long MODULEPATH drastically reduces performance #2226

pescobar · 2017-05-16T19:53:41Z

I did this test with latest EasyBuld 3.2.1 and Lmod-7.4.5 in a Centos7.3 machine:

With a long $MODULEPATH the execution time is quite long:

$> echo $MODULEPATH
/scicore/soft/modules/base:/scicore/soft/modules/bio:/scicore/soft/modules/cae:/scicore/soft/modules/chem:/scicore/soft/modules/compiler:/scicore/soft/modules/data:/scicore/soft/modules/debugger:/scicore/soft/modules/devel:/scicore/soft/modules/geo:/scicore/soft/modules/ide:/scicore/soft/modules/lang:/scicore/soft/modules/lib:/scicore/soft/modules/math:/scicore/soft/modules/mpi:/scicore/soft/modules/numlib:/scicore/soft/modules/perf:/scicore/soft/modules/phys:/scicore/soft/modules/system:/scicore/soft/modules/toolchain:/scicore/soft/modules/tools:/scicore/soft/modules/vis

$> time eb foss-2016a.eb -r -D
real	0m57.002s
user	0m36.900s
sys	0m8.828s

If I just reduce the $MODULEPATH length the execution time is much better:

$> export MODULEPATH=/scicore/soft/modules/all

$> time eb foss-2016a.eb -r -D
real	0m8.054s
user	0m4.925s
sys	0m1.361s

I don't know if this is the root cause but It seem that when MODULEPATH is so long EasyBuild is executing Lmod many more times:

$ echo $MODULEPATH 
/scicore/soft/modules/base:/scicore/soft/modules/bio:/scicore/soft/modules/cae:/scicore/soft/modules/chem:/scicore/soft/modules/compiler:/scicore/soft/modules/data:/scicore/soft/modules/debugger:/scicore/soft/modules/devel:/scicore/soft/modules/geo:/scicore/soft/modules/ide:/scicore/soft/modules/lang:/scicore/soft/modules/lib:/scicore/soft/modules/math:/scicore/soft/modules/mpi:/scicore/soft/modules/numlib:/scicore/soft/modules/perf:/scicore/soft/modules/phys:/scicore/soft/modules/system:/scicore/soft/modules/toolchain:/scicore/soft/modules/tools:/scicore/soft/modules/vis

$> time strace -f -o /tmp/eb-strace.log eb foss-2016a.eb -r -D

$> which lmod
/export/soft/lua_lmod/centos7/lmod/lmod/libexec/lmod

$> grep /export/soft/lua_lmod/centos7/lmod/lmod/libexec/lmod /tmp/eb-strace.log | wc -l
948

$> export MODULEPATH=/scicore/soft/modules/all

$> time strace -f -o /tmp/eb-strace2.log eb foss-2016a.eb -r -D

$> which lmod
/export/soft/lua_lmod/centos7/lmod/lmod/libexec/lmod

$ grep /export/soft/lua_lmod/centos7/lmod/lmod/libexec/lmod /tmp/eb-strace2.log | wc -l
272

The text was updated successfully, but these errors were encountered:

pescobar · 2017-05-16T20:07:35Z

To make this issue more weird, if I try the same using EB-3.2.1 in Centos6 machine with Lmod-6.0.9 the long $MODULEPATH doesn't seem to be a problem:

echo $MODULEPATH 
/scicore/soft/modules/base:/scicore/soft/modules/bio:/scicore/soft/modules/chem:/scicore/soft/modules/compiler:/scicore/soft/modules/data:/scicore/soft/modules/devel:/scicore/soft/modules/lang:/scicore/soft/modules/lib:/scicore/soft/modules/math:/scicore/soft/modules/mpi:/scicore/soft/modules/numlib:/scicore/soft/modules/perf:/scicore/soft/modules/phys:/scicore/soft/modules/system:/scicore/soft/modules/toolchain:/scicore/soft/modules/tools:/scicore/soft/modules/vis

$ time eb foss-2016a.eb -r -D
real	0m4.169s
user	0m2.980s
sys	0m0.728s

boegel · 2017-05-16T20:13:49Z

@pescobar That could be because of internal changes to Lmod...

