Re: [mdnalysis-discussion] Digest for mdnalysis-discussion@googlegroups.com - 2 Messages in 1 Topic
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bipin singh
Nov 5, 2012, 1:07:52 AM11/5/12
to mdnalysis-...@googlegroups.com
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 ?
--
-----------------------
Regards,
Bipin Singh
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-...@googlegroups.com> wrote:
Group: http://groups.google.com/group/mdnalysis-discussion/topics
- Error during installation [2 Updates]
bipin singh <bipin...@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" <sebastie...@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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--
-----------------------
Regards,
Bipin Singh
Oliver Beckstein
Nov 5, 2012, 11:53:03 AM11/5/12
to mdnalysis-...@googlegroups.com
Hi,
On 4 Nov, 2012, at 23:07, bipin singh wrote:
> 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 ?
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 * orbe...@gmx.net
skype: orbeckst * orbe...@gmail.com
On 4 Nov, 2012, at 23:07, bipin singh wrote:
> 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 ?
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 * orbe...@gmx.net
skype: orbeckst * orbe...@gmail.com
bipin singh
Nov 6, 2012, 12:38:46 AM11/6/12
to mdnalysis-...@googlegroups.com, orbe...@gmail.com
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.
I followed your suggestion and used the following commands:
>import MDAnalysis
>u = MDAnalysis.Universe('md.gro','traj.xtc')
On Tue, Nov 6, 2012 at 10:54 AM, <mdnalysis-...@googlegroups.com> wrote:
bipin singh <bipin...@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-...@googlegroups.com>wrote:
--
-----------------------
*Regards,*
Bipin Singh
Oliver Beckstein <orbe...@gmail.com> Nov 05 09:53AM -0700
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Oliver Beckstein
Nov 6, 2012, 12:09:47 PM11/6/12
to mdnalysis-...@googlegroups.com, bipin singh
Hi Bipin Singh,
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-0.7.6.tar.gz unpack 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/_libxdrfile.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/segmentation$20fault/mdnalysis-discussion/52Npnr2M2GE/cK7KWXRUNEgJ
But until we have some better idea where the problem lies I cannot say much more.
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.
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-0.7.6.tar.gz unpack 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/_libxdrfile.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/segmentation$20fault/mdnalysis-discussion/52Npnr2M2GE/cK7KWXRUNEgJ
But until we have some better idea where the problem lies I cannot say much more.
bipin singh
Nov 6, 2012, 12:46:24 PM11/6/12
to mdnalysis-...@googlegroups.com, orbe...@gmail.com
Hello Sir,
Thank you for your help. I am mentioning below the information you asked to provide.
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
I will try to send the detail output of the build process ASAP.--
-----------------------
Thanks and Regards,
Bipin Singh
Thank you for your help. I am mentioning below the information you asked to provide.
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
I will try to send the detail output of the build process ASAP.
-----------------------
Thanks and Regards,
Bipin Singh
Oliver Beckstein
Nov 6, 2012, 12:55:46 PM11/6/12
to mdnalysis-...@googlegroups.com
On 6 Nov, 2012, at 10:46, bipin singh wrote:
> Thank you for your help. I am mentioning below the information you asked to provide.
>
> 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
>
> I will try to send the detail output of the build process ASAP.
I added a page https://code.google.com/p/mdanalysis/wiki/QuestionsAndAnswers#Why_do_I_get_a_segmentation_fault? and maybe this already gives you some ideas what to try next.
Sébastien Buchoux
Nov 6, 2012, 2:58:37 PM11/6/12
to mdnalysis-...@googlegroups.com
On 11/06/2012 06:46 PM, bipin singh wrote:
> Hello Sir,
>
> Thank you for your help. I am mentioning below the information you asked to
> provide.
>
> *Operating system*:Ubuntu 10.10
> Hello Sir,
>
> Thank you for your help. I am mentioning below the information you asked to
> provide.
>
Ubuntu 10.10 (Codename Maverick Meerkat) is not supported since last
April (See: 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.
bug.
S�b
Oliver Beckstein
Nov 6, 2012, 3:11:06 PM11/6/12
to mdnalysis-...@googlegroups.com
On 6 Nov, 2012, at 12:58, Sébastien Buchoux wrote:
>> Thank you for your help. I am mentioning below the information you asked to
>> provide.
>>
>> *Operating system*:Ubuntu 10.10
http://code.google.com/p/mdanalysis/wiki/Install#Installing_using_binary_packages_%28for_Ubuntu/Debian_users%29
bipin singh
Nov 6, 2012, 11:31:05 PM11/6/12
to mdnalysis-...@googlegroups.com, sebastie...@gmail.com
Thank you sebastien for your suggestion. I know that Ubuntu10.10 is outdated. Sorry but currently I can not afford to upgrade it to 12.XX because I think I have to reinstall all the other programs (huge in number), which are currently installed on my current Ubuntu version.
