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Description
Hi ,
We are currently in a situation where in we installed a R bundle using easybuild. but with the generated module files, the module load and module purge are taking more than 15 seconds.
I f this was a code, I would have attached a debugger to see which line of code is taking longer. Could you please help me to understand how and thich tools can I debug the root cause of slowness here ?
Here is the command I use to reproduce the slowness -
So far we have observed slowness issues with only this particular module.
Example:
[singhpuv@server ~]$ time module load R-bundle-Novartis
real 0m16.866s
user 0m15.105s
sys 0m0.082s
[singhpuv@Pserver~]$ module list
Currently Loaded Modulefiles:
- GCCcore/11.2.0 83) Mesa/22.0.3-GCCcore-11.2.0
- zlib/1.2.11-GCCcore-11.2.0 84) libGLU/9.0.2-GCCcore-11.2.0
- binutils/2.37-GCCcore-11.2.0 85) nodejs/18.17.1-GCCcore-11.2.0
- GCC/11.2.0 86) MPFR/4.1.0-GCCcore-11.2.0
- numactl/2.0.14-GCCcore-11.2.0 87) OpenJPEG/2.5.0-GCCcore-11.2.0
- XZ/5.2.5-GCCcore-11.2.0 88) Pandoc/3.1.2
- libxml2/2.9.13-GCCcore-11.2.0 89) NSPR/4.34-GCCcore-11.2.0
- libpciaccess/0.16-GCCcore-11.2.0-BuildNAOS 90) NSS/3.79-GCCcore-11.2.0
- hwloc/2.7.1-GCCcore-11.2.0 91) double-conversion/3.2.0-GCCcore-11.2.0
- OpenSSL/1.1 92) graphite2/1.3.14-GCCcore-11.2.0
- libevent/2.1.12-GCCcore-11.2.0 93) DBus/1.14.0-GCCcore-11.2.0
- UCX/1.12.1-GCCcore-11.2.0 94) snappy/1.1.9-GCCcore-11.2.0
- libfabric/1.15.1-GCCcore-11.2.0 95) Qt5/5.15.5-GCCcore-11.2.0-MEISSA
- PMIx/4.1.2-GCCcore-11.2.0 96) Boost/1.81.0-GCC-11.2.0
- UCC/1.0.0-GCCcore-11.2.0 97) poppler/22.01.0-GCC-11.2.0-MEISSA
- OpenMPI/4.1.4-GCC-11.2.0 98) OpenPGM/5.2.122-GCCcore-11.2.0
- gompi/2022a 99) libsodium/1.0.18-GCCcore-11.2.0
- imkl/2022.1.0-gompi-2022a 100) ZeroMQ/4.3.4-GCCcore-11.2.0-BuildNAOS
- gomkl/2022a 101) FFTW/3.3.10-gompi-2022a
- OracleInstantClient/21.12-el9 102) Szip/2.1.1-GCCcore-11.2.0
- ncurses/6.2-GCCcore-11.2.0 103) HDF5/1.12.1-gompi-2022a
- libreadline/8.1-GCCcore-11.2.0 104) libogg/1.3.5-GCCcore-11.2.0
- bzip2/1.0.8-GCCcore-11.2.0 105) FLAC/1.3.4-GCCcore-11.2.0
- PCRE2/10.40-GCCcore-11.2.0 106) libvorbis/1.3.7-GCCcore-11.2.0
- cURL/7.78.0-GCCcore-11.2.0 107) libopus/1.3.1-GCCcore-11.2.0
- M4/1.4.20-GCCcore-11.2.0 108) LAME/3.100-GCCcore-11.2.0
- expat/2.4.8-GCCcore-11.2.0 109) libsndfile/1.1.0-GCCcore-11.2.0
- DB/18.1.40-GCCcore-11.2.0 110) libpipeline/1.5.7-GCC-11.2.0
- Perl/5.34.0-GCCcore-11.2.0-BuildNAOS 111) man-db/2.11.2-GCC-11.2.0
- Autoconf/2.71-GCCcore-11.2.0-BuildNAOS 112) NLopt/2.7.1-GCCcore-11.2.0
- Automake/1.16.5-GCCcore-11.2.0-BuildNAOS 113) UDUNITS/2.2.28-GCCcore-11.2.0
- libtool/2.4.6-GCCcore-11.2.0 114) netCDF/4.9.0-gompi-2022a
- Autotools/20220317-GCCcore-11.2.0 115) GEOS/3.11.1-GCC-11.2.0
- libpng/1.6.37-GCCcore-11.2.0 116) nlohmann_json/3.11.2-GCCcore-11.2.0
- Brotli/1.0.9-GCCcore-11.2.0 117) PROJ/9.0.0-GCCcore-11.2.0
- freetype/2.12.1-GCCcore-11.2.0 118) libgeotiff/1.7.1-GCCcore-11.2.0
- pixman/0.40.0-GCCcore-11.2.0 119) pybind11/2.10.3-GCCcore-11.2.0
