Remove the file $AMBERHOME/include/netcdf.mod and
$AMBERHOME/lib/libnetcdf.a and try
./configure -cuda gnu
make install
again.
On Thu, Jun 6, 2013 at 11:28 AM, Matthew Wampole <
Matthew.Wampole.jefferson.edu> wrote:
> Hi Amber users,
>
> I have run into a compilation error with the latest updates to amber.
> Attached to this email is a log of the 'make install' output from a
> standard './configure -cuda gnu'.
>
> ::snippet::
> ./cuda/cuda.a -L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcurand
> -lcufft -lcudart -L/usr/lib64 -lstdc++ -L/usr/local/amber12/lib
> -L/usr/local/amber12/lib -lnetcdf
> bintraj.o: In function `__bintraj_mod_MOD_checkerror.part.0':
> bintraj.F90:(.text+0x6e): undefined reference to
> `__netcdf_MOD_nf90_strerror'
> bintraj.o: In function `__bintraj_mod_MOD_end_binary_frame':
> 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'
> ...
>
> I was able to bypass this error by configuring without netcdf,
> './configure -cuda -nobintraj gnu'. It doesn't fix the issue but gives me a
> workable pmemd.cuda to test. (I've been following the titan discussion)
>
> System specs:
> Ubuntu 12.04
> gcc 4.6.3
> gfortran 4.6.3
>
> Cuda cards:
> Titan
> GTX 680
> Quadro 5600
>
> Thanks,
>
> ~Matt
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 06 2013 - 09:00:04 PDT