A long $MODULEPATH is currently going to make EB run a lot of module use commands, which may be handled very differently by Lmod 6 & Lmod 7. Thoughts @rtmclay?

rtmclay · 2017-05-16T20:41:26Z

I have a few ideas but I can't really say without more data. Try timing a module avail and a module load (without the spider cache) for both a long MODULEPATH and a short one. For the test to be fair, it would be nice if the total number of modules was the same.

Also please do the same thing for Lmod 6.

pescobar · 2017-05-16T21:03:27Z

I think I located the issue. I did this other test in the Centos6-Lmod6.9 environment and I got totally puzzled because I was getting the same bad runtime and the difference in $MODULEPATH was 17 folders vs 21 folders:

$ echo $MODULEPATH
/scicore/soft/modules/base:/scicore/soft/modules/bio:/scicore/soft/modules/chem:/scicore/soft/modules/compiler:/scicore/soft/modules/data:/scicore/soft/modules/devel:/scicore/soft/modules/lang:/scicore/soft/modules/lib:/scicore/soft/modules/math:/scicore/soft/modules/mpi:/scicore/soft/modules/numlib:/scicore/soft/modules/perf:/scicore/soft/modules/phys:/scicore/soft/modules/system:/scicore/soft/modules/toolchain:/scicore/soft/modules/tools:/scicore/soft/modules/vis

[easybuild@login10 ~]$ time eb foss-2016a.eb -r -D
real	0m4.293s
user	0m2.958s
sys	0m0.809s

export MODULEPATH=/scicore/soft/modules/base:/scicore/soft/modules/bio:/scicore/soft/modules/cae:/scicore/soft/modules/chem:/scicore/soft/modules/compiler:/scicore/soft/modules/data:/scicore/soft/modules/debugger:/scicore/soft/modules/devel:/scicore/soft/modules/geo:/scicore/soft/modules/ide:/scicore/soft/modules/lang:/scicore/soft/modules/lib:/scicore/soft/modules/math:/scicore/soft/modules/mpi:/scicore/soft/modules/numlib:/scicore/soft/modules/perf:/scicore/soft/modules/phys:/scicore/soft/modules/system:/scicore/soft/modules/toolchain:/scicore/soft/modules/tools:/scicore/soft/modules/vis

$> time eb foss-2016a.eb -r -D
real	1m4.156s
user	0m40.182s
sys	0m10.166s

Then I realized that my $MODULEPATH in Centos7 contains non existing folders like /scicore/soft/modules/cae .When I configured Lmod in centos7 I added all the EasyBuild's moduleclasses to the $MODULEPATH so in case I add extra modules to those folders in the future the $MODULEPATH wouldn't need any update but it seems that this is affecting EasyBuild's or Lmod's performance.

After removing non existing folders from MODULEPATH the performance seems to be much better but I couldn't figure out how the non-existing folders are affecting to the performance

Thanks @boegel and @rtmclay for your help and suggestions!

wpoely86 · 2017-05-22T13:17:42Z

I'm have 10 directories in $MODULEPATH and I count 154 calls to ml use. This makes it all very slow.

boegel · 2017-06-09T15:41:49Z

module use supports multiple arguments, that would be an easy way to fix this...

akesandgren · 2018-02-01T11:48:34Z

I can also see a big improvement by removing non-existing dirs from MODULEPATH.

echo $MODULEPATH
/hpc2n/eb/modules/all/Core:/hpc2n/eb/modules/all/Linux:/hpc2n/eb/software/lmod/lmod/modulefiles/Core
time eb goolfc-2017b.eb --stop=fetch
== temporary log file in case of crash /scratch/eb-Kp_AeF/easybuild-U1V3ni.log
== Core/goolfc/2017b is already installed (module found), skipping
== No easyconfigs left to be built.
== Build succeeded for 0 out of 0
== Temporary log file(s) /scratch/eb-Kp_AeF/easybuild-U1V3ni.log* have been removed.
== Temporary directory /scratch/eb-Kp_AeF has been removed.

real    2m52.153s
user    0m45.004s
sys     0m44.092s

time env MODULEPATH=/hpc2n/eb/modules/all/Core:/hpc2n/eb/software/lmod/lmod/modulefiles/Core eb goolfc-2017b.eb --stop=fetch
== temporary log file in case of crash /scratch/eb-vzFCwJ/easybuild-frRWLR.log
== Core/goolfc/2017b is already installed (module found), skipping
== No easyconfigs left to be built.
== Build succeeded for 0 out of 0
== Temporary log file(s) /scratch/eb-vzFCwJ/easybuild-frRWLR.log* have been removed.
== Temporary directory /scratch/eb-vzFCwJ has been removed.

real    0m7.559s
user    0m3.000s
sys     0m1.804s

The /hpc2n/eb/modules/all/Linux dir doesn't exist.

