Ayla,

I fixed the problem! I had to clear my PATH environment variable of everything except /usr/bin, /bin, and the path to my gcc 4.8 compiler (export PATH=/opt/rh/devtoolset-2/root/usr/bin:/usr/local/bin:/bin:/usr/bin:/usr/sbin:/sbin). I'd been careful about LDFLAGS, CFLAGS and LD_LIBRARY_PATH already.  Since my system is not unusual, perhaps the CMAKE script needs to be edited to more carefully check PATH, to ensure that internally provided binaries aren't being ignored in favor of incompatible system provided binaries. I'd expect an error to occur at the beginning of the build during the configure stage, rather than right at the end. 

I hope from the build log you can find out where things went wrong, since I have no idea which specific binary was the problem. If you want me to try building again or doing anything else to help diagnose the root cause, let me know.

Cheers

Daniel Duke

Postdoctoral Appointee
Energy Systems Division
Argonne National Laboratory

dduke@anl.gov
daniel.j.duke@gmail.com

+1 (630) 252-9175 (Office)
+1 (630) 823-6867 (Mobile)

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From: Ayla Khan [ayla@sci.utah.edu]
Sent: Tuesday, February 23, 2016 3:26 PM
To: Duke, Daniel J.
Cc: seg3d@sci.utah.edu
Subject: Re: [Seg3D] Cmake error linking python static libraries

Hi Daniel,

Can you try building 2.3.0 RC1 (https://github.com/SCIInstitute/Seg3D/releases/tag/v2.3.0_rc1) and see if you get the same error?

Ayla

On Feb 23, 2016, at 2:04 PM, Duke, Daniel J. wrote:

Hi guys 

I am compiling Seg3D on several Red Hat Enterprise Linux machines. Everything builds fine up until the very final step where the Seg3D2 binary is linked, then I get this:

Linking CXX executable ../Seg3D2
/local/fuelspray/Seg3D-2.2.1/bin/Externals/Source/Boost_external/lib/libboost_python-mt.a(builtin_converters.o): In function `boost::python::converter::(anonymous namespace)::signed_int_rvalue_from_python_base::get_pytype()':
builtin_converters.cpp:(.text+0x13): undefined reference to `PyInt_Type'
...
and many other similar errors follow (PyString_Type, PyString_Size, etc are undefined).

Looks to me like a missing static libpython, but looking at the CMakeCache files, it looks like the right libraries are being linked. Maybe libraries linked out-of-order?
This seems like some kind of bug in the cmake scripts, since there is nothing special about my Linux setup that should cause hassle. We've compiled Seg3D on other machines in the past without trouble.

OS is Red Hat Enterprise 6.7. Compiler version is gcc 4.8.2 20140120
uname output: 2.6.32-573.8.1.el6.x86_64 #1 SMP Fri Sep 25 19:24:22 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux
My shell has LDFLAGS and CFLAGS unset.  
LD_LIBRARY_PATH is pointing to my gcc 4.8.2 libs, LD_LIBRARY_PATH=opt/rh/devtoolset-2/root/usr/lib64:/opt/rh/devtoolset-2/root/usr/lib, since otherwise Red Hat will use gcc 4.4.7 by default.
Is this likely to cause trouble for the python3.2 build inside Seg3D?
 
I have attached a complete log of the build process. Let me know what other information I can provide to help solve the issue. It's a great program by the way.

Cheers,
Dr Daniel Duke

Postdoctoral Appointee
Energy Systems Division
Argonne National Laboratory

<build.log>

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