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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Nov 22, 2011, at 9:28 AM, Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de> wrote: > Well, it seems that the python bundled with AMBER is not able to load > standard modules. > When I run on a console $AMBERHOME/AmberTools/bin/python ... I get lots > of import errors on different modules (e.g. readline, atexit and so on) > > I tried to set $PYTHONHOME to $AMBERHOME/AmberTools/lib/python2.6 but > this also did not fix the problems > > Best, > Vlad > > On 11/22/2011 03:00 PM, Vlad Cojocaru wrote: >> Hi Jason, >> >> Thank for your suggestion. I did that and now I see that python has >> problems to import the module datetime (see new errors below) ... At >> this point I don't completely understand whether AMBER is using the >> bundled python 2.6.6 or my system python 2.7.2 ... >> However, when I try in a separate window to import datetime on my system >> python, it works ... Well, no surprise here as this is a standard module ... >> >> Best, >> Vlad >> >> ./py_setup.sh >> Using AmberTools' python >> Could not find platform dependent libraries<exec_prefix> >> Consider setting $PYTHONHOME to<prefix>[:<exec_prefix>] >> Traceback (most recent call last): >> File "<string>", line 1, in<module> >> File "chemistry/amber/readparm.py", line 32, in<module> >> from datetime import datetime >> ImportError: No module named datetime >> Error importing cpinutil.py python modules! cpinutil will not work. >> make[1]: *** [python] Error 1 >> make[1]: Leaving directory >> `/usr/local/build-apps/amber/11-1.5/AmberTools/src/etc' >> make: *** [serial] Error 2 >> >> >> On 11/22/2011 01:20 PM, Jason Swails wrote: >>> This is indeed a strange error. Can you modify the py_setup.sh script and remove the redirects to /dev/null and rerun make install in that directory? Then post the resulting error messages here. >>> >>> The error output from the failed module imports is the only way I'd be able to diagnose what's happening. >>> >>> It's also possible that the bundled Python is not compiling properly. If this is the case, you should remove all of the amber Python parts (remove the whole bin and lib directories in AMBERHOME) and reconfigure with -nopython. >>> >>> -- >>> Jason Swails >>> Quantum Theory Project, >>> University of Florida >>> Ph.D. Candidate >>> 352-392-4032 >>> >>> On Nov 22, 2011, at 5:27 AM, Vlad Cojocaru<vlad.cojocaru.mpi-muenster.mpg.de> wrote: >>> >>>> Dear ambers, >>>> >>>> I recently updated the operating system to openSUSE 12.1 and I am >>>> recompiling AMBER 11 with AmberTools 1.5 ... >>>> I decided to do it from scratch with all new bugfixes (the tree is clean). >>>> >>>> After applying all bugfixes for AT (downloaded today), the compilation >>>> of AT fails with the error: >>>> ./py_setup.sh >>>> Using AmberTools' python >>>> Error importing cpinutil.py python modules! cpinutil will not work. >>>> make[1]: *** [python] Error 1 >>>> make[1]: Leaving directory >>>> `/usr/local/build-apps/amber/11-1.5/AmberTools/src/etc' >>>> make: *** [serial] Error 2 >>>> >>>> I searched the archive and it seemed that other people went through >>>> similar troubles ... however not exactly the same, as in those reported >>>> cases the error either did not come during the AT compilation (but >>>> rather after applying the python script before A11 compilation) or it >>>> was accompanied by other errors. The solution proposed to start with a >>>> clean tree does not apply to me as I did exactly that. >>>> >>>> Is there a known fix for this error? >>>> >>>> Architecture: x86_64 , AMD, gnu 4.6.2 (configure works just fine), >>>> python 2.7.2 >>>> >>>> Thank you >>>> >>>> Best wishes >>>> Vlad >>>> >>>> >>>> -- >>>> Dr. Vlad Cojocaru >>>> Max Planck Institute for Molecular Biomedicine >>>> Department of Cellular and Developmental Biology >>>> Roentgenstrasse 20 >>>> 48149 Muenster, Germany >>>> tel: +49-251-70365-324 >>>> fax: +49-251-70365-399 >>>> email: vlad.cojocaru[at]mpi-muenster.mpg.de >>>> >>>> >>>> >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> > > -- > Dr. Vlad Cojocaru > Max Planck Institute for Molecular Biomedicine > Department of Cellular and Developmental Biology > Roentgenstrasse 20 > 48149 Muenster, Germany > tel: +49-251-70365-324 > fax: +49-251-70365-399 > email: vlad.cojocaru[at]mpi-muenster.mpg.de > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Nov 22 2011 - 07:30:02 PST