Re: [easybuild] imkl log directory
On Mar 21, 2017, at 7:02 PM, Kenneth Hoste wrote: > It is highly recommended to use a local directory as temporary directory in > EasyBuild, see also > https://github.com/hpcugent/easybuild-easyconfigs/issues/3375 . also, I'd sometimes suppress/trigger failure modes by using /dev/shm instead, which also gives a speed boost. Explanation: /dev/shm will not suffer from parallel fs quirks, therefor several build issues go away, however fast execution might bring in the surface build/installation bugs, fi. for values higher than parallel=1 (I’m sure that there is at least one version of `install` which can be used in such unsafe ways under Makefiles) More broadly, I’ve found that all these build processes put together serve as a good measure of a system’s health. It is particularly entertaining to identify heisenbugs, which repeat themselves with a characteristic probability.. Fotis -- echo "sysadmin know better bash than english" | sed s/min/mins/ \ | sed 's/better bash/bash better/' # signal detected in a CERN forum
Re: [easybuild] imkl log directory
Hi Shahzeb, On 21/03/2017 13:59, Siddiqui, Shahzeb wrote: Hello, I would like to find out if you know how to make sure imkl does a clean build. I am doing repetitive builds and sometimes I keep running into this issue where imkl fails at sanity check because it fails to clean up the directory. My tmp directory is set to /hpc/grid/scratch/easybuild. In this directory, imkl would write its log for all its build. It is highly recommended to use a local directory as temporary directory in EasyBuild, see also https://github.com/hpcugent/easybuild-easyconfigs/issues/3375 . regards, Kenneth failed (first 300 chars): Cleaning up intel dir /hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel failed: [Errno 39] Directory not empty: '/hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel/ism/rm'") l/2017.1.132... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == testing... == installing... == taking care of extensions... == postprocessing... == sanity checking... == cleaning up... == FAILED: Installation ended unsuccessfully (build directory: /nfs/grid/software/RHEL7-BUILD/easybuild/build/imkl/2017.1.132/iimpi-2017.01-GCC-5.4.0-2.27): build failed (first 300 chars): Cleaning up intel dir /hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel failed: [Errno 39] Directory not empty: '/hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel/ism/rm' == Results of the build can be found in the log file(s) /hpc/grid/scratch/easybuild/eb-yIih_R/easybuild-imkl-2017.1.132-20170321.005413.TJszC.log [hpcswadm@amrndhl1157 easybuild]$ tail /hpc/grid/scratch/easybuild/eb-yIih_R/easybuild-imkl-2017.1.132-20170321.005413.TJszC.log == 2017-03-21 01:49:56,556 environment.py:97 INFO Environment variable EBVARI_MPI_CC set to icc (previously undefined) == 2017-03-21 01:49:56,558 environment.py:97 INFO Environment variable CFLAGS set to -fPIC (previously undefined) == 2017-03-21 01:49:56,560 environment.py:97 INFO Environment variable EBVARI_MPI_F77 set to ifort (previously undefined) == 2017-03-21 01:49:56,562 environment.py:97 INFO Environment variable LOCAL_INSTALL_VERBOSE set to 1 (previously undefined) == 2017-03-21 01:49:56,564 build_log.py:216 INFO cleaning up... == 2017-03-21 01:49:56,566 easyblock.py:2288 INFO Starting cleanup step == 2017-03-21 01:49:56,568 easyblock.py:2291 INFO Running method cleanup_step part of step cleanup == 2017-03-21 01:49:56,856 build_log.py:147 ERROR EasyBuild crashed with an error (at easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/vsc_base-2.5.7-py2.7.egg/vsc/utils/exceptions.py:124 in __init__): Cleaning up intel dir /hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel failed: [Errno 39] Directory not empty: '/hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel/ism/rm' (at easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyblocks-3.1.1-py2.7.egg/easybuild/easyblocks/generic/intelbase.py:171 in clean_home_subdir) == 2017-03-21 01:49:56,858 easyblock.py:2520 WARNING build failed (first 300 chars): Cleaning up intel dir /hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel failed: [Errno 39] Directory not empty: '/hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel/ism/rm' == 2017-03-21 01:49:56,861 easyblock.py:276 INFO Closing log for application name imkl version 2017.1.132 [hpcswadm@amrndhl1157 easybuild]$ tail -n 20 /hpc/grid/scratch/easybuild/eb-yIih_R/easybuild-imkl-2017.1.132-20170321.005413.TJszC.log == 2017-03-21 01:49:56,536 environment.py:97 INFO Environment variable LDFLAGS set to -L/nfs/grid/software/testing/RHEL7/easybuild/software/Core/icc/2017.1.132-GCC-5.4.0-2.27/lib/intel64 (previously undefined) == 2017-03-21 01:49:56,539 environment.py:97 INFO Environment variable I_MPI_CXX set to icpc (previously undefined) == 2017-03-21 01:49:56,541 environment.py:97 INFO Environment variable _ModuleTable004_ set to 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 (previous value: 'LGJpbnV0aWxzPXtbIkZOIl09Ii9uZnMvZ3JpZC9zb2Z0d2FyZS90ZXN0aW5nL1JIRUw3L2Vhc3lidWlsZC9tb2R1bGVzL2FsbC9Db21waWxlci9HQ0Njb3JlLzUuNC4wL2JpbnV0aWxzLy4yLjI3Lmx1YSIsWyJkZWZhdWx0Il09MCxbImZ1bGxOYW1lIl09ImJpbnV0aWxzLy4yLjI3IixbImxvYWRPcmRlciJdPTQscHJvcFQ9e30sWyJzaG9ydCJdPSJiaW51dGlscyIsWyJzdGF0dXMiXT0iYWN0aXZlIix9LGljYz17WyJGTiJdPSIvbmZzL2dyaWQvc29mdHdhcmUvdGVzdGluZy9SSEVMNy9lYXN5YnVpbGQvbW9kdWxlcy9hbGwvQ29yZS9pY2MvLjIwMTcuMS4xMzItR0NDLTU