Séb
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bipin singh
Nov 6, 2012, 11:43:48 PM11/6/12
to mdnalysis-...@googlegroups.com, orbe...@gmail.com
Please find below the output from the build process, using the command
>python setup.py build
#########################################################################################
running build
running build_py
creating build
creating build/lib.linux-i686-2.6
creating build/lib.linux-i686-2.6/MDAnalysis
copying MDAnalysis/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis
creating build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/log.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/transformations.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/util.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/units.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/Timeseries.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/AtomGroup.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/Selection.py -> build/lib.linux-i686-2.6/MDAnalysis/core
creating build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PrimitivePDBParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
creating build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
creating build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
creating build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/XTC.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/libxdrfile.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/TRR.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/statno.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/core.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
creating build/lib.linux-i686-2.6/MDAnalysis/coordinates/pdb
copying MDAnalysis/coordinates/pdb/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/pdb
copying MDAnalysis/coordinates/pdb/extensions.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/pdb
creating build/lib.linux-i686-2.6/MDAnalysis/util
copying MDAnalysis/util/LAMMPSParser.py -> build/lib.linux-i686-2.6/MDAnalysis/util
copying MDAnalysis/util/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/util
copying MDAnalysis/util/Transformation.py -> build/lib.linux-i686-2.6/MDAnalysis/util
creating build/lib.linux-i686-2.6/MDAnalysis/KDTree
copying MDAnalysis/KDTree/KDTree.py -> build/lib.linux-i686-2.6/MDAnalysis/KDTree
copying MDAnalysis/KDTree/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/KDTree
copying MDAnalysis/KDTree/CKDTree.py -> build/lib.linux-i686-2.6/MDAnalysis/KDTree
copying MDAnalysis/KDTree/NeighborSearch.py -> build/lib.linux-i686-2.6/MDAnalysis/KDTree
creating build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/helanal.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/hbonds.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
creating build/lib.linux-i686-2.6/MDAnalysis/builder
copying MDAnalysis/builder/charmm.py -> build/lib.linux-i686-2.6/MDAnalysis/builder
copying MDAnalysis/builder/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/builder
creating build/lib.linux-i686-2.6/MDAnalysis/tests
copying MDAnalysis/tests/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.linux-i686-2.6/MDAnalysis/tests
running build_ext
building 'coordinates._dcdmodule' extension
creating build/temp.linux-i686-2.6
creating build/temp.linux-i686-2.6/src
creating build/temp.linux-i686-2.6/src/dcd
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -Isrc/dcd/include -I/usr/include/python2.6 -c src/dcd/dcd.c -o build/temp.linux-i686-2.6/src/dcd/dcd.o
src/dcd/include/endianswap.h:32: warning: ‘swap2_unaligned’ defined but not used
src/dcd/include/endianswap.h:96: warning: ‘swap2_aligned’ defined but not used
src/dcd/include/fastio.h:140: warning: ‘fio_open’ defined but not used
src/dcd/include/fastio.h:159: warning: ‘fio_fclose’ defined but not used
src/dcd/include/fastio.h:232: warning: ‘fio_read_int32’ defined but not used
src/dcd/include/fastio.h:236: warning: ‘fio_write_str’ defined but not used
src/dcd/include/readdcd.h:626: warning: ‘jump_to_dcdstep’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/dcd/dcd.o -o build/lib.linux-i686-2.6/MDAnalysis/coordinates/_dcdmodule.so
building 'coordinates.dcdtimeseries' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -Isrc/dcd/include -I/usr/include/python2.6 -c src/dcd/dcdtimeseries.c -o build/temp.linux-i686-2.6/src/dcd/dcdtimeseries.o
src/dcd/include/endianswap.h:32: warning: ‘swap2_unaligned’ defined but not used
src/dcd/include/endianswap.h:96: warning: ‘swap2_aligned’ defined but not used
src/dcd/include/fastio.h:140: warning: ‘fio_open’ defined but not used
src/dcd/include/fastio.h:159: warning: ‘fio_fclose’ defined but not used
src/dcd/include/fastio.h:219: warning: ‘fio_ftell’ defined but not used
src/dcd/include/fastio.h:232: warning: ‘fio_read_int32’ defined but not used
src/dcd/include/fastio.h:236: warning: ‘fio_write_str’ defined but not used
src/dcd/include/readdcd.h:169: warning: ‘read_dcdheader’ defined but not used
src/dcd/include/readdcd.h:502: warning: ‘read_dcdstep’ defined but not used
src/dcd/include/readdcd.h:758: warning: ‘close_dcd_read’ defined but not used
src/dcd/include/readdcd.h:690: warning: ‘write_dcdheader’ defined but not used
src/dcd/include/readdcd.h:653: warning: ‘write_dcdstep’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/dcd/dcdtimeseries.o -o build/lib.linux-i686-2.6/MDAnalysis/coordinates/dcdtimeseries.so
building 'core.distances' extension
creating build/temp.linux-i686-2.6/src/numtools
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -Isrc/numtools -I/usr/include/python2.6 -c src/numtools/distances.c -o build/temp.linux-i686-2.6/src/numtools/distances.o
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/numtools/distances.o -lm -o build/lib.linux-i686-2.6/MDAnalysis/core/distances.so
building 'core.qcprot' extension
creating build/temp.linux-i686-2.6/src/pyqcprot
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/pyqcprot/pyqcprot.c -o build/temp.linux-i686-2.6/src/pyqcprot/pyqcprot.o -O3 -ffast-math
src/pyqcprot/pyqcprot.c: In function ‘__Pyx_GetBuffer’:
src/pyqcprot/pyqcprot.c:7398: warning: unused variable ‘getbuffer_cobj’
src/pyqcprot/pyqcprot.c: In function ‘__Pyx_ReleaseBuffer’:
src/pyqcprot/pyqcprot.c:7438: warning: unused variable ‘releasebuffer_cobj’
src/pyqcprot/pyqcprot.c: At top level:
/usr/lib/python2.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:968: warning: ‘_import_array’ defined but not used
/usr/lib/python2.6/dist-packages/numpy/core/include/numpy/__ufunc_api.h:182: warning: ‘_import_umath’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/pyqcprot/pyqcprot.o -o build/lib.linux-i686-2.6/MDAnalysis/core/qcprot.so
building 'core._transformations' extension
creating build/temp.linux-i686-2.6/src/transformations
