> Group: http://groups.google.com/group/mdnalysis-discussion/topics

>    - Error during installation <#13ac9db3842e3614_group_thread_0> [2
>    Updates]

>   Error during installation<http://groups.google.com/group/mdnalysis-discussion/t/798859a8c6a1be1>

>    bipin singh <bipinel...@gmail.com> Nov 03 07:12AM -0700

>    Hi all,

>    I got the following error during the installation of the package.
>    Please
>    help me to rectify it:

>    --------------------------------------------------------------------------- ----------------------------------------------------------
>    Installed
>    /usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg
>    Processing dependencies for MDAnalysisTests==0.7.6
>    Searching for MDAnalysis==0.7.6
>    Reading http://pypi.python.org/simple/MDAnalysis/
>    Download error: [Errno 111] Connection refused -- Some packages may
>    not be
>    found!
>    Reading http://pypi.python.org/simple/MDAnalysis/
>    Download error: [Errno 111] Connection refused -- Some packages may
>    not be
>    found!
>    Couldn't find index page for 'MDAnalysis' (maybe misspelled?)
>    Scanning index of all packages (this may take a while)
>    Reading http://pypi.python.org/simple/
>    Download error: [Errno 111] Connection refused -- Some packages may
>    not be
>    found!
>    No local packages or download links found for MDAnalysis==0.7.6
>    error: Could not find suitable distribution for
>    Requirement.parse('MDAnalysis==0.7.6')

>    --------------------------------------------------------------------------- ------------------------------------------------

>    Thanks and Regards
>    Bipin Singh

>    "Sébastien Buchoux" <sebastien.buch...@gmail.com> Nov 03 08:59AM -0700

>    Hi,

>    On Saturday, November 3, 2012 3:12:10 PM UTC+1, bipin singh wrote:
>    > error: Could not find suitable distribution for
>    > Requirement.parse('MDAnalysis==0.7.6')

>    --------------------------------------------------------------------------- ------------------------------------------------

>    What command did you run to get this error?

>    I just tried the "easy_install" command without any problem.

>    Séb

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> >import MDAnalysis
> >import MDAnalysis.analysis.contacts
> >C = MDAnalysis.analysis.contacts.ContactAnalysis('md.gro','traj.xtc')

> which resulted in segmentation fault. Am I doing this in correct way or I have to provide the PSF/DCD format of topology and trajectory respectively ?

> Group: http://groups.google.com/group/mdnalysis-discussion/topics

>    - Digest for mdnalysis-discussion@googlegroups.com - 2 Messages in 1
>    Topic <#13ad42ce3c46b355_group_thread_0> [2 Updates]

>   Digest for mdnalysis-discussion@googlegroups.com - 2 Messages in 1 Topic<http://groups.google.com/group/mdnalysis-discussion/t/ce2453551f249df9>

>    bipin singh <bipinel...@gmail.com> Nov 05 11:37AM +0530

>    Thanks Sebastian for your reply.
>    I was able to install the MDAnalysis package after installing some
>    dependencies required for it.
>    Now I am trying to use Native contact module of this program as
>    follows, at
>    the python interpreter:

>    >import MDAnalysis
>    >import MDAnalysis.analysis.contacts
>    >C = MDAnalysis.analysis.contacts.ContactAnalysis('md.gro','traj.xtc')

>    which resulted in segmentation fault. Am I doing this in correct way
>    or I
>    have to provide the PSF/DCD format of topology and trajectory
>    respectively ?

>    On Sun, Nov 4, 2012 at 10:48 AM, <mdnalysis-discussion@googlegroups.com
>    >wrote:

>    --
>    -----------------------
>    *Regards,*
>    Bipin Singh

>    Oliver Beckstein <orbec...@gmail.com> Nov 05 09:53AM -0700

>    Hi,

>    On 4 Nov, 2012, at 23:07, bipin singh wrote:

>    > >import MDAnalysis.analysis.contacts
>    > >C =
>    MDAnalysis.analysis.contacts.ContactAnalysis('md.gro','traj.xtc')

>    > which resulted in segmentation fault. Am I doing this in correct way
>    or I have to provide the PSF/DCD format of topology and trajectory
>    respectively ?

