Hi,
Thank you very much for the suggestion. The problem seems to be solved.
Though all the required executables, such as cpptraj, sander, mmpbsa, etc.,
are
in the bin directory, I am wondering whether I need to worry about the
following that I got after make install
/opt/oscer/software/GCCcore/6.4.0/include/c++/6.4.0/bits/basic_string.h:5340:5:
note: template argument deduction/substitution failed:
GraphToHoldScores.cpp:1153:7: note: ‘std::ostream {aka
std::basic_ostream<char>}’ is not derived from ‘const
std::__cxx11::basic_string<_CharT, _Traits, _Alloc>’
std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]"
<< std::endl;
^~~~
make[3]: *** [GraphToHoldScores.o] Error 1
make[3]: Leaving directory
`/home/prabir/SOFTWARE/AMBER/amber14/AmberTools/src/reduce/reduce_src'
make[2]: *** [install] Error 2
make[2]: Leaving directory
`/home/prabir/SOFTWARE/AMBER/amber14/AmberTools/src/reduce'
make[1]: *** [serial] Error 2
make[1]: Leaving directory
`/home/prabir/SOFTWARE/AMBER/amber14/AmberTools/src'
make: *** [install] Error 2
Thanks,
Prabir
On Mon, Feb 4, 2019 at 11:05 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
> _______________________________________________
> 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.*
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Received on Mon Feb 04 2019 - 14:30:03 PST
