basemap099.4 and geos

xiaoni wrote:

Jeff,
    Just to be safe because I am going to operate on the root:
1) ls -l /usr/local/lib: libgeos-3.2.0.so
libgeos.so -> libgeos-3.2.0.so

Xianoi: I'm assuming you installed libgeos 3.2.0rc1 yourself in /usr/local, and nothing is linked against it besides your non-working basemap? If so, it should be safe to do

rm /usr/local/lib/libgeos*

shall I just remove libgeos-3.2.0.so ? But then the link for libgeos.so may not work.

2) ls /usr/local/include:
geos geos_c.h geos.h

rm /usr/local/include/geos*h

and in the folder of geos, there are a lot of files and headers.
To remove the geos3.2 headers, shall I just remove /usr/local/include/geos_c.h and /usr/local/include/geos.h ? I can not tell where the headers of geos3.1.

presumably in /usr/include. If not, you probably need to install a libgeos-dev package or somesuch.

-Jeff

···

Many thanks again !

xiaoni

------------------------------------------------------------------------
*From:* Jeff Whitaker <jswhit@...146...>
*To:* xiaoni <wangxni@...9...>
*Cc:* Matplotlib Users <matplotlib-users@lists.sourceforge.net>
*Sent:* Wed, December 2, 2009 5:55:58 PM
*Subject:* Re: [Matplotlib-users] basemap099.4 and geos

xiaoni wrote:
> Jeff,
> Many thanks !
>
> ----ldd /usr/local/lib/python2.6/dist-packages/_geoslib.so
> The results are:
> linux-gate.so <http://linux-gate.so>.1 => (0x00cf2000)
> libgeos_c.so <http://libgeos_c.so>.1 => /usr/local/lib/libgeos_c.so.1 (0x00944000)
> libgeos-3.1.0.so <http://libgeos-3.1.0.so> => /usr/lib/libgeos-3.1.0.so (0x005cd000)
> libpthread.so <http://libpthread.so>.0 => /lib/tls/i686/cmov/libpthread.so.0 (0x00a0e000)
> libc.so <http://libc.so>.6 => /lib/tls/i686/cmov/libc.so.6 (0x00165000)
> libgeos-3.2.0.so <http://libgeos-3.2.0.so> => /usr/local/lib/libgeos-3.2.0.so (0xb75c1000)
> libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00d5c000)
> libm.so <http://libm.so>.6 => /lib/tls/i686/cmov/libm.so.6 (0x00cf7000)
> libgcc_s.so <http://libgcc_s.so>.1 => /lib/libgcc_s.so.1 (0x00f77000)
> /lib/ld-linux.so.2 (0x00148000)
>
> It seems that it mixed geos3.1 and 3.2 ?

Xianoi: Yep, there's your problem right there. My suggestion is to remove the 3.2.0 geos lib and headers from /usr/local/lib and /usr/local/include and try again.

