Can't compile Julia on Mac OS X 10.7 (Lion) #636

ksvanhorn · 2012-03-24T04:36:22Z

I upgraded from 10.5 (Leopard) to 10.6 (Snow Leopard) and then to 10.7.3 (Lion). Then I uninstalled my existing gfortran, downloaded and installed the 64-bit gfortran for Lion (gfortran-4.6.2-x86_64-Lion.dmg), downloaded julia with git, and ran make. The compilation continued for some time (albeit with a lot of warnings) and ultimately failed at this point near the end:

Making install in m4
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1216k 100 1216k 0 0 207k 0 0:00:05 0:00:05 --:--:-- 277k
CC src/jltypes.o
CC src/gf.o
CC src/support/hashing.o
CC src/support/timefuncs.o
CC src/support/dblprint.o
CC src/support/ptrhash.o
CC src/support/operators.o
CC src/support/socket.o
CC src/support/utf8.o
CC src/support/ios.o
CC src/support/dirpath.o
CC src/support/htable.o
CC src/support/bitvector.o
CC src/support/int2str.o
CC src/support/dump.o
CC src/support/libsupportinit.o
CC src/support/arraylist.o
LINK src/support/libsupport.a
CC src/flisp/flisp.o
CC src/flisp/builtins.o
CC src/flisp/string.o
CC src/flisp/equalhash.o
CC src/flisp/table.o
CC src/flisp/iostream.o
CC src/flisp/julia_extensions.o
LINK src/flisp/libflisp.a
CC src/flisp/flmain.o
CC src/flisp/flisp
FLISP src/julia_flisp.boot
FLISP src/julia_flisp.boot.inc
CC src/ast.o
CC src/builtins.o
CC src/module.o
CC src/codegen.o
CC src/interpreter.o
CC src/alloc.o
CC src/dlload.o
CC src/sys.o
CC src/init.o
CC src/task.o
CC src/array.o
CC src/dump.o
CC src/gc.o
LINK src/libjulia-release.a
LINK libjulia-release.dylib
PERL base/pcre_h.jl
cc1: warning: unrecognized gcc debugging option: M
PERL base/errno_h.jl
cc1: warning: unrecognized gcc debugging option: M
cc1: warning: unrecognized gcc debugging option: M
CC ui/repl.o
CC ui/repl-basic.o
LINK uijulia-release-basic
CC ui/repl-readline.o
LINK uijulia-release-readline
LINK ui/webserverjulia-release-webserver
JULIA sys0.ji
dlopen(/Users/kevin/Tmp/julia/lib/libsuitesparse.dylib, 2): Symbol not found: ___addtf3
Referenced from: /usr/local/gfortran/lib/libquadmath.0.dylib
Expected in: /usr/lib/libSystem.B.dylib
in /usr/local/gfortran/lib/libquadmath.0.dylib

make[1]: *** [sys0.ji] Error 1
make: *** [release] Error 2

I can provide the complete make output if desired.

ksvanhorn · 2012-03-24T08:27:28Z

Seems the build of readline also fails:

Target: i686-apple-darwin11
Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2336.922/src/configure --disable-checking --enable-werror --prefix=/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]_$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.922/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.9.00)
i686-apple-darwin11-llvm-gcc-4.2: -compatibility_version only allowed with -dynamiclib
make[4]: *_* [libreadline.6.2.dylib] Error 1

It's 2:30 a.m. and I have been trying since early in the evening to get this thing to build...

nolta · 2012-03-24T17:33:43Z

i686-apple-darwin11-llvm-gcc-4.2: -compatibility_version only allowed with -dynamiclib

Does this help:

http://techdebug.com/blog/2009/01/03/compiling-readline-on-an-osx-105-intel-x86_64/

?

ksvanhorn · 2012-03-24T18:17:52Z

Thanks, that fixed the readline problem. For anyone else who has this problem, I went to the external directory and issued this command to rebuild readline:

make -B install-readline SHOBJ_LDFLAGS=-dynamiclib

Now if I can just get this "Symbol not found" business straightened out.

StefanKarpinski · 2012-03-24T18:45:48Z

That cc1 warning is worrying. What version of gcc and gfortran do you have?

ksvanhorn · 2012-03-24T19:32:53Z

mac> gcc --version
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.9.00)

mac> gfortran --version
GNU Fortran (GCC) 4.6.2 20111019 (prerelease)

After upgrading to Lion I installed XCode 4.3.2 and and its Command Line Tools, presuming that this would get me reasonably up-to-date versions of all the developer tools. For gfortran I followed the Julia "Source Download and Compilation" instructions:

Either download and install gfortran from hpc.sf.net, or 64-bit gfortran from gcc.gnu.org.

I opted for the latter, specifically, http://quatramaran.ens.fr/~coudert/gfortran/gfortran-4.6.2-x86_64-Lion.dmg

StefanKarpinski · 2012-03-24T19:35:15Z

Ok, those versions are all perfectly reasonable. Hmm...

ksvanhorn · 2012-03-24T19:49:36Z

Here's another datum that might (or might not) be relevant. When I try to run the prebuilt julia binaries for Mac OS X, I get this error:

dlopen(/Users/kevin/Downloads/julia/lib/libamos.dylib, 2): Library not loaded: /usr/local/lib/libgfortran.3.dylib
Referenced from: /Users/kevin/Downloads/julia/lib/libamos.dylib
Reason: image not found
error during init:
could not load module libamos
in dlopen at /Users/viral/julia/jl/base.jl:98
at string:15

If I add /usr/local/gfortran/lib to DYLD_LIBRARY_PATH it takes care of that error, but I still get pretty much the same error I'm getting when I build julia myself:

dlopen(/Users/kevin/Downloads/julia/lib/libamos.dylib, 2): Symbol not found: ___addtf3
Referenced from: /usr/local/gfortran/lib/libquadmath.0.dylib
Expected in: /usr/lib/libSystem.B.dylib
in /usr/local/gfortran/lib/libquadmath.0.dylib
error during init:
could not load module libamos
in dlopen at /Users/viral/julia/jl/base.jl:98
at string:15

ksvanhorn · 2012-03-24T19:54:32Z

One other thing -- I've tried it both with and without using the system BLAS and LAPACK, by uncommenting

ifeq ($(OS), Darwin)
USE_SYSTEM_BLAS=1
USE_SYSTEM_LAPACK=1
endif

in Make.inc. The only difference I've seen is (no suprise) in build time.

