Korzystanie z modułów
Wersja z dnia 09:31, 5 wrz 2019 autorstwa Teresa Sas (dyskusja | edycje) (Aktualizacja listy modułów.)
< Podręcznik użytkownika KDM < Korzystanie z modułów
Moduły
Moduł - moduły pozwalają na łatwą i szybką konfigurację środowiska sesji użytkownika. Każda wersja zainstalowanych na klastrze programów lub bibliotek produkcyjnych posiada własny moduł w formacie nazwa_aplikacji/wersja, np.gaussian/g09.E.01 . Moduły dodają odpowiednie zmienne środowiskowe lub podmieniają ich wartości. Do zmiennych środowiskowych należą standardowe w Linux-ach zmienne PATH oraz LD_LIBRARY_PATH, lecz także te, które są wyjątkowe dla aplikacji działających na klastrze.
| ! | Z mechanizmu należy korzystać na węzłach roboczych - w zadaniach (czy to wsadowych czy interaktywnych). |
Polecenie:
- module avail - listuje dostępne moduły, polecana metoda do sprawdzenia zasobów oprogramowania
---------- /usr/local/Modules ---------- abaqus/2017 mkl/10.3 plgrid/apps/r/3.5.3-intel15.0 abaqus/6.14-2(default) mkl/13.1 plgrid/apps/raspa/2.0-gcc6.2.0 abinit/7.10.4-intel13.1 mkl/15.0(default) plgrid/apps/siesta/3.2-intel16.0 abinit/8.0.7-intel15.0 mode/7.12.1731(default) plgrid/apps/siesta/4.0.2-intel16.0 abinit/8.10.2-intel16.0.3 mode/7.5.387 plgrid/apps/siesta/4.0-intel16.0 abinit/8.2.2-intel15.0 mode/7.7.758 plgrid/apps/turbomole/5.10 abinit/8.4.4-intel16.0(default) molcas/7.9-gcc4.7.4(default) plgrid/apps/turbomole/6.3 abinit/8.8.3-intel16.0 molcas/8.0-gcc4.7.4 plgrid/apps/turbomole/6.6 adf/2014.01 molden/5.2-gcc4.9.2 plgrid/apps/turbomole/7.0 adf/2014.10 molden/5.7-gcc6.2.0(default) plgrid/apps/turbomole/7.1.1 adf/2016.108 molpro/2010.1.80-intel16.0 plgrid/apps/turbomole/7.3 adf/2017.105(default) molpro/2012.1.12-intel13.1(default) plgrid/apps/xaim/1.0 adf/2017.110.r61742.0.718 molpro/2012.1.57-intel13.1 plgrid/apps/xcrysden/1.5.60 adf/2018.104 mopac/2016 plgrid/libs/blacs/1.1 adf/2019.102 mpc/1.0.3-gcc4.9.2 plgrid/libs/blacs/1.1-intel15.0 allinea-forge/6.1.2 mpc/1.1.0-gcc7.4.0(default) plgrid/libs/boost/1.59.0-gcc4.9.2 amber/14-intel15.0(default) mpfr/3.1.3-gcc4.9.2 plgrid/libs/boost/1.62.0-gcc6.2.0 amber/tools18-gcc4.9.2 mpfr/4.0.2-gcc7.4.0(default) plgrid/libs/boost/1.68.0-gcc6.2.0 ansys/18.2 mrbayes/3.2.5-gcc5.1.0(default) plgrid/libs/fftw/2.1.5-intel15.0 ansys/19.0 mrbayes/3.2.6-gcc6.2.0 plgrid/libs/fftw/3.3.4-gcc4.7.4 argtable2/13-gcc4.9.2 mvapich2/2.1-gcc6.1.0 plgrid/libs/fftw/3.3.4-gcc4.9.2 aster/12.6.0-gcc4.9.2 mvapich2/2.1-intel15.0 plgrid/libs/fftw/3.3.4-intel15.0 