And after creating it...

mkdir /hpc2n/eb/modules/all/Linux
b-an02 [goolfc]$ time eb goolfc-2017b.eb --stop=fetch
== temporary log file in case of crash /scratch/eb-9zeVil/easybuild-P2Xcvp.log
== Core/goolfc/2017b is already installed (module found), skipping
== No easyconfigs left to be built.
== Build succeeded for 0 out of 0
== Temporary log file(s) /scratch/eb-9zeVil/easybuild-P2Xcvp.log* have been removed.
== Temporary directory /scratch/eb-9zeVil has been removed.

real    0m7.530s
user    0m3.152s
sys     0m1.720s

boegel · 2018-02-06T13:56:04Z

@rtmclay Does this ring a bell for you? Why would Lmod be significantly slower with a bunch of non-existing paths included in $MODULEPATH?

Note that this is with Lmod under EasyBuild's control, so with $LMOD_IGNORE_CACHE set...

SethosII · 2018-02-20T06:39:11Z

I encountered the same issue with non-existing directories in MODULEPATH slowing down EasyBuild considerably (see #2408, for me the initialization of EasyBuild takes more than 10 minutes). Here is the log: easybuild-aML_jl.log. Notice how lmod python use ... is executed over and over again for the same directories (grep -o "lmod python use.*ran fine" easybuild-aML_jl.log | sort | uniq -c says 17 times each).

And maybe the title of this issue should reflect that this only happens with non-existing directories in MODULEPATH?

boegel · 2018-03-30T19:42:40Z

I'm having trouble reproducing this...

I tried adding a whole bunch of non-existing directories in $MODULEPATH using:

for i in $(seq 1 100); do export MODULEPATH=/tmp/$USER/dir${i}:$MODULEPATH; done

But I'm not seeing any noticeable slowdown. Am I overlooking something?

SethosII · 2018-04-10T11:48:28Z

@boegel The issue might be amplified due to our file system having a very bad latency/small read behaviour. Do you have a measurable slow down with non existing directories?

boegel · 2018-04-15T08:36:43Z

OK, I gave this another try, with:

$HOME an NFS mount (so quite slow)
1000 non-existent directories in $MODULEPATH, added via module use

$ ml --version

Modules based on Lua: Version 7.7.26  2018-04-03 23:18 -05:00
    by Robert McLay mclay@tacc.utexas.edu

$ echo $MODULEPATH | wc -c
213
$ time eb foss-2016a.eb -r -D
...
real	0m6.044s
user	0m2.760s
sys	0m1.081s

$ for i in $(seq 1 1000); do echo $i; module use $HOME/nosuchdir${i}; done

$ time eb foss-2016a.eb -r -D
...
real	0m30.824s
user	0m25.835s
sys	0m2.558s

So there's a noticeable slowdown of about 5x, but I don't think that's a surprise with 1000 (non-existing) directories, since Lmod will check each of those locations whether it has modules present in those locations.

Creating the directories makes things a lot worse, to the point where eb foss-2016a.eb -r -D didn't finish in ~1 hour; I guess Lmod tries harder to find modules if the top directory exists.

If someone can still reproduce this, with a recent version of Lmod, please provide debug logs for both a 'fast' run (short $MODULEPATH, only existing directories) and a 'slow' run (long $MODULEPATH with several non-existing directories).

