BioPython installation compile error

BioPython installation compile error

I've installed the Intel® Distribution for Python Tech Preview 3.5 on a Linux system (2.6.32-431.el6.x86_64) and now want to install the BioPython 1.66 packages to support a molecular docking application. 

Following the download and installation instructions from the BioPython wiki page (, the Python bits for installation went well. When I get to the compiled C code, I run into an error dealing with undefined identifiers from the Intel Python include files. Specifically, I get the following errors:

/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(58): error: identifier "__ATOMIC_RELAXED" is undefined

/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(59): error: identifier "__ATOMIC_ACQUIRE" is undefined

/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(60): error: identifier "__ATOMIC_RELEASE" is undefined

/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(61): error: identifier "__ATOMIC_ACQ_REL" is undefined

/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(62): error: identifier "__ATOMIC_SEQ_CST" is undefined

I've greped for these identifiers in the include directory, but there is no definition. They are only used in pyatomic.h, which is being included into Python.h. Just to check, I've been able to build and test the BioPython install on a different system with the default Python (2.6) without problems. 

Any ideas on where these ATOMIC identifiers are defined? I've attached the compilation command with flags and the errors generated during the installation.


Downloadtext/plain biopython error.txt2.35 KB
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Hi Clay,

I tested installing biopython with our upcoming release - I was able to install the package. We are releasing our beta soon, you should be able to install biopython with it.



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