Re: [easybuild] Build of iomkl-2018a.eb fails
Building from PR 5949 worked for me: $ eb --from-pr 5949 OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb == temporary log file in case of crash /tmp/eb-WgkLyV/easybuild-d11n9L.log == processing EasyBuild easyconfig /tmp/eb-WgkLyV/files_pr5949/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb == building and installing OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == testing... == installing... == taking care of extensions... == postprocessing... == sanity checking... == cleaning up... == creating module... == permissions... == packaging... == COMPLETED: Installation ended successfully == Results of the build can be found in the log file(s) /home/modules/software/OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28/easybuild/easybuild-OpenMPI-2.1.2-20180306.100945.log == Build succeeded for 1 out of 1 == Temporary log file(s) /tmp/eb-WgkLyV/easybuild-d11n9L.log* have been removed. == Temporary directory /tmp/eb-WgkLyV has been removed. Thanks a lot! /Ole On 03/05/2018 03:43 PM, Kenneth Hoste wrote: Dear Ole, See also https://github.com/easybuilders/easybuild-easyconfigs/issues/5805. Maybe we should just include --without-ucx in the easyconfig, since the installation can never work for OpenMPI 2.1.1 (and 2.1.2?) with UCX enabled? regards, Kenneth On 05/03/2018 15:36, Balázs Hajgató wrote: Dear Ole, use configopts += '--without-ucx ' in the OpenMPI easyconfig Sincerely, Balazs On 05/03/2018 15:27, Ole Holm Nielsen wrote: Using EB 3.5.2 I'm trying to build the latest iomkl: eb iomkl-2018a.eb -r This works like a charm on 2 of our 3 binary architectures, but on our Sandy Bridge nodes with Mellanox Infiniband the build aborts: # eb iomkl-2018a.eb -r == temporary log file in case of crash /tmp/eb-Dnjmix/easybuild-6WeIK9.log == resolving dependencies ... == processing EasyBuild easyconfig /home/modules/software/EasyBuild/3.5.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.2-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb == building and installing OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == FAILED: Installation ended unsuccessfully (build directory: /home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28): build failed (first 300 chars): cmd " make -j 16 " exited with exit code 2 and output: Making all in config make[1]: Entering directory `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/config' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/icc ... The end of the log file /tmp/eb-Dnjmix/easybuild-OpenMPI-2.1.2-20180305.144907.SAFtP.log contains: libtool: error: require no space between '-L' and '-lrt' make[2]: *** [libmca_pml_ucx.la] Error 1 make[2]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/ompi/mca/pml/ucx' make[1]: *** [all-recursive] Error 1 I can't make out what's causing this. Perhaps the build server has a library installed triggering an error? Thanks for any suggestions!
Re: [easybuild] Build of iomkl-2018a.eb fails
To clarify, it's a bug in the OpenMPI configure script when dealing with UCX which they haven't fixed. On 03/05/2018 03:36 PM, Balázs Hajgató wrote: > Dear Ole, > > use > configopts += '--without-ucx ' > > in the OpenMPI easyconfig > > Sincerely, > > Balazs > > > On 05/03/2018 15:27, Ole Holm Nielsen wrote: >> Using EB 3.5.2 I'm trying to build the latest iomkl: >> >> eb iomkl-2018a.eb -r >> >> This works like a charm on 2 of our 3 binary architectures, but on our >> Sandy Bridge nodes with Mellanox Infiniband the build aborts: >> >> # eb iomkl-2018a.eb -r >> == temporary log file in case of crash >> /tmp/eb-Dnjmix/easybuild-6WeIK9.log >> == resolving dependencies ... >> == processing EasyBuild easyconfig >> /home/modules/software/EasyBuild/3.5.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.2-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb >> >> == building and installing >> OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28... >> == fetching files... >> == creating build dir, resetting environment... >> == unpacking... >> == patching... >> == preparing... >> == configuring... >> == building... >> == FAILED: Installation ended unsuccessfully (build directory: >> /home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28): >> build failed (first 300 chars): cmd " make -j 16 " exited with exit >> code 2 and output: >> Making all in config >> make[1]: Entering directory >> `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/config' >> >> make[1]: Nothing to be done for `all'. >> make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/icc >> ... >> >> The end of the log file >> /tmp/eb-Dnjmix/easybuild-OpenMPI-2.1.2-20180305.144907.SAFtP.log >> contains: >> >> libtool: error: require no space between '-L' and '-lrt' >> make[2]: *** [libmca_pml_ucx.la] Error 1 >> make[2]: Leaving directory >> `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/ompi/mca/pml/ucx' >> >> make[1]: *** [all-recursive] Error 1 >> >> I can't make out what's causing this. Perhaps the build server has a >> library installed triggering an error? >> >> Thanks for any suggestions! >> > -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
