Strange problem with non-root users

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Strange problem with non-root users

David García Aristegui
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 owned by
this user.

The users can do a babel -V, but not to perform conversions... any
ideas, please? with root user OB works like a charm.

Thank you in advanced!!! best regards




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Re: Strange problem with non-root users

Tim Vandermeersch
Hi,

On Tue, Mar 23, 2010 at 7:29 PM, David García Aristegui
<[hidden email]> 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 owned by
> this user.
>
> The users can do a babel -V, but not to perform conversions... any
> ideas, please? with root user OB works like a charm.

Does the root user or normal user have the BABEL_LIBDIR environment
variable set? Did you use some special install prefix (other than
/usr/local)?

> Thank you in advanced!!! best regards
>
>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Strange problem with non-root users

David García Aristegui
El mar, 23-03-2010 a las 20:03 +0100, Tim Vandermeersch escribió:
> BABEL_LIBDIR


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Re: Strange problem with non-root users

David García Aristegui
In reply to this post by Tim Vandermeersch
Hello, OB is installed on /usr/bin/babel /usr/local/bin/babel
The BABEL_LIBDIR is not set (for root or the others).

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 García Aristegui
> <[hidden email]> 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 owned
> by
> > this user.
> >
> > The users can do a babel -V, but not to perform conversions... any
> > ideas, please? with root user OB works like a charm.
>
> Does the root user or normal user have the BABEL_LIBDIR environment
> variable set? Did you use some special install prefix (other than
> /usr/local)?
>
> > Thank you in advanced!!! best regards
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Download Intel&#174; 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
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
>


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Re: Strange problem with non-root users

Tim Vandermeersch
On Tue, Mar 23, 2010 at 8:08 PM, David García Aristegui
<[hidden email]> 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 García Aristegui
>> <[hidden email]> 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 owned
>> by
>> > this user.
>> >
>> > The users can do a babel -V, but not to perform conversions... any
>> > ideas, please? with root user OB works like a charm.
>>
>> Does the root user or normal user have the BABEL_LIBDIR environment
>> variable set? Did you use some special install prefix (other than
>> /usr/local)?
>>
>> > Thank you in advanced!!! best regards
>> >
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Download Intel&#174; 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
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>>
>
>

------------------------------------------------------------------------------
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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.
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Re: Strange problem with non-root users

David García Aristegui
Same input file prop.smi (CCC), and in the examples of my user prop.smi
is owned by "aristegui"

With root:

root@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:

aristegui@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.

aristegui@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 García Aristegui
> <[hidden email]> 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 García Aristegui
> >> <[hidden email]> 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
> owned
> >> by
> >> > this user.
> >> >
> >> > The users can do a babel -V, but not to perform conversions...
> any
> >> > ideas, please? with root user OB works like a charm.
> >>
> >> Does the root user or normal user have the BABEL_LIBDIR environment
> >> variable set? Did you use some special install prefix (other than
> >> /usr/local)?
> >>
> >> > Thank you in advanced!!! best regards
> >> >
> >> >
> >> >
> >> >
> >> >
> >>
> ------------------------------------------------------------------------------
> >> > Download Intel&#174; 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
> >> > [hidden email]
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >> >
> >>
> >
> >
>


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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.
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Re: Strange problem with non-root users (reinstallation)

David García Aristegui
After a new OpenBabel 2.2.3 reinstallation i have the same problem...

aristegui@thema:/tmp/test_dir_2$ babel --gen3D -ismi prop.smi -osdf
prop2.sdf

babel: cannot read input format!
Open Babel 2.2.3 -- Mar 24 2010 -- 11:52:35
Usage: babel [-i<input-type>] <name> [-o<output-type>] <name>
Try  -H option for more information.

El mié, 24-03-2010 a las 10:24 +0100, David García Aristegui escribió:

> Same input file prop.smi (CCC), and in the examples of my user prop.smi
> is owned by "aristegui"
>
> With root:
>
> root@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:
>
> aristegui@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.
>
> aristegui@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 García Aristegui
> > <[hidden email]> 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 García Aristegui
> > >> <[hidden email]> 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
> > owned
> > >> by
> > >> > this user.
> > >> >
> > >> > The users can do a babel -V, but not to perform conversions...
> > any
> > >> > ideas, please? with root user OB works like a charm.
> > >>
> > >> Does the root user or normal user have the BABEL_LIBDIR environment
> > >> variable set? Did you use some special install prefix (other than
> > >> /usr/local)?
> > >>
> > >> > Thank you in advanced!!! best regards
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >>
> > ------------------------------------------------------------------------------
> > >> > Download Intel&#174; 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
> > >> > [hidden email]
> > >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> > >> >
> > >>
> > >
> > >
> >
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


