to go OK and 'make install' copied the > directories > > lib > rdkit > > to the NFS share where the software should reside. I then do > > export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3 > export PYTHONPATH=$PYTHONPATH:$RDBASE > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib > > However when I then run Python (2.6.6) and try > Just to do some expectation management: python 2.6 is pretty ancient and there's no guarantee that all of the RDKit code will work with it. Python 2.7 is the minimum version that we "officially" support. It's a very good idea to update. > import rdkit > > I get > > ImportError: No module named rdkit > > I am not a Python person and my naive expectation was that there should > be a file called > > rdkit.py > Based on the info provided so far, there should be a directory called rdkit in the directory: /cm/shared/apps/rdkit/rdkit_2017_03_3 That directory should contain a number of sub dirs, other files, and a file called __init__.py (this is the one that tells Python that it can import the directory as a package). What do you see there? > which has to be on my PYTHONPATH. However, since the unpacked sources > together with the build don't seem to contain such a file, either > something is broken or the rdkit module should be found by some other > mechanism. > Again, based on the info above, I would expect that you want "make install" to copy the "rdkit" and "lib" directories (as well as a couple others) to /cm/shared/apps/rdkit/rdkit_2017_03_3. Once we figure out what actually happened I can maybe help you figure out how to fix it. best. -greg > Any ideas what I'm doing wrong or what initialisation file I should > ensure is on my PYTHONPATH? > > Cheers, > > Loris > > -- > Dr. Loris Bennett (Mr.) > ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] ImportError: No module named rdkit
Hi, I am trying to install RDKit on a university cluster running Linux from source. The build seem to go OK and 'make install' copied the directories lib rdkit to the NFS share where the software should reside. I then do export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3 export PYTHONPATH=$PYTHONPATH:$RDBASE export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib However when I then run Python (2.6.6) and try import rdkit I get ImportError: No module named rdkit I am not a Python person and my naive expectation was that there should be a file called rdkit.py which has to be on my PYTHONPATH. However, since the unpacked sources together with the build don't seem to contain such a file, either something is broken or the rdkit module should be found by some other mechanism. Any ideas what I'm doing wrong or what initialisation file I should ensure is on my PYTHONPATH? Cheers, Loris -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss