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

From: mirko hennig <>
Date: Tue, 16 Aug 2016 07:18:10 +0000 (UTC)

got one step further I guess...
>​You need to specify the appropriate variant for the netcdf-fortran package
>on a Mac to make sure it is built with the desired compiler.
>sudo port install netcdf
>sudo port install netcdf-fortran +gcc49

I thought I had done that before, but uninstalled and re-installed netcdf and -netcdf-fortran as you pointed configure is getting past the netcdf, but goes into an endless loop (meaning never terminates w/ any error, waited for >30min) while configuring fftw-3.3:
[Mirkos-MBP:~/my_CNS/Amber/amber14] mirko% ./configure -macAccelerate --with-netcdf /opt/local gnuChecking for updates...Checking for available patches online. This may take a few seconds...
Available AmberTools 15 patches:
No patches available
Available Amber 14 patches:
No patches availableSearching for python2... Found python2.7: /opt/local/bin/python2.7
Obtaining the gnu compiler suite versions, e.g.:     gcc -vThe C version is 4.9.3The Fortran version is 4.9.3
Testing the gcc compiler:     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o testp testp.cOK
Testing the g++ compiler:     g++ -fPIC -o testp testp.cppOK
Testing the gfortran compiler:     gfortran -fPIC -O0 -o testp testp.fOK
Testing mixed C/Fortran compilation:     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -c -o testp.c.o testp.c     gfortran -fPIC -O0 -c -o testp.f.o testp.f     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w -framework AccelerateOK
Testing pointer size:     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o test_pointer_size test_pointer_size.cDetected 64 bit operating system.
Testing flex: OK
Checking NetCDF... Using external NetCDF in '/opt/local'
Checking for zlib:      gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ  -lz -o testp testp.cOK
Checking for libbz2:      gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ  -lbz2 -o testp testp.cOK
Configuring fftw-3.3 (may be time-consuming)...
same result using clang compilers, taking out the -macAccelerate also makes no differenceany idea how to take this hurdle?many thanksMirko

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Received on Tue Aug 16 2016 - 00:30:02 PDT
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