Dear all
I am trying to install Ambertools 17 onto Macbook Sierra 10.12
and I followed "all" available instructions, including installation of
Xquartz, Xcode and Gfortran.
However, I used './configure -macAccelerate clang' and kept getting the
following error messages... HELP, please!!
~~~~~~
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 17 patches:
No patches available
AMBER_PREFIX=/Users/vincent/bin/amber16
AMBER_SOURCE=/Users/vincent/bin/amber16
Using the AmberTools miniconda installation in
/Users/vincent/bin/amber16/miniconda
version 2.7.13
Obtaining the clang compiler suite versions, e.g.:
clang -v
The C version is 9.0.0
The Fortran version is 配置為：../gcc-6.3.0/configure
6.3.0
Testing the clang compiler:
clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
testp.c
OK
Testing the clang++ compiler:
clang++ -fPIC -o testp testp.cpp
OK
Testing the gfortran compiler:
gfortran -fPIC -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
clang -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
clang -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
testp.c.o testp.f.o -L -lgfortran -w -framework Accelerate
Undefined symbols for architecture x86_64:
"__gfortran_st_write", referenced from:
_hello_ in testp.f.o
"__gfortran_st_write_done", referenced from:
_hello_ in testp.f.o
"__gfortran_transfer_character_write", referenced from:
_hello_ in testp.f.o
ld: symbol(s) not found for architecture x86_64
clang: *error: *linker command failed with exit code 1 (use -v to see
invocation)
./configure2: line 2495: ./testp: No such file or directory
Error: Unable to compile mixed C/Fortran code.
Please check your compiler settings and configure flags.
Configure failed due to the errors above!
~~~~~~
And the 'clang -v' output is ::
~~
Apple LLVM version 9.0.0 (clang-900.0.37)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
~~
In addition, the 'port installed' output is ::
~~
The following ports are currently installed:
bzip2 .1.0.6_0 (active)
cctools .895_4+llvm40 (active)
cloog .0.18.4_1 (active)
cmake .3.9.3_0
cmake .3.9.4_0 (active)
curl .7.55.1_0+ssl
curl @7.56.0_0+ssl (active)
curl-ca-bundle .7.55.1_0
curl-ca-bundle @7.56.0_0 (active)
db48 .4.8.30_4 (active)
expat .2.2.4_0 (active)
gcc6 .6.4.0_0
gcc7 .7.2.0_0
gcc48 .4.8.5_2
gcc49 .4.9.4_2 (active)
gcc_select @0.1_8 (active)
gettext .0.19.8.1_0 (active)
gmake .4.2.1_0 (active)
gmp .6.1.2_1 (active)
hdf5 @1.10.1_1+cxx+gcc48+hl (active)
isl .0.18_0 (active)
isl14 .0.14.1_0 (active)
ld64 .3_0 (active)
ld64-latest @274.2_1+llvm40 (active)
libarchive .3.3.2_1 (active)
libcxx .3.9.1_0+universal (active)
libedit @20170329-3.1_1
libedit .20170329-3.1_2 (active)
libffi @3.2.1_0 (active)
libgcc .7.2.0_0
libgcc .7.2.0_1 (active)
libgcc6 .6.4.0_1 (active)
libiconv .1.15_0 (active)
libmpc .1.0.3_0 (active)
libuv .1.14.1_0
libuv .1.15.0_0 (active)
libxml2 .2.9.5_0
libxml2 @2.9.6_0 (active)
llvm-4.0 .4.0.1_0
llvm-4.0 @4.0.1_1 (active)
llvm_select .2_0 (active)
lz4 .1.8.0_0 (active)
lzo2 .2.10_0 (active)
molden .5.7-20170920124800_0+gcc6
molden .5.7-20170920124800_0+gcc7 (active)
mpfr .3.1.6_0 (active)
mpi-doc .3.2_0 (active)
mpi_select .0.0_3 (active)
mpich-gcc49 .3.2_4+fortran (active)
ncurses .6.0-20170916_0 (active)
netcdf @4.4.1.1_0+dap+gcc48+netcdf4 (active)
netcdf-fortran @4.4.4_0+gcc7
netcdf-fortran .4.4.4_0+gcc48 (active)
openssl .1.0.2l_0 (active)
python2_select .0.0_2 (active)
python27 .2.7.14_0 (active)
python_select @0.3_7 (active)
sqlite3 .3.20.1_0 (active)
xar .1.6.1_0 (active)
xorg-kbproto .1.0.7_0 (active)
xorg-libpthread-stubs @0.3_0 (active)
xorg-libX11 .1.6.5_0 (active)
xorg-libXau .1.0.8_0 (active)
xorg-libxcb @1.12_2+python27 (active)
xorg-libXdmcp .1.1.2_0 (active)
xorg-xcb-proto .1.12_1+python27 (active)
xorg-xproto @7.0.31_0 (active)
xz .5.2.3_0 (active)
zlib @1.2.11_0 (active)
~~
Any advice or suggestions will be greatly appreciated.
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Received on Thu Oct 12 2017 - 23:00:02 PDT