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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
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Re: Strange problem with non-root users

Craig James-2
In reply to this post by David García Aristegui
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:
>
> root@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:
>
> aristegui@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.
>
> aristegui@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 García Aristegui
>> <[hidden email]>  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 García Aristegui
>>>> <[hidden email]>  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

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Re: Strange problem with non-root users

David García Aristegui
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:
> >
> > root@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:
> >
> > aristegui@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.
> >
> > aristegui@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 García Aristegui
> >> <[hidden email]>  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 García Aristegui
> >>>> <[hidden email]>  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
>


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Re: Strange problem with non-root users

Igor Filippov
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.

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:
> > >
> > > root@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:
> > >
> > > aristegui@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.
> > >
> > > aristegui@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 García Aristegui
> > >> <[hidden email]>  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 García Aristegui
> > >>>> <[hidden email]>  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&#174; 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss



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Re: Strange problem with non-root users

Tim Vandermeersch
On Wed, Mar 24, 2010 at 3:43 PM, Igor Filippov
<[hidden email]> 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:

tim@ubuntu:~/openbabel-2010/build$ ls -l /usr/local/lib/openbabel/
drwxr-xr-x 2 root root 4096 Mar 24 15:32 2.2.99
tim@ubuntu:~/openbabel-2010/build$ babel -H   # wroks fine
tim@ubuntu:~/openbabel-2010/build$ sudo chmod 744
/usr/local/lib/openbabel/2.2.99/
tim@ubuntu:~/openbabel-2010/build$ babel -H   # doesn't work
tim@ubuntu:~/openbabel-2010/build$ sudo chmod 755
/usr/local/lib/openbabel/2.2.99/
tim@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:
>> > >
>> > > root@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:
>> > >
>> > > aristegui@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.
>> > >
>> > > aristegui@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 García Aristegui
>> > >> <[hidden email]>  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 García Aristegui
>> > >>>> <[hidden email]>  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&#174; 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
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Strange problem with non-root users

David García Aristegui
In reply to this post by Igor Filippov
Is not a stupid question at all...

root@thema:/biodata2/software/openbabel-2.2.3# locate smilesformat.so

/biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.so
/biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.soT
/usr/local/lib/openbabel/2.2.3/smilesformat.so

--- The /biodata2/software/openbabel-2.2.3 directory is the installation
directory (no "other" permissions)

-rwxr-x--- 1 root root 918770 2010-03-24
12:47 /biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.so

--- And /usr/local/lib/openbabel is the installation itself and there
are the proper permissions for "others"

-rwxr-xr-x 1 root root 918770 2010-03-24
13:03 /usr/local/lib/openbabel/2.2.3/smilesformat.so


So, should i change the installation directory permissions and
reinstall? why the executable "babel" looks for this files instead of
the installed files on /usr/local/lib/openbabel/2.2.3 with "other"
permissions? am i missing something?

Thank you for your help!!!

El mié, 24-03-2010 a las 10:43 -0400, Igor Filippov escribió:

> 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.
>
> 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:
> > > >
> > > > root@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:
> > > >
> > > > aristegui@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.
> > > >
> > > > aristegui@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 García Aristegui
> > > >> <[hidden email]>  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 García Aristegui
> > > >>>> <[hidden email]>  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&#174; 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
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>


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Re: Strange problem with non-root users

Noel O'Boyle
Administrator
On 24 March 2010 07:56, David García Aristegui <[hidden email]> wrote:

> Is not a stupid question at all...
>
> root@thema:/biodata2/software/openbabel-2.2.3# locate smilesformat.so
>
> /biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.so
> /biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.soT
> /usr/local/lib/openbabel/2.2.3/smilesformat.so
>
> --- The /biodata2/software/openbabel-2.2.3 directory is the installation
> directory (no "other" permissions)
>
> -rwxr-x--- 1 root root 918770 2010-03-24
> 12:47 /biodata2/software/openbabel-2.2.3/src/formats/.libs/smilesformat.so
>
> --- And /usr/local/lib/openbabel is the installation itself and there
> are the proper permissions for "others"
>
> -rwxr-xr-x 1 root root 918770 2010-03-24
> 13:03 /usr/local/lib/openbabel/2.2.3/smilesformat.so
>
>
> So, should i change the installation directory permissions and
> reinstall?

