Hi Dan,
I've attached a log of libnetcdf.a from the command you gave. Everything looks to be in order for libnetcdf.a that is contained in amber12. Branching from your idea, I searched my computer for other copies of libnetcdf.a and found one in my usr/lib directory installed with the libnetcdf developer kit. That version of libnetcdf.a does not contain nf90 routines so I'm wondering if AMBER could be using the Synaptic installed version instead of the one built by AMBER.
I removed the developer kit of libnetcdf from my Ubuntu machine and was able to install like normal without removing the bintraj functionality. I've had the developer kit installed for a while for other programs and this is the first time this has occurred, curious but it provided a temporary fix.
~Matt
-------------
Hi,
On Thu, Jun 6, 2013 at 9:28 AM, Matthew Wampole
<Matthew.Wampole.jefferson.edu> wrote:
> bintraj.F90:(.text+0x332): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
> bintraj.F90:(.text+0x35e): undefined reference to `__netcdf_MOD_nf90_sync'
> bintraj.F90:(.text+0x4ba): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
> bintraj.F90:(.text+0x4cf): undefined reference to `__netcdf_MOD_nf90_sync'
These errors make me think that for some reason the NetCDF install
process got messed up and the fortran 90 netcdf routines didn't make
it into the netcdf library. I would say first check out your
libnetcdf.a and make sure the nf90 symbols are in there:
nm $AMBERHOME/lib/libnetcdf.a | grep nf90
If nothing is output from this then for some reason the netcdf install
went wrong. I remember seeing this happen once on one of my machines a
while back but I couldn't track down why. I think the way I fixed it
was by going into the netcdf directory manually and doing a 'make
uninstall' or 'make distclean', then 'make install', e.g.
cd $AMBERHOME/AmberTools/src/netcdf/src
make uninstall
make install
If you still do not have nf90 symbols in your libnetcdf.a after this
then there may be a larger problem.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 11 2013 - 13:30:03 PDT
