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bartoldeman avatar bartoldeman commented on June 7, 2024

Hi @Omer80 those instructions are indeed outdated. The AUTO manual has correct instructions; you can also refer to @BjornSandstede's instructions here: https://github.com/sandstede-lab/Auto07p/blob/master/auto07p_installation_guide.md

The GFortran binaries from https://github.com/fxcoudert/gfortran-for-macOS/releases should work. Alternatively you can use Homebrew. I've run AUTO on a Mac myself using Homebrew.

I haven't tested the hpc binaries at all, and for that reason they are no longer mentioned in the AUTO manual.

If all fails, please attach your config.log file to this issue.

from auto-07p.

Omer80 avatar Omer80 commented on June 7, 2024

Hi @bartoldeman , I have installed GFortran from the bineries you've mentioned, but there is still an error. Here is a copy of the config.log file:

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by configure, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure 

## --------- ##
## Platform. ##
## --------- ##

hostname = Omers-MBP
uname -m = x86_64
uname -r = 18.7.0
uname -s = Darwin
uname -v = Darwin Kernel Version 18.7.0: Sun Dec  1 18:59:03 PST 2019; root:xnu-4903.278.19~1/RELEASE_X86_64

/usr/bin/uname -p = i386
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = Mach kernel version:
	 Darwin Kernel Version 18.7.0: Sun Dec  1 18:59:03 PST 2019; root:xnu-4903.278.19~1/RELEASE_X86_64
Kernel configured for up to 8 processors.
4 processors are physically available.
8 processors are logically available.
Processor type: x86_64h (Intel x86-64h Haswell)
Processors active: 0 1 2 3 4 5 6 7
Primary memory available: 16.00 gigabytes
Default processor set: 421 tasks, 2137 threads, 8 processors
Load average: 1.33, Mach factor: 6.66
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /opt/anaconda3/bin
PATH: /opt/anaconda3/condabin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /Library/TeX/texbin
PATH: /opt/X11/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2389: checking for gcc
configure:2416: result: x86_64-apple-darwin13.4.0-clang
configure:2645: checking for C compiler version
configure:2654: x86_64-apple-darwin13.4.0-clang --version >&5
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin13.4.0
Thread model: posix
InstalledDir: /opt/anaconda3/bin
configure:2665: $? = 0
configure:2654: x86_64-apple-darwin13.4.0-clang -v >&5
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin13.4.0
Thread model: posix
InstalledDir: /opt/anaconda3/bin
configure:2665: $? = 0
configure:2654: x86_64-apple-darwin13.4.0-clang -V >&5
clang-4.0: error: argument to '-V' is missing (expected 1 value)
clang-4.0: error: no input files
configure:2665: $? = 1
configure:2654: x86_64-apple-darwin13.4.0-clang -qversion >&5
clang-4.0: error: unknown argument: '-qversion'
clang-4.0: error: no input files
configure:2665: $? = 1
configure:2685: checking whether the C compiler works
configure:2707: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs conftest.c  >&5
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
ld: dynamic main executables must link with libSystem.dylib for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
configure:2711: $? = 1
configure:2749: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| 
|   ;
|   return 0;
| }
configure:2754: error: in `/Users/omertzuk/auto/07p':
configure:2756: error: C compiler cannot create executables
See `config.log' for more details

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=x86_64-apple-darwin13.4.0-clang
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe'
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value='-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9'
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXFLAGS_set=set
ac_cv_env_CXXFLAGS_value='-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0'
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=x86_64-apple-darwin13.4.0-clang++
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=
ac_cv_env_FC_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs'
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_MPIFC_set=
ac_cv_env_MPIFC_value=
ac_cv_env_XMKMF_set=
ac_cv_env_XMKMF_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_prog_ac_ct_CC=x86_64-apple-darwin13.4.0-clang

## ----------------- ##
## Output variables. ##
## ----------------- ##

CC='x86_64-apple-darwin13.4.0-clang'
CFLAGS='-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe'
COMPAT=''
CPP=''
CPPFLAGS='-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9'
CXX='x86_64-apple-darwin13.4.0-clang++'
CXXFLAGS='-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0'
DEFS=''
DEPS_INCLUDES=''
DEPS_LIBS=''
ECHO_C='\c'
ECHO_N=''
ECHO_T=''
EGREP=''
EXEEXT=''
FC=''
FCFLAGS=''
FCFLAGS_f90=''
FCLIBS=''
FFLAGS=''
GREP=''
GUI=''
HAVE_COIN_CONFIG=''
HAVE_SOQT_CONFIG=''
HAVE_SOXT_CONFIG=''
INSTALL_DATA=''
INSTALL_PROGRAM=''
INSTALL_SCRIPT=''
LDFLAGS='-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs'
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
MOC=''
MPIFC=''
MPIFILE='nompi.f90'
OBJEXT=''
OPT_FLAG='-O'
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_URL=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
PLAUT04=''
PLAUT=''
SET_MAKE=''
SHELL='/bin/sh'
SOXT_OBJS=''
SOXT_OBJS_R3B=''
TEK2PS=''
XMKMF=''
X_CFLAGS=''
X_EXTRA_LIBS=''
X_LIBS=''
X_PRE_LIBS=''
ac_ct_CC='x86_64-apple-darwin13.4.0-clang'
ac_ct_CXX=''
ac_ct_FC=''
bindir='${exec_prefix}/bin'
build=''
build_alias=''
build_cpu=''
build_os=''
build_vendor=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE}'
dvidir='${docdir}'
exec_prefix='NONE'
host=''
host_alias=''
host_cpu=''
host_os=''
host_vendor=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
runstatedir='${localstatedir}/run'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define PACKAGE_STRING ""
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""

configure: exit 77

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BjornSandstede avatar BjornSandstede commented on June 7, 2024

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Omer80 avatar Omer80 commented on June 7, 2024

Dear Bjorn,
Yes I have installed xcode, but maybe there is some conflict with the anaconda installation. When I type xcode-select --install I get:
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
When I check gcc version I get:

$ gcc -v
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

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BjornSandstede avatar BjornSandstede commented on June 7, 2024

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bartoldeman avatar bartoldeman commented on June 7, 2024

Yes indeed Anaconda messes it up. There is a long thread about it here:
ContinuumIO/anaconda-issues#9096

Try this:
./configure CC=/usr/bin/gcc CXX=/usr/bin/g++
or (if the above doesn't work) the path order:
export PATH=/usr/bin:$PATH

from auto-07p.

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