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 - 07:00:04 PDT