SethosII · 2018-06-11T07:08:42Z

@boegel I finnaly came around testing this again with the latest versions. I can confirm that it's still the case for me. A dry run takes over 20 minutes if I have non-existing directories in my MODULEPATH and if I create all the missing directories it goes down to 20 seconds:

# versions involved
$ eb --version
This is EasyBuild 3.6.1 (framework: 3.6.1, easyblocks: 3.6.1) on host node015.
$ ml --version

Modules based on Lua: Version 7.7.34  2018-05-27 17:42 -05:00
    by Robert McLay mclay@tacc.utexas.edu

# clear MODULEPATH
$ unset MODULEPATH
# add all possible module classes
$ ml use $MODULEPATH_EASYBUILD_ROOT/base $MODULEPATH_EASYBUILD_ROOT/bio $MODULEPATH_EASYBUILD_ROOT/cae $MODULEPATH_EASYBUILD_ROOT/chem $MODULEPATH_EASYBUILD_ROOT/compiler $MODULEPATH_EASYBUILD_ROOT/data $MODULEPATH_EASYBUILD_ROOT/debugger $MODULEPATH_EASYBUILD_ROOT/devel $MODULEPATH_EASYBUILD_ROOT/geo $MODULEPATH_EASYBUILD_ROOT/lang $MODULEPATH_EASYBUILD_ROOT/lib $MODULEPATH_EASYBUILD_ROOT/math $MODULEPATH_EASYBUILD_ROOT/mpi $MODULEPATH_EASYBUILD_ROOT/numlib $MODULEPATH_EASYBUILD_ROOT/perf $MODULEPATH_EASYBUILD_ROOT/phys $MODULEPATH_EASYBUILD_ROOT/system $MODULEPATH_EASYBUILD_ROOT/toolchain $MODULEPATH_EASYBUILD_ROOT/tools $MODULEPATH_EASYBUILD_ROOT/vis
# existing directories
$ ls $MODULEPATH_EASYBUILD_ROOT 
all  base  bio  compiler  data  devel  lang  lib  math  mpi  numlib  system  toolchain  tools  vis
# dry-run takes long time
$ time eb --buildpath=/dev/shm --optarch=march=corei7 --prefix=/easybuild/16.04 SAMtools-1.4-foss-2016b.eb -dr -D
== temporary log file in case of crash /tmp/eb-5plycS/easybuild-MdHiPZ.log
Dry run: printing build status of easyconfigs and dependencies
CFGS=/easybuild/16.04/software/EasyBuild/3.6.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.1-py2.7.egg/easybuild/easyconfigs
 * [x] $CFGS/m/M4/M4-1.4.17.eb (module: M4/1.4.17)
 * [x] $CFGS/b/Bison/Bison-3.0.4.eb (module: Bison/3.0.4)
 * [x] $CFGS/n/ncurses/ncurses-6.0.eb (module: ncurses/6.0)
 * [x] $CFGS/g/gettext/gettext-0.19.8.eb (module: gettext/0.19.8)
 * [x] $CFGS/f/flex/flex-2.6.0.eb (module: flex/2.6.0)
 * [x] $CFGS/z/zlib/zlib-1.2.8.eb (module: zlib/1.2.8)
 * [x] $CFGS/b/binutils/binutils-2.26.eb (module: binutils/2.26)
 * [x] $CFGS/g/GCCcore/GCCcore-5.4.0.eb (module: GCCcore/5.4.0)
 * [x] $CFGS/m/M4/M4-1.4.17-GCCcore-5.4.0.eb (module: M4/1.4.17-GCCcore-5.4.0)
 * [x] $CFGS/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb (module: zlib/1.2.8-GCCcore-5.4.0)