>    Segmentation fault is bad.

>    Can you do the following in python:

>    import MDAnalysis
>    u = MDAnalysis.Universe('md.gro','traj.xtc')
>    print u

>    If this works then also install the test cases and run all the unit
>    tests as described at
>    https://code.google.com/p/mdanalysis/wiki/UnitTests

>    import MDAnalysis.tests
>    MDAnalysis.tests.test(label="full")

>    Let us know the results.

>    Oliver

>    --
>    Oliver Beckstein * orbec...@gmx.net
>    skype: orbeckst * orbec...@gmail.com

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>  >import MDAnalysis
>  >u = MDAnalysis.Universe('md.gro','traj.xtc')

> But again it resulted in segmentation fault.

> On 5 Nov, 2012, at 22:38, bipin singh wrote:

> > Thank you Sir, for your reply.
> > I followed your suggestion and used the following commands:

> >  >import MDAnalysis
> >  >u = MDAnalysis.Universe('md.gro','traj.xtc')

> > But again it resulted in segmentation fault.

> This looks like a problem with incompatible libraries.

> You'll need to tell us exactly

> - your operating system
> - your version of the gcc compiler (gcc -V)
> - your version of Python, NumPy, SciPy

> Download the tar file from
> https://code.google.com/p/mdanalysis/downloads/detail?name=MDAnalysis... and build

> tar zxvf MDAnalysis-0.7.6.tar.gz
> cd MDAnalysis-0.7.6
> python setup.py build

> Send the whole output from the 'build' process. For me this looks like
> (with most of it omitted as '...') like this:

> $ python setup.py build
> running build
> running build_py
> creating build
> creating build/lib.macosx-10.6-universal-2.6
> creating build/lib.macosx-10.6-universal-2.6/MDAnalysis
> ...
> gcc-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -arch i386 -arch ppc
> -arch x86_64
> build/temp.macosx-10.6-universal-2.6/src/xdrfile/libxdrfile_wrap.o
> build/temp.macosx-10.6-universal-2.6/src/xdrfile/xdrfile.o
> build/temp.macosx-10.6-universal-2.6/src/xdrfile/xdrfile_trr.o
> build/temp.macosx-10.6-universal-2.6/src/xdrfile/xdrfile_xtc.o -o
> build/lib.macosx-10.6-universal-2.6/MDAnalysis/coordinates/xdrfile/_libxdrf ile.so

> On the mailing list there was one other instance of segfault, which was
> fixed by reinstalling numpy and scipy:

> https://groups.google.com/forum/#!searchin/mdnalysis-discussion/segme...

> But until we have some better idea where the problem lies I cannot say
> much more.

> Oliver

> --
> Oliver Beckstein * orbec...@gmx.net
> skype: orbeckst  * orbec...@gmail.com

> Operating system:Ubuntu 10.10
> gcc compiler version: 4.4.5
> Python version: 2.6.6
> Numpy version: 1:1.3.0-3build1
> Scipy version: 0.7.2-2ubuntu1

> Thank you for your help. I am mentioning below the information you asked to
> provide.

> *Operating system*:Ubuntu 10.10

>> *Operating system*:Ubuntu 10.10

>> Hello Sir,

>> Thank you for your help. I am mentioning below the information you asked
>> to
>> provide.

>> *Operating system*:Ubuntu 10.10

> Ubuntu 10.10 (Codename Maverick Meerkat) is not supported since last April
> (See: https://wiki.ubuntu.com/**Releases<https://wiki.ubuntu.com/Releases>).
> I would suggest you upgrade your system to Ubuntu 12.04 LTS (Codename
> Precise Pangolin, the latest "Long Time Support" version) or Ubuntu 12.10
> (Codename Quantic Quetzal, the lastest version)

>  *gcc compiler version*: 4.4.5
>> *Python version*: 2.6.6
>> *Numpy version*: 1:1.3.0-3build1
>> *Scipy version*: 0.7.2-2ubuntu1

> As mentioned by Oliver, this setup should be OK.

>  I will try to send the detail output of the build process ASAP.