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/transformations/transformations.c -o build/temp.linux-i686-2.6/src/transformations/transformations.o
src/transformations/transformations.c: In function ‘py_superimposition_matrix’:
src/transformations/transformations.c:1845: warning: ignoring #pragma vector always
src/transformations/transformations.c:1962: warning: ignoring #pragma vector always
src/transformations/transformations.c:1986: warning: ignoring #pragma vector always
src/transformations/transformations.c: In function ‘py_vector_norm’:
src/transformations/transformations.c:3427: warning: ignoring #pragma vector always
src/transformations/transformations.c:3508: warning: ignoring #pragma vector always
src/transformations/transformations.c: In function ‘py_unit_vector’:
src/transformations/transformations.c:3610: warning: ignoring #pragma vector always
src/transformations/transformations.c:3615: warning: ignoring #pragma vector always
src/transformations/transformations.c:3679: warning: ignoring #pragma vector always
src/transformations/transformations.c:3684: warning: ignoring #pragma vector always
src/transformations/transformations.c: At top level:
src/transformations/transformations.c:774: warning: ‘PyConverter_DoubleArray’ defined but not used
src/transformations/transformations.c:804: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used
src/transformations/transformations.c:910: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/transformations/transformations.o -lm -o build/lib.linux-i686-2.6/MDAnalysis/core/_transformations.so
building 'KDTree._CKDTree' extension
creating build/temp.linux-i686-2.6/src/KDTree
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/KDTree/KDTree.cpp -o build/temp.linux-i686-2.6/src/KDTree/KDTree.o
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/KDTree/KDTree.swig.cpp -o build/temp.linux-i686-2.6/src/KDTree/KDTree.swig.o
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/KDTree/KDTree.o build/temp.linux-i686-2.6/src/KDTree/KDTree.swig.o -lstdc++ -o build/lib.linux-i686-2.6/MDAnalysis/KDTree/_CKDTree.so
building 'coordinates.xdrfile._libxdrfile' extension
creating build/temp.linux-i686-2.6/src/xdrfile
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/xdrfile/libxdrfile_wrap.c -o build/temp.linux-i686-2.6/src/xdrfile/libxdrfile_wrap.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/xdrfile/xdrfile.c -o build/temp.linux-i686-2.6/src/xdrfile/xdrfile.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/xdrfile/xdrfile_trr.c -o build/temp.linux-i686-2.6/src/xdrfile/xdrfile_trr.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/xdrfile/xdrfile_xtc.c -o build/temp.linux-i686-2.6/src/xdrfile/xdrfile_xtc.o
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/xdrfile/libxdrfile_wrap.o build/temp.linux-i686-2.6/src/xdrfile/xdrfile.o build/temp.linux-i686-2.6/src/xdrfile/xdrfile_trr.o build/temp.linux-i686-2.6/src/xdrfile/xdrfile_xtc.o -o build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile/_libxdrfile.so
#########################################################################################
>python setup.py build
#########################################################################################
running build
running build_py
creating build
creating build/lib.linux-i686-2.6/MDAnalysis
copying MDAnalysis/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis
creating build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/log.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/transformations.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/util.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/units.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/Timeseries.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/AtomGroup.py -> build/lib.linux-i686-2.6/MDAnalysis/core
copying MDAnalysis/core/Selection.py -> build/lib.linux-i686-2.6/MDAnalysis/core
creating build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PrimitivePDBParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.linux-i686-2.6/MDAnalysis/topology
creating build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.linux-i686-2.6/MDAnalysis/selections
creating build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates
creating build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/XTC.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/libxdrfile.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/TRR.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/statno.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
copying MDAnalysis/coordinates/xdrfile/core.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile
creating build/lib.linux-i686-2.6/MDAnalysis/coordinates/pdb
copying MDAnalysis/coordinates/pdb/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/pdb
copying MDAnalysis/coordinates/pdb/extensions.py -> build/lib.linux-i686-2.6/MDAnalysis/coordinates/pdb
creating build/lib.linux-i686-2.6/MDAnalysis/util
copying MDAnalysis/util/LAMMPSParser.py -> build/lib.linux-i686-2.6/MDAnalysis/util
copying MDAnalysis/util/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/util
copying MDAnalysis/util/Transformation.py -> build/lib.linux-i686-2.6/MDAnalysis/util
creating build/lib.linux-i686-2.6/MDAnalysis/KDTree
copying MDAnalysis/KDTree/KDTree.py -> build/lib.linux-i686-2.6/MDAnalysis/KDTree
copying MDAnalysis/KDTree/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/KDTree
copying MDAnalysis/KDTree/CKDTree.py -> build/lib.linux-i686-2.6/MDAnalysis/KDTree
copying MDAnalysis/KDTree/NeighborSearch.py -> build/lib.linux-i686-2.6/MDAnalysis/KDTree
creating build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/helanal.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/hbonds.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.linux-i686-2.6/MDAnalysis/analysis
creating build/lib.linux-i686-2.6/MDAnalysis/builder
copying MDAnalysis/builder/charmm.py -> build/lib.linux-i686-2.6/MDAnalysis/builder
copying MDAnalysis/builder/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/builder
creating build/lib.linux-i686-2.6/MDAnalysis/tests
copying MDAnalysis/tests/__init__.py -> build/lib.linux-i686-2.6/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.linux-i686-2.6/MDAnalysis/tests
running build_ext
building 'coordinates._dcdmodule' extension
creating build/temp.linux-i686-2.6
creating build/temp.linux-i686-2.6/src
creating build/temp.linux-i686-2.6/src/dcd
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -Isrc/dcd/include -I/usr/include/python2.6 -c src/dcd/dcd.c -o build/temp.linux-i686-2.6/src/dcd/dcd.o
src/dcd/include/endianswap.h:32: warning: ‘swap2_unaligned’ defined but not used
src/dcd/include/endianswap.h:96: warning: ‘swap2_aligned’ defined but not used
