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From: Paul M. <pau...@gm...> - 2025-12-03 14:59:55
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This seems insanely long: TIMER module load R-bundle-organozation (163945.261 ms) You might want to make sure it is modules, by side installing 5.3.0 on one of your RHEL 7 machines, and seeing if it has the same problem (it may be something inside one of your modules that has a problem on the newer OS, or a selection in the modulefile that id different on the different OSes). The 3.2.10 modulecmd is likely a compiled binary (particularly on RHEL). 5.3.0 modulecmd is a tclsh script (which includes an optional binary helper library ..../modules/5.3.0/lib/libtclenvmodules.so ). Also, if there are .modulecache files in your module tree; they may have been created by the older version, and likely are causing problems for the newer version. I note two things about my own setup: 1. I use a central (network) installation of modules, so I remove lib/libtclenvmodules.so from the installation (actually I move it to another folder modules/$VERSION/NOT_USED/lib/ ) as it is compiled for a specific OS (and we use the same modules installation on a variety of OSes - including FreeBSD, so that library could be problematic). The library is optional, and only used if present (perhaps the the one installed on your machines is corrupted somehow). 2. In my progress through modules versions, I skipped 5.3.0 for some reason and went directly from 5.2.0 to 5.3.1 (so there may be some bug in 5.3.0). See: https://modules.readthedocs.io/en/latest/NEWS.html#modules-5-3-1-2023-06-27 On 2025-12-02 9:50 PM, Singh, Puneet-2 (Ext) via Modules-interest wrote: > Thank you for the response Xavier > > we have 2 environments : > old environment based on RHEL 7) > ~]$ time module load R-bundle-Novartis > > real 0m2.327s > user 0m1.677s > sys 0m0.177s > ~]$ module --version > VERSION=3.2.10 > DATE=2012-12-21 > > AUTOLOADPATH=undef > BASEPREFIX="/usr/share" > BEGINENV=99 > CACHE_AVAIL=undef > DEF_COLLATE_BY_NUMBER=undef > > > new environment based on RHEL 9.5) > module version: > ~]$ module --version > Modules Release 5.3.0 (2023-05-14) > > > Yes, Module files are located over the network in both the situations. > That’s why we believe that either the latest version of module is unable to handle the module loads efficiently > or there is something within the module files which causes the loads to take more time. > > > I tried using –time and –debug, and I got a lot of information. Will try to see if I am able to understand the root cause > ………. > TIMER charEscaped 2.1.12 (0.018 ms) > TIMER charEscaped /CHBS/apps/EB/software/NASM/2.15.05-GCCcore-11.2.0/easybuild/NASM-2.15.05-GCCcore-11.2.0-easybuild-devel (0.013 ms) > TIMER charEscaped /CHBS/apps/EB/software/OpenSSL/1.1 (0.011 ms) > TIMER charEscaped 2.38 (0.010 ms) > TIMER charEscaped 1.12 (0.012 ms) > TIMER charEscaped {echo -e "cmdstan THREADS" && make -f /apps/EB-DEV/software/cmdstan/2.32.2-gomkl-2022a/makefile -C /apps/EB-DEV/software/cmdstan/2.32.2-gomkl-2022a "${PWD}/$1"} (0.062 ms) > TIMER charEscaped {R --no-restore-data --no-save} (0.016 ms) > TIMER renderTrue (1.653 ms) > TIMER renderSettings (162.068 ms) > TIMER module load R-bundle-organozation (163945.261 ms) > TIMER renderFlush (2.275 ms) > > TIMER Total execution took 163951.384 ms > > real 2m44.000s > user 0m38.132s > sys 0m15.587s > [user@rhel9server ~]$ ls -lrth out > -rw-------. 1 user ug 93M Dec 3 04:46 out > [user@rhel9server ~]$ > > > > Regards > Puneet > > > From: Xavier Delaruelle <xav...@gm...> > Sent: 01 December 2025 23:51 > To: Singh, Puneet-2 (Ext) <pun...@no...> > Subject: Fwd: [Modules] tcl module load slowness debug > > Le lun. 1 déc. 2025 à 19: 19, Xavier Delaruelle <xavier. delaruelle@ gmail. com> a écrit : Hi, To debug such situation you may add the "--timer --debug" options to your module commands. You will get precise list of operations with > ZjQcmQRYFpfptBannerStart > This Message Is From an Untrusted Sender > You have not previously corresponded with this sender. > ZjQcmQRYFpfptBannerEnd > > Le lun. 1 déc. 2025 à 19:19, Xavier Delaruelle <xav...@gm...<mailto:xav...@gm...>> a écrit : > Hi, > > To debug such situation you may add the "--timer --debug" options to your module commands. You will get precise list of operations with their timing. > > What version of Modules are you using ? > Is the modulefiles located on a network filesystem? Have you tried building a module cache to speed-up the reads? > > Regards, > Xavier > > Le lun. 1 déc. 2025 à 19:09, Singh, Puneet-2 (Ext) via Modules-interest <mod...@li...<mailto:mod...@li...>> a écrit : > > Hi , > We are currently in a situation where in a 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 onserved 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: > 1) GCCcore/11.2.0 83) Mesa/22.0.3-GCCcore-11.2.0 > 2) zlib/1.2.11-GCCcore-11.2.0 84) libGLU/9.0.2-GCCcore-11.2.0 > 3) binutils/2.37-GCCcore-11.2.0 85) nodejs/18.17.1-GCCcore-11.2.0 > 4) GCC/11.2.0 86) MPFR/4.1.0-GCCcore-11.2.0 > 5) numactl/2.0.14-GCCcore-11.2.0 87) OpenJPEG/2.5.0-GCCcore-11.2.0 > 6) XZ/5.2.5-GCCcore-11.2.0 88) Pandoc/3.1.2 > 7) libxml2/2.9.13-GCCcore-11.2.0 89) NSPR/4.34-GCCcore-11.2.0 > 8) libpciaccess/0.16-GCCcore-11.2.0-BuildNAOS 90) NSS/3.79-GCCcore-11.2.0 > 9) hwloc/2.7.1-GCCcore-11.2.0 91) double-conversion/3.2.0-GCCcore-11.2.0 > 10) OpenSSL/1.1 92) graphite2/1.3.14-GCCcore-11.2.0 > 11) libevent/2.1.12-GCCcore-11.2.0 93) DBus/1.14.0-GCCcore-11.2.0 > 12) UCX/1.12.1-GCCcore-11.2.0 94) snappy/1.1.9-GCCcore-11.2.0 > 13) libfabric/1.15.1-GCCcore-11.2.0 