Dear Easybuilders,
we recently installed FSL/6.0.3-foss-2019b-Python-3.7.4 on our cluster, but not with GPU support. The available Easyconfig was not quite working for us but we were able to fix the problems with a few additional patches. One patch adds the missing im* scripts, and two other patches fix compilation errors in two of the modules. These patches add using namespaces, an include guard and one function call was missing an argument. The last one was a bit tricky and needed an educated guess what the missing argument should be. There is a PR with the changes: https://github.com/easybuilders/easybuild-easyconfigs/pull/10461 Best wishes and good luck Stefan ________________________________ From: [email protected] <[email protected]> on behalf of Sam Moors <[email protected]> Sent: Friday, April 17, 2020 2:51:29 PM To: [email protected] Subject: Re: [easybuild] Build FSL fail Hi Yann, In your log file the software depending on MPI are in the directory /opt/ebsofts/MPI/GCC-CUDA whereas your EBROOTBOOST points to /opt/ebsofts/MPI/GCC Could this be the source of your problem? Sam On Fri, Apr 17, 2020 at 11:54 AM Yann Sagon <[email protected]<mailto:[email protected]>> wrote: Hello, Le 17.04.2020 à 10:26, Kenneth Hoste a écrit : This looks like a Boost module that was not installed with EasyBuild, or was it? Does it define the $EBROOTBOOST environment variable? If not, that explains why "get_software_root" is failing for Boost... ml show Boost --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- /opt/ebmodules/all/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Boost/1.67.0.lua: --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- help([[ Description =========== Boost provides free peer-reviewed portable C++ source libraries. More information ================ - Homepage: http://www.boost.org/ ]]) whatis("Description: Boost provides free peer-reviewed portable C++ source libraries.") whatis("Homepage: http://www.boost.org/";) conflict("Boost") prepend_path("CPATH","/opt/ebsofts/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Boost/1.67.0/include") prepend_path("LD_LIBRARY_PATH","/opt/ebsofts/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Boost/1.67.0/lib") prepend_path("LIBRARY_PATH","/opt/ebsofts/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Boost/1.67.0/lib") setenv("EBROOTBOOST","/opt/ebsofts/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Boost/1.67.0") setenv("EBVERSIONBOOST","1.67.0") setenv("EBDEVELBOOST","/opt/ebsofts/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Boost/1.67.0/easybuild/MPI-GCC-7.3.0-2.30-OpenMPI-3.1.1-Boost-1.67.0-easybuild-devel") setenv("BOOST_ROOT","/opt/ebsofts/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Boost/1.67.0") == 2019-06-06 14:02:15,378 easyblock.py:278 INFO This is EasyBuild 3.9.0 (framework: 3.9.0, easyblocks: 3.9.0) on host master.cluster. As this version of Boost was installed on our old server with CentOS6, I rebuilt it right now on CentOS7 just in case. [sagon@node025 f] $ ml show Boost --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- /opt/ebmodules/all/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/Boost/1.67.0.lua: --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- help([[ Description =========== Boost provides free peer-reviewed portable C++ source libraries. More information ================ - Homepage: http://www.boost.org/ ]]) whatis("Description: Boost provides free peer-reviewed portable C++ source libraries.") whatis("Homepage: http://www.boost.org/";) whatis("URL: http://www.boost.org/";) conflict("Boost") prepend_path("CPATH","/opt/ebsofts/Boost/1.67.0-foss-2018b/include") prepend_path("LD_LIBRARY_PATH","/opt/ebsofts/Boost/1.67.0-foss-2018b/lib") prepend_path("LIBRARY_PATH","/opt/ebsofts/Boost/1.67.0-foss-2018b/lib") setenv("EBROOTBOOST","/opt/ebsofts/Boost/1.67.0-foss-2018b") setenv("EBVERSIONBOOST","1.67.0") setenv("EBDEVELBOOST","/opt/ebsofts/Boost/1.67.0-foss-2018b/easybuild/MPI-GCC-7.3.0-2.30-OpenMPI-3.1.1-Boost-1.67.0-easybuild-devel") setenv("BOOST_ROOT","/opt/ebsofts/Boost/1.67.0-foss-2018b") you can see it is now installed with fixed-installdir-naming-scheme = 1, it wasn't the case for the previous build. I tried to rebuild FSL and I got the same error message. Here is the log with the debug flag: https://gist.github.com/ysagon/428b4ecc12a6499c41ab147dd456405e/raw/f52133077c309387a981015434bd9557e45404d5/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb Best