 * [x] $CFGS/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb (module: Bison/3.0.4-GCCcore-5.4.0)
 * [x] $CFGS/f/flex/flex-2.6.0-GCCcore-5.4.0.eb (module: flex/2.6.0-GCCcore-5.4.0)
 * [x] $CFGS/b/binutils/binutils-2.26-GCCcore-5.4.0.eb (module: binutils/2.26-GCCcore-5.4.0)
 * [x] $CFGS/g/GCC/GCC-5.4.0-2.26.eb (module: GCC/5.4.0-2.26)
 * [x] $CFGS/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb (module: OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1)
 * [x] $CFGS/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb (module: M4/1.4.17-GCC-5.4.0-2.26)
 * [x] $CFGS/a/Autoconf/Autoconf-2.69-GCC-5.4.0-2.26.eb (module: Autoconf/2.69-GCC-5.4.0-2.26)
 * [x] $CFGS/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb (module: Automake/1.15-GCC-5.4.0-2.26)
 * [x] $CFGS/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb (module: libtool/2.4.6-GCC-5.4.0-2.26)
 * [x] $CFGS/a/Autotools/Autotools-20150215-GCC-5.4.0-2.26.eb (module: Autotools/20150215-GCC-5.4.0-2.26)
 * [x] $CFGS/n/numactl/numactl-2.0.11-GCC-5.4.0-2.26.eb (module: numactl/2.0.11-GCC-5.4.0-2.26)
 * [x] $CFGS/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb (module: hwloc/1.11.3-GCC-5.4.0-2.26)
 * [x] $CFGS/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb (module: OpenMPI/1.10.3-GCC-5.4.0-2.26)
 * [x] $CFGS/g/gompi/gompi-2016b.eb (module: gompi/2016b)
 * [x] $CFGS/f/FFTW/FFTW-3.3.4-gompi-2016b.eb (module: FFTW/3.3.4-gompi-2016b)
 * [x] $CFGS/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1.eb (module: ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1)
 * [x] $CFGS/f/foss/foss-2016b.eb (module: foss/2016b)
 * [x] $CFGS/b/bzip2/bzip2-1.0.6-foss-2016b.eb (module: bzip2/1.0.6-foss-2016b)
 * [x] $CFGS/m/M4/M4-1.4.17-foss-2016b.eb (module: M4/1.4.17-foss-2016b)
 * [x] $CFGS/l/libtool/libtool-2.4.6-foss-2016b.eb (module: libtool/2.4.6-foss-2016b)
 * [x] $CFGS/n/ncurses/ncurses-6.0-foss-2016b.eb (module: ncurses/6.0-foss-2016b)
 * [x] $CFGS/z/zlib/zlib-1.2.8-foss-2016b.eb (module: zlib/1.2.8-foss-2016b)
 * [x] $CFGS/a/Autoconf/Autoconf-2.69-foss-2016b.eb (module: Autoconf/2.69-foss-2016b)
 * [x] $CFGS/a/Automake/Automake-1.15-foss-2016b.eb (module: Automake/1.15-foss-2016b)
 * [x] $CFGS/a/Autotools/Autotools-20150215-foss-2016b.eb (module: Autotools/20150215-foss-2016b)
 * [x] $CFGS/x/XZ/XZ-5.2.2-foss-2016b.eb (module: XZ/5.2.2-foss-2016b)
 * [ ] $CFGS/s/SAMtools/SAMtools-1.4-foss-2016b.eb (module: SAMtools/1.4-foss-2016b)
== Temporary log file(s) /tmp/eb-5plycS/easybuild-MdHiPZ.log* have been removed.
== Temporary directory /tmp/eb-5plycS has been removed.