95) Qt5/5.15.5-GCCcore-11.2.0-MEISSA > 14) PMIx/4.1.2-GCCcore-11.2.0 96) Boost/1.81.0-GCC-11.2.0 > 15) UCC/1.0.0-GCCcore-11.2.0 97) poppler/22.01.0-GCC-11.2.0-MEISSA > 16) OpenMPI/4.1.4-GCC-11.2.0 98) OpenPGM/5.2.122-GCCcore-11.2.0 > 17) gompi/2022a 99) libsodium/1.0.18-GCCcore-11.2.0 > 18) imkl/2022.1.0-gompi-2022a 100) ZeroMQ/4.3.4-GCCcore-11.2.0-BuildNAOS > 19) gomkl/2022a 101) FFTW/3.3.10-gompi-2022a > 20) OracleInstantClient/21.12-el9 102) Szip/2.1.1-GCCcore-11.2.0 > 21) ncurses/6.2-GCCcore-11.2.0 103) HDF5/1.12.1-gompi-2022a > 22) libreadline/8.1-GCCcore-11.2.0 104) libogg/1.3.5-GCCcore-11.2.0 > 23) bzip2/1.0.8-GCCcore-11.2.0 105) FLAC/1.3.4-GCCcore-11.2.0 > 24) PCRE2/10.40-GCCcore-11.2.0 106) libvorbis/1.3.7-GCCcore-11.2.0 > 25) cURL/7.78.0-GCCcore-11.2.0 107) libopus/1.3.1-GCCcore-11.2.0 > 26) M4/1.4.20-GCCcore-11.2.0 108) LAME/3.100-GCCcore-11.2.0 > 27) expat/2.4.8-GCCcore-11.2.0 109) libsndfile/1.1.0-GCCcore-11.2.0 > 28) DB/18.1.40-GCCcore-11.2.0 110) libpipeline/1.5.7-GCC-11.2.0 > 29) Perl/5.34.0-GCCcore-11.2.0-BuildNAOS 111) man-db/2.11.2-GCC-11.2.0 > 30) Autoconf/2.71-GCCcore-11.2.0-BuildNAOS 112) NLopt/2.7.1-GCCcore-11.2.0 > 31) Automake/1.16.5-GCCcore-11.2.0-BuildNAOS 113) UDUNITS/2.2.28-GCCcore-11.2.0 > 32) libtool/2.4.6-GCCcore-11.2.0 114) netCDF/4.9.0-gompi-2022a > 33) Autotools/20220317-GCCcore-11.2.0 115) GEOS/3.11.1-GCC-11.2.0 > 34) libpng/1.6.37-GCCcore-11.2.0 116) nlohmann_json/3.11.2-GCCcore-11.2.0 > 35) Brotli/1.0.9-GCCcore-11.2.0 117) PROJ/9.0.0-GCCcore-11.2.0 > 36) freetype/2.12.1-GCCcore-11.2.0 118) libgeotiff/1.7.1-GCCcore-11.2.0 > 37) pixman/0.40.0-GCCcore-11.2.0 119) pybind11/2.10.3-GCCcore-11.2.0 > 38) libffi/3.4.4-GCCcore-11.2.0 120) hypothesis/6.14.6-gomkl-2022a > 39) gettext/0.21-GCCcore-11.2.0-BuildNAOS 121) numpy/1.23.5-gomkl-2022a > 40) PCRE/8.45-GCCcore-11.2.0 122) SciPy-bundle/2022.05-gomkl-2022a > 41) util-linux/2.38-GCCcore-11.2.0 123) libtirpc/1.3.2-GCCcore-11.2.0 > 42) GLib/2.72.1-GCCcore-11.2.0 124) HDF/4.2.15-GCCcore-11.2.0 > 43) fontconfig/2.14.0-GCCcore-11.2.0 125) Eigen/3.4.0-GCCcore-11.2.0 > 44) xorg-macros/1.19.3-GCCcore-11.2.0-BuildNAOS 126) arpack-ng/3.8.0-gomkl-2022a > 45) X11/20220504-GCCcore-11.2.0 127) Armadillo/11.4.3-gomkl-2022a-MEISSA > 46) cairo/1.17.4-GCCcore-11.2.0 128) CFITSIO/4.2.0-GCCcore-11.2.0 > 47) Java/17.0.6 129) giflib/5.2.1-GCCcore-11.2.0 > 48) ICU/74.1-GCCcore-11.2.0 130) json-c/0.16-GCCcore-11.2.0 > 49) NASM/2.15.05-GCCcore-11.2.0 131) Xerces-C++/3.2.4-GCCcore-11.2.0 > 50) libjpeg-turbo/2.1.3-GCCcore-11.2.0 132) Imath/3.1.5-GCCcore-11.2.0 > 51) jbigkit/2.1-GCCcore-11.2.0 133) OpenEXR/3.1.5-GCCcore-11.2.0 > 52) gzip/1.12-GCCcore-11.2.0 134) Highway/1.0.3-GCCcore-11.2.0 > 53) lz4/1.9.3-GCCcore-11.2.0 135) Brunsli/0.1-GCCcore-11.2.0 > 54) zstd/1.5.2-GCCcore-11.2.0 136) Qhull/2020.2-GCCcore-11.2.0 > 