[AMBER-Developers] Problems with AmberTools 15 and netcdf-fortran-4.2 compile

From: Ross Walker <rosscwalker.gmail.com>
Date: Tue, 20 Oct 2015 14:59:21 -0700

Hi All,

I am trying to get an AWS AMI of AMBER up and running. This involves using Amazon's hacked up version of Linux which is loosely based on Redhat but has then been 'tweaked' in tons of ways. Anyway, long story short AmberTools 15 configure is dying:

./configure gnu
Checking 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 available
Searching for python2... Found python2.7: /usr/bin/python2.7

Obtaining the gnu compiler suite versions, e.g.:
     gcc -v
The C version is 4.8.3
The Fortran version is 4.8.3

Testing the gcc compiler:
     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c

Testing the g++ compiler:
     g++ -fPIC -o testp testp.cpp

Testing the gfortran compiler:
     gfortran -fPIC -O0 -o testp testp.f

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

Testing pointer size:
     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.

Testing flex: OK

Checking NetCDF...
        Using bundled NetCDF library.
        Starting NetCDF build.
        Configuring NetCDF C interface (may be time-consuming)...
        Compiling the NetCDF C interface (may be time-consuming)...
        Configuring NetCDF Fortran interface (may be time-consuming)...
        Compiling the NetCDF Fortran interface (may be time-consuming)...
Error: NetCDF Fortran compile failed.
       Check /usr/local/amber14/AmberTools/src/netcdf-fortran-4.2/netcdf.fortran.compile.log
       for errors.
Configure failed due to the errors above!

tail netcdf.fortran.compile.log

/bin/sh ../libtool --tag=FC --mode=link gfortran -fPIC -O3 -mtune=native -version-number 5:3:1 -L/usr/local/amber14/lib -o libnetcdff.la -rpath /usr/local/amber14/lib fort-attio.lo fort-control.lo fort-dim.lo fort-genatt.lo fort-geninq.lo fort-genvar.lo fort-lib.lo fort-misc.lo fort-v2compat.lo fort-vario.lo fort-var1io.lo fort-varaio.lo fort-varmio.lo fort-varsio.lo ../f90/libnetcdff90.la -lnetcdf
libtool: link: gfortran -shared .libs/fort-attio.o .libs/fort-control.o .libs/fort-dim.o .libs/fort-genatt.o .libs/fort-geninq.o .libs/fort-genvar.o .libs/fort-lib.o .libs/fort-misc.o .libs/fort-v2compat.o .libs/fort-vario.o .libs/fort-var1io.o .libs/fort-varaio.o .libs/fort-varmio.o .libs/fort-varsio.o -Wl,--whole-archive ../f90/.libs/libnetcdff90.a -Wl,--no-whole-archive -Wl,-rpath -Wl,/usr/local/amber14/lib -Wl,-rpath -Wl,/usr/local/amber14/lib -L/usr/local/amber14/lib /usr/local/amber14/lib/libnetcdf.so -lm -mtune=native -Wl,-soname -Wl,libnetcdff.so.5 -o .libs/libnetcdff.so.5.3.1
/usr/bin/ld: /usr/lib/gcc/x86_64-amazon-linux/4.8.3/libgfortran.a(reshape_i4.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-amazon-linux/4.8.3/libgfortran.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [libnetcdff.la] Error 1
make[2]: Leaving directory `/usr/local/amber14/AmberTools/src/netcdf-fortran-4.2/fortran'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/usr/local/amber14/AmberTools/src/netcdf-fortran-4.2/fortran'
make: *** [install-recursive] Error 1

Which would be all well and good except that everything is already being built with -fPIC.

Anybody else come across this problem / know a simple way to fix it?

All the best

|\oss Walker

| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |

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Received on Tue Oct 20 2015 - 15:00:03 PDT
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