-Jeff
>
> If I have to clean out all the old versions of basemap, _geoslib.so <http://_geoslib.so> and libgeos, then rebuild again, What is the safe way to do so ? I am afraid that I may damage the system if I simplely apply "rm". Do you have some suggestion about the steps of deleting ?
>
> Many thanks !!
>
> xiaoni
>
> ------------------------------------------------------------------------
> *From:* Jeff Whitaker <jswhit@…146… <mailto:jswhit@…146…>>
> *To:* xiaoni <wangxni@…9… <mailto:wangxni@…9…>>; Matplotlib Users <matplotlib-users@lists.sourceforge.net <mailto:matplotlib-users@lists.sourceforge.net>>
> *Sent:* Wed, December 2, 2009 5:42:17 PM
> *Subject:* Re: [Matplotlib-users] basemap099.4 and geos
>
> xiaoni wrote:
> > Jeff,
> > Many thanks for your help ! The problem was : there was a segmentation error when I call Basemap. I applied the following steps, and then tried to launch ipython, it still has the same problem.
> > --add export GEOS_DIR=/usr/local/lib
> > --download basemap 099.4 to /home/xiaoni/software, where the previous version099.3 is saved also
> > – sudo python setup.py <http://setup.py> <http://setup.py> install
> >
> > The installation is OK. Then I test:
> > --ls -l /usr/local/lib/libgeos.so : /usr/local/lib/libgeos.so -> libgeos-3.2.0.so <http://libgeos-3.2.0.so>
> > --ls -l /usr/lib/libgeos.so : /usr/lib/libgeos.so -> libgeos-3.1.0.so <http://libgeos-3.1.0.so>
> > --ls -l /usr/local/lib/libgeos.so : /usr/local/lib/libgeos.so -> libgeos-3.2.0.so
> > --locate libgeos.so <http://libgeos.so> <http://libgeos.so> : /usr/lib/libgeos.so , and /usr/local/lib/libgeos.so
> > --locate _geoslib :
> > /home/xiaoni/software/basemap-0.99.3/build/lib.linux-i686-2.6/_geoslib.so
> > /home/xiaoni/software/basemap-0.99.3/build/temp.linux-i686-2.6/src/_geoslib.o
> > /home/xiaoni/software/basemap-0.99.3/src/_geoslib.c
> > /home/xiaoni/software/basemap-0.99.3/src/_geoslib.pyx
> > /usr/local/lib/python2.6/dist-packages/_geoslib.so
> > (in fact I have saved both basemap -099.3 and basemap-0.99.4 in the /home/xiaoni/software. This result only shows 0.99.3 and is strange to me).
> >
> > Many thanks again !!
> >
> > xiaoni
>
> Xiaoni: Is there no traceback? Can you run ldd on the _geoslib.so <http://_geoslib.so> that you are actually importing when the error occurs (presumably /usr/local/lib/python2.6/dist-packages/_geoslib.so)? That will tell you what version of the geos library you actually linked. I don't think I can be of much help here - all I can suggest is that you clean out all old versions of basemap, _geoslib.so and libgeos, then rebuild again. The fact that there are so may versions floating around increases the chance that you have a version mismatch somewhere.
>
> Also check the build output and make sure there were no errors building _geoslib.so.
>
> -Jeff
>
> >
> > ------------------------------------------------------------------------
> > *From:* Jeff Whitaker <jswhit@…146… <mailto:jswhit@…146…> <mailto:jswhit@…146…>>
> > *To:* xiaoni <wangxni@…9… <mailto:wangxni@…9…> <mailto:wangxni@…9…>>
> > *Cc:* matplotlib-users@lists.sourceforge.net <mailto:matplotlib-users@lists.sourceforge.net> <mailto:matplotlib-users@lists.sourceforge.net>
> > *Sent:* Wed, December 2, 2009 4:47:51 PM
> > *Subject:* Re: [Matplotlib-users] basemap099.4 and geos
> >
> > xiaoni wrote:
> > > Hello, all,
> > > I have some problem with basemap and geos, and can not use Basemap。
> > > In the below I list the information about basemap and geos in my computer. Hope someone would help me to figure out why it does not work. Many thanks in adance !
> > >
> > > 1) I type:
> > > —from mpl_toolkits.basemap import Basemap;
> > > —mpl_toolkits.basemap.__path__
> > > —mpl_toolkits.basemap.__version__
> > > The results:
> > > /usr/local/lib/python2.6/dist-packages/mpl_toolkits/basemap
> > > '0.99.4'
> > >
> > > 2) I also checked the same for matplotlib:
> > > /usr/lib/pymodules/python2.6/matplotlib
> > > 0.99.0
> > >
> > > 3) I type: locate _geoslib:
> > >
> > > /home/xiaoni/software/basemap-0.99.3/build/lib.linux-i686-2.6/_geoslib.so
> > > /home/xiaoni/software/basemap-0.99.3/build/temp.linux-i686-2.6/src/_geoslib.o
> > > /home/xiaoni/software/basemap-0.99.3/src/_geoslib.c > /home/xiaoni/software/basemap-0.99.3/src/_geoslib.pyx /usr/local/lib/python2.6/dist-packages/_geoslib.so
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/build/lib.linux-i686-2.6/_geoslib.so
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/src/_geoslib.c
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/src/_geoslib.pyx