Re: [easybuild] Build of iomkl-2018a.eb fails
Dear Ole, See also https://github.com/easybuilders/easybuild-easyconfigs/issues/5805. Maybe we should just include --without-ucx in the easyconfig, since the installation can never work for OpenMPI 2.1.1 (and 2.1.2?) with UCX enabled? regards, Kenneth On 05/03/2018 15:36, Balázs Hajgató wrote: Dear Ole, use configopts += '--without-ucx ' in the OpenMPI easyconfig Sincerely, Balazs On 05/03/2018 15:27, Ole Holm Nielsen wrote: Using EB 3.5.2 I'm trying to build the latest iomkl: eb iomkl-2018a.eb -r This works like a charm on 2 of our 3 binary architectures, but on our Sandy Bridge nodes with Mellanox Infiniband the build aborts: # eb iomkl-2018a.eb -r == temporary log file in case of crash /tmp/eb-Dnjmix/easybuild-6WeIK9.log == resolving dependencies ... == processing EasyBuild easyconfig /home/modules/software/EasyBuild/3.5.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.2-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb == building and installing OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == FAILED: Installation ended unsuccessfully (build directory: /home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28): build failed (first 300 chars): cmd " make -j 16 " exited with exit code 2 and output: Making all in config make[1]: Entering directory `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/config' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/icc ... The end of the log file /tmp/eb-Dnjmix/easybuild-OpenMPI-2.1.2-20180305.144907.SAFtP.log contains: libtool: error: require no space between '-L' and '-lrt' make[2]: *** [libmca_pml_ucx.la] Error 1 make[2]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/ompi/mca/pml/ucx' make[1]: *** [all-recursive] Error 1 I can't make out what's causing this. Perhaps the build server has a library installed triggering an error? Thanks for any suggestions!
Re: [easybuild] Build of iomkl-2018a.eb fails
Dear Ole, use configopts += '--without-ucx ' in the OpenMPI easyconfig Sincerely, Balazs On 05/03/2018 15:27, Ole Holm Nielsen wrote: Using EB 3.5.2 I'm trying to build the latest iomkl: eb iomkl-2018a.eb -r This works like a charm on 2 of our 3 binary architectures, but on our Sandy Bridge nodes with Mellanox Infiniband the build aborts: # eb iomkl-2018a.eb -r == temporary log file in case of crash /tmp/eb-Dnjmix/easybuild-6WeIK9.log == resolving dependencies ... == processing EasyBuild easyconfig /home/modules/software/EasyBuild/3.5.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.2-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb == building and installing OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == FAILED: Installation ended unsuccessfully (build directory: /home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28): build failed (first 300 chars): cmd " make -j 16 " exited with exit code 2 and output: Making all in config make[1]: Entering directory `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/config' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/icc ... The end of the log file /tmp/eb-Dnjmix/easybuild-OpenMPI-2.1.2-20180305.144907.SAFtP.log contains: libtool: error: require no space between '-L' and '-lrt' make[2]: *** [libmca_pml_ucx.la] Error 1 make[2]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/ompi/mca/pml/ucx' make[1]: *** [all-recursive] Error 1 I can't make out what's causing this. Perhaps the build server has a library installed triggering an error? Thanks for any suggestions! -- HPC consultant HPC/VSC Support and System Administration Computing Center ULB/VUB Avenue Adolphe Buyllaan 91 - CP 197 1050 Brussels Belgium
[easybuild] Build of iomkl-2018a.eb fails
Using EB 3.5.2 I'm trying to build the latest iomkl: eb iomkl-2018a.eb -r This works like a charm on 2 of our 3 binary architectures, but on our Sandy Bridge nodes with Mellanox Infiniband the build aborts: # eb iomkl-2018a.eb -r == temporary log file in case of crash /tmp/eb-Dnjmix/easybuild-6WeIK9.log == resolving dependencies ... == processing EasyBuild easyconfig /home/modules/software/EasyBuild/3.5.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.2-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb == building and installing OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == FAILED: Installation ended unsuccessfully (build directory: /home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28): build failed (first 300 chars): cmd " make -j 16 " exited with exit code 2 and output: Making all in config make[1]: Entering directory `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/config' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/icc ... The end of the log file /tmp/eb-Dnjmix/easybuild-OpenMPI-2.1.2-20180305.144907.SAFtP.log contains: libtool: error: require no space between '-L' and '-lrt' make[2]: *** [libmca_pml_ucx.la] Error 1 make[2]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/ompi/mca/pml/ucx' make[1]: *** [all-recursive] Error 1 I can't make out what's causing this. Perhaps the build server has a library installed triggering an error? Thanks for any suggestions! -- Ole Holm Nielsen
