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<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Folks,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I am having problems installing NeXus on Linux. I have a Fedora
Core 10 system. I followed the instructions on the NeXus site:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>http://www.nexusformat.org/Download#NeXus_Binary_Distributions<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I did the:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>yum install hdf hdf-devel hdf5 hdf5-devel mxml mxml-devel<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I then tried to install Nexus as directed but it fails:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>corvette:~>sudo rpm -Uhv nexus-4.1.0-0.i386.rpm <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>[sudo] password for epics: <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>error: Failed dependencies:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> libhdf5.so.0 is needed by nexus-4.1.0-0.i386<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>It cannot find libhdf5.so.0, which indeed does not exist. These
are the hdf5 files and links in /usr/lib.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>corvette:~>ls -l /usr/lib/libhdf5*<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rw-r--r-- 1 root root 3434232 Jun 5 2008
/usr/lib/libhdf5.a<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 16 Sep
4 2008 /usr/lib/libhdf5.so -> libhdf5.so.5.0.1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 16 Sep
4 2008 /usr/lib/libhdf5.so.5 -> libhdf5.so.5.0.1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rwxr-xr-x 1 root root 2487304 Jun 5 2008
/usr/lib/libhdf5.so.5.0.1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rw-r--r-- 1 root root 572100 Jun 5 2008 /usr/lib/libhdf5_cpp.a<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 20 Sep
4 2008 /usr/lib/libhdf5_cpp.so -> libhdf5_cpp.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 20 Sep
4 2008 /usr/lib/libhdf5_cpp.so.0 -> libhdf5_cpp.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rwxr-xr-x 1 root root 400808 Jun 5 2008 /usr/lib/libhdf5_cpp.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rw-r--r-- 1 root root 267126 Jun 5 2008
/usr/lib/libhdf5_fortran.a<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 24 Sep
4 2008 /usr/lib/libhdf5_fortran.so -> libhdf5_fortran.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 24 Sep
4 2008 /usr/lib/libhdf5_fortran.so.0 -> libhdf5_fortran.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rwxr-xr-x 1 root root 223128 Jun 5 2008
/usr/lib/libhdf5_fortran.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rw-r--r-- 1 root root 138888 Jun 5 2008
/usr/lib/libhdf5_hl.a<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 19 Sep
4 2008 /usr/lib/libhdf5_hl.so -> libhdf5_hl.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 19 Sep
4 2008 /usr/lib/libhdf5_hl.so.0 -> libhdf5_hl.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rwxr-xr-x 1 root root 114968 Jun 5 2008
/usr/lib/libhdf5_hl.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rw-r--r-- 1 root root 6454 Jun 5 2008
/usr/lib/libhdf5_hl_cpp.a<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 23 Sep
4 2008 /usr/lib/libhdf5_hl_cpp.so -> libhdf5_hl_cpp.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 23 Sep
4 2008 /usr/lib/libhdf5_hl_cpp.so.0 -> libhdf5_hl_cpp.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rwxr-xr-x 1 root root 7492 Jun 5 2008
/usr/lib/libhdf5_hl_cpp.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rw-r--r-- 1 root root 56366 Jun 5 2008
/usr/lib/libhdf5hl_fortran.a<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 26 Sep
4 2008 /usr/lib/libhdf5hl_fortran.so -> libhdf5hl_fortran.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>lrwxrwxrwx 1 root root 26 Sep
4 2008 /usr/lib/libhdf5hl_fortran.so.0 -> libhdf5hl_fortran.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-rwxr-xr-x 1 root root 51400 Jun 5 2008
/usr/lib/libhdf5hl_fortran.so.0.0.0<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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. <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>(I also installed hdf5-static and hdf-devel-static because I want those
libraries too).<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I forced rpm to install NeXus with the –nodeps to ignore the
problem.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>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:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>corvette:1-5beta/ADApp/simDetectorSrc>nm
../../lib/linux-x86/libNeXus.a | grep H5Acreate<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> U H5Acreate<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>If I run nm on libhdf5.a I see that it defines some similar symbols,
H5Acreate1, H5Acreate2, H5Acreate_by_name, but not H5Acreate.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>corvette:1-5beta/ADApp/simDetectorSrc>nm /usr/lib/libhdf5.a | grep
H5Acreate<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>00006990 T H5Acreate2<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>00006570 T H5Acreate_by_name<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>00000a90 T H5Acreate1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Any idea what the problem is?<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Mark<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
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