> Yes, this output will be useful to solve your problem and/or a potential
> bug.

> Séb

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> On 6 Nov, 2012, at 21:43, bipin singh wrote:

> > Please find below the output from the build process, using the command
> > >python setup.py build

> At first glance I don't see anything weird.

> Have you tried the Ubuntu packages?

> Otherwise the next step is to run the debugger as described under
> https://code.google.com/p/mdanalysis/wiki/QuestionsAndAnswers#Why_do_...
> so that we find out where the seg fault occurs.

> Oliver

> --
> Oliver Beckstein * orbec...@gmx.net
> skype: orbeckst  * orbec...@gmail.com

> On 7 Nov, 2012, at 10:06, bipin singh wrote:

> > I was trying the Ubuntu packages but they require some more recent
> versions of python (>= 2.7.1-0ubuntu2) and has some other dependency
> requirements.

> You might be able to install python2.7 in additon to 2.6 but Séb knows
> more about that.

> > In the mean time I tried the debugger as suggested by you. But all the
> program exited normally without any seg. fault. I am appending the output
> got by running the debugger:

> > #######################################################################
> > (gdb) run -c "import MDAnalysis; print MDAnalysis.__version__"
> > Starting program: /usr/bin/python -c "import MDAnalysis; print
> MDAnalysis.__version__"
> > [Thread debugging using libthread_db enabled]
> > 0.7.6

> > Program exited normally.
> > (gdb) run -c "import MDAnalysis; print MDAnalysis.Universe"
> > Starting program: /usr/bin/python -c "import MDAnalysis; print
> MDAnalysis.Universe"
> > [Thread debugging using libthread_db enabled]
> > <class 'MDAnalysis.core.AtomGroup.Universe'>

> > Program exited normally.

> ##########################################################################

> Ok, that's a good first step, great that you got that working. The very
> basics seem to be working.

> Now try

> (gdb) run -c "import MDAnalysis; print MDAnalysis.Universe('system.pdb',
> 'traj.xtc')"

> where you're loading the pdb and xtc file from your original example. What
> does it show?

> Oliver

> --
> Oliver Beckstein * orbec...@gmx.net
> skype: orbeckst  * orbec...@gmail.com

> On 7 Nov, 2012, at 11:01, bipin singh wrote:

> > I am appending the output got by running the suggested command on my
> .xtc trajectory:

> ########################################################################### ###############
> > (gdb) run -c "import MDAnalysis; print MDAnalysis.Universe('md.pdb',
> 'traj.xtc')"
> > Starting program: /usr/bin/python -c "import MDAnalysis; print
> MDAnalysis.Universe('b4md.pdb', 'sixb_rerun_widvelfromnpt_md450_nopbc.xtc')"
> > [Thread debugging using libthread_db enabled]

> > Program received signal SIGSEGV, Segmentation fault.
> > 0x0127274b in xdrfile_write_int (ptr=0xbfffde9c, ndata=1, xfp=0x0) at
> src/xdrfile/xdrfile.c:258
> > 258        while(i<ndata && xdr_int((XDR *)(xfp->xdr),ptr+i))
> > (gdb)

> ########################################################################### ###############

> That shows us the problem: the file pointer xfp for the trajectory is a
> NULL pointer and when trying NULL->xdr we get a seg fault. I haven't seen
> this one before.

> And I have no idea why.

> First, let's see if this is specific to your trajectory:

> Please install the MDAnalysis test cases (see
> https://code.google.com/p/mdanalysis/wiki/UnitTests ) and

> 1. run specific tests

> from MDAnalysis.tests.datafiles import PSF, DCD, GRO, XTC, TRR

> print MDAnalysis.Universe(PSF, DCD)
> print MDAnalysis.Universe(GRO, XTC)
> print MDAnalysis.Universe(GRO, TRR)

> 2. run the whole test suite

> import MDAnalysis.tests
> MDAnalysis.tests.test(label="full")

> Which tests fail?