> > >
> > > 4) I type: locate libgeos.so <http://libgeos.so> <http://libgeos.so/>
> > >
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/geos-2.2.3/source/geom/.libs/libgeos.so
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/geos-2.2.3/source/geom/.libs/libgeos.so.2
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/geos-2.2.3/source/geom/.libs/libgeos.so.2.2.3
> > > /home/xiaoni/software/temp/geos-3.2.0rc1/source/.libs/libgeos.so
> > > /home/xiaoni/software/temp/lib/libgeos.so
> > > /home/xiaoni/software/temp/lib/libgeos.so.2
> > > /home/xiaoni/software/temp/lib/libgeos.so.2.2.3
> > > /usr/lib/libgeos.so
> > > /usr/local/lib/libgeos.so
> > > /usr/local/lib/backup2/libgeos.so
> > > /usr/local/lib/backup2/libgeos.so.2
> > > /usr/local/lib/backup2/libgeos.so.2.2.3
> > >
> > > 5) locate libgeos_c.so <http://libgeos_c.so> <http://libgeos_c.so> <http://libgeos_c.so/>
> > >
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/geos-2.2.3/source/capi/.libs/libgeos_c.so
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/geos-2.2.3/source/capi/.libs/libgeos_c.so.1
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/geos-2.2.3/source/capi/.libs/libgeos_c.so.1.1.1
> > > /home/xiaoni/software/temp/basemap-0.99.3-backup/geos-2.2.3/source/capi/.libs/libgeos_c.so.1.1.1T
> > > /home/xiaoni/software/temp/geos-3.2.0rc1/capi/.libs/libgeos_c.so
> > > /home/xiaoni/software/temp/geos-3.2.0rc1/capi/.libs/libgeos_c.so.1
> > > /home/xiaoni/software/temp/geos-3.2.0rc1/capi/.libs/libgeos_c.so.1.6.0
> > > /home/xiaoni/software/temp/geos-3.2.0rc1/capi/.libs/libgeos_c.so.1.6.0T
> > > /home/xiaoni/software/temp/lib/libgeos_c.so
> > > /home/xiaoni/software/temp/lib/libgeos_c.so.1
> > > /home/xiaoni/software/temp/lib/libgeos_c.so.1.1.1
> > > /usr/lib/libgeos_c.so
> > > /usr/lib/libgeos_c.so.1
> > > /usr/lib/libgeos_c.so.1.5.0
> > > /usr /local/lib/libgeos_c.so.1
> > > /us r/local/lib/libgeos_c.so.1.6.0
> > > /usr/local/lib/backup2/libgeos_c.so
> > > /usr/local/lib/backup2/libgeos_c.so.1
> > > /usr/local/lib/backup2/libgeos_c.so.1.1.1
> > >
> > > > 6) I also type:
> > > ls -l /usr/local/lib/python2.6/dist-packages/_geoslib.so
> > > It does not linked to any files (no pointer)
> > >
> > > 2) ls -l /usr/local/lib/libgeos.so
> > > /usr/local/lib/libgeos.so -> libgeos-3.2.0.so <http://libgeos-3.2.0.so> <http://libgeos-3.2.0.so/>
> > >
> > > 3) ls -l /usr/local/lib/libgeos.so
> > > /usr/local/lib/libgeos.so -> libgeos-3.2.0.so
> > >
> > > 4) ls -l /usr/local/lib/backup2/libgeos.so.2
> > > /usr/local/lib/backup2/libgeos.so.2 -> libgeos.so <http://libgeos.so/>.2.2.3
> > >
> > > 5) ls -l /usr/local/lib/backup2/libgeos.so.2.2.3
> > > /usr/local/lib/backup2/libgeos.so.2.2.3, no links
> > >
> > > It seems that Basemap can not be used because of something wrong with the installation of GEOS ? Anyone would give some hints for help ? I appreciate it a lot !!
> > >
> > > xiaoni
> > >
> > Xianoi: You never said what the actual problem is with basemap. I have seen segfaults when there are two versions of geos installed (version 2 and version 3) and you pick up the header from one version and lib from the other version. I suggest setting the GEOS_DIR env var to /usr/local/lib and re-running the basemap install (python setup.py <http://setup.py> install), after deleting the existing build directory. Hopefully then it will grab both the header and lib for version 3.2.0 (which by the way is a pre-release, as yet untested with basemap).
> >
> > -Jeff
> >
> > – Jeffrey S. Whitaker Phone : (303)497-6313
> > Meteorologist FAX : (303)497-6449
> > NOAA/OAR/PSD R/PSD1 Email : Jeffrey.S.Whitaker@…259… <mailto:Jeffrey.S.Whitaker@…259…> <mailto:Jeffrey.S.Whitaker@…259…> <mailto:Jeffrey.S.Whitaker@…259… <mailto:Jeffrey.S.Whitaker@…259…>>
> > 325 Broadway Office : Skaggs Research Cntr 1D-113
> > Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg
> >
>
> – Jeffrey S. Whitaker Phone : (303)497-6313
> Meteorologist FAX : (303)497-6449
> NOAA/OAR/PSD R/PSD1 Email : Jeffrey.S.Whitaker@…259… <mailto:Jeffrey.S.Whitaker@…259…> <mailto:Jeffrey.S.Whitaker@…259…>
> 325 Broadway Office : Skaggs Research Cntr 1D-113
> Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg
>

– Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jeffrey.S.Whitaker@…259… <mailto:Jeffrey.S.Whitaker@…259…>
325 Broadway Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg

--
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jeffrey.S.Whitaker@...259...
325 Broadway Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg