[Nexus] Problems installing NeXus on Linux
Carlos Pascual Izarra
carlos.pascual at cells.es
Wed Aug 12 09:23:38 BST 2009
Some time ago I created a Ubuntu/debian 64b binary deb package which is
available at the nexus kits page:
http://download.nexusformat.org/kits/
(perhaps it should be linked from the downloads page as well?)
Apart from that, I also wrote a small step-by-step howto for installing from
sources for Ubuntu, SuSe 10.2 and SuSe11.1:
http://www.cells.es/Members/cpascual/docs/HowTo%20Install%20Nexus
I did it mainly for my personal records, but maybe it helps...
Carlos
On Tuesday 11 August 2009 21:30:11 Pete R. Jemian wrote:
> I followed Mark's path, but on my Ubuntu 8.04LTS system.
> (downloaded the nexus rpm, converted it to a .deb using "alien" and
> installed it) and also installed the required libmxml package.
> nxbrowse TOFRAW.nxs
> indicated the same "could not find libhdf5.so.0" error.
>
> [prjemian at morel,3016,test]$ nxbrowse TOFRAW.nxs
> nxbrowse: error while loading shared libraries: libhdf5.so.0: cannot open
> shared object file: No such file or directory
>
>
> I built all the NeXus components from scratch (2009-01-28) and it works.
> Only the prebuilt NeXus cannot find libhdf5.so.0.
> This is sensible since that is not on my system and it did not install
> with the libhdf5 on the NeXus downloads page
> (http://www.nexusformat.org/Download).
>
>
> [prjemian at morel,3008,log]$ locate libhdf5.so
> /usr/local/lib/libhdf5.so
> /usr/local/lib/libhdf5.so.6
> /usr/local/lib/libhdf5.so.6.0.1
> /usr/local/src/hdf/hdf5-1.8.2/src/.libs/libhdf5.so
> /usr/local/src/hdf/hdf5-1.8.2/src/.libs/libhdf5.so.6
> /usr/local/src/hdf/hdf5-1.8.2/src/.libs/libhdf5.so.6.0.1
> [prjemian at morel,3009,log]$ ll /usr/local/lib/libhdf5*
> -rw-r--r-- 1 root root 4.0M 2009-01-28 14:13 /usr/local/lib/libhdf5.a
> -rw-r--r-- 1 root root 135K 2009-01-28 14:13 /usr/local/lib/libhdf5_hl.a
> -rwxr-xr-x 1 root root 989 2009-01-28 14:13 /usr/local/lib/libhdf5_hl.la*
> lrwxrwxrwx 1 root root 19 2009-01-28 14:13 /usr/local/lib/libhdf5_hl.so
> -> libhdf5_hl.so.0.0.0* lrwxrwxrwx 1 root root 19 2009-01-28 14:13
> /usr/local/lib/libhdf5_hl.so.0 -> libhdf5_hl.so.0.0.0* -rwxr-xr-x 1 root
> root 128K 2009-01-28 14:13 /usr/local/lib/libhdf5_hl.so.0.0.0* -rwxr-xr-x 1
> root root 968 2009-01-28 14:13 /usr/local/lib/libhdf5.la* -rw-r--r-- 1
> root root 2.6K 2009-01-28 14:13 /usr/local/lib/libhdf5.settings lrwxrwxrwx
> 1 root root 16 2009-01-28 14:13 /usr/local/lib/libhdf5.so ->
> libhdf5.so.6.0.1* lrwxrwxrwx 1 root root 16 2009-01-28 14:13
> /usr/local/lib/libhdf5.so.6 -> libhdf5.so.6.0.1* -rwxr-xr-x 1 root root
> 3.0M 2009-01-28 14:13 /usr/local/lib/libhdf5.so.6.0.1*
>
>
> [prjemian at morel,3017,test]$ ll /usr/lib/libhdf5*
> lrwxrwxrwx 1 root root 22 2008-05-09 21:16 /usr/lib/libhdf5-1.6.5.so.0 ->
> libhdf5-1.6.5.so.0.0.0 -rw-r--r-- 1 root root 1.2M 2008-03-25 14:00
> /usr/lib/libhdf5-1.6.5.so.0.0.0 lrwxrwxrwx 1 root root 26 2008-05-09
> 21:16 /usr/lib/libhdf5_cpp-1.6.5.so.0 -> libhdf5_cpp-1.6.5.so.0.0.0
> -rw-r--r-- 1 root root 400K 2008-03-25 14:00
> /usr/lib/libhdf5_cpp-1.6.5.so.0.0.0 lrwxrwxrwx 1 root root 25 2008-05-09
> 21:16 /usr/lib/libhdf5_hl-1.6.5.so.0 -> libhdf5_hl-1.6.5.so.0.0.0
> -rw-r--r-- 1 root root 51K 2008-03-25 14:00
> /usr/lib/libhdf5_hl-1.6.5.so.0.0.0
>
> Mark Rivers wrote:
> > Folks,
> >
> >
> >
> > I am having problems installing NeXus on Linux. I have a Fedora Core 10
> > system. I followed the instructions on the NeXus site:
> >
> >
> >
> > http://www.nexusformat.org/Download#NeXus_Binary_Distributions
> >
> >
> >
> > I did the:
> >
> >
> >
> > yum install hdf hdf-devel hdf5 hdf5-devel mxml mxml-devel
> >
> >
> >
> > I then tried to install Nexus as directed but it fails:
> >
> >
> >
> > corvette:~>sudo rpm -Uhv nexus-4.1.0-0.i386.rpm
> >
> > [sudo] password for epics:
> >
> > error: Failed dependencies:
> >
> > libhdf5.so.0 is needed by nexus-4.1.0-0.i386
> >
> >
> >
> > It cannot find libhdf5.so.0, which indeed does not exist. These are the
> > hdf5 files and links in /usr/lib.
> >
> >
> >
> > corvette:~>ls -l /usr/lib/libhdf5*
> >
> > -rw-r--r-- 1 root root 3434232 Jun 5 2008 /usr/lib/libhdf5.a
> >
> > lrwxrwxrwx 1 root root 16 Sep 4 2008 /usr/lib/libhdf5.so ->
> > libhdf5.so.5.0.1
> >
> > lrwxrwxrwx 1 root root 16 Sep 4 2008 /usr/lib/libhdf5.so.5 ->
> > libhdf5.so.5.0.1
> >
> > -rwxr-xr-x 1 root root 2487304 Jun 5 2008 /usr/lib/libhdf5.so.5.0.1
> >
> > -rw-r--r-- 1 root root 572100 Jun 5 2008 /usr/lib/libhdf5_cpp.a
> >
> > lrwxrwxrwx 1 root root 20 Sep 4 2008 /usr/lib/libhdf5_cpp.so ->
> > libhdf5_cpp.so.0.0.0
> >
> > lrwxrwxrwx 1 root root 20 Sep 4 2008 /usr/lib/libhdf5_cpp.so.0 ->
> > libhdf5_cpp.so.0.0.0
> >
> > -rwxr-xr-x 1 root root 400808 Jun 5 2008 /usr/lib/libhdf5_cpp.so.0.0.0
> >
> > -rw-r--r-- 1 root root 267126 Jun 5 2008 /usr/lib/libhdf5_fortran.a
> >
> > lrwxrwxrwx 1 root root 24 Sep 4 2008 /usr/lib/libhdf5_fortran.so
> > -> libhdf5_fortran.so.0.0.0
> >
> > lrwxrwxrwx 1 root root 24 Sep 4 2008
> > /usr/lib/libhdf5_fortran.so.0 -> libhdf5_fortran.so.0.0.0
> >
> > -rwxr-xr-x 1 root root 223128 Jun 5 2008
> > /usr/lib/libhdf5_fortran.so.0.0.0
> >
> > -rw-r--r-- 1 root root 138888 Jun 5 2008 /usr/lib/libhdf5_hl.a
> >
> > lrwxrwxrwx 1 root root 19 Sep 4 2008 /usr/lib/libhdf5_hl.so ->
> > libhdf5_hl.so.0.0.0
> >
> > lrwxrwxrwx 1 root root 19 Sep 4 2008 /usr/lib/libhdf5_hl.so.0 ->
> > libhdf5_hl.so.0.0.0
> >
> > -rwxr-xr-x 1 root root 114968 Jun 5 2008 /usr/lib/libhdf5_hl.so.0.0.0
> >
> > -rw-r--r-- 1 root root 6454 Jun 5 2008 /usr/lib/libhdf5_hl_cpp.a
> >
> > lrwxrwxrwx 1 root root 23 Sep 4 2008 /usr/lib/libhdf5_hl_cpp.so
> > -> libhdf5_hl_cpp.so.0.0.0
> >
> > lrwxrwxrwx 1 root root 23 Sep 4 2008 /usr/lib/libhdf5_hl_cpp.so.0
> > -> libhdf5_hl_cpp.so.0.0.0
> >
> > -rwxr-xr-x 1 root root 7492 Jun 5 2008
> > /usr/lib/libhdf5_hl_cpp.so.0.0.0
> >
> > -rw-r--r-- 1 root root 56366 Jun 5 2008 /usr/lib/libhdf5hl_fortran.a
> >
> > lrwxrwxrwx 1 root root 26 Sep 4 2008
> > /usr/lib/libhdf5hl_fortran.so -> libhdf5hl_fortran.so.0.0.0
> >
> > lrwxrwxrwx 1 root root 26 Sep 4 2008
> > /usr/lib/libhdf5hl_fortran.so.0 -> libhdf5hl_fortran.so.0.0.0
> >
> > -rwxr-xr-x 1 root root 51400 Jun 5 2008
> > /usr/lib/libhdf5hl_fortran.so.0.0.0
> >
> >
> >
> > So I have libhdf5.so.5.0.1 as the actual file. Making a symbolic link
> > to that file from libhdf5.so.0 does not help, same rpm error as above.
> >
> >
> >
> > (I also installed hdf5-static and hdf-devel-static because I want those
> > libraries too).
> >
> >
> >
> > I forced rpm to install NeXus with the –nodeps to ignore the problem.
> >
> >
> >
> > Once I do that I try to link my application, and I get a bunch of
> > unresolved symbols. It looks like it could be an HDF5 version problem.
> > One of the undefined symbols is H5Acreate. If I run “nm” on libNeXus.a
> > I see that it has an undefined symbol H5Acreate:
> >
> > corvette:1-5beta/ADApp/simDetectorSrc>nm ../../lib/linux-x86/libNeXus.a
> >
> > | grep H5Acreate
> >
> > U H5Acreate
> >
> >
> >
> > If I run nm on libhdf5.a I see that it defines some similar symbols,
> > H5Acreate1, H5Acreate2, H5Acreate_by_name, but not H5Acreate.
> >
> >
> >
> > corvette:1-5beta/ADApp/simDetectorSrc>nm /usr/lib/libhdf5.a | grep
> > H5Acreate
> >
> > 00006990 T H5Acreate2
> >
> > 00006570 T H5Acreate_by_name
> >
> > 00000a90 T H5Acreate1
> >
> >
> >
> > Any idea what the problem is?
> >
> >
> >
> > Thanks,
> >
> > Mark
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > NeXus mailing list
> > NeXus at nexusformat.org
> > http://lists.nexusformat.org/mailman/listinfo/nexus
--
+----------------------------------------------------+
Carlos Pascual Izarra
Scientific Software Contact
Computing Division
Cells / Alba Synchrotron [http:/www.cells.es]
Carretera BP 1413 de Cerdanyola-Sant Cugat, Km. 3.3
E-08290 Cerdanyola del Valles (Barcelona), Spain
E-mail: carlos.pascual at cells.es
Phone: +34 93 592 4428
+----------------------------------------------------+
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