atk/2.18.0-gcc4.9.2 namd/2.11-intel15.0 plgrid/libs/fftw/3.3.8-gcc7.4.0 atk-spi2/2.19.2-gcc4.9.2 namd/2.13-intel16.0(default) plgrid/libs/fftw2/2.1.5 autoconf/2.69 namd/2.7-intel15.0 plgrid/libs/fftw3/3.3.4 autodock/4.2.6(default) namd/2.9-intel15.0 plgrid/libs/fftw-mpi/3.3.4-intel15.0 autodock_vina/1.1.2(default) nbo/6.0 plgrid/libs/fftw-mpi/3.3.4-intel_mpi_15.0 avogadro/1.1.1 nbo/6.0.18a plgrid/libs/fftw-mpi/3.3.8-gcc7.4.0 bagel/2018.07.04-git nbo/6.0.18a-g16b01 plgrid/libs/gmp/6.0.0-gcc4.9.2 beagle/2.1.2-gcc5.1.0(default) nbo/6.0-g09d01 plgrid/libs/gmp/6.1.2-gcc7.4.0 beagle/3.0.2-gcc6.2.0 nbo/6.0-g09e01 plgrid/libs/gsl/2.2.1-gcc6.2.0 beast/2.5.1-with_JRE(default) nbo/6.0-orca4 plgrid/libs/lapack/3.6.0 binutils/2.25(default) nbo/current plgrid/libs/lapack/3.6.0-gcc4.9.2 binutils/2.28.1 ncarg/6.3.0-intel15.0(default) plgrid/libs/lapack/3.6.0-intel15.0 bison/3.0.4 nciplot/3.0-intel15.0 plgrid/libs/mkl/10.3 blacs/1.1 nco/4.4.8-intel15.0(default) plgrid/libs/mkl/13.1 blacs/1.1-intel15.0 nco/4.5.2-intel15.0 plgrid/libs/mkl/15.0 blas/3.6.0 nco/4.6.0-beta05-intel15.0 plgrid/libs/mpfr/3.1.3-gcc4.9.2 blas/3.6.0-intel15.0 netcdf/4.3.2-intel13.1 plgrid/libs/mpfr/4.0.2-gcc7.4.0 boost/1.59.0-gcc4.9.2 netcdf/4.3.3.1 plgrid/libs/netcdf/4.3.2-intel13.1 boost/1.62.0-gcc6.2.0 netcdf/4.3.3.1-gcc4.9.2 plgrid/libs/netcdf/4.3.3.1 boost/1.68.0-gcc6.2.0(default) netcdf/4.3.3.1-intel13.1 plgrid/libs/netcdf/4.3.3.1-gcc4.9.2 cairo/1.14.2 netcdf/4.3.3.1-intel15.0 plgrid/libs/netcdf/4.3.3.1-intel13.1 cairo/1.14.6-gcc4.9.2(default) netcdf/4.3.3.1-intel15.0dbg plgrid/libs/netcdf/4.3.3.1-intel15.0 cairomm/1.12.0-gcc4.9.2 netcdf/4.3.3.1-intel15.0-openmpi1.10.1 plgrid/libs/netcdf/4.3.3.1-intel15.0dbg castep/17.2-parallel netcdf/4.4.1.1-gcc6.2.0 plgrid/libs/netcdf/4.3.3.1-intel15.0-openmpi1.10.1 castep/17.2-serial netcdf/4.4.1-intel16.0 plgrid/libs/netcdf/4.4.1.1-gcc6.2.0 castep/18.1-parallel netcdf/4.4.1-pgi16.5 plgrid/libs/netcdf/4.4.1-intel16.0 castep/18.1-serial netcdf/4.6.2-gcc7.4.0(default) plgrid/libs/netcdf/4.4.1-pgi16.5 cfour/1.0-gcc5.1.0(default) netcdf-fortran/4.2-intel13.1 plgrid/libs/netcdf/4.6.2-gcc7.4.0 cfour/1.0-gcc7.4.0 netcdf-fortran/4.4.2-gcc4.9.2 plgrid/libs/openblas/0.2.14-gcc4.9.2 cfour/2.1-gcc7.4.0 netcdf-fortran/4.4.2-intel13.1 plgrid/libs/openblas/0.2.14-gcc5.1.0 cfx/16.0 netcdf-fortran/4.4.2-intel15.0 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plgrid/tools/blas/3.6.0-intel15.0 cpmd/4.1-gcc4.9.2 nwchem/6.8-intel15.0 plgrid/tools/cmake/3.10.2 