bump to Lmod 6.5.7 - Githubissues

boegel commented 7 years ago

Lmod 6.5.7 fixes a bug that we encountered in EasyBuild where a module for a dependency that sets $LD_PRELOAD (e.g. jemalloc) breaks subsequent loads of other dependencies (e.g. PCRE) when a Tcl module file is being loaded (e.g. MariaDB), due to EasyBuild resetting $LD_LIBRARY_PATH after having loading the toolchain first

This problem can be reproduced with:

$ ml intel/2016a && LD_LIBRARY_PATH='' LD_PRELOAD='' ml MariaDB/10.1.14-intel-2016a
sh: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
sh: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
Lmod has detected the following error:  Failed to find 'Lmod Capture Exit Code' in output: 
While processing the following module(s):
    Module fullname              Module Filename
    ---------------              ---------------
    PCRE/8.38-intel-2016a        /apps/gent/SL6/sandybridge/modules/all/PCRE/8.38-intel-2016a
    MariaDB/10.1.14-intel-2016a  /apps/gent/SL6/sandybridge/modules/all/MariaDB/10.1.14-intel-2016a

If you don't understand the warning or error, contact the helpdesk at hpc@ugent.be

Note that although the resetting of $LD_LIBRARY_PATH as done by EasyBuild should be followed by properly merging the original $LD_LIBRARY_PATH with the value obtained from the ml load statement; if not, lots of commands will be broken because of $LD_PRELOAD listing a library that needs other libraries which are no longer available via $LD_LIBRARY_PATH...

boegel commented 7 years ago

This issue arose while testing https://github.com/hpcugent/easybuild-easyconfigs/pull/3511, see (last) failing test reports.

boegel commented 7 years ago

@wpoely86 do _NOT_ merge this yet, WIP because:

[x] Lmod 6.5.7 needs to be tagged by @rtmclay first
[x] our SitePackage.lua should be updated to use the os.execute wrapper that will be provided by Lmod to run the logger command, since that suffers from the same problem basically, i.e. os.execute forks a subshell which may be broken due to an improper combo of $LD_PRELOAD and (incomplete) $LD_LIBRARY_PATH
[x] HPC-UGent integration tests should be confirmed to fully pass with Lmod 6.5.7

boegel commented 7 years ago

Lmod 6.5.7 is now tagged, and works like a charm:

[20:17:04] vsc40023@test2802:~/vsc-testing/module $ ./run_all_tests.sh 
Lmod-6.5.7-1.ug.el6.noarch
vsc-cluster-modules-0.19-1.noarch
vsc-cluster-modules-tier2-0.19-1.noarch

> module --version

Modules based on Lua: Version 6.5.7  2016-09-02 12:54 -05:00 (CDT)
$MODULEPATH: /apps/gent/SL6/westmere/modules/all:/etc/modulefiles/vsc

*** 001_list.sh ***

> module list

>>> 001_list.sh: PASS

*** 002_avail.sh ***

> module avail 
> module avail GCC
> module avail GCC/4.9.3

>>> 002_avail.sh: PASS

*** 003_load.sh ***

> module load GCC
> module load GCC/4.9.3
> module load intel
> module load foss
> module load Python/2.7.11-intel-2016a
> module load GCC/4.9.3-2.25 OpenMPI/1.10.2-GCC-4.9.3-2.25 OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0 FFTW/3.3.4-gompi-2016a

>>> 003_load.sh: PASS

*** 004_purge.sh ***

> module load Python/2.7.11-intel-2016a
> module purge
> module load cluster
> module purge -force
> module load cluster
> module purge -force
> module load cluster/.banette

>>> 004_purge.sh: PASS

*** 005_swap.sh ***

> module load GCC/4.7.2
> module swap GCC/4.9.3
> module swap GCC GCC/4.7.2
> module swap GCC/4.7.2 GCC/4.9.3

>>> 005_swap.sh: PASS

*** 006_unload.sh ***

> module load GCC/4.9.3
> module unload GCC
> module load GCC/4.9.3
> module unload GCC/4.9.3

>>> 006_unload.sh: PASS

*** 007_spider.sh ***

> module spider intel
> module spider intel/2016a
> module --show-hidden spider intel/2016a

>>> 007_spider.sh: PASS

*** 010_stdout_stderr.sh ***

> module list
> module avail

>>> 010_stdout_stderr.sh: PASS

*** 050_ml.sh ***

> ml av GCC/4.9.3
> ml
> ml GCC/4.9.3
> ml
> ml -GCC/4.9.3
> ml

>>> 050_ml.sh: PASS

*** 051_collections.sh ***

> ml foss/2016a
> ml Python/2.7.11-intel-2016a
> ml save this_is_just_a_test_collection_for_module_integration_test_051
> ml describe this_is_just_a_test_collection_for_module_integration_test_051
> ml purge
> ml restore this_is_just_a_test_collection_for_module_integration_test_051
> ml purge
> module swap cluster/.banette cluster/delcatty
> ml purge
> ml restore this_is_just_a_test_collection_for_module_integration_test_051
> ml purge

>>> 051_collections.sh: PASS

*** 100_lmod_cache.sh ***

> module avail  # 2s time limit

>>> 100_lmod_cache.sh: PASS

*** 101_LD_LIBRARY_PATH.sh ***

> module load GCC/4.9.3-2.25
> module load OpenMPI/1.10.2-GCC-4.9.3-2.25
> checking $LD_LIBRARY_PATH...