src/dcd/include/fastio.h:140: warning: ‘fio_open’ defined but not used
src/dcd/include/fastio.h:159: warning: ‘fio_fclose’ defined but not used
src/dcd/include/fastio.h:232: warning: ‘fio_read_int32’ defined but not used
src/dcd/include/fastio.h:236: warning: ‘fio_write_str’ defined but not used
src/dcd/include/readdcd.h:626: warning: ‘jump_to_dcdstep’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/dcd/dcd.o -o build/lib.linux-i686-2.6/MDAnalysis/coordinates/_dcdmodule.so
building 'coordinates.dcdtimeseries' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -Isrc/dcd/include -I/usr/include/python2.6 -c src/dcd/dcdtimeseries.c -o build/temp.linux-i686-2.6/src/dcd/dcdtimeseries.o
src/dcd/include/endianswap.h:32: warning: ‘swap2_unaligned’ defined but not used
src/dcd/include/endianswap.h:96: warning: ‘swap2_aligned’ defined but not used
src/dcd/include/fastio.h:140: warning: ‘fio_open’ defined but not used
src/dcd/include/fastio.h:159: warning: ‘fio_fclose’ defined but not used
src/dcd/include/fastio.h:219: warning: ‘fio_ftell’ defined but not used
src/dcd/include/fastio.h:232: warning: ‘fio_read_int32’ defined but not used
src/dcd/include/fastio.h:236: warning: ‘fio_write_str’ defined but not used
src/dcd/include/readdcd.h:169: warning: ‘read_dcdheader’ defined but not used
src/dcd/include/readdcd.h:502: warning: ‘read_dcdstep’ defined but not used
src/dcd/include/readdcd.h:758: warning: ‘close_dcd_read’ defined but not used
src/dcd/include/readdcd.h:690: warning: ‘write_dcdheader’ defined but not used
src/dcd/include/readdcd.h:653: warning: ‘write_dcdstep’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/dcd/dcdtimeseries.o -o build/lib.linux-i686-2.6/MDAnalysis/coordinates/dcdtimeseries.so
building 'core.distances' extension
creating build/temp.linux-i686-2.6/src/numtools
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -Isrc/numtools -I/usr/include/python2.6 -c src/numtools/distances.c -o build/temp.linux-i686-2.6/src/numtools/distances.o
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/numtools/distances.o -lm -o build/lib.linux-i686-2.6/MDAnalysis/core/distances.so
building 'core.qcprot' extension
creating build/temp.linux-i686-2.6/src/pyqcprot
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/pyqcprot/pyqcprot.c -o build/temp.linux-i686-2.6/src/pyqcprot/pyqcprot.o -O3 -ffast-math
src/pyqcprot/pyqcprot.c: In function ‘__Pyx_GetBuffer’:
src/pyqcprot/pyqcprot.c:7398: warning: unused variable ‘getbuffer_cobj’
src/pyqcprot/pyqcprot.c: In function ‘__Pyx_ReleaseBuffer’:
src/pyqcprot/pyqcprot.c:7438: warning: unused variable ‘releasebuffer_cobj’
src/pyqcprot/pyqcprot.c: At top level:
/usr/lib/python2.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:968: warning: ‘_import_array’ defined but not used
/usr/lib/python2.6/dist-packages/numpy/core/include/numpy/__ufunc_api.h:182: warning: ‘_import_umath’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/pyqcprot/pyqcprot.o -o build/lib.linux-i686-2.6/MDAnalysis/core/qcprot.so
building 'core._transformations' extension
creating build/temp.linux-i686-2.6/src/transformations
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/transformations/transformations.c -o build/temp.linux-i686-2.6/src/transformations/transformations.o
src/transformations/transformations.c: In function ‘py_superimposition_matrix’:
src/transformations/transformations.c:1845: warning: ignoring #pragma vector always
src/transformations/transformations.c:1962: warning: ignoring #pragma vector always
src/transformations/transformations.c:1986: warning: ignoring #pragma vector always
src/transformations/transformations.c: In function ‘py_vector_norm’:
src/transformations/transformations.c:3427: warning: ignoring #pragma vector always
src/transformations/transformations.c:3508: warning: ignoring #pragma vector always
src/transformations/transformations.c: In function ‘py_unit_vector’:
src/transformations/transformations.c:3610: warning: ignoring #pragma vector always
src/transformations/transformations.c:3615: warning: ignoring #pragma vector always
src/transformations/transformations.c:3679: warning: ignoring #pragma vector always
src/transformations/transformations.c:3684: warning: ignoring #pragma vector always
src/transformations/transformations.c: At top level:
src/transformations/transformations.c:774: warning: ‘PyConverter_DoubleArray’ defined but not used
src/transformations/transformations.c:804: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used
src/transformations/transformations.c:910: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/transformations/transformations.o -lm -o build/lib.linux-i686-2.6/MDAnalysis/core/_transformations.so
building 'KDTree._CKDTree' extension
creating build/temp.linux-i686-2.6/src/KDTree
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/KDTree/KDTree.cpp -o build/temp.linux-i686-2.6/src/KDTree/KDTree.o
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/KDTree/KDTree.swig.cpp -o build/temp.linux-i686-2.6/src/KDTree/KDTree.swig.o
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/KDTree/KDTree.o build/temp.linux-i686-2.6/src/KDTree/KDTree.swig.o -lstdc++ -o build/lib.linux-i686-2.6/MDAnalysis/KDTree/_CKDTree.so
building 'coordinates.xdrfile._libxdrfile' extension
creating build/temp.linux-i686-2.6/src/xdrfile
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/xdrfile/libxdrfile_wrap.c -o build/temp.linux-i686-2.6/src/xdrfile/libxdrfile_wrap.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/xdrfile/xdrfile.c -o build/temp.linux-i686-2.6/src/xdrfile/xdrfile.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/xdrfile/xdrfile_trr.c -o build/temp.linux-i686-2.6/src/xdrfile/xdrfile_trr.o
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/include/python2.6 -c src/xdrfile/xdrfile_xtc.c -o build/temp.linux-i686-2.6/src/xdrfile/xdrfile_xtc.o
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-i686-2.6/src/xdrfile/libxdrfile_wrap.o build/temp.linux-i686-2.6/src/xdrfile/xdrfile.o build/temp.linux-i686-2.6/src/xdrfile/xdrfile_trr.o build/temp.linux-i686-2.6/src/xdrfile/xdrfile_xtc.o -o build/lib.linux-i686-2.6/MDAnalysis/coordinates/xdrfile/_libxdrfile.so
#########################################################################################
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bipin singh
Nov 7, 2012, 12:06:09 PM11/7/12
to mdnalysis-...@googlegroups.com, orbe...@gmail.com
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.
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.
##########################################################################
On Wed, Nov 7, 2012 at 8:55 PM, Oliver Beckstein <orbe...@gmail.com> wrote:
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_I_get_a_segmentation_fault? so that we find out where the seg fault occurs.
--
-----------------------
Regards,
Bipin Singh
bipin singh
Nov 7, 2012, 1:01:23 PM11/7/12
to mdnalysis-...@googlegroups.com, orbe...@gmail.com
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)
##########################################################################################
##########################################################################################
(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]
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)
##########################################################################################
On Wed, Nov 7, 2012 at 11:21 PM, Oliver Beckstein <orbe...@gmail.com> wrote:
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?
bipin singh
Nov 7, 2012, 11:59:00 PM11/7/12
to mdnalysis-...@googlegroups.com, Oliver Beckstein
Hello Sir,
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.
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.
On Wed, Nov 7, 2012 at 11:49 PM, Oliver Beckstein <orbe...@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?
bipin singh
Nov 8, 2012, 12:08:32 AM11/8/12
to mdnalysis-...@googlegroups.com, orbe...@gmail.com
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>
>>> import MDAnalysis.tests
>>> MDAnalysis.tests.test(label="full")
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
OK
<nose.result.TextTestResult run=0 errors=0 failures=0>
############################################################################
############################################################################
>>> from MDAnalysis.tests.datafiles import PSF, DCD, GRO, XTC, TRR
>>> print MDAnalysis.Universe(PSF, DCD)
>>> print MDAnalysis.Universe(GRO, XTC)
<Universe with 47681 atoms>
>>> print MDAnalysis.Universe(GRO, TRR)
<Universe with 47681 atoms>
>>> import MDAnalysis.tests
>>> MDAnalysis.tests.test(label="full")
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
OK
<nose.result.TextTestResult run=0 errors=0 failures=0>
############################################################################
bipin singh
Nov 9, 2012, 12:20:43 AM11/9/12
to mdnalysis-...@googlegroups.com, Oliver Beckstein
I am trying to provide the answers of the questions asked by you:
1) How did you create your xtcs?
I have created my .xtc from .trr using trjconv module of GROMACS.
2) Which version of Gromacs?
I have used GROMACS 4.5.3 version.
3) What does 'gmxcheck -f your.xtc' produce?
# Atoms 29751
Precision 0.001 (nm)
Last frame 50000 time 100000.000
Item #frames Timestep (ps)
Step 50001 2
Time 50001 2
Lambda 0
Coords 50001 2
Velocities 0
Forces 0
Box 50001 2
I am dumping the output produced by running
>>> MDAnalysis.tests.test(label="full", extra_argv=["--exe"])
############################################################################################################
>>> 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
Fitted frame 98/98 [100.0%]
..E..creating /tmp/bipin/python26_intermediate/compiler_aa0a423c34a704de9b08c95a98137791
0.0 percent done
.HBonds frame 1/1 [100.0%]
.HBonds frame 1/1 [100.0%]
.HBonds frame 1/1 [100.0%]
./usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/analysis/hbonds.py:571: DeprecationWarning: _get_bonded_hydrogens_list() does not always find all hydrogens; detect_hydrogens='distance' is safer.
category=DeprecationWarning)
HBonds frame 1/1 [100.0%]
.HBonds frame 1/1 [100.0%]
.HBonds frame 1/1 [100.0%]
................F......................../usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/core/AtomGroup.py:1081: DeprecationWarning: velocities() will become an attribute 'velocities' in 0.8
category=DeprecationWarning)
..../usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'N' for Atom (name=N) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HT1' for Atom (name=HT1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HT2' for Atom (name=HT2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HT3' for Atom (name=HT3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'CA' for Atom (name=CA) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HA' for Atom (name=HA) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CB' for Atom (name=CB) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HB1' for Atom (name=HB1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HB2' for Atom (name=HB2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CG' for Atom (name=CG) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HG1' for Atom (name=HG1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HG2' for Atom (name=HG2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'SD' for Atom (name=SD) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'CE' for Atom (name=CE) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HE1' for Atom (name=HE1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HE2' for Atom (name=HE2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HE3' for Atom (name=HE3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'C' for Atom (name=C) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'O' for Atom (name=O) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HN' for Atom (name=HN) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'CD' for Atom (name=CD) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HD1' for Atom (name=HD1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HD2' for Atom (name=HD2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'NE' for Atom (name=NE) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'HE' for Atom (name=HE) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CZ' for Atom (name=CZ) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'NH1' for Atom (name=NH1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HH11) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HH12) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'NH2' for Atom (name=NH2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HH21) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HH22) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HB' for Atom (name=HB) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CG2' for Atom (name=CG2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG21) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG22) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG23) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CG1' for Atom (name=CG1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG11) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG12) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HD3' for Atom (name=HD3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'HG' for Atom (name=HG) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CD1' for Atom (name=CD1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD11) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD12) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD13) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CD2' for Atom (name=CD2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD21) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD22) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD23) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HA1' for Atom (name=HA1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HA2' for Atom (name=HA2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HB3' for Atom (name=HB3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'NZ' for Atom (name=NZ) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HZ1' for Atom (name=HZ1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HZ2' for Atom (name=HZ2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HZ3' for Atom (name=HZ3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OG1' for Atom (name=OG1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OE1' for Atom (name=OE1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'NE2' for Atom (name=NE2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HE21) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HE22) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CE1' for Atom (name=CE1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HZ' for Atom (name=HZ) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CE2' for Atom (name=CE2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OE2' for Atom (name=OE2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OH' for Atom (name=OH) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HH' for Atom (name=HH) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OG' for Atom (name=OG) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OD1' for Atom (name=OD1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OD2' for Atom (name=OD2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG13) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'SG' for Atom (name=SG) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'ND2' for Atom (name=ND2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'ND1' for Atom (name=ND1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OT1' for Atom (name=OT1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OT2' for Atom (name=OT2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
.................................................< Timestep 298 with unit cell dimensions array([ 0., 0., 0., 0., 0., 0.], dtype=float32) > 298
....KK................................................................................................................................................................................................................K.......................K...................................F................................../usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/topology/PSFParser.py:208: FileFormatWarning: Guessing that this is actually a NAMD-type PSF file... continuing with fingers crossed!