real    25m36.102s
user    2m29.416s
sys     3m38.544s
# create all non-existing directories
$ mkdir $MODULEPATH_EASYBUILD_ROOT/cae $MODULEPATH_EASYBUILD_ROOT/chem $MODULEPATH_EASYBUILD_ROOT/debugger $MODULEPATH_EASYBUILD_ROOT/geo $MODULEPATH_EASYBUILD_ROOT/perf $MODULEPATH_EASYBUILD_ROOT/phys
# dry-run is much faster
$ time eb --buildpath=/dev/shm --optarch=march=corei7 --prefix=/easybuild/16.04 SAMtools-1.4-foss-2016b.eb -dr -D
== temporary log file in case of crash /tmp/eb-IJ2KeW/easybuild-6V5fli.log
Dry run: printing build status of easyconfigs and dependencies
CFGS=/easybuild/16.04/software/EasyBuild/3.6.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.1-py2.7.egg/easybuild/easyconfigs
 * [x] $CFGS/m/M4/M4-1.4.17.eb (module: M4/1.4.17)
 * [x] $CFGS/b/Bison/Bison-3.0.4.eb (module: Bison/3.0.4)
 * [x] $CFGS/n/ncurses/ncurses-6.0.eb (module: ncurses/6.0)
 * [x] $CFGS/g/gettext/gettext-0.19.8.eb (module: gettext/0.19.8)
 * [x] $CFGS/f/flex/flex-2.6.0.eb (module: flex/2.6.0)
 * [x] $CFGS/z/zlib/zlib-1.2.8.eb (module: zlib/1.2.8)
 * [x] $CFGS/b/binutils/binutils-2.26.eb (module: binutils/2.26)
 * [x] $CFGS/g/GCCcore/GCCcore-5.4.0.eb (module: GCCcore/5.4.0)
 * [x] $CFGS/m/M4/M4-1.4.17-GCCcore-5.4.0.eb (module: M4/1.4.17-GCCcore-5.4.0)
 * [x] $CFGS/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb (module: zlib/1.2.8-GCCcore-5.4.0)
 * [x] $CFGS/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb (module: Bison/3.0.4-GCCcore-5.4.0)
 * [x] $CFGS/f/flex/flex-2.6.0-GCCcore-5.4.0.eb (module: flex/2.6.0-GCCcore-5.4.0)
 * [x] $CFGS/b/binutils/binutils-2.26-GCCcore-5.4.0.eb (module: binutils/2.26-GCCcore-5.4.0)
 * [x] $CFGS/g/GCC/GCC-5.4.0-2.26.eb (module: GCC/5.4.0-2.26)
 * [x] $CFGS/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb (module: OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1)
 * [x] $CFGS/m/M4/M4-1.4.17-GCC-5.4.0-2.26.eb (module: M4/1.4.17-GCC-5.4.0-2.26)
 * [x] $CFGS/a/Autoconf/Autoconf-2.69-GCC-5.4.0-2.26.eb (module: Autoconf/2.69-GCC-5.4.0-2.26)
 * [x] $CFGS/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb (module: Automake/1.15-GCC-5.4.0-2.26)
 * [x] $CFGS/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb (module: libtool/2.4.6-GCC-5.4.0-2.26)
 * [x] $CFGS/a/Autotools/Autotools-20150215-GCC-5.4.0-2.26.eb (module: Autotools/20150215-GCC-5.4.0-2.26)
 * [x] $CFGS/n/numactl/numactl-2.0.11-GCC-5.4.0-2.26.eb (module: numactl/2.0.11-GCC-5.4.0-2.26)
 * [x] $CFGS/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb (module: hwloc/1.11.3-GCC-5.4.0-2.26)
 * [x] $CFGS/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb (module: OpenMPI/1.10.3-GCC-5.4.0-2.26)
 * [x] $CFGS/g/gompi/gompi-2016b.eb (module: gompi/2016b)
 * [x] $CFGS/f/FFTW/FFTW-3.3.4-gompi-2016b.eb (module: FFTW/3.3.4-gompi-2016b)
 * [x] $CFGS/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1.eb (module: ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1)
 * [x] $CFGS/f/foss/foss-2016b.eb (module: foss/2016b)
 * [x] $CFGS/b/bzip2/bzip2-1.0.6-foss-2016b.eb (module: bzip2/1.0.6-foss-2016b)
 * [x] $CFGS/m/M4/M4-1.4.17-foss-2016b.eb (module: M4/1.4.17-foss-2016b)
 * [x] $CFGS/l/libtool/libtool-2.4.6-foss-2016b.eb (module: libtool/2.4.6-foss-2016b)
 * [x] $CFGS/n/ncurses/ncurses-6.0-foss-2016b.eb (module: ncurses/6.0-foss-2016b)
 * [x] $CFGS/z/zlib/zlib-1.2.8-foss-2016b.eb (module: zlib/1.2.8-foss-2016b)
 * [x] $CFGS/a/Autoconf/Autoconf-2.69-foss-2016b.eb (module: Autoconf/2.69-foss-2016b)
 * [x] $CFGS/a/Automake/Automake-1.15-foss-2016b.eb (module: Automake/1.15-foss-2016b)
 * [x] $CFGS/a/Autotools/Autotools-20150215-foss-2016b.eb (module: Autotools/20150215-foss-2016b)
 * [x] $CFGS/x/XZ/XZ-5.2.2-foss-2016b.eb (module: XZ/5.2.2-foss-2016b)
 * [ ] $CFGS/s/SAMtools/SAMtools-1.4-foss-2016b.eb (module: SAMtools/1.4-foss-2016b)
== Temporary log file(s) /tmp/eb-IJ2KeW/easybuild-6V5fli.log* have been removed.
== Temporary directory /tmp/eb-IJ2KeW has been removed.

