In the past few months, I encountered issues and asked various questions for installation of hscPipe 7.9.1 in Fedora 30, which default compiler is gcc 9.2.1 (see the topics I asked: libicudata.so, undefined symbol, libiomp5.so). With help from a project scientist here, we figured out that most of the issues are related to gcc version, which had been noted at pipeline prerequisites. However, the devtoolset-6 seems unavailable in Fedora 30 for now, and user-installation of gcc 6.3.1 (or later) is somehow difficult and takes time. We think that Conda should be able to handle/solve issues (I think, this is also the reason for using Conda in lsstpipe/hscPipe). Here I share the settings for the installation of hscPipe 7.9.1 in Fedora 30.
bash bash newinstall.sh source loadLSST.bash export INCLUDE="${CONDA_PREFIX}/include" export LD_LIBRARY_PATH="${CONDA_PREFIX}/lib" export LD_RUN_PATH="${LD_LIBRARY_PATH}" conda install -c anaconda gxx_linux-64=7.3.0 conda install -c anaconda libstdcxx-ng=7.3.0 conda install -c anaconda make conda install -c anaconda pkgconfig conda install -c anaconda cmake conda install -c anaconda flex conda install -c anaconda bison conda install -c anaconda boost=1.67.0 conda install -c anaconda boost-cpp=1.67.0 conda install -c anaconda cairo cd $CONDA_PREFIX/bin ln -s x86_64-conda_cos6-linux-gnu-gcc gcc ln -s x86_64-conda_cos6-linux-gnu-g++ g++ ln -s x86_64-conda_cos6-linux-gnu-c++ c++ ln -s x86_64-conda_cos6-linux-gnu-cc cc ln -s x86_64-conda_cos6-linux-gnu-ld ld ln -s x86_64-conda_cos6-linux-gnu-ar ar eups distrib install hscPipe 7.9.1
Then installation will die at [ 52/97 ] sconsUtils 7.0-hsc, which has a checking procedure for compiler name (current $CC is x86_64-conda_cos6-linux-gnu-cc). If you don’t want to manually install sconsUtils via eups, the quick solution for sconsUtils is
export CC=gcc export CXX=g++ eups distrib install sconsUtils 7.0-hsc source loadLSST.bash
The step of “source loadLSST.bash” again is necessary, otherwise the following installations will be confused with gcc in OS, and encounter ld path issue.
However, the checking procedure in installed sconsUtils is still called by following package installations, which will raise the “Unrecognised compiler” error again. So you need to
1. open [install directory]/stack/miniconda3-4.5.12-1172c30/Linux64/sconsUtils/7.0-hsc/python/lsst/sconsUtils/state.py
2. remove the character “^” in front of gcc, icc, clang, and cc, i.e. these in line 336-349.
After the fix of sconsUtils, just start the installation of hscPipe again
eups distrib install hscPipe 7.9.1
Then everything should go smoothly.
Some inputs:
- Using the compilers in Conda is an alternative solution for OS without
devtoolset. - We suggest modifying the code of compiler checking in sconsUtils.
- We notice that, in the installations of some packages, eups will export PATH=/bin:$PATH (something like that, I forgot the exact codes), which forces the installation to use gcc in OS (9.2.1 for Fedora 30). Fortunately, we don’t encounter the issue of
GLIBCXXversion in these packages.