category=FileFormatWarning)
..................................................................................................F.................F
======================================================================
ERROR: test align.fasta2select() with calling ClustalW (Issue 113)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_analysis.py", line 195, in test_fasta2select_ClustalW
sel = fasta2select(self.seq, is_aligned=False, alnfilename=self.alnfile, treefilename=self.treefile)
File "/usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/analysis/align.py", line 597, in fasta2select
stdout, stderr = run_clustalw()
File "/usr/local/lib/python2.6/dist-packages/Bio/Application/__init__.py", line 437, in __call__
stdout_str, stderr_str)
ApplicationError: Command 'clustalw2 -infile=/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/test.fasta -align -type=protein -outfile=/tmp/tmpMvxVk0.aln -newtree=/tmp/tmpfoAhoX.dnd' returned non-zero exit status 127, '/bin/sh: clustalw2: not found'
-------------------- >> begin captured logging << --------------------
MDAnalysis.analysis.align: DEBUG: Aligning sequences in '/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/test.fasta' with 'clustalw2'.
MDAnalysis.analysis.align: DEBUG: ClustalW commandline: 'clustalw2 -infile=/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/test.fasta -align -type=protein -outfile=/tmp/tmpMvxVk0.aln -newtree=/tmp/tmpfoAhoX.dnd'
MDAnalysis.analysis.align: ERROR: ClustalW 'clustalw2' failed
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/analysis/align.py", line 597, in fasta2select
stdout, stderr = run_clustalw()
File "/usr/local/lib/python2.6/dist-packages/Bio/Application/__init__.py", line 437, in __call__
stdout_str, stderr_str)
ApplicationError: Command 'clustalw2 -infile=/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/test.fasta -align -type=protein -outfile=/tmp/tmpMvxVk0.aln -newtree=/tmp/tmpfoAhoX.dnd' returned non-zero exit status 127, '/bin/sh: clustalw2: not found'
MDAnalysis.analysis.align: INFO: (You can get clustalw2 from http://www.clustal.org/clustal2/)
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: test_dihedral_omega (MDAnalysisTests.test_atomgroup.TestAtomGroup)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_atomgroup.py", line 226, in test_dihedral_omega
assert_almost_equal(osel.dihedral(), -179.93439, 3)
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 265, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: -179.93742
DESIRED: -179.93439000000001
-------------------- >> begin captured logging << --------------------
MDAnalysis.topology.PSF: DEBUG: PSF file '/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/adk.psf': format 'STANDARD'
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: test_torsions (MDAnalysisTests.test_nuclinfo.TestNucl)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_nuclinfo.py", line 54, in test_torsions
assert_almost_equal(nucl_acid, expected_nucl_acid, err_msg="Backbone torsion does not have expected values for alpha, beta, gamma, epsilon, zeta, chi.")
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 262, in assert_almost_equal
return assert_array_almost_equal(actual, desired, decimal, err_msg)
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 537, in assert_array_almost_equal
header='Arrays are not almost equal')
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 395, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal
Backbone torsion does not have expected values for alpha, beta, gamma, epsilon, zeta, chi.
(mismatch 14.2857142857%)
x: array([ 296.45596313, 177.79353333, 48.67910767, 81.81109619,
205.58882141, 286.37353516, 198.09185791], dtype=float32)
y: array([ 296.45596313, 177.79353333, 48.67910767, 81.81109619,
205.58882141, 286.37353516, 198.09187317], dtype=float32)
======================================================================
FAIL: testAngleNullVector (MDAnalysisTests.test_util.TestGeometryFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_util.py", line 69, in testAngleNullVector
assert_equal(util.angle(self.e1, self.null), numpy.nan)
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 189, in assert_equal
raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: nan
DESIRED: nan
======================================================================
FAIL: testParse_velocities (MDAnalysisTests.test_velocities.TestGROVelocities)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_velocities.py", line 39, in testParse_velocities
assert_equal(all_atoms.velocities(), self.reference_velocities, "problem reading .gro file velocities")
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 186, in assert_equal
return assert_array_equal(actual, desired, err_msg, verbose)
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 463, in assert_array_equal
verbose=verbose, header='Arrays are not equal')
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 395, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not equal
problem reading .gro file velocities
(mismatch 33.3333333333%)
x: array([[ 1.227 , -0.57999998, 0.43400002],
[ 8.08500004, 3.19099998, -7.79099989],
[ -9.04500008, -26.46899986, 13.17999935],...
y: array([[ 1.227 , -0.57999998, 0.43399999],
[ 8.08500004, 3.19099998, -7.79099989],
[ -9.04500008, -26.46899986, 13.18000031],...
----------------------------------------------------------------------
Ran 531 tests in 529.966s
FAILED (KNOWNFAIL=4, errors=1, failures=4)
<nose.result.TextTestResult run=531 errors=1 failures=4>
############################################################################################################
1) How did you create your xtcs?
I have created my .xtc from .trr using trjconv module of GROMACS.
2) Which version of Gromacs?
I have used GROMACS 4.5.3 version.
3) What does 'gmxcheck -f your.xtc' produce?