crystal09/2.0.1-intel13.1(default) octave/4.4.1-gcc7.4.0(default) plgrid/tools/cmake/3.13.4-gcc7.4.0 crystal09/2.0.1-intel15.0 openbabel/2.3.2-gcc4.9.2 plgrid/tools/cmake/3.2.1 cuda/8.0 openbabel/2.4.1 plgrid/tools/gcc/4.7.4 cuda/9.1(default) openblas/0.2.14-gcc4.9.2 plgrid/tools/gcc/4.9.2 cuda-software/namd-2.13-intel16.0.3 openblas/0.2.14-gcc5.1.0 plgrid/tools/gcc/5.1.0 cuda-software/openblas-0.2.20-pgi18.10 openblas/0.2.15-gcc5.2.0 plgrid/tools/gcc/5.2.0 cuda-software/openmpi-3.1.3-gcc7.4.0 openblas/0.2.20-gcc7.4.0(default) plgrid/tools/gcc/5.4.0 cuda-software/openmpi-3.1.3-pgi18.10 opencv/3.0.0 plgrid/tools/gcc/6.1.0 cuda-software/pgi-18.10 openfoam/2.1.1-gcc4.7.4 plgrid/tools/gcc/6.2.0 dalton/2015-intel13.1 openfoam/v1612+-gcc5.2.0 plgrid/tools/gcc/7.3.0 dalton/2015-intel13.1-MXDIST openmolcas/2018.08.29-git-gcc6.2.0 plgrid/tools/gcc/7.4.0 dalton/2015-intel13.1-rspvec 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plgrid/tools/openmpi/2.1.0-gcc6.2.0 gaussian/g03.E.01 plgrid/apps/adf/2016.108 plgrid/tools/openmpi/2.1.0-intel16.0 gaussian/g09.B.01 plgrid/apps/adf/2017.105 plgrid/tools/openmpi/2.1.2-gcc6.2.0 gaussian/g09.D.01 plgrid/apps/adf/2017.110.r61742.0.718 plgrid/tools/openmpi/2.1.3-gcc7.3.0 gaussian/g09.D.01-justa plgrid/apps/adf/2018.104 plgrid/tools/openmpi/3.1.3-gcc7.4.0 gaussian/g09.E.01(default) plgrid/apps/adf/2019.102 plgrid/tools/openmpi/3.1.3-intel16.0.3 gaussian/g16.A.03 plgrid/apps/amber/14-intel15.0 plgrid/tools/pgi/15.3 gaussian/g16.B.01 plgrid/apps/amber/tools18-gcc4.9.2 plgrid/tools/pgi/16.5 gaussian/g16.C.01 plgrid/apps/ansys/18.2 plgrid/tools/prcc/15.0 gcc/4.7.4 plgrid/apps/ansys/19.0 plgrid/tools/prcpp/15.0 gcc/4.9.2 plgrid/apps/aster/12.6.0-gcc4.9.2 plgrid/tools/prftn/15.0 gcc/5.1.0 plgrid/apps/autodock/4.2.6 plgrid/tools/pymol/1.7.6 gcc/5.2.0 plgrid/apps/autodock_vina/1.1.2 plgrid/tools/python/2.7.13-gcc6.2.0 gcc/5.4.0 plgrid/apps/cfour/1.0-gcc5.1.0 plgrid/tools/python/2.7.15-gcc7.4.0 gcc/6.1.0 plgrid/apps/cfour/1.0-gcc7.4.0 plgrid/tools/python/2.7.15-intel16.0.3 gcc/6.2.0 plgrid/apps/cfour/2.1-gcc7.4.0 plgrid/tools/python/2.7.8-gcc4.9.2 gcc/7.3.0 plgrid/apps/cfx/16.0 plgrid/tools/python/2.7.8-gcc4.9.2-iSpec gcc/7.4.0(default) plgrid/apps/cfx/16.2 plgrid/tools/python/2.7.8-gcc4.9.2-meteo gdal/1.11.2-gcc4.9.2 plgrid/apps/cfx/17.2 plgrid/tools/python/2.7.8-gcc4.9.2-pyyaml gdal/1.11.2-intel15.0(default) plgrid/apps/cfx/18.2 plgrid/tools/python/3.4.4-gcc5.2.0 gdal/2.3.1-gcc7.3.0 plgrid/apps/cfx/19.0 plgrid/tools/python/3.6.2-gcc6.2.0 gdk-pixbuf/2.33.2-gcc4.9.2 