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All Python applications in use in LCLS production must be tested and verified against the updated version before changing the default version of Python.
Testers must can use the following environment settings to properly test their applications against Python 2.7.13 64-bit:
Configuring LCLS production environment for testing
Method 1
If you would like full control over your user environment settings, use the following instructions.
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The following instructions assume that you are using the Bash shell, and that ${LCLS_ROOT}=/usr/local/lcls. Steps 1-4 are required. |
Add the new Python path instance to your environment:
Code Block language bash theme Confluence export PYTHON_ROOT=${LCLS_ROOT}/package/python/python2.7.13/linux-x86_64
Add the new Python binaries to the PATH environment variable:
Code Block language bash theme Confluence export PATH=${QT_HOME}/bin:${ORACLE_HOME}/bin:${PYTHON_ROOT}/bin:${PATH}
Add the new Python libraries and their dependencies (EPICS 64-bit, Matlab, etc.) to the LD_LIBRARY_PATH environment variable. This is to ensure that the new 64-bit versions of Python modules built against those dependencies will work:
Code Block language bash theme Confluence export LD_LIBRARY_PATH=${LCLS_ROOT}/matlab/2016b/extern/lib:${EPICS_BASE_RELEASE}/lib/linux-x86_64:${EPICS_EXTENSIONS}/lib/linux-x86_64:${EPICS_BASE_TOP}/base-cpp-R4-6-0/lib/linux-x86_64:${PYTHON_ROOT}/lib:${PYTHON_ROOT}/build/Python2.7.13/Lib:${LD_LIBRARY_PATH}
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Set the PYTHONPATH environment variable. This is to ensure that there are no false positives when testing applications, since the current PYTHONPATH may still have access to older versions of Python modules and override the new libraries:
Info title Note The ${EPICS_BASE_TOP}/base-cpp-R4-6-0/pvaPy/lib/python/2.7/linux-x86_64 directory contains EPICS V4 Python modules.
The /usr/local/lcls/tools/python/toolbox directory contains SLAC-maintained Python modules.Code Block language bash theme Confluence export PYTHONPATH=${EPICS_BASE_TOP}/base-cpp-R4-6-0/pvaPy/lib/python/2.7/linux-x86_64:${LCLS_ROOT}/tools/python/toolbox
[Optional] If your application(s) import the "cx_Oracle" module, add /change the following in to your environment:
export ORACLE_HOME= ${LCLS_ROOT} /package/oracle/product/ 11 . 2 . 0 . 2 .0_x86_64/client_1exportCode Block language bash theme Confluence export PATH=${ORACLE_HOME}/bin:${PATH}
export LD_LIBRARY_PATH=${ORACLE_HOME}/lib:${LD_LIBRARY_PATH}
[Optional] If your application(s) import "PyQt", "PyQwt", or any other Python modules that depend on QtQt4 64-bit, add /change the following in to your environment:
Code Block language bash theme Confluence export QT_HOME=${LCLS_ROOT}/package/Qt/Qt-4.8.6/linux-x86_64 export PATH=${QT_HOME}/bin:${PATH} export LD_LIBRARY_PATH=${QT_HOME}/lib:${LD_LIBRARY_PATH}
If your application uses Qt5 64-bit, add the following to your environment (needs updated gcc and glibc):Code Block language bash theme Confluence export LD_LIBRARY_PATH=${LCLS_ROOT}/package/gcc/gcc-4.9.4/lib:${LD_LIBRARY_PATH} export LD_LIBRARY_PATH=/usr/local/lcls/package/gcc/gcc-4.9.4/lib64:$LD_LIBRARY_PATH export QT_HOME=${LCLS_ROOT}/package/Qt/Qt-5.9.1/linux-x86_64 export PATH=${QT_HOME}/bin:${PATH}
export LD_LIBRARY_PATH=${QT_HOME}/lib:${LD_LIBRARY_PATH}
Method 2