# Atoms 29751
Precision 0.001 (nm)
Last frame 50000 time 100000.000
Item #frames Timestep (ps)
Step 50001 2
Time 50001 2
Lambda 0
Coords 50001 2
Velocities 0
Forces 0
Box 50001 2
I am dumping the output produced by running
>>> MDAnalysis.tests.test(label="full", extra_argv=["--exe"])
############################################################################################################
>>> 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
..E..creating /tmp/bipin/python26_intermediate/compiler_aa0a423c34a704de9b08c95a98137791
0.0 percent done
.HBonds frame 1/1 [100.0%]
.HBonds frame 1/1 [100.0%]
.HBonds frame 1/1 [100.0%]
./usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/analysis/hbonds.py:571: DeprecationWarning: _get_bonded_hydrogens_list() does not always find all hydrogens; detect_hydrogens='distance' is safer.
category=DeprecationWarning)
HBonds frame 1/1 [100.0%]
.HBonds frame 1/1 [100.0%]
.HBonds frame 1/1 [100.0%]
................F......................../usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/core/AtomGroup.py:1081: DeprecationWarning: velocities() will become an attribute 'velocities' in 0.8
category=DeprecationWarning)
..../usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'N' for Atom (name=N) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HT1' for Atom (name=HT1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HT2' for Atom (name=HT2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HT3' for Atom (name=HT3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'CA' for Atom (name=CA) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HA' for Atom (name=HA) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CB' for Atom (name=CB) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HB1' for Atom (name=HB1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HB2' for Atom (name=HB2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CG' for Atom (name=CG) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HG1' for Atom (name=HG1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HG2' for Atom (name=HG2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'SD' for Atom (name=SD) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'CE' for Atom (name=CE) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HE1' for Atom (name=HE1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HE2' for Atom (name=HE2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HE3' for Atom (name=HE3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'C' for Atom (name=C) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'O' for Atom (name=O) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HN' for Atom (name=HN) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'CD' for Atom (name=CD) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HD1' for Atom (name=HD1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HD2' for Atom (name=HD2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'NE' for Atom (name=NE) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'HE' for Atom (name=HE) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CZ' for Atom (name=CZ) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'NH1' for Atom (name=NH1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HH11) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HH12) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'NH2' for Atom (name=NH2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HH21) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HH22) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HB' for Atom (name=HB) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CG2' for Atom (name=CG2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG21) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG22) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG23) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CG1' for Atom (name=CG1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG11) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG12) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HD3' for Atom (name=HD3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'HG' for Atom (name=HG) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CD1' for Atom (name=CD1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD11) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD12) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD13) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CD2' for Atom (name=CD2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD21) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD22) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HD23) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HA1' for Atom (name=HA1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HA2' for Atom (name=HA2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HB3' for Atom (name=HB3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'NZ' for Atom (name=NZ) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HZ1' for Atom (name=HZ1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HZ2' for Atom (name=HZ2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HZ3' for Atom (name=HZ3) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OG1' for Atom (name=OG1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OE1' for Atom (name=OE1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'NE2' for Atom (name=NE2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HE21) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HE22) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CE1' for Atom (name=CE1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HZ' for Atom (name=HZ) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'CE2' for Atom (name=CE2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OE2' for Atom (name=OE2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OH' for Atom (name=OH) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'HH' for Atom (name=HH) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OG' for Atom (name=OG) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OD1' for Atom (name=OD1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OD2' for Atom (name=OD2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'H' for Atom (name=HG13) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Used element 'SG' for Atom (name=SG) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'ND2' for Atom (name=ND2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'ND1' for Atom (name=ND1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OT1' for Atom (name=OT1) with given element ''
warnings.warn(msg, PDBConstructionWarning)
/usr/local/lib/python2.6/dist-packages/Bio/PDB/Atom.py:99: PDBConstructionWarning: Could not assign element 'OT2' for Atom (name=OT2) with given element ''
warnings.warn(msg, PDBConstructionWarning)
.................................................< Timestep 298 with unit cell dimensions array([ 0., 0., 0., 0., 0., 0.], dtype=float32) > 298
....KK................................................................................................................................................................................................................K.......................K...................................F................................../usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/topology/PSFParser.py:208: FileFormatWarning: Guessing that this is actually a NAMD-type PSF file... continuing with fingers crossed!
category=FileFormatWarning)
..................................................................................................F.................F
======================================================================
ERROR: test align.fasta2select() with calling ClustalW (Issue 113)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_analysis.py", line 195, in test_fasta2select_ClustalW
sel = fasta2select(self.seq, is_aligned=False, alnfilename=self.alnfile, treefilename=self.treefile)
File "/usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/analysis/align.py", line 597, in fasta2select
stdout, stderr = run_clustalw()
File "/usr/local/lib/python2.6/dist-packages/Bio/Application/__init__.py", line 437, in __call__
stdout_str, stderr_str)
ApplicationError: Command 'clustalw2 -infile=/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/test.fasta -align -type=protein -outfile=/tmp/tmpMvxVk0.aln -newtree=/tmp/tmpfoAhoX.dnd' returned non-zero exit status 127, '/bin/sh: clustalw2: not found'
-------------------- >> begin captured logging << --------------------
MDAnalysis.analysis.align: DEBUG: Aligning sequences in '/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/test.fasta' with 'clustalw2'.
MDAnalysis.analysis.align: DEBUG: ClustalW commandline: 'clustalw2 -infile=/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/test.fasta -align -type=protein -outfile=/tmp/tmpMvxVk0.aln -newtree=/tmp/tmpfoAhoX.dnd'
MDAnalysis.analysis.align: ERROR: ClustalW 'clustalw2' failed
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysis-0.7.6-py2.6-linux-i686.egg/MDAnalysis/analysis/align.py", line 597, in fasta2select
stdout, stderr = run_clustalw()
File "/usr/local/lib/python2.6/dist-packages/Bio/Application/__init__.py", line 437, in __call__
stdout_str, stderr_str)
ApplicationError: Command 'clustalw2 -infile=/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/test.fasta -align -type=protein -outfile=/tmp/tmpMvxVk0.aln -newtree=/tmp/tmpfoAhoX.dnd' returned non-zero exit status 127, '/bin/sh: clustalw2: not found'
MDAnalysis.analysis.align: INFO: (You can get clustalw2 from http://www.clustal.org/clustal2/)
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: test_dihedral_omega (MDAnalysisTests.test_atomgroup.TestAtomGroup)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_atomgroup.py", line 226, in test_dihedral_omega
assert_almost_equal(osel.dihedral(), -179.93439, 3)
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 265, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: -179.93742
DESIRED: -179.93439000000001
-------------------- >> begin captured logging << --------------------
MDAnalysis.topology.PSF: DEBUG: PSF file '/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/data/adk.psf': format 'STANDARD'
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: test_torsions (MDAnalysisTests.test_nuclinfo.TestNucl)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_nuclinfo.py", line 54, in test_torsions
assert_almost_equal(nucl_acid, expected_nucl_acid, err_msg="Backbone torsion does not have expected values for alpha, beta, gamma, epsilon, zeta, chi.")