[easybuild] imkl log directory
Hello, I would like to find out if you know how to make sure imkl does a clean build. I am doing repetitive builds and sometimes I keep running into this issue where imkl fails at sanity check because it fails to clean up the directory. My tmp directory is set to /hpc/grid/scratch/easybuild. In this directory, imkl would write its log for all its build. failed (first 300 chars): Cleaning up intel dir /hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel failed: [Errno 39] Directory not empty: '/hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel/ism/rm'") l/2017.1.132... == fetching files... == creating build dir, resetting environment... == unpacking... == patching... == preparing... == configuring... == building... == testing... == installing... == taking care of extensions... == postprocessing... == sanity checking... == cleaning up... == FAILED: Installation ended unsuccessfully (build directory: /nfs/grid/software/RHEL7-BUILD/easybuild/build/imkl/2017.1.132/iimpi-2017.01-GCC-5.4.0-2.27): build failed (first 300 chars): Cleaning up intel dir /hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel failed: [Errno 39] Directory not empty: '/hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel/ism/rm' == Results of the build can be found in the log file(s) /hpc/grid/scratch/easybuild/eb-yIih_R/easybuild-imkl-2017.1.132-20170321.005413.TJszC.log [hpcswadm@amrndhl1157 easybuild]$ tail /hpc/grid/scratch/easybuild/eb-yIih_R/easybuild-imkl-2017.1.132-20170321.005413.TJszC.log == 2017-03-21 01:49:56,556 environment.py:97 INFO Environment variable EBVARI_MPI_CC set to icc (previously undefined) == 2017-03-21 01:49:56,558 environment.py:97 INFO Environment variable CFLAGS set to -fPIC (previously undefined) == 2017-03-21 01:49:56,560 environment.py:97 INFO Environment variable EBVARI_MPI_F77 set to ifort (previously undefined) == 2017-03-21 01:49:56,562 environment.py:97 INFO Environment variable LOCAL_INSTALL_VERBOSE set to 1 (previously undefined) == 2017-03-21 01:49:56,564 build_log.py:216 INFO cleaning up... == 2017-03-21 01:49:56,566 easyblock.py:2288 INFO Starting cleanup step == 2017-03-21 01:49:56,568 easyblock.py:2291 INFO Running method cleanup_step part of step cleanup == 2017-03-21 01:49:56,856 build_log.py:147 ERROR EasyBuild crashed with an error (at easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/vsc_base-2.5.7-py2.7.egg/vsc/utils/exceptions.py:124 in __init__): Cleaning up intel dir /hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel failed: [Errno 39] Directory not empty: '/hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel/ism/rm' (at easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_easyblocks-3.1.1-py2.7.egg/easybuild/easyblocks/generic/intelbase.py:171 in clean_home_subdir) == 2017-03-21 01:49:56,858 easyblock.py:2520 WARNING build failed (first 300 chars): Cleaning up intel dir /hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel failed: [Errno 39] Directory not empty: '/hpc/grid/scratch/easybuild/hpcswadm/easybuild_intel/ism/rm' == 2017-03-21 01:49:56,861 easyblock.py:276 INFO Closing log for application name imkl version 2017.1.132 [hpcswadm@amrndhl1157 easybuild]$ tail -n 20 /hpc/grid/scratch/easybuild/eb-yIih_R/easybuild-imkl-2017.1.132-20170321.005413.TJszC.log == 2017-03-21 01:49:56,536 environment.py:97 INFO Environment variable LDFLAGS set to -L/nfs/grid/software/testing/RHEL7/easybuild/software/Core/icc/2017.1.132-GCC-5.4.0-2.27/lib/intel64 (previously undefined) == 2017-03-21 01:49:56,539 environment.py:97 INFO Environment variable I_MPI_CXX set to icpc (previously undefined) == 2017-03-21 01:49:56,541 environment.py:97 INFO Environment variable _ModuleTable004_ set to 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 (previous value: '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') == 2017-03-21 01:49:56,543 environment.py:97 INFO Environment variable EBVARMPICC set to mpiicc (previously undefined) == 2017-03-21 01:49:56,545 environment.py:97 INFO Environment variable I_MPI_FC set to
