On Wed, Mar 24, 2010 at 3:43 PM, Igor Filippov <igor.v.filip...@gmail.com> wrote: > Sorry for a stupid question - is the directory with all the format > shared libs readable by a non-root user? > Check where you have smilesformat.so for example.
Do you get similar results when doing this: t...@ubuntu:~/openbabel-2010/build$ ls -l /usr/local/lib/openbabel/ drwxr-xr-x 2 root root 4096 Mar 24 15:32 2.2.99 t...@ubuntu:~/openbabel-2010/build$ babel -H # wroks fine t...@ubuntu:~/openbabel-2010/build$ sudo chmod 744 /usr/local/lib/openbabel/2.2.99/ t...@ubuntu:~/openbabel-2010/build$ babel -H # doesn't work t...@ubuntu:~/openbabel-2010/build$ sudo chmod 755 /usr/local/lib/openbabel/2.2.99/ t...@ubuntu:~/openbabel-2010/build$ babel -H # wroks fine > Igor > > > On Wed, 2010-03-24 at 10:35 -0400, David García Aristegui wrote: >> Working with a fresh OpenBabel 2.2.3 installation... There are no >> diferences related with BABEL* variables, they are not defined. PATH: i >> "force" to run the same executable (there is one babel installation at >> this time), and i retrieve different outputs with different users. >> >> A problem detected: with a non-root user, i retrieve a "formats is not a >> recognized plugin type" with babel -H command >> >> --- --- ---With a non-root user, >> >> /usr/local/bin/babel -H >> Open Babel converts chemical structures from one file format to another >> >> Usage: babel <input spec> <output spec> [Options] >> Conversion options >> -f <#> Start import at molecule # specified >> -l <#> End import at molecule # specified >> -e Continue with next object after error, if possible >> -z Compress the output with gzip >> -k Attempt to translate keywords >> -H Outputs this help text >> -Hxxx (xxx is file format ID e.g. -Hcml) gives format info >> -Hall Outputs details of all formats >> -V Outputs version number >> -L <BaseType> Lists plugin classes of this type >> e.g. <fingerprints>, or <plugins> for a list of BaseTypes >> -m Produces multiple output files, to allow: >> Splitting: e.g. babel infile.mol new.smi -m >> puts each molecule into new1.smi new2.smi etc >> Batch conversion: e.g. babel *.mol -osmi -m >> converts each input file to a .smi file >> The following file formats are recognized: >> >> formats is not a recognized plugin type [<= HERE HERE HERE] >> >> Those with instances of sub-types loaded are: >> descriptors >> fingerprints >> forcefields >> loaders >> ops >> >> See further specific info and options using -H<format-type>, e.g. -Hcml >> >> >> El mié, 24-03-2010 a las 07:09 -0700, Craig A. James escribió: >> > On 3/24/10 2:24 AM, David García Aristegui wrote: >> > > Same input file prop.smi (CCC), and in the examples of my user >> > prop.smi >> > > is owned by "aristegui" >> > > >> > > With root: >> > > >> > > r...@thema:/tmp/test_dir_1# babel --gen3D -ismi prop.smi -osdf >> > prop.sdf >> > > 1 molecule converted >> > > 1 info messages 55 audit log messages 1 debugging messages >> > > >> > > and a proper prop.sdf with 3D coordinates is generated >> > > >> > > With my user: >> > > >> > > ariste...@thema:/tmp/test_dir_2$ /usr/bin/babel --gen3D -ismi >> > prop.smi >> > > -osdf prop.sdf >> > > >> > > babel: cannot read input format! >> > > Open Babel 2.2.0 -- Jul 17 2008 -- 11:53:19 >> > > Usage: babel [-i<input-type>]<name> [-o<output-type>]<name> >> > > Try -H option for more information. >> > > >> > > ariste...@thema:/tmp/test_dir_2$ /usr/local/bin/babel --gen3D -ismi >> > > prop.smi -osdf prop.sdf >> > > >> > > babel: cannot read input format! >> > > Open Babel 2.2.3 -- Jan 18 2010 -- 13:11:01 >> > > Usage: babel [-i<input-type>]<name> [-o<output-type>]<name> >> > > Try -H option for more information. >> > > >> > > babel: cannot read input format! >> > > Open Babel 2.2.0 -- Jul 17 2008 -- 11:53:19 >> > > Usage: babel [-i<input-type>]<name> [-o<output-type>]<name> >> > > Try -H option for more information. >> > > >> > > Thank you for your help!!! >> > > >> > > El mar, 23-03-2010 a las 20:39 +0100, Tim Vandermeersch escribió: >> > >> On Tue, Mar 23, 2010 at 8:08 PM, David GarcÃa Aristegui >> > >> <ariste...@cbm.uam.es> wrote: >> > >>> Hello, OB is installed on /usr/bin/babel /usr/local/bin/babel >> > >>> The BABEL_LIBDIR is not set (for root or the others). >> > >> >> > >> Sorry for all the questions, but it's hard to guess what's wrong... >> > >> >> > >> Do you have two versions of OB installed? >> > >> Does "/usr/bin/babel -H" produce the same results as >> > >> "/usr/local/bin/babel -H"? >> > >> Does /usr/local/bin versus /usr/bin have the same priority for >> > user& >> > >> root? (i.e. are they in the same order in PATH env. var.) >> > >> >> > >>> Best regards. >> > >>> >> > >>> El mar, 23-03-2010 a las 20:03 +0100, Tim Vandermeersch escribió: >> > >>>> Hi, >> > >>>> >> > >>>> On Tue, Mar 23, 2010 at 7:29 PM, David GarcÃa Aristegui >> > >>>> <ariste...@cbm.uam.es> wrote: >> > >>>>> Hello, i have a strange problem with non-root users and >> > >> OpenBabel, >> > >>>> and >> > >>>>> tested with two different versions of the program: >> > >>>>> >> > >>>>> Open Babel 2.2.3 -- Jan 18 2010 >> > >>>>> Open Babel 2.2.0 -- Jul 17 2008 >> > >>>>> >> > >>>>> OB is installed in a PC with Ubuntu 8x (Hardy Neron) >> > >>>>> Linux 2.6.27-14-server (the root account is activated). >> > >>>>> >> > >>>>> My problem: with non-root users i always retrieve an >> > >>>>> "babel: cannot read input format!" error, even if the file is >> > >> > As root, then a regular user, type: >> > >> > env | sort >> > >> > and look for differences. The environment variables of interest are >> > >> > BABEL_* (any variable with BABEL_ prefix) >> > LD_LIBRARY_PATH >> > PATH >> > >> > Or alternatively, look for these same variables in your >> > shell-initialization scripts (.cshrc for csh, .bash_profile >> > and .bash_rc for bash, but I don't remember which one Cygwin uses). >> > >> > Craig >> > >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