If you would like to use the full Python 2.7.13 64-bit environment and all of its dependencies, invoke or copy the lines in source the following setup script provided in $TOOLS/script:
, which does all of the steps in Method 1, including the optional ones:
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Be aware of your environment settings before and after testing your Python applications. |
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source /usr/local/lcls/tools/script/go_python2.7.13.bash |
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#!/bin/bash # Sets the user environment to use Python2.7.13 if [ -d /afs/slac/g/lcls ]; then export LCLS_ROOT=/afs/slac/g/lcls else export LCLS_ROOT=/usr/local/lcls fi # Set default Java to 64-bit export JAVA_HOME=${LCLS_ROOT}/package/java/jdk1.8.0_144 if [ -z `echo "${PATH}" | grep "${JAVA_HOME}/bin"` ]; then export PATH=${JAVA_HOME}/bin:${PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${JAVA_HOME}/lib"` ]; then export LD_LIBRARY_PATH=${JAVA_HOME}/lib:${LD_LIBRARY_PATH} fi # Add Qt4 to 64-bit for PyQwt and PyQt4 compatibility export QT_HOME=${LCLS_ROOT}/package/Qt/Qt-4.8.6/linux-x86_64 if [ -z `echo "${PATH}" | grep "${QT_HOME}/bin"` ]; then export PATH=${QT_HOME}/bin:${PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${QT_HOME}/lib"` ]; then export LD_LIBRARY_PATH=${QT_HOME}/lib:${LD_LIBRARY_PATH} fi # Add Qt5 64-bit for PyQwt and PyQt5 compatibility (requires updated gcc and glibc, # sets default Qt to Qt5) if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${LCLS_ROOT}/package/gcc/gcc-4.9.4/lib"` ]; then export LD_LIBRARY_PATH=${LCLS_ROOT}/package/gcc/gcc-4.9.4/lib:${LD_LIBRARY_PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${LCLS_ROOT}/package/gcc/gcc-4.9.4/lib64"` ]; then export LD_LIBRARY_PATH=${LCLS_ROOT}/package/gcc/gcc-4.9.4/lib64:${LD_LIBRARY_PATH} fi export QT_HOME=${LCLS_ROOT}/package/Qt/Qt-5.9.1/linux-x86_64 if [ -z `echo "${PATH}" | grep "${QT_HOME}/bin"` ]; then export PATH=${QT_HOME}/bin:${PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${QT_HOME}/lib"` ]; then export LD_LIBRARY_PATH=${QT_HOME}/lib:${LD_LIBRARY_PATH} fi # Set default Oracle client to 11.2.0.2.0 64-bit for cx_Oracle compatibility export ORACLE_HOME=${LCLS_ROOT}/package/oracle/product/11.2.0.2.0_x86_64/client_1 if [ -z `echo "${PATH}" | grep "${ORACLE_HOME}/bin"` ]; then export PATH=${ORACLE_HOME}/bin:${PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${ORACLE_HOME}/lib"` ]; then export LD_LIBRARY_PATH=${ORACLE_HOME}/lib:${LD_LIBRARY_PATH} fi # Set default Matlab to 2016b 64-bit for matlab_wrapper compatibility if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${LCLS_ROOT}/matlab/2016b/extern/lib"` ]; then export LD_LIBRARY_PATH=${LCLS_ROOT}/matlab/2016b/extern/lib:${LD_LIBRARY_PATH} fi # Set default EPICS to 64-bit for pyca and psp compatibility if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${EPICS_BASE_RELEASE}/lib/linux-x86_64"` ]; then export LD_LIBRARY_PATH=${EPICS_BASE_RELEASE}/lib/linux-x86_64:${LD_LIBRARY_PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${EPICS_EXTENSIONS}/lib/linux-x86_64"` ]; then export LD_LIBRARY_PATH=${EPICS_EXTENSIONS}/lib/linux-x86_64:${LD_LIBRARY_PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${EPICS_BASE_TOP}/base-cpp-R4-6-0/lib/linux-x86_64"` ]; then export LD_LIBRARY_PATH=${EPICS_BASE_TOP}/base-cpp-R4-6-0/lib/linux-x86_64:${LD_LIBRARY_PATH} fi # Set default Python to 2.7.13 64-bit export