>>> 101_LD_LIBRARY_PATH.sh: PASS

*** 102_symlink_modulepath.sh ***

> module use /tmp/vsc40023/PmsOLM/symlinked_modules
> module avail test/1.2.3

>>> 102_symlink_modulepath.sh: PASS

*** 103_load-via-list.sh ***

>>> 103_load-via-list.sh: PASS

*** 103_tcl2lua_LD_PRELOAD.sh ***

> module load jemalloc
> module show jemalloc

>>> 103_tcl2lua_LD_PRELOAD.sh: PASS

TEST RESULT: all 15 passed!

boegel commented 7 years ago

@wpoely86 please merge? ;)

boegel commented 7 years ago

@wpoely86 all is good with Lmod 6.5.8

I will look into an extra test for the $LD_PRELOAD crap that was fixed with Lmod 6.5.7 though

[10:26:17] vsc40023@test2802:~/vsc-testing/module $ ./run_all_tests.sh 
Lmod-6.5.8-1.ug.el6.noarch
vsc-cluster-modules-0.19-1.noarch
vsc-cluster-modules-tier2-0.19-1.noarch

> module --version

Modules based on Lua: Version 6.5.8  2016-09-03 13:41 -05:00 (CDT)
$MODULEPATH: /apps/gent/SL6/westmere/modules/all:/etc/modulefiles/vsc

*** 001_list.sh ***

> module list

>>> 001_list.sh: PASS

*** 002_avail.sh ***

> module avail 
> module avail GCC
> module avail GCC/4.9.3

>>> 002_avail.sh: PASS

*** 003_load.sh ***

> module load GCC
> module load GCC/4.9.3
> module load intel
> module load foss
> module load Python/2.7.11-intel-2016a
> module load GCC/4.9.3-2.25 OpenMPI/1.10.2-GCC-4.9.3-2.25 OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0 FFTW/3.3.4-gompi-2016a

>>> 003_load.sh: PASS

*** 004_purge.sh ***

> module load Python/2.7.11-intel-2016a
> module purge
> module load cluster
> module purge -force
> module load cluster
> module purge -force
> module load cluster/.banette

>>> 004_purge.sh: PASS

*** 005_swap.sh ***

> module load GCC/4.7.2
> module swap GCC/4.9.3
> module swap GCC GCC/4.7.2
> module swap GCC/4.7.2 GCC/4.9.3

>>> 005_swap.sh: PASS

*** 006_unload.sh ***

> module load GCC/4.9.3
> module unload GCC
> module load GCC/4.9.3
> module unload GCC/4.9.3

>>> 006_unload.sh: PASS

*** 007_spider.sh ***

> module spider intel
> module spider intel/2016a
> module --show-hidden spider intel/2016a

>>> 007_spider.sh: PASS

*** 010_stdout_stderr.sh ***

> module list
> module avail

>>> 010_stdout_stderr.sh: PASS

*** 050_ml.sh ***

> ml av GCC/4.9.3
> ml
> ml GCC/4.9.3
> ml
> ml -GCC/4.9.3
> ml

>>> 050_ml.sh: PASS

*** 051_collections.sh ***

> ml foss/2016a
> ml Python/2.7.11-intel-2016a
> ml save this_is_just_a_test_collection_for_module_integration_test_051
> ml describe this_is_just_a_test_collection_for_module_integration_test_051
> ml purge
> ml restore this_is_just_a_test_collection_for_module_integration_test_051
> ml purge
> module swap cluster/.banette cluster/delcatty
> ml purge
> ml restore this_is_just_a_test_collection_for_module_integration_test_051
> ml purge

>>> 051_collections.sh: PASS

*** 100_lmod_cache.sh ***

> module avail  # 2s time limit

>>> 100_lmod_cache.sh: PASS

*** 101_LD_LIBRARY_PATH.sh ***

> module load GCC/4.9.3-2.25
> module load OpenMPI/1.10.2-GCC-4.9.3-2.25
> checking $LD_LIBRARY_PATH...

>>> 101_LD_LIBRARY_PATH.sh: PASS

*** 102_symlink_modulepath.sh ***

> module use /tmp/vsc40023/GI7X3V/symlinked_modules
> module avail test/1.2.3

>>> 102_symlink_modulepath.sh: PASS

*** 103_load-via-list.sh ***

>>> 103_load-via-list.sh: PASS

*** 103_tcl2lua_LD_PRELOAD.sh ***

> module load jemalloc
> module show jemalloc

>>> 103_tcl2lua_LD_PRELOAD.sh: PASS

TEST RESULT: all 15 passed!

hpcugent / Lmod-UGent

bump to Lmod 6.5.7 #8