Cython: custom blas_lapack_dir crashes Cython compilation / build_thread_safe breaks cti2ctml

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What steps will reproduce the problem?
1. compile latest svn-git(r2546)

What is the expected output? What do you see instead?
compilation crashes

What version of the product are you using? On what operating system?
r2546 on fedora 19

Please provide any additional information below.

compiled using:
$ scons build prefix=/opt/cantera-r2546 \
use_sundials=y sundials_include='/usr/include' sundials_libdir='/usr/lib64' \
python3_package=y python_package=new \
blas_lapack_dir='/usr/lib64/atlas' blas_lapack_libs='lapack,atlas,f77blas' \
doxygen_docs=y build_thread_safe=y boost_thread_lib='boost_thread,boost_system'

adding '/usr/lib64/atlas' to setup2.py and setup3.py (at the 
exts[0].library_dirs entries) manually after they are created fixes the issue 
with Cython. 

For cti2ctml (right after the compilation of python2.7), the following crashes

g++ -o build/bin/cti2ctml -pthread build/src/apps/cti2ctml.o -Lbuild/lib 
-L/usr/lib64/atlas -L/usr/lib64 -lcantera -lsundials_cvodes -lsundials_ida 
-lsundials_nvecserial -latlas
build/lib/libcantera.a(ctexceptions.os): In function 
`__static_initialization_and_destruction_0':
/usr/include/boost/system/error_code.hpp:214: undefined reference to 
`boost::system::generic_category()'
[...]

is missing a -lboost_system to link without errors (which I was unable to force 
passing flags to scons)

Original issue reported on code.google.com by ischo...@gmail.com on 28 Sep 2013 at 3:47

Attachments:

• crash.log
• crash.log

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Here's my cantera.conf for completeness

Original comment by ischo...@gmail.com on 28 Sep 2013 at 3:50

Attachments:

• cantera.conf_thread_safe

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These issues should be addressed by r2554 and r2555.

Original comment by yarmond on 30 Sep 2013 at 2:16

• Changed state: Fixed

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Ray: thanks for the fixes in the build script, but now scons fails during 
testing ... see attached error.log (produced via 'scons test')

Original comment by ischo...@gmail.com on 30 Sep 2013 at 2:29

Attachments:

• error.log

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Original comment by yarmond on 30 Sep 2013 at 3:33

• Changed state: InProgress

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I think r2556 should be a more global fix for this linking problem. Let me know 
if it works.

Original comment by yarmond on 30 Sep 2013 at 4:03

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Ray: I just confirmed that r2556 works (at least on a linux machine with gcc)

Original comment by ischo...@gmail.com on 30 Sep 2013 at 10:49

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Original comment by yarmond on 1 Oct 2013 at 1:51

• Changed state: Fixed