55) LibTIFF/4.3.0-GCCcore-11.2.0 137) LERC/4.0.0-GCCcore-11.2.0 > 56) HarfBuzz/8.2.2-GCCcore-11.2.0-MEISSA 138) libwebp/1.3.1-GCCcore-11.2.0 > 57) FriBidi/1.0.12-GCCcore-11.2.0 139) GDAL/3.6.2-gomkl-2022a-MEISSA > 58) Pango/1.50.7-GCCcore-11.2.0-MEISSA 140) unixODBC/2.3.11-gomkl-2022a > 59) Tcl/8.6.12-GCCcore-11.2.0 141) GObject-Introspection/1.72.0-GCCcore-11.2.0 > 60) Tk/8.6.12-GCCcore-11.2.0 142) pkg-config/0.29.2-GCCcore-11.2.0 > 61) Zip/3.0-GCCcore-11.2.0 143) librsvg/2.54.2-gomkl-2022a-MEISSA > 62) CMake/3.25.0-GCCcore-11.2.0 144) phantomjs/2.1.1-gomkl-2022a > 63) cmdstan/2.32.2-gomkl-2022a 145) MPC/1.2.1-GCCcore-11.2.0 > 64) ATK/2.38.0-GCCcore-11.2.0 146) gmpy2/2.1.2-GCC-11.2.0 > 65) SQLite/3.39.4-GCCcore-11.2.0 147) sympy/1.9-gomkl-2022a > 66) GMP/6.2.1-GCCcore-11.2.0 148) PostgreSQL/14.4-GCCcore-11.2.0 > 67) Python/3.10.7-GCCcore-11.2.0-BuildNAOS 149) libpq/13.20-el9_5 > 68) Gdk-Pixbuf/2.42.8-GCCcore-11.2.0 150) texlive/20210325-GCCcore-11.2.0-MEISSA > 69) six/1.16.0-gomkl-2022a 151) rpmrebuild/2.11 > 70) GTK2/2.24.33-GCCcore-11.2.0-MEISSA 152) shinycannon/1.1.3-linux-x86_64 > 71) Ghostscript/9.56.1-GCCcore-11.2.0-MEISSA 153) MariaDB-connector-c/3.3.5-gomkl-2022a > 72) JasPer/4.0.0-GCCcore-11.2.0 154) quartocli/1.6.40 > 73) LittleCMS/2.13.1-GCCcore-11.2.0 155) tbb/2018_U5-GCCcore-11.2.0 > 74) ImageMagick/7.1.0-4-GCCcore-11.2.0-MEISSA 156) libarchive/3.7.7-GCCcore-11.2.0 > 75) GLPK/5.0-GCCcore-11.2.0 157) texinfo/7.1-GCCcore-11.2.0 > 76) GSL/2.7-GCC-11.2.0 158) hiredis/1.3.0-GCCcore-11.2.0 > 77) JAGS/4.3.2-gomkl-2022a 159) libxslt/1.1.43-GCCcore-11.2.0 > 78) libgit2/1.4.3-GCCcore-11.2.0 160) Abseil/20250512.1-GCCcore-11.2.0 > 79) libdrm/2.4.110-GCCcore-11.2.0 161) protobuf/31.1-GCCcore-11.2.0 > 80) libglvnd/1.4.0-GCCcore-11.2.0 162) R/4.3.1-gomkl-2022a-0.4 > 81) libunwind/1.6.2-GCCcore-11.2.0 163) R-bundle-Novartis/0.5-gomkl-2022a-R-4.3.1 > 82) 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 ~]$ > _______________________________________________ > Modules-interest mailing list > Mod...@li...<mailto:Mod...@li...> > https://lists.sourceforge.net/lists/listinfo/modules-interest<https://urldefense.com/v3/__https:/lists.sourceforge.net/lists/listinfo/modules-interest__;!!N3hqHg43uw!sNArrmBrygltUfMOX-dS-7baQKtka4F4PDBxyH5NTJHzy3uikm_0JVJeqyxhWicpzr1mzedkU-bkZ9oPYA87zKIMWC0_MMGL6nv16Q$> > > > This body part will be downloaded on demand. > > > This body part will be downloaded on demand. > -- -------------------------------------------------------- The views and opinions expressed above are strictly those of the author(s). The content of this message has not been reviewed nor approved by any entity whatsoever. -------------------------------------------------------- Paul FM Info: http://paulfm.com/~paulfm/ -------------------------------------------------------- |
