> Segmentation fault is… unexpected to say the least. A couple of things I’m > curious about here: > > 1) Does this happen consistently on the same stage if you try again?
Yes. However, if I try very same binary, like this: /p/project/ccstao/cstao05/easybuild/juwelsbooster/software/R/4.1.2-gcccoremkl-11.2.0-2021.4.0/lib64/R/bin/R R version 4.1.2 (2021-11-01) -- "Bird Hippie" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Easybuild’s log doesn’t tell me WHAT caused the segfault. So I don’t know how to fix or what to. > 2) What kind of hardware does this run on? This is Juwels Booster. And AMD cluster. > There is the possibility that you are running out of memory, but that seems > odd to happen during testing. There might be something more useful in the log > file, and dmesg might say something if we are seeing memory pressure. Other > than that I’d probably try to build on /tmp to see if that changes anything. It’s strange. I installed R before on all our machines. I’m testing the exact same install on our other machines, to see where I get. > >> On 24 Jan 2022, at 22:25, Strube, Alexandre <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hi, >> >> I get this at the end of 3 hours of R >> >> >> make[1]: Leaving directory >> '/dev/shm/strube1/juwelsbooster/R/4.1.2/gcccoremkl-11.2.0-2021.4.0/rgl/rgl/src/useNULL' >> installing to >> /p/project/ccstao/cstao05/easybuild_hard/juwelsbooster/software/R/4.1.2-gcccoremkl-11.2.0-2021.4.0/lib64/R/library/00LOCK-rgl/00new/rgl/libs >> ** R >> ** demo >> ** inst >> ** byte-compile and prepare package for lazy loading >> ** help >> *** installing help indices >> *** copying figures >> ** building package indices >> ** installing vignettes >> ** testing if installed package can be loaded from temporary location >> sh: line 1: 30109 Segmentation fault R_TESTS= >> '/p/project/ccstao/cstao05/easybuild/juwelsbooster/software/R/4.1.2-gcccoremkl-11.2.0-2021.4.0/lib64/R/bin/R' >> --no-save --no-restore --no-echo 2>&1 < >> '/tmp/eb-uw4uv1em/RtmpWzB0Zp/file68e16ce6d926' >> ERROR: loading failed >> (at easybuild/tools/run.py:618 in parse_cmd_output) >> == 2022-01-24 22:19:39,096 build_log.py:265 INFO ... (took 1 min 26 >> secs) >> == 2022-01-24 22:19:39,099 build_log.py:265 INFO ... (took 3 hours 8 mins 51 >> secs) >> == 2022-01-24 22:19:39,101 filetools.py:1976 INFO Removing lock >> /p/project/ccstao/cstao05/easybuild/juwelsbooster/software/.locks/_p_project_ccstao_cstao05_easybuild_juwelsbooster_software_R_4.1.2-gcccoremkl-11.2.0-2021.4.0.lock... >> == 2022-01-24 22:19:39,545 filetools.py:380 INFO Path >> /p/project/ccstao/cstao05/easybuild/juwelsbooster/software/.locks/_p_project_ccstao_cstao05_easybuild_juwelsbooster_software_R_4.1.2-gcccoremkl-11.2.0-2021.4.0.lock >> successfully removed. >> == 2022-01-24 22:19:39,546 filetools.py:1980 INFO Lock removed: >> /p/project/ccstao/cstao05/easybuild/juwelsbooster/software/.locks/_p_project_ccstao_cstao05_easybuild_juwelsbooster_software_R_4.1.2-gcccoremkl-11.2.0-2021.4.0.lock >> == 2022-01-24 22:19:39,546 easyblock.py:4032 WARNING build failed (first 300 >> chars): cmd " R CMD INSTALL >> /dev/shm/strube1/juwelsbooster/R/4.1.2/gcccoremkl-11.2.0-2021.4.0/rgl/rgl >> --library=/p/project/ccstao/cstao05/easybuild/juwelsbooster/software/R/4.1.2-gcccoremkl-11.2.0-2021.4.0/lib64/R/library >> --no-clean-on-error " exited with exit code 1 and output: >> * installing *source* pack >> == 2022-01-24 22:19:39,546 easyblock.py:318 INFO Closing log for application >> name R version 4.1.2 > > -- > Terje Kvernes > Driftsansvarlig > Matematisk Institutt > Universitetet i Oslo >
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