Seems like /usr/local/src/amber18/lib/libcpptraj.so is out of date for
some reason. I'm not really an expert on how cmake tries to figure out
dependencies so I'm not exactly sure what's going on, but maybe try to
remove /usr/local/src/amber18/lib/libcpptraj.so so it gets regenerated
with references to the proper libnetcdf.so? Someone better versed in
cmake may want to chime in here.
-Dan
On Mon, Jul 20, 2020 at 9:56 AM Karolina Mitusińska (Markowska)
<markowska.kar.gmail.com> wrote:
>
> Dear Amber Users,
>
> I'm having problem with upgrading AmberTools 18 to AmberTools19 on Ubuntu
> 18.04.
> I run
> ./update_amber --upgrade to upgrade from AmberTools18 to AmberTools19. I
> downloaded all available patches and then run
> ./configure gnu
> and
> make install
>
> The installation starts but after few minutes it ends with such info:
> [AMBPDB] CXX ambpdb
> /usr/bin/ld: warning: libnetcdf.so.7, needed by
> /usr/local/src/amber18/lib/libcpptraj.so, not found (try using -rpath or
> -rpath-link)
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_def_dim'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_get_var_double'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_vara_float'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_var_int'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to `nc_redef'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_inq_dimid'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_get_var1_float'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_inq_attlen'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to `nc_open'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_inq_dimlen'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_att_int'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_att_double'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to `nc_close'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to `nc_enddef'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_inq_varname'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_inq_varndims'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_var1_float'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to `nc_sync'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_get_att_text'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_set_fill'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_get_var_int'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_vara_double'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_var_double'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_vara_text'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_get_vara_int'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_get_vara_float'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_att_text'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to `nc_inq'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_def_var'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_get_vara_double'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_inq_varid'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_strerror'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_put_vara_int'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to
> `nc_get_vara_text'
> /usr/local/src/amber18/lib/libcpptraj.so: undefined reference to `nc_create'
> collect2: error: ld returned 1 exit status
> Makefile:28: recipe for target 'ambpdb' failed
> make[3]: *** [ambpdb] Error 1
> make[3]: Leaving directory '/usr/local/src/amber18/AmberTools/src/ambpdb'
> Makefile:26: recipe for target 'serial' failed
> make[2]: *** [serial] Error 2
> make[2]: Leaving directory '/usr/local/src/amber18/AmberTools/src'
> Makefile:7: recipe for target 'install' failed
> make[1]: *** [install] Error 2
> make[1]: Leaving directory '/usr/local/src/amber18'
> mkfiles/amber.mk:34: recipe for target 'amber' failed
> make: *** [amber] Error 2
>
> I sourced amber.sh and add the LD_LIBRARY_PATH variable
> source /usr/local/src/amber18/amber.sh
> export LD_LIBRARY_PATH=$AMBERHOME/lib:$LD_LIBRARY_PATH
> but still without any luck.
>
> I saw some posts on the list here, but I'm not sure how to apply those
> fixes in my case.
> Can someone help please?
> Best regards,
> Karolina Mitusińska
> PhD student
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Received on Mon Jul 20 2020 - 07:00:05 PDT
