On 2019-09-23 13:47, Hai Nguyen wrote:
> On Mon, Sep 23, 2019 at 4:19 PM David Mathog <mathog.caltech.edu>
> wrote:
>
>> Greetings.
>>
>> Just installed AmberTools which ended up in a directory amber18. We
>> do
>> not at this time have a license for Amber 18. Did this:
>>
>>
>> TOPDIR=/usr/common/modules/el7/x86_64/software/amber/19-CentOS-vanilla
>> mkdir -p $TOPDIR
>> export PATH=/opt/ompi401/bin:$PATH #or it cannot figure out which
>> mpi, fails in fftw
>> ./configure --python-install local -mpi --with-python
>> /usr/bin/python
>> --prefix $TOPDIR gnu
>>
>
> Please try again without the `--prefix` option. It might not setup
> properly
> for testing cpptraj.
Is it possible to install to the --prefix directory after running the
test?
Also, I tried in a rebuild earlier to get it to see the netcdf installed
on CentOS. (Because the first error was netcdf related, and I thought
that might be the problem.) It wants
the netcdf.mod file, which is here:
/usr/lib64/gfortran/modules/netcdf.mod
The only way I could get this to configure was by
#as root
ln -s /usr/lib64/gfortran/modules/netcdf.mod /usr/include/netcdf.mod
then
TOPDIR=/usr/common/modules/el7/x86_64/software/amber/19-CentOS-vanilla
export PATH=/opt/ompi401/bin:$PATH #or it cannot figure out which
mpi, fails in fftw s
./configure --python-install local -mpi \
--with-python /usr/bin/python --prefix $TOPDIR \
--with-netcdf /usr gnu
all the other attempts constructed odd paths for the fortran test
program which sees if netcdf is present. Is there a way to do that
which does not require adding that link? The problem is that the build
seems to expect a particular netcdf directory structure, and it can
either find
the mod file, or the headers and libraries, but not both!
Thanks,
David Mathog
mathog.caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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Received on Mon Sep 23 2019 - 14:30:02 PDT