> Oliver

> --
> Oliver Beckstein * orbec...@gmx.net
> skype: orbeckst  * orbec...@gmail.com

> On Wed, Nov 7, 2012 at 11:49 PM, Oliver Beckstein <orbec...@gmail.com>wrote:

>> On 7 Nov, 2012, at 11:01, bipin singh wrote:

>> > I am appending the output got by running the suggested command on my
>> .xtc trajectory:

>> ########################################################################### ###############
>> > (gdb) run -c "import MDAnalysis; print MDAnalysis.Universe('md.pdb',
>> 'traj.xtc')"
>> > Starting program: /usr/bin/python -c "import MDAnalysis; print
>> MDAnalysis.Universe('b4md.pdb', 'sixb_rerun_widvelfromnpt_md450_nopbc.xtc')"
>> > [Thread debugging using libthread_db enabled]

>> > Program received signal SIGSEGV, Segmentation fault.
>> > 0x0127274b in xdrfile_write_int (ptr=0xbfffde9c, ndata=1, xfp=0x0) at
>> src/xdrfile/xdrfile.c:258
>> > 258        while(i<ndata && xdr_int((XDR *)(xfp->xdr),ptr+i))
>> > (gdb)

>> ########################################################################### ###############

>> That shows us the problem: the file pointer xfp for the trajectory is a
>> NULL pointer and when trying NULL->xdr we get a seg fault. I haven't seen
>> this one before.

>> And I have no idea why.

>> First, let's see if this is specific to your trajectory:

>> Please install the MDAnalysis test cases (see
>> https://code.google.com/p/mdanalysis/wiki/UnitTests ) and

>> 1. run specific tests

>> from MDAnalysis.tests.datafiles import PSF, DCD, GRO, XTC, TRR

>> print MDAnalysis.Universe(PSF, DCD)
>> print MDAnalysis.Universe(GRO, XTC)
>> print MDAnalysis.Universe(GRO, TRR)

>> 2. run the whole test suite

>> import MDAnalysis.tests
>> MDAnalysis.tests.test(label="full")

>> Which tests fail?

>> Oliver

>> --
>> Oliver Beckstein * orbec...@gmx.net
>> skype: orbeckst  * orbec...@gmail.com

> --
> -----------------------
> *Regards,*
> Bipin Singh

> On 7 Nov, 2012, at 22:08, bipin singh wrote:

> > Just for your information. I want to convey that, I have tried six
> different trajectories(.xtc) and the same error occurred in every case, so
> I think the error is not specific to a particular trajectory.

> And:

> > I am appending the output got by running test cases:

> ########################################################################### #
> > >>> from MDAnalysis.tests.datafiles import PSF, DCD, GRO, XTC, TRR
> > >>> print MDAnalysis.Universe(PSF, DCD)
> > <Universe with 3341 atoms>
> > >>> print MDAnalysis.Universe(GRO, XTC)
> > <Universe with 47681 atoms>
> > >>> print MDAnalysis.Universe(GRO, TRR)
> > <Universe with 47681 atoms>

> This shows that the standard test directories work.

> 1. How did you create your xtcs?
> 2. Which version of Gromacs?
> 3. What does 'gmxcheck -f your.xtc' produce?

> If 3. does not show any errrors then:

> 4. Can you produce a short XTC that fails (only 3 frames) and send it
>  just to me (orbec...@gmail.com) together with the PDB file? I'll need to
> reproduce the problem here.

> > >>> import MDAnalysis.tests
> > >>> MDAnalysis.tests.test(label="full")

> Ah, sorry, it seems you need to run

> >>> MDAnalysis.tests.test(label="full", extra_argv=["--exe"])

> > Running unit tests for numpy
> > NumPy version 1.3.0
> > NumPy is installed in /usr/lib/python2.6/dist-packages/numpy
> > Python version 2.6.6 (r266:84292, Sep 15 2010, 15:52:39) [GCC 4.4.5]
> > nose version 0.11.1

> > ----------------------------------------------------------------------
> > Ran 0 tests in 0.015s

> Should really produce ~500 tests and take ~6 mins. But that should work
> with the --exe flag.

> Oliver

> --
> Oliver Beckstein * orbec...@gmx.net
> skype: orbeckst  * orbec...@gmail.com