Hi Lars, The next error is
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed == 2020-03-12 08:01:00,556 run.py:546 WARNING Found 1 errors in command output (output: -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed) == 2020-03-12 08:01:00,556 build_log.py:265 INFO building... == 2020-03-12 08:01:00,556 easyblock.py:2857 INFO Starting build step == 2020-03-12 08:01:00,556 easyblock.py:2863 INFO Running method build_step part of step build == 2020-03-12 08:01:00,556 run.py:219 INFO running cmd: make -j 20 == 2020-03-12 08:02:22,425 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/software/EasyBuild/4.1.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:124 in __init__): cmd " make -j 20 " exited with exit code 2 and output: /trinity/shared/easybuild/software/CMake/3.15.3-GCCcore-8.3.0/bin/cmake -S/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/openmm-7.4.1 -B/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/easybuild_obj --check-build-system CMakeFiles/Makefile.cmake 0 /trinity/shared/easybuild/software/CMake/3.15.3-GCCcore-8.3.0/bin/cmake -E cmake_progress_start /trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/easybuild_obj/CMakeFiles /trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/easybuild_obj/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all Would it be more helpful to do this on the Github page for the PR? Cheers, Loris Lars Viklund <[email protected]> writes: > Hi Loris, > > The "error" seems to be somewhat expected, in my log it's followed by the > following: > > == 2020-03-12 11:57:32,550 github.py:427 WARNING Ignoring problem that > occured when applying PR patch: u"Can't determine patch level for patch > /tmp/eb-VOiAyu/files_pr9620/9620.diff from directory > /tmp/eb-VOiAyu/tmp3yaMTD/easybuilders/easybuild-easyconfigs-develop" > == 2020-03-12 11:57:32,551 github.py:440 INFO Downloading > o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb from > https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/bcee7910e9425801246f3edebd5fd0a152bb3649/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b > -Python-3.7.4.eb > > That is, it tries to apply the PR as a patch, but as a fallback it retrieves > individual files into the tree instead. > > It's quite likely that the retrieval step worked fine despite the "error" and > there's other problems further down. Please look for other errors and > identify at which step it seems to fail. > > // Lars > > -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > From: [email protected] <[email protected]> on > behalf of Loris Bennett <[email protected]> > Sent: Thursday, March 12, 2020 9:39:47 AM > To: [email protected] > Subject: Re: [easybuild] Error building fosscuda version of OpenMM > > Hi Lars, > > Lars Viklund <[email protected]> writes: > >> Hi, >> >> When something using `make` fails with something like your "Error 2" the >> actual >> error is way earlier in the log as the whole tail is Make propagating the >> error >> state up through the invocations. The path fragment you mention is indeed >> from >> truncation, the "first 300 chars" thing is mostly to give you bit of context >> to >> what's wrong, you need to look at the actual logged information to see what's >> up. >> >> Is that CUDA_SDK_ROOT_DIR really supposed to point into that part of the CUDA >> SDK tree as you cite it? > > That was a bit of a shot in the dark. I found the suggestion here: > > https://github.com/PixarAnimationStudios/OpenSubdiv/issues/616 > > * cmake fails to set CUDA_TOOLKIT_ROOT_DIR · Issue #616 · > PixarAnimationStudios/OpenSubdiv · GitHub > github.com > As mentioned in #472, the variable, CUDA_SDK_ROOT_DIR doesn't get set for > Linux users using cmake even though it does find Cuda. On Linux ( Ubuntu > 14.04.1 ) this variable doesn't get automatically > set during installation of Cuda ( like i... > * > > but it didn't make much sense to me either. > >> Please note that there's an open pull request currently