- libffi/3.4.4-GCCcore-11.2.0 120) hypothesis/6.14.6-gomkl-2022a
- gettext/0.21-GCCcore-11.2.0-BuildNAOS 121) numpy/1.23.5-gomkl-2022a
- PCRE/8.45-GCCcore-11.2.0 122) SciPy-bundle/2022.05-gomkl-2022a
- util-linux/2.38-GCCcore-11.2.0 123) libtirpc/1.3.2-GCCcore-11.2.0
- GLib/2.72.1-GCCcore-11.2.0 124) HDF/4.2.15-GCCcore-11.2.0
- fontconfig/2.14.0-GCCcore-11.2.0 125) Eigen/3.4.0-GCCcore-11.2.0
- xorg-macros/1.19.3-GCCcore-11.2.0-BuildNAOS 126) arpack-ng/3.8.0-gomkl-2022a
- X11/20220504-GCCcore-11.2.0 127) Armadillo/11.4.3-gomkl-2022a-MEISSA
- cairo/1.17.4-GCCcore-11.2.0 128) CFITSIO/4.2.0-GCCcore-11.2.0
- Java/17.0.6 129) giflib/5.2.1-GCCcore-11.2.0
- ICU/74.1-GCCcore-11.2.0 130) json-c/0.16-GCCcore-11.2.0
- NASM/2.15.05-GCCcore-11.2.0 131) Xerces-C++/3.2.4-GCCcore-11.2.0
- libjpeg-turbo/2.1.3-GCCcore-11.2.0 132) Imath/3.1.5-GCCcore-11.2.0
- jbigkit/2.1-GCCcore-11.2.0 133) OpenEXR/3.1.5-GCCcore-11.2.0
- gzip/1.12-GCCcore-11.2.0 134) Highway/1.0.3-GCCcore-11.2.0
- lz4/1.9.3-GCCcore-11.2.0 135) Brunsli/0.1-GCCcore-11.2.0
- zstd/1.5.2-GCCcore-11.2.0 136) Qhull/2020.2-GCCcore-11.2.0
- LibTIFF/4.3.0-GCCcore-11.2.0 137) LERC/4.0.0-GCCcore-11.2.0
- HarfBuzz/8.2.2-GCCcore-11.2.0-MEISSA 138) libwebp/1.3.1-GCCcore-11.2.0
- FriBidi/1.0.12-GCCcore-11.2.0 139) GDAL/3.6.2-gomkl-2022a-MEISSA
- Pango/1.50.7-GCCcore-11.2.0-MEISSA 140) unixODBC/2.3.11-gomkl-2022a
- Tcl/8.6.12-GCCcore-11.2.0 141) GObject-Introspection/1.72.0-GCCcore-11.2.0
- Tk/8.6.12-GCCcore-11.2.0 142) pkg-config/0.29.2-GCCcore-11.2.0
- Zip/3.0-GCCcore-11.2.0 143) librsvg/2.54.2-gomkl-2022a-MEISSA
- CMake/3.25.0-GCCcore-11.2.0 144) phantomjs/2.1.1-gomkl-2022a
- cmdstan/2.32.2-gomkl-2022a 145) MPC/1.2.1-GCCcore-11.2.0
- ATK/2.38.0-GCCcore-11.2.0 146) gmpy2/2.1.2-GCC-11.2.0
- SQLite/3.39.4-GCCcore-11.2.0 147) sympy/1.9-gomkl-2022a
- GMP/6.2.1-GCCcore-11.2.0 148) PostgreSQL/14.4-GCCcore-11.2.0
- Python/3.10.7-GCCcore-11.2.0-BuildNAOS 149) libpq/13.20-el9_5
- Gdk-Pixbuf/2.42.8-GCCcore-11.2.0 150) texlive/20210325-GCCcore-11.2.0-MEISSA
- six/1.16.0-gomkl-2022a 151) rpmrebuild/2.11
- GTK2/2.24.33-GCCcore-11.2.0-MEISSA 152) shinycannon/1.1.3-linux-x86_64
- Ghostscript/9.56.1-GCCcore-11.2.0-MEISSA 153) MariaDB-connector-c/3.3.5-gomkl-2022a
- JasPer/4.0.0-GCCcore-11.2.0 154) quartocli/1.6.40
- LittleCMS/2.13.1-GCCcore-11.2.0 155) tbb/2018_U5-GCCcore-11.2.0
- ImageMagick/7.1.0-4-GCCcore-11.2.0-MEISSA 156) libarchive/3.7.7-GCCcore-11.2.0
- GLPK/5.0-GCCcore-11.2.0 157) texinfo/7.1-GCCcore-11.2.0
- GSL/2.7-GCC-11.2.0 158) hiredis/1.3.0-GCCcore-11.2.0
- JAGS/4.3.2-gomkl-2022a 159) libxslt/1.1.43-GCCcore-11.2.0
- libgit2/1.4.3-GCCcore-11.2.0 160) Abseil/20250512.1-GCCcore-11.2.0
- libdrm/2.4.110-GCCcore-11.2.0 161) protobuf/31.1-GCCcore-11.2.0
- libglvnd/1.4.0-GCCcore-11.2.0 162) R/4.3.1-gomkl-2022a-0.4
- libunwind/1.6.2-GCCcore-11.2.0 163) R-bundle-Novartis/0.5-gomkl-2022a-R-4.3.1
- LLVM/12.0.1-GCCcore-11.2.0
Key:
auto-loaded
[singhpuv@server ~]$ time module purge
real 0m18.310s
user 0m17.923s
sys 0m0.045s
[singhpuv@server ~]$