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 262, in assert_almost_equal
return assert_array_almost_equal(actual, desired, decimal, err_msg)
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 537, in assert_array_almost_equal
header='Arrays are not almost equal')
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 395, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal
Backbone torsion does not have expected values for alpha, beta, gamma, epsilon, zeta, chi.
(mismatch 14.2857142857%)
x: array([ 296.45596313, 177.79353333, 48.67910767, 81.81109619,
205.58882141, 286.37353516, 198.09185791], dtype=float32)
y: array([ 296.45596313, 177.79353333, 48.67910767, 81.81109619,
205.58882141, 286.37353516, 198.09187317], dtype=float32)
======================================================================
FAIL: testAngleNullVector (MDAnalysisTests.test_util.TestGeometryFunctions)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_util.py", line 69, in testAngleNullVector
assert_equal(util.angle(self.e1, self.null), numpy.nan)
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 189, in assert_equal
raise AssertionError(msg)
AssertionError:
Items are not equal:
ACTUAL: nan
DESIRED: nan
======================================================================
FAIL: testParse_velocities (MDAnalysisTests.test_velocities.TestGROVelocities)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.6/dist-packages/MDAnalysisTests-0.7.6-py2.6.egg/MDAnalysisTests/test_velocities.py", line 39, in testParse_velocities
assert_equal(all_atoms.velocities(), self.reference_velocities, "problem reading .gro file velocities")
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 186, in assert_equal
return assert_array_equal(actual, desired, err_msg, verbose)
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 463, in assert_array_equal
verbose=verbose, header='Arrays are not equal')
File "/usr/lib/python2.6/dist-packages/numpy/testing/utils.py", line 395, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not equal
problem reading .gro file velocities
(mismatch 33.3333333333%)
x: array([[ 1.227 , -0.57999998, 0.43400002],
[ 8.08500004, 3.19099998, -7.79099989],
[ -9.04500008, -26.46899986, 13.17999935],...
y: array([[ 1.227 , -0.57999998, 0.43399999],
[ 8.08500004, 3.19099998, -7.79099989],
[ -9.04500008, -26.46899986, 13.18000031],...
----------------------------------------------------------------------
Ran 531 tests in 529.966s
FAILED (KNOWNFAIL=4, errors=1, failures=4)
<nose.result.TextTestResult run=531 errors=1 failures=4>
############################################################################################################
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 (orbe...@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.
bipin singh
Nov 9, 2012, 12:25:33 AM11/9/12
to mdnalysis-...@googlegroups.com, Oliver Beckstein
Regarding your 4th question, I have tested the same commands with trajectory (.xtc) containing 3 frames but this time it did not showed any error.
On Thu, Nov 8, 2012 at 11:34 PM, Oliver Beckstein <orbe...@gmail.com> wrote:
Hi Bipin,
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 (orbe...@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 Beckstein
Nov 13, 2012, 1:19:10 PM11/13/12
to mdnalysis-...@googlegroups.com, Oliver Beckstein
Hi Bipin,
On 9 Nov, 2012, at 10:58, bipin singh wrote:
I tried your test trajectory with MDAnalysis-0.7.7-devel (but there shouldn't be any differences compared to the 0.7.6 that you used, at least not in this respect because that part of the code did not change):
and both work:
I'm also able to analyze it, e.g.
Thus, I cannot reproduce your error, which makes it more difficult to fix.
One possibility is that it has something to do with the size of your trajectory. Under certain circumstances (32-bit linux without setting certain compilation flags for large file support) there's a 2 GB file size limit. Can you try to produce
check which ones lead to the seg fault.
Also send the output of 'uname -a', perhaps you have a 32-bit system?
If anyone else has any ideas what could be going on, I'd be happy to hear them!
Thanks,
Oliver
Regarding your 4th question, I have tested the same commands with trajectory (.xtc) containing 3 frames but this time it did not showed any error.
I have tried to produce the minimum size "test" trajectory which can produce the seg. fault (turn out to be in ~2.5GB). I am giving the link for the same, Please try to download and check for the error on your side.
I tried your test trajectory with MDAnalysis-0.7.7-devel (but there shouldn't be any differences compared to the 0.7.6 that you used, at least not in this respect because that part of the code did not change):
- on Linux Ubuntu 12.04.1 x86_64
Linux 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
Python 2.7.3
Python 2.7.3
- on Mac OS X 10.6.8 i386
Darwin 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 i386
and both work:
>>> u = MDAnalysis.Universe("test.pdb", "test.xtc")
>>> print u
<Universe with 32956 atoms>
>>> print u.trajectory
< XTCReader 'test.xtc' with 25001 frames of 32956 atoms (0 fixed) >
>>> print u
<Universe with 32956 atoms>
>>> print u.trajectory
< XTCReader 'test.xtc' with 25001 frames of 32956 atoms (0 fixed) >
I'm also able to analyze it, e.g.
protein = u.selectAtoms("protein")
rgyr = [(u.trajectory.time, protein.radiusOfGyration()) for ts in u.trajectory[::10]]
rgyr = [(u.trajectory.time, protein.radiusOfGyration()) for ts in u.trajectory[::10]]
Thus, I cannot reproduce your error, which makes it more difficult to fix.
One possibility is that it has something to do with the size of your trajectory. Under certain circumstances (32-bit linux without setting certain compilation flags for large file support) there's a 2 GB file size limit. Can you try to produce
- a very short trajectory (only a few frames)
- a trajectory a bit smaller than 2GB and
- one a bit larger than 2GB
check which ones lead to the seg fault.
Also send the output of 'uname -a', perhaps you have a 32-bit system?
If anyone else has any ideas what could be going on, I'd be happy to hear them!
Thanks,
Oliver
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