StefanKarpinski · 2012-03-24T19:55:53Z

The function __addtf3 is a GCC software floating point routine:

http://www.opensource.apple.com/source/gcc/gcc-5666.3/gcc/config/soft-fp/addtf3.c

It looks like GCC isn't finding that function for some reason.

ksvanhorn · 2012-03-25T02:06:10Z

I ran a script to run nm on every *.dylib file under /usr; these are the only ones that mention ___addtf3:

/usr/local/gfortran/lib/i386/libgfortran.3.dylib : U ___addtf3
/usr/local/gfortran/lib/i386/libgfortran.dylib : U ___addtf3
/usr/local/gfortran/lib/i386/libquadmath.0.dylib : U ___addtf3
/usr/local/gfortran/lib/i386/libquadmath.dylib : U ___addtf3
/usr/local/gfortran/lib/libgcc_ext.10.4.dylib : 0000000000005330 T ___addtf3
/usr/local/gfortran/lib/libgcc_ext.10.5.dylib : 0000000000005330 T ___addtf3
/usr/local/gfortran/lib/libgcc_s.1.dylib : 0000000000005330 T ___addtf3
/usr/local/gfortran/lib/libgcc_s_ppc64.1.dylib : 0000000000005330 T ___addtf3
/usr/local/gfortran/lib/libgcc_s_x86_64.1.dylib : 0000000000005330 T ___addtf3
/usr/local/gfortran/lib/libgfortran.3.dylib : U ___addtf3
/usr/local/gfortran/lib/libgfortran.dylib : U ___addtf3
/usr/local/gfortran/lib/libquadmath.0.dylib : U ___addtf3
/usr/local/gfortran/lib/libquadmath.dylib : U ___addtf3

aviks · 2012-03-25T17:49:32Z

FWIW, I recently upgraded from SnowLeopard to Lion, and successfully re-compiled julia and its dependencies using

Gfortran from http://quatramaran.ens.fr/~coudert/gfortran/gfortran-4.6.2-x86_64-Lion.dmg

$gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin11/4.6.2/lto-wrapper
Target: x86_64-apple-darwin11
Configured with: ../gcc-4.6.2-RC-20111019/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/deps-static/x86_64 --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin11
Thread model: posix
gcc version 4.6.2 20111019 (prerelease) (GCC)

and GCC

$gcc -v
Using built-in specs.
Target: i686-apple-darwin11
Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2336.9~22/src/configure --disable-checking --enable-werror --prefix=/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.9~22/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.9.00)

ksvanhorn · 2012-03-25T18:41:19Z

I found the solution: putting /usr/local/gfortran/lib at the beginning of DYLD_LIBRARY_PATH solved the problem. Previously I had .../gfortran/lib at the end of DYLD_LIBRARY_PATH.

StefanKarpinski · 2012-03-25T18:55:23Z

Ah. That's interesting. I generally don't have DYLD_LIBRARY_PATH set at all.

StefanKarpinski · 2012-03-25T19:46:12Z

Should we put some kind of note about DY/LD_LIBRARY_PATH in the install docs?

ViralBShah · 2012-03-26T02:59:18Z

With this version of gfortran, -static-gfortran would solve this problem, but create problems on some older versions of gfortran. Of course that flag does not include libquadmath, so it is only a partial solution, if at all it works.

…uliaLang#636)

JeffBezanson closed this as completed in f3b295c Apr 14, 2012

keflavich mentioned this issue Oct 6, 2013

Mac OS install issues JohannesBuchner/PyMultiNest#21

Closed

LilithHafner pushed a commit to LilithHafner/julia that referenced this issue Oct 11, 2021

add replace and ordered keywords for sample! method (JuliaLang#633) (J…

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Can't compile Julia on Mac OS X 10.7 (Lion) #636

Can't compile Julia on Mac OS X 10.7 (Lion) #636

ksvanhorn commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

nolta commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

StefanKarpinski commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

StefanKarpinski commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

StefanKarpinski commented Mar 24, 2012

ksvanhorn commented Mar 25, 2012

aviks commented Mar 25, 2012

ksvanhorn commented Mar 25, 2012

StefanKarpinski commented Mar 25, 2012

StefanKarpinski commented Mar 25, 2012

ViralBShah commented Mar 26, 2012

Can't compile Julia on Mac OS X 10.7 (Lion) #636

Can't compile Julia on Mac OS X 10.7 (Lion) #636

Comments

ksvanhorn commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

nolta commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

StefanKarpinski commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

StefanKarpinski commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

ksvanhorn commented Mar 24, 2012

StefanKarpinski commented Mar 24, 2012

ksvanhorn commented Mar 25, 2012

aviks commented Mar 25, 2012

ksvanhorn commented Mar 25, 2012

StefanKarpinski commented Mar 25, 2012

StefanKarpinski commented Mar 25, 2012

ViralBShah commented Mar 26, 2012