DSDP: Undefined symbols: _ATL_cGetNB _ATL_dGetNB _ATL_sGetNB _ATL_zGetNB __gfortran_compare_string __gfortran_concat_string

[yotam@…]

DSDP is a dependency of py27-cvxopt, which I am trying to install.

It failed during build with a bunch of linker errors (regarding ATLAS and gfortran) inside liblapack.a (see attached "DSDP main.log 1.txt"). (The error log also has a line 'could not read "/opt/local/lib/libtatlas.dylib": no such file or directory' but it definitely exists.)

Trying again to install DSDP complains sometimes that 'couldn't open "/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tclIndex": no such file or directory' (see attached "DSDP main.log 2.txt") --- that file does *not* exist on my fresh Mountain Lion 10.8.1 machine.

[ryandesign (Ryan Carsten Schmidt)]

Replying to yotam@…:

It failed during build with a bunch of linker errors (regarding ATLAS and gfortran) inside liblapack.a (see attached "DSDP main.log 1.txt").

Yes, that seems to be the relevant error that needs to be addressed:

:info:build Undefined symbols for architecture x86_64:
:info:build   "_ATL_cGetNB", referenced from:
:info:build       _ATL_ilaenv in liblapack.a(ATL_ilaenv.o)
:info:build   "_ATL_dGetNB", referenced from:
:info:build       _ATL_ilaenv in liblapack.a(ATL_ilaenv.o)
:info:build   "_ATL_sGetNB", referenced from:
:info:build       _ATL_ilaenv in liblapack.a(ATL_ilaenv.o)
:info:build   "_ATL_zGetNB", referenced from:
:info:build       _ATL_ilaenv in liblapack.a(ATL_ilaenv.o)
:info:build   "__gfortran_compare_string", referenced from:
:info:build       _ilaenv_ in liblapack.a(ilaenv.o)
:info:build   "__gfortran_concat_string", referenced from:
:info:build       _dormtr_ in liblapack.a(dormtr.o)
:info:build       _dormql_ in liblapack.a(dormql.o)
:info:build       _dormqr_ in liblapack.a(dormqr.o)
:info:build ld: symbol(s) not found for architecture x86_64

You might try if building DSDP with a different compiler would help.

(The error log also has a line 'could not read "/opt/local/lib/libtatlas.dylib": no such file or directory' but it definitely exists.)

I've occasionally seen MacPorts print inexplicable errors like this about files that are not related to the port currently being installed. Probably it's some stale information left in memory from a previous port install. We should fix it, but it's unimportant to error you're experiencing.

Trying again to install DSDP complains sometimes that 'couldn't open "/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tclIndex": no such file or directory' (see attached "DSDP main.log 2.txt") --- that file does *not* exist on my fresh Mountain Lion 10.8.1 machine.

This message should be ignored. Another problem that is unrelated but that we should eventually fix if we can figure out how.

[yotam@…]

I tried building DSDP with a different compiler, as per the wiki instructions:

Xcode 4.2 and later

If a port foo fails to build and you're using Xcode 4.2 or later, the default compiler is clang; try compiling with llvm-gcc-4.2 instead:

sudo port clean foo
sudo port install foo configure.compiler=llvm-gcc-4.2

If that fails, try installing the apple-gcc42 port and compiling with that:

sudo port clean foo
sudo port install apple-gcc42
sudo port install foo configure.compiler=apple-gcc-4.2 configure.cxx=g++-apple-4.2

<<<

Both alternate compilers (llvm-gcc-4.2 and apple-gcc42) produced the exact same linker errors.

[garydoranjr@…]

Cc Me!

[miranda.henrique@…]

Cc Me!

[proteinyang@…]

main.log from DSDP installation

[proteinyang@…]

I got the same problem:

:info:build /usr/bin/llvm-gcc-4.2 -O3 -arch x86_64 -o maxcut maxcut.o /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_DSDP/DSDP/work/DSDP5.8/lib/libdsdp.a -llapack -lblas -lm
:info:build Undefined symbols for architecture x86_64:
:info:build   "_ATL_cGetNB", referenced from:

I tried different compiler, e.g. llvm-gcc-4.2 and apple-gcc-4.2, but not help...

[proteinyang@…]

Cc Me!

[fred.jendrzejewski@…]

Hi,

I tried everything proposed in the bug reports, but I were not able to solve it. Any other ideas?

Replying to yotam@…:

DSDP is a dependency of py27-cvxopt, which I am trying to install.

It failed during build with a bunch of linker errors (regarding ATLAS and gfortran) inside liblapack.a (see attached "DSDP main.log 1.txt"). (The error log also has a line 'could not read "/opt/local/lib/libtatlas.dylib": no such file or directory' but it definitely exists.)

Trying again to install DSDP complains sometimes that 'couldn't open "/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tclIndex": no such file or directory' (see attached "DSDP main.log 2.txt") --- that file does *not* exist on my fresh Mountain Lion 10.8.1 machine.

[yotam@…]

A solution to get py27-cvxopt installed is to use the -dsdp variant.

[jjstickel (Jonathan Stickel)]

Cc Me!

[jjstickel (Jonathan Stickel)]

I suspect that DSDP needs to be patched to work with current version of atlas. Upstream development of DSDP has stalled (I see no activity since 2006).

#37097 is related, but is not necessarily a duplicate (request for +/-atlas variant).

py-cvxopt has its own atlas problems: see #38887.

[mf2k (Frank Schima)]

mnick has retired.

[ryandesign (Ryan Carsten Schmidt)]

Duplicate #42016 includes a patch.

[ryandesign (Ryan Carsten Schmidt)]

#39152 may be a duplicate, and includes a patch.

[ryandesign (Ryan Carsten Schmidt)]

Has duplicate #38172.

[ryandesign (Ryan Carsten Schmidt)]

Replying to ryandesign@…:

#39152 may be a duplicate, and includes a patch.

The patch fixes the problem. Committed in r115520.

[accounts@…]

I still received a linker error regarding atlas with macports version: 2.3.3 It seems the DSDP dependency on atlas hasn't been added to the port.

I worked around this by installing "atlas" explicitly.

$ sudo port install atlas

[tiagofrepereira2012 (Tiago Freitas Pereira)]

Hi,

I detected the same issue. Follow attached my log files.

Thanks Tiago