> == 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
I'm pretty sure I've seen this for patches that create new files. Is your patch doing that? I think EasyBuild tries to automatically determine the patch level, but fails to do so when new files are created. I seem to remember you can specify in the EasyConfig explicitely what the patch level should be, but can't find it right now... :S Cheers, Caspar ----- Original Message ----- From: "lars viklund" <lars.vikl...@umu.se> To: "easybuild" <easybuild@lists.ugent.be> Sent: Thursday, 12 March, 2020 13:28:35 Subject: Re: [easybuild] Error building fosscuda version of OpenMM You could definitely open an issue referencing the PR number, preferably providing a gist with your complete easybuild log. The pthread test you mention there seems to happen in my build as well, so it's probably not fatal. On 2020-03-12 13:09, Loris Bennett wrote: > 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 <lars.vikl...@umu.se> 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: easybuild-requ...@lists.ugent.be <easybuild-requ...@lists.ugent.be> on >> behalf of Loris Bennett <loris.benn...@fu-berlin.de> >> Sent: Thursday, March 12, 2020 9:39:47 AM >> To: easybuild@lists.ugent.be >> Subject: Re: [easybuild] Error building fosscuda version of OpenMM >> >> Hi Lars, >> >> Lars Viklund <lars.vikl...@umu.se> 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 >>>>