real    0m23.276s
user    0m4.188s
sys     0m2.960s

How can I tell EasyBuild to keep the logs so I can provide them for further inspection?

boegel · 2018-06-11T07:30:00Z

@SethosII Please try with --disable-cleanup-tmpdir

SethosII · 2018-06-11T09:12:30Z

Here are the logs.

…d test to verify that easybuilders#2226 and easybuilders#3084 are fixed)

boegel · 2019-11-25T19:09:11Z

This problem was reported again via #3084, and after some digging @Micket managed to figure out the culprit.

It's basically caused by an inconsistency in the code w.r.t. handling of non-existing directories in $MODULEPATH.

Fixed by #3099, which will be included in the upcoming EasyBuild v4.1.0 release...

boegel added this to the 3.3.0 milestone May 16, 2017

boegel modified the milestones: 3.3.0, 3.3.1 Jun 26, 2017

boegel modified the milestones: 3.3.1, 3.4.0 Jul 9, 2017

boegel modified the milestones: 3.4.0, 3.5.0 Sep 4, 2017

boegel modified the milestones: 3.5.0, next release Dec 6, 2017

boegel modified the milestones: 3.5.1, 3.6.0 Jan 12, 2018

boegel mentioned this issue Feb 19, 2018

Endless loop during initialization with non-existing directories in MODULEPATH #2408

Closed

boegel modified the milestones: 3.5.2, 3.6.0 Feb 22, 2018

boegel added the problem report label Mar 14, 2018

boegel modified the milestones: 3.6.0, 3.x Mar 30, 2018

boegel mentioned this issue Nov 25, 2019

prepend_module_path is very slow #3084

Closed

boegel added a commit to boegel/easybuild-framework that referenced this issue Nov 25, 2019

add tests for curr_module_paths + check_module_path (incl. a dedicate…

99aa264

…d test to verify that easybuilders#2226 and easybuilders#3084 are fixed)

boegel mentioned this issue Nov 25, 2019

add tests for curr_module_paths + check_module_path Micket/easybuild-framework#1

Merged

boegel modified the milestones: 3.x, 4.1.0 Nov 25, 2019

Micket mentioned this issue Nov 25, 2019

Fix inconsistent module path usage that leads to repeated reloading in HMNS #3099

Merged

migueldiascosta closed this as completed in #3099 Nov 26, 2019

vsoch mentioned this issue Dec 9, 2021

Access to private Docker container registry singularityhub/singularity-hpc#465

Closed

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long MODULEPATH drastically reduces performance #2226

long MODULEPATH drastically reduces performance #2226

pescobar commented May 16, 2017 •

edited

pescobar commented May 16, 2017

boegel commented May 16, 2017

rtmclay commented May 16, 2017

pescobar commented May 16, 2017

wpoely86 commented May 22, 2017

boegel commented Jun 9, 2017

akesandgren commented Feb 1, 2018 •

edited

boegel commented Feb 6, 2018

SethosII commented Feb 20, 2018 •

edited

boegel commented Mar 30, 2018

SethosII commented Apr 10, 2018 •

edited

boegel commented Apr 15, 2018

SethosII commented Jun 11, 2018

boegel commented Jun 11, 2018

SethosII commented Jun 11, 2018

boegel commented Nov 25, 2019

long MODULEPATH drastically reduces performance #2226

long MODULEPATH drastically reduces performance #2226

Comments

pescobar commented May 16, 2017 • edited

pescobar commented May 16, 2017

boegel commented May 16, 2017

rtmclay commented May 16, 2017

pescobar commented May 16, 2017

wpoely86 commented May 22, 2017

boegel commented Jun 9, 2017

akesandgren commented Feb 1, 2018 • edited

boegel commented Feb 6, 2018

SethosII commented Feb 20, 2018 • edited

boegel commented Mar 30, 2018

SethosII commented Apr 10, 2018 • edited

boegel commented Apr 15, 2018

SethosII commented Jun 11, 2018

boegel commented Jun 11, 2018

SethosII commented Jun 11, 2018

boegel commented Nov 25, 2019

pescobar commented May 16, 2017 •

edited

akesandgren commented Feb 1, 2018 •

edited

SethosII commented Feb 20, 2018 •

edited

SethosII commented Apr 10, 2018 •

edited