Hi,
According to that log, here's your problem:
```
checking how to run the C preprocessor... /lib/cpp
configure: error: in
`/home/prabir/SOFTWARE/AMBER/amber14/AmberTools/src/netcdf-4.3.0':
configure: error: C preprocessor "/lib/cpp" fails sanity check
```
Does that program exist? Can you run it successfully? This seems to be
a problem with your system configuration, so you may want to take it
up with your system's administrators.
-Dan
On Mon, Feb 4, 2019 at 12:22 PM Prabir Khatua <prabir07chem.gmail.com> wrote:
>
> By mistake, I gave the wrong information about serial version in this
> server where I got the similar problem too. Once again, I could not
> understand the problem by looking
> at the mentioned log file. Following is the error.
> Checking NetCDF...
> Using bundled NetCDF library.
> Starting NetCDF build.
> Configuring NetCDF C interface (may be time-consuming)...
> Error: NetCDF C configure returned 1
> NetCDF configure failed! Check the netcdf_config.log file
> in the /home/prabir/SOFTWARE/AMBER/amber14/AmberTools/src directory.
> Configure failed due to the errors above!
> [prabir.c474 amber14]$ vi
> /home/prabir/SOFTWARE/AMBER/amber14/AmberTools/src/netcdf_config.log
>
> Attached is the corresponding log file.
>
> On Mon, Feb 4, 2019 at 10:36 PM Prabir Khatua <prabir07chem.gmail.com>
> wrote:
>
> > Dear Sir,
> >
> > Thank you very much for your reply. It is to be noted that the server
> > where I am trying to install amber has openmpi enabled mpi.
> > mpicc is located in
> > /opt/oscer/software/openmpi/1.10.3/intel/avx-shm-mxm/bin. I am loading this
> > module before configuring amber
> > with mpi. I am trying to install amber in the following $AMBERHOME
> > directory
> > /home/prabir/SOFTWARE/AMBER/AMBER14/amber14
> > mpicc is in the $PATH as per my understanding. However, I am not sure
> > whether compiler used for serial version is same as that
> > of mpi version. Can you please tell me the command to check it. I tried to
> > check it by typing "mpicc -show". However, it showed that
> > this commad does not exist. I am sharing the log file. I really did not
> > understand the error from this log file. Please advice me to fix
> > this problem.
> >
> > Thank you,
> > Sincerely,
> >
> > Prabir
> >
> > On Sat, Feb 2, 2019 at 10:38 PM David Case <david.case.rutgers.edu> wrote:
> >
> >> On Fri, Feb 01, 2019, Prabir Khatua wrote:
> >> >
> >> >I am experiencing a problem in installing Amber 14 with Amber15Tools with
> >> >mpi. Following is the error that I am getting while I was trying to
> >> >configure it with mpi
> >> >
> >> >Error: FFTW configure returned 1
> >> > FFTW configure failed! Check the fftw3_config.log file
> >> > in the /home/prabir/SOFTWARE/AMBER/AMBER14/amber14/AmberTools/src
> >> >directory.
> >>
> >> So: what was the result of looking at the log file described above?
> >> That will tell you what the problem is. Be sure that files like mpicc
> >> are in your $PATH, and that the compilers used match those you used of
> >> the serial installation--type "mpicc -show" to find this out.
> >>
> >> But this is all guesswork: look at the log file and see if that helps.
> >> If you still have problems, please let us know what is in that file.
> >>
> >> ...good luck....dac
> >>
> >> p.s. Amber14 is five years old, which is a long time in software terms.
> >> Consider upgrading to AmberTools18.
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> >
> > *Prabir Khatua*
> > *Postdoctoral Research Associate*
> > *Department of Chemistry & Biochemistry*
> > *University of Oklahoma*
> > *Norman, Oklahoma 73019*
> > *U. S. A.*
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
> --
>
> *Prabir Khatua*
> *Postdoctoral Research Associate*
> *Department of Chemistry & Biochemistry*
> *University of Oklahoma*
> *Norman, Oklahoma 73019*
> *U. S. A.*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Feb 04 2019 - 10:00:02 PST
