Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan

From: mirko hennig <>
Date: Mon, 15 Aug 2016 17:03:04 +0000 (UTC)

 so far ...not much...
[Mirkos-MacBook-Pro:AmberTools/src/netcdf-4.3.0] mirko% make installmake: Nothing to be done for `install'.
[Mirkos-MacBook-Pro:AmberTools/src/netcdf-fortran-4.2] mirko% make installmake: *** No rule to make target `install'.  Stop.
      From: Hai Nguyen <>
 To: mirko hennig <>; AMBER Mailing List <>
 Sent: Monday, August 15, 2016 9:50 AM
 Subject: Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan

what happens if you

cd $AMBERHOME/AmberTools/src/netcdf-fortran-4.2
make install

cd $AMBERHOME/AmberTools/src/netcdf-4.3.0
make install


On Mon, Aug 15, 2016 at 12:26 PM, mirko hennig <>

> Dear allI'm still trying to install Ambertools15 and Amber14 on a Macbook
> pro (OS X 10.11.6) and continue to have issues when executing ./configure
> w/ and w/o -macAccelerate using either gnu or clang compilers.
> Specifically, the installation hangs when configuring NetCDF:
> Checking NetCDF... Using bundled NetCDF library. Starting NetCDF build.
> Configuring NetCDF C interface (may be time-consuming)...
> meaning that ./configure never finishes (no errors, no prompt after hours
> and hours of waiting which has been described before by myself and on Mon
> Nov 30 2015 "mac hangs when compile amber tools on el capitan" by  YY) but
> rather has to be manually killed. Every test before like gcc, g++, gfortran
> etc passes.
> I have attached a txt file illustrating the outputs of the
> corresponding netcdf_config.log and the gcc -v output.
> the netcdf versions that appear in ~/amber14/AmberTools/src
> arenetcdf-4.3.0 andnetcdf-fortran-4.2
> 'port list installed active' returnsnetcdf                        @4.4.1
>        science/netcdfnetcdf-fortran                @4.4.3
> science/netcdf-fortran
> what really confuses me is the fact that 'port list installed INACTIVE'
> lists the same versions (netcdf-4.4.1 and netcdf-fortran-4.4.3) and the
> latter netcdf's are only found under e.g:[Mirkos-MacBook-Pro:/opt/local]
> mirko% find . -name netcdf-fortran -print./var/macports/
> distfiles/netcdf-fortran./var/macports/software/netcdf-
> fortran./var/macports/sources/
> tarballs/ports/science/netcdf-fortranwhich makes using the
> '--with-netcdf' flag difficult.any help would be greatly appreciatedmany
> thanks-mirko
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Received on Mon Aug 15 2016 - 10:30:02 PDT
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