Just chmod a+x the directory.

> why the executable "babel" looks for this files instead of
> the installed files on /usr/local/lib/openbabel/2.2.3 with "other"
> permissions? am i missing something?

Hi David,

In the past, I have found that many problems with permissions are due
to users who compile as root. I would recommend you just delete
everything related to openbabel, and then follow *exactly* the
instructions on our website. The *only* step that you should run as
root is "make install". Everything else should be done as a regular
user. If not, you will have lots of weird permissions problems.

- Noel

> Thank you for your help!!!
>
> El mié, 24-03-2010 a las 10:43 -0400, Igor Filippov escribió:
>> 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.
>>
>> 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:
>> > > >
>> > > > root@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:
>> > > >
>> > > > aristegui@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.
>> > > >
>> > > > aristegui@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 García Aristegui
>> > > >> <[hidden email]>  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 García Aristegui
>> > > >>>> <[hidden email]>  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&#174; 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
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; 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
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Strange problem with non-root users

user.name
Dear Babel User,
                     Recently i installed babel through yast (SuSe 11.3), however i got similar problem like the one posted in this thread before.

       When i give "sudo babel -H" it prints all the file formats

"....
The following file formats are recognized:
acr -- ACR format [Read-only]
..........
..........
zin -- ZINDO input format [Write-only]
See further specific info and options using -H<format-type>, e.g. -Hcml"

      However "babel -H" (non-root user mode) i don't get file formats, and hence could'nt able to convert files. Then i tried to login as root and execute the command "babel -H" i get similar output without all file formats.

      Only "sudo babel -H" results in proper verbose, although "sudo babel -ixxx input.xx -oyyy output.yyy
does work, and creates a empty file output.yyy

Thanks
Andri

         

 
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Re: Strange problem with non-root users

David García Aristegui
Check the directories permissions, this is was what happened to me (only
root permissions in the file definitions files).

Best regardas.

>
> Dear Babel User,
>                      Recently i installed babel through yast (SuSe 11.3),
> however i got similar problem like the one posted in this thread before.
>
>        When i give "sudo babel -H" it prints all the file formats
>
> "....
> The following file formats are recognized:
> acr -- ACR format [Read-only]
> ..........
> ..........
> zin -- ZINDO input format [Write-only]
> See further specific info and options using -H<format-type>, e.g. -Hcml"
>
>       However "babel -H" (non-root user mode) i don't get file formats,
> and
> hence could'nt able to convert files. Then i tried to login as root and
> execute the command "babel -H" i get similar output without all file
> formats.
>
>       Only "sudo babel -H" results in proper verbose, although "sudo babel
> -ixxx input.xx -oyyy output.yyy
> does work, and creates a empty file output.yyy
>
> Thanks
> Andri
>
>
>
>
> --
> View this message in context:
> http://open-babel.957263.n4.nabble.com/Strange-problem-with-non-root-users-tp1679525p2548280.html
> Sent from the openbabel-discuss mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>



------------------------------------------------------------------------------
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Re: Strange problem with non-root users

user.name
 Thanks for the hints
   
 For the purpose of archive, let me post what makes it to work, there was a conflict with BABEL_DATADIR and BABEL_LIBDIR assignment with earlier installation of "avogadro"

Thanks a lot

On 22 September 2010 12:21, <[hidden email]> wrote:
Check the directories permissions, this is was what happened to me (only
root permissions in the file definitions files).

Best regardas.

>
> Dear Babel User,
>                      Recently i installed babel through yast (SuSe 11.3),
> however i got similar problem like the one posted in this thread before.
>
>        When i give "sudo babel -H" it prints all the file formats
>
> "....
> The following file formats are recognized:
> acr -- ACR format [Read-only]
> ..........
> ..........
> zin -- ZINDO input format [Write-only]
> See further specific info and options using -H<format-type>, e.g. -Hcml"
>
>       However "babel -H" (non-root user mode) i don't get file formats,
> and
> hence could'nt able to convert files. Then i tried to login as root and
> execute the command "babel -H" i get similar output without all file
> formats.
>
>       Only "sudo babel -H" results in proper verbose, although "sudo babel
> -ixxx input.xx -oyyy output.yyy
> does work, and creates a empty file output.yyy
>
> Thanks
> Andri
>
>
>
>
> --
> View this message in context:
> http://open-babel.957263.n4.nabble.com/Strange-problem-with-non-root-users-tp1679525p2548280.html
> Sent from the openbabel-discuss mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>




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