PYTHON_ROOT=${LCLS_ROOT}/package/python/python2.7.13/linux-x86_64 if [ -z `echo "${PATH}" | grep "${PYTHON_ROOT}/bin"` ]; then export PATH=${PYTHON_ROOT}/bin:${PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${PYTHON_ROOT}/lib"` ]; then export LD_LIBRARY_PATH=${PYTHON_ROOT}/lib:${LD_LIBRARY_PATH} fi if [ -z `echo "${LD_LIBRARY_PATH}" | grep "${PYTHON_ROOT}/build/Python2.7.13/Lib"` ]; then export LD_LIBRARY_PATH=${PYTHON_ROOT}/build/Python2.7.13/Lib:${LD_LIBRARY_PATH} fi # Update PYTHONPATH for EPICS V4 64-bit and SLAC-maintained module dependencies export PYTHONPATH=${EPICS_BASE_TOP}/base-cpp-R4-6-0/pvaPy/lib/python/2.7/linux-x86_64:${LCLS_ROOT}/tools/python/toolbox |
Workarounds
After testing, it may be discovered that certain applications may not run with Python 2.7.13 64-bit due to unresolved/conflicting dependencies (e.g., Python modules only available for 32-bit Python, Matlab2016b, Qt, etc.) or other reasons. If such dependencies cannot currently be resolved, Python developers may invoke the following environment settings in a wrapper script or similar to launch the application using the older instance of Python instead:
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| The script above may introduce duplicate paths into your environment settings. Be aware of your environment settings before and after testing your Python applications.
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The following instructions assume that you are using the Bash shell, and that ${LCLS_ROOT}=/usr/local/lcls. The steps below will set your default Python instance to Python 2.7.4 32-bit. Any Python applications that have 64-bit dependencies will no longer work with this environment setup. |
Add the previous Python instance (Python 2.7.4 32-bit) to your environment:
Code Block language bash theme Confluence export PYTHON_ROOT=${LCLS_ROOT}/package/python/python2.7.4
Add the previous Python binaries to your environment:
Code Block language bash theme Confluence export PATH=${PYTHON_ROOT}/bin:${PATH}
Add the 32-bit Python libraries and their dependencies to your environment:
Code Block language bash theme Confluence export LD_LIBRARY_PATH=${PYTHON_ROOT}/lib:${LD_LIBRARY_PATH} export LD_LIBRARY_PATH=${PYTHON_ROOT}/lib/python2.7/lib-dynload:${LD_LIBRARY_PATH}
[Optional] If your application(s) import the 32-bit "cx_Oracle" module, add the following to your environment:
Code Block language bash theme Confluence export ORACLE_HOME=${LCLS_ROOT}/package/oracle/product/11.1.0.6/client export PATH=${ORACLE_HOME}/bin:${PATH} export LD_LIBRARY_PATH=${ORACLE_HOME}/lib:${LD_LIBRARY_PATH}
[Optional] If your application(s) import "PyQt4", "PyQwt", or any other 32-bit Qt dependencies, add the following to your environment:
Code Block language bash theme Confluence export QT_HOME=${LCLS_ROOT}/package/Qt-4.8.5 export PATH=${QT_HOME}/bin:${PATH} export LD_LIBRARY_PATH=${QT_HOME}/lib:${LD_LIBRARY_PATH}
[Optional] If your application(s) import "matlab_wrapper" or any other 32-bit Matlab 2012a dependent modules, add the following to your environment:
Code Block language bash theme Confluence export LD_LIBRARY_PATH=${LCLS_ROOT}/matlab/2012a/extern/lib:${LD_LIBRARY_PATH}
[Optional] If your application has dependencies on 32-bit pvaPy, set the following in your Python path:
Code Block language bash theme Confluence export PYTHONPATH=${EPICS_BASE_TOP}/base-cpp-R4-6-0/pvaPy/lib/python/2.7/linux-x86:${TOOLS}/python/toolbox