Kenneth, That did the trick. Thank you!
-- Davide Vanzo, PhD Application Developer Adjunct Assistant Professor of Chemical and Biomolecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 (615)-875-9137 www.accre.vanderbilt.edu On 2018-01-02 14:34:58-06:00 [email protected] wrote: Hi Davide, On 02/01/2018 21:29, Vanzo, Davide wrote: Hello EasyBuilders! I am trying to build Python-2.7.12-iccifort-2016.3.210-GCC-5.4.0-2.26.eb (from the intel-2016b easyconfig file I have simply removed the python packages that depend on MPI and MKL) on CentOS 7.2.1511 and for some reason it fails with the error below. I have never seen this error when I built it under CentOS 6.x. Does it ring any bell to any of you? This sounds a lot like the issue we encountered in https://github.com/easybuilders/easybuild-easyconfigs/issues/3646<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feasybuilders%2Feasybuild-easyconfigs%2Fissues%2F3646&data=02%7C01%7Cdavide.vanzo%40vanderbilt.edu%7C60492f13dc124c9b145508d552203a60%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636505220979932081&sdata=F7lWMjqwLJ1n6n1mXsiXt%2B37t2DV4VGIzY87FI5zwqw%3D&reserved=0>, which basically boils down to this version of the Intel compilers not being compatible with CentOS 7.2. The official (!) fix is to copy libintlc.so.5 from a more recent version of the Intel compilers, see also https://bugzilla.redhat.com/show_bug.cgi?id=1377895<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbugzilla.redhat.com%2Fshow_bug.cgi%3Fid%3D1377895&data=02%7C01%7Cdavide.vanzo%40vanderbilt.edu%7C60492f13dc124c9b145508d552203a60%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636505220979932081&sdata=D6yK6055NdMSdv7paJpQIMxRNc1NjbupWsOskRAr6pM%3D&reserved=0> and https://software.intel.com/en-us/articles/intel-compiler-version-16-not-compatible-with-recent-libcso6<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsoftware.intel.com%2Fen-us%2Farticles%2Fintel-compiler-version-16-not-compatible-with-recent-libcso6&data=02%7C01%7Cdavide.vanzo%40vanderbilt.edu%7C60492f13dc124c9b145508d552203a60%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636505220979932081&sdata=ECsUSf3or8X%2BQh17hgDSGOxMJeYK7TCrGD21vOvu7Bw%3D&reserved=0> . regards, Kenneth Attached you can find the full log. Thanks! Modules/posixmodule.o: In function `posix_tmpnam': /mnt/ramdisk/Python/2.7.12/iccifort-2016.3.210/Python-2.7.12/./Modules/posixmodule.c:7631: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp' Modules/posixmodule.o: In function `posix_tempnam': posixmodule.c:(.text+0x4fba): warning: the use of `tempnam' is dangerous, better use `mkstemp' icc -L/accre/arch/easybuild/software/Core/icc/2016.3.210/lib/intel64 -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/bzip2/1.0.6/lib -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/zlib/1.2.8/li\ b -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libreadline/6.3/lib -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/ncurses/6.0/lib -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/SQLi\ te/3.13.0/lib -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/Tk/8.6.5/lib -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/GMP/6.1.1/lib -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/l\ ibffi/3.2.1/lib64 -L/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libffi/3.2.1/lib -Xlinker -export-dynamic -o python \ Modules/python.o \ -L. -lpython2.7 -ldl -liomp5 -lpthread -lutil /accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libreadline/6.3/lib/libreadline.a /accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/ncurse\ s/6.0/lib/libncurses.a -lm LD_LIBRARY_PATH=/mnt/ramdisk/Python/2.7.12/iccifort-2016.3.210/Python-2.7.12:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libffi/3.2.1/lib64:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libffi\ /3.2.1/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/GMP/6.1.1/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/Tk/8.6.5/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/X11/201608\ 19/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/fontconfig/2.12.1/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/expat/2.2.0/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/fre\ etype/2.6.5/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libpng/1.6.24/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/SQLite/3.13.0/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.\ 4.0/Tcl/8.6.5/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libreadline/6.3/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/ncurses/6.0/lib:/accre/arch/easybuild/software/Compiler/GCCcore/\ 5.4.0/zlib/1.2.8/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/bzip2/1.0.6/lib:/accre/arch/easybuild/software/Core/ifort/2016.3.210/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64:/acc\ re/arch/easybuild/software/Core/icc/2016.3.210/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/binutils/2.26/lib:/accre/arch/easybuild/softwar\ e/Core/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/accre/arch/easybuild/software/Core/GCCcore/5.4.0/lib64:/accre/arch/easybuild/software/Core/GCCcore/5.4.0/lib ./python -E -S -m sysconfig --generate-p\ osix-vars ;\ if test $? -ne 0 ; then \ echo "generate-posix-vars failed" ; \ rm -f ./pybuilddir.txt ; \ exit 1 ; \ fi /bin/sh: line 5: 23389 Segmentation fault LD_LIBRARY_PATH=/mnt/ramdisk/Python/2.7.12/iccifort-2016.3.210/Python-2.7.12:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libffi/3.2.1/lib64:/accre/arch/e\ asybuild/software/Compiler/GCCcore/5.4.0/libffi/3.2.1/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/GMP/6.1.1/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/Tk/8.6.5/lib:/accre/arch/easyb\ uild/software/Compiler/GCCcore/5.4.0/X11/20160819/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/fontconfig/2.12.1/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/expat/2.2.0/lib:/accre/arc\ h/easybuild/software/Compiler/GCCcore/5.4.0/freetype/2.6.5/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libpng/1.6.24/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/SQLite/3.13.0/lib:/ac\ cre/arch/easybuild/software/Compiler/GCCcore/5.4.0/Tcl/8.6.5/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/libreadline/6.3/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/ncurses/6.0/lib:/\ accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/zlib/1.2.8/lib:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/bzip2/1.0.6/lib:/accre/arch/easybuild/software/Core/ifort/2016.3.210/compilers_and_libra\ ries_2016.3.210/linux/compiler/lib/intel64:/accre/arch/easybuild/software/Core/icc/2016.3.210/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64:/accre/arch/easybuild/software/Compiler/GCCcore/5.4.0/\ binutils/2.26/lib:/accre/arch/easybuild/software/Core/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/accre/arch/easybuild/software/Core/GCCcore/5.4.0/lib64:/accre/arch/easybuild/software/Core/GCCcore/5.4\ .0/lib ./python -E -S -m sysconfig --generate-posix-vars generate-posix-vars failed make: *** [pybuilddir.txt] Error 1 (at easybuild/EB-develop/easybuild-framework/easybuild/tools/run.py:481 in parse_cmd_output) -- Davide Vanzo, PhD Application Developer Adjunct Assistant Professor of Chemical and Biomolecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 (615)-875-9137 www.accre.vanderbilt.edu<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.accre.vanderbilt.edu&data=02%7C01%7Cdavide.vanzo%40vanderbilt.edu%7C60492f13dc124c9b145508d552203a60%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636505220979932081&sdata=9PEM0uUo5H4g%2BZM34arwv%2BmOqqu%2FEDQYMH47Xc03uck%3D&reserved=0>