for exactly the >> version >> you're trying to build, I've built it successfully on my system with a >> development EasyBuild installation. >> >> https://github.com/easybuilders/easybuild-easyconfigs/pull/9620 > > * {bio}[fosscuda/2019b] OpenMM v7.4.1 w/ Python 3.7.4 by boegel · Pull > Request #9620 · easybuilders/easybuild-easyconfigs · GitHub > github.com > (created using eb --new-pr) requires #9613 (OpenMM patch) > * > > Thanks for the link. I tried the PR, but fails with the following as > the first error: > > == 2020-03-12 08:00:26,578 build_log.py:169 ERROR EasyBuild crashed with an > error (at > easybuild/software/EasyBuild/4.1.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:124 > in __init__): Can't > determine patch level for patch /tmp/eb-ER72Yd/files_pr9620/9620.diff from > directory /tmp/eb-ER72Yd/tmpJ3tyjg/easybuilders/easybuild-easyconfigs-develop > (at > easybuild/software/EasyBuild/4.1.1/lib/python2.7/site-packages/easybuild/tools/filetools.py:1058 > in apply_patch) > > Does that mean anything to you? > > Cheers, > > Loris > >> // Lars >> >> On 2020-03-11 15:28, Loris Bennett wrote: >>> Hi, >>> >>> I'm trying to build a GPU-enabled version of OpenMM. Starting with >>> >>> OpenMM-7.4.1-foss-2019b-Python-3.7.4 >>> >>> (which built fine) I changed the toolchain to 'fosscuda' and added >>> >>> configopts = "-DOPENMM_BUILD_CUDA_LIB=ON >>> -DCUDA_SDK_ROOT_DIR=$CUDA_HOME/extras/CUPTI/samples" >>> >>> The build then fails with: >>> >>> [ 57%] Built target OpenMMCUDA >>> make[1]: Leaving directory >>> `/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/easybuild_obj' >>> make: *** [all] Error 2 >>> (at >>> easybuild/software/EasyBuild/4.1.1/lib/python2.7/site-packages/easybuild/tools/run.py:529 >>> in parse_cmd_output) >>> == 2020-03-11 10:50:31,848 easyblock.py:3109 WARNING build failed (first >>> 300 chars): cmd " make -j 20 " exited with exit code 2 and output: >>> /trinity/shared/easybuild/software/CMake/3.15.3-GCCcore-8.3.0/bin/cmake >>> -S/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/openmm-7.4.1 > -B/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/easybuild_ >>> == 2020-03-11 10:50:31,848 easyblock.py:295 INFO Closing log for >>> application name OpenMM version 7.4.1 >>> == 2020-03-11 10:50:31,849 build_log.py:265 INFO FAILED: Installation >>> ended unsuccessfully (build directory: >>> /trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4): >>> build failed (first > 300 chars): cmd " make -j 20 " exited with exit code 2 and output: >>> /trinity/shared/easybuild/software/CMake/3.15.3-GCCcore-8.3.0/bin/cmake >>> -S/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/openmm-7.4.1 > -B/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/easybuild_ > (took 2 min 16 sec) >>> == 2020-03-11 10:50:31,849 build_log.py:265 INFO Results of the build >>> can be found in the log file(s) >>> /tmp/eb-KFw1Uj/easybuild-OpenMM-7.4.1-20200311.104815.vsMFt.log >>> == 2020-03-11 10:50:31,850 build_log.py:169 ERROR EasyBuild crashed with >>> an error (at >>> easybuild/software/EasyBuild/4.1.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:124 >>> in __init__): build > failed (first 300 chars): cmd " make -j 20 " exited with exit code 2 and > output: >>> /trinity/shared/easybuild/software/CMake/3.15.3-GCCcore-8.3.0/bin/cmake >>> -S/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/openmm-7.4.1 > -B/trinity/shared/easybuild/build/OpenMM/7.4.1/fosscuda-2019b-Python-3.7.4/easybuild_ > (at > easybuild/software/EasyBuild/4.1.1/lib/python2.7/site-packages/easybuild/main.py:116 > in build_and_install_software) >>> >>> Is the reference to >>> >>> easybuild_ >>> >>> real and therefore something to do with the actual error, or has the >>> path just fallen victim to some form of truncation? >>> >>> Either way, does anyone have an idea about what the problem is? >>> >>> Cheers, >>> >>> Loris >>> >> -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email [email protected]
