https://community.intel.com/t5/Intel-Distribution-for-Python/BioPython-installation-compile-error/m-p/1064697#M117 <P>I've installed the Intel® Distribution for Python Tech Preview&nbsp;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.&nbsp;</P> <P>Following the download and installation instructions from the BioPython wiki page (http://biopython.org/wiki/Download), 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:</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(58): error: identifier "__ATOMIC_RELAXED" is undefined</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(59): error: identifier "__ATOMIC_ACQUIRE" is undefined</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(60): error: identifier "__ATOMIC_RELEASE" is undefined</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(61): error: identifier "__ATOMIC_ACQ_REL" is undefined</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(62): error: identifier "__ATOMIC_SEQ_CST" is undefined</P> <P>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.&nbsp;<SPAN style="font-size: 1em; line-height: 1.5;">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.&nbsp;</SPAN></P> <P><SPAN style="font-size: 1em; line-height: 1.5;">Any ideas on where these ATOMIC identifiers are defined? I've attached the compilation command with flags and the errors generated during the installation.</SPAN></P> <P>&nbsp;</P> Tue, 29 Mar 2016 18:22:41 GMT ClayB 2016-03-29T18:22:41Z https://community.intel.com/t5/Intel-Distribution-for-Python/BioPython-installation-compile-error/m-p/1064697#M117 <P>I've installed the Intel® Distribution for Python Tech Preview&nbsp;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.&nbsp;</P> <P>Following the download and installation instructions from the BioPython wiki page (http://biopython.org/wiki/Download), 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:</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(58): error: identifier "__ATOMIC_RELAXED" is undefined</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(59): error: identifier "__ATOMIC_ACQUIRE" is undefined</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(60): error: identifier "__ATOMIC_RELEASE" is undefined</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(61): error: identifier "__ATOMIC_ACQ_REL" is undefined</P> <P>/opt/intel/python/3.5.20150803_185146/include/python3.5m/pyatomic.h(62): error: identifier "__ATOMIC_SEQ_CST" is undefined</P> <P>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.&nbsp;<SPAN style="font-size: 1em; line-height: 1.5;">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.&nbsp;</SPAN></P> <P><SPAN style="font-size: 1em; line-height: 1.5;">Any ideas on where these ATOMIC identifiers are defined? I've attached the compilation command with flags and the errors generated during the installation.</SPAN></P> <P>&nbsp;</P> Tue, 29 Mar 2016 18:22:41 GMT https://community.intel.com/t5/Intel-Distribution-for-Python/BioPython-installation-compile-error/m-p/1064697#M117 ClayB 2016-03-29T18:22:41Z https://community.intel.com/t5/Intel-Distribution-for-Python/BioPython-installation-compile-error/m-p/1064698#M118 <P>Hi Clay,</P> <P>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.</P> <P>Thanks,</P> <P><SPAN style="font-size: 1em; line-height: 1.5;">Rohit</SPAN></P> Tue, 29 Mar 2016 19:09:53 GMT https://community.intel.com/t5/Intel-Distribution-for-Python/BioPython-installation-compile-error/m-p/1064698#M118 Rohit_J_Intel 2016-03-29T19:09:53Z