plgrid/apps/clustal-omega/1.2.1-gcc4.9.2 plgrid/tools/python/3.6.8-gcc7.3.0 geos/3.4.2-gcc4.9.2 plgrid/apps/clustalw/2.1-intel15.0 plgrid/tools/slepc/3.7.2-intel16.0 geos/3.4.2-intel15.0(default) plgrid/apps/cp2k/2.6.1-gcc4.9.2 plgrid/tools/sparsehash/2.0.2-gcc4.9.2 gettext/0.19.7 plgrid/apps/cpmd/3.15.3-intel15.0 plgrid/tools/sqlite/3.7.17 git/2.7.1 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FFTW/3.3.7-gompi-2018a libdrm/2.4.91-GCCcore-6.4.0 Rosetta/3.10-foss-2016b FFTW/3.3.7-iomkl-2018a libdrm/2.4.92-GCCcore-7.3.0 ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1 FFTW/3.3.8-gompi-2018b libffi/3.2.1-foss-2016b ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20 FFTW/3.3.8-gompic-2018b libffi/3.2.1-GCCcore-6.4.0 ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1 FFTW/3.3.8-intel-2018b libffi/3.2.1-GCCcore-7.3.0 ScaLAPACK/2.0.2-gompic-2018b-OpenBLAS-0.3.1 flex/2.5.39(default) libgeotiff/1.4.2-intel-2018b SCons/2.5.0-foss-2016b-Python-2.7.12 flex/2.5.39-GCC-4.9.3-binutils-2.25 libGLU/9.0.0-intel-2018b Singularity/2.4.2-GCC-5.4.0-2.26 flex/2.6.0 libGLU/9.0.0-iomkl-2018a SQLite/3.13.0-foss-2016b flex/2.6.0-GCCcore-5.4.0 libjpeg-turbo/1.5.3-GCCcore-6.4.0 SQLite/3.20.1-GCCcore-6.4.0 flex/2.6.3 libjpeg-turbo/2.0.0-GCCcore-7.3.0 SQLite/3.21.0-GCCcore-6.4.0 flex/2.6.4 libpciaccess/0.14-GCCcore-6.4.0 SQLite/3.24.0-GCCcore-7.3.0 flex/2.6.4-GCCcore-6.4.0 libpciaccess/0.14-GCCcore-7.3.0 SQLite/3.8.10.2-intel-2015b flex/2.6.4-GCCcore-7.3.0 libpng/1.6.34-GCCcore-6.4.0 SWIG/3.0.12-foss-2018a-Python-2.7.14 fontconfig/2.12.6-GCCcore-6.4.0 libpng/1.6.34-GCCcore-7.3.0 SWIG/3.0.12-intel-2018b-Python-3.6.6 fontconfig/2.13.0-GCCcore-7.3.0 libreadline/6.3-foss-2016b SWIG/3.0.12-iomkl-2018a-Python-3.6.4 foss/2016b libreadline/6.3-intel-2015b Szip/2.1.1-GCCcore-6.4.0 foss/2018a libreadline/7.0-GCCcore-6.4.0 Szip/2.1.1-GCCcore-7.3.0 foss/2018b libreadline/7.0-GCCcore-7.3.0 Tcl/8.6.4-intel-2015b fosscuda/2018b libsndfile/1.0.28-GCCcore-6.4.0 Tcl/8.6.5-foss-2016b freetype/2.9.1-GCCcore-7.3.0 libsndfile/1.0.28-GCCcore-7.3.0 Tcl/8.6.7-GCCcore-6.4.0 freetype/2.9-GCCcore-6.4.0 LibTIFF/4.0.9-GCCcore-6.4.0 Tcl/8.6.8-GCCcore-6.4.0 GCC/4.9.3-binutils-2.25 LibTIFF/4.0.9-intel-2018b Tcl/8.6.8-GCCcore-7.3.0 GCC/5.4.0-2.26 libtool/2.4.6-foss-2016b TensorFlow/1.13.1-foss-2018b-Python-3.6.6 GCC/6.4.0-2.28 libtool/2.4.6-GCC-5.4.0-2.26 TensorFlow/1.8.0-foss-2018a-Python-3.6.4 GCC/7.3.0-2.30 libtool/2.4.6-GCCcore-6.4.0 Tk/8.6.4-intel-2015b-no-X11 GCCcore/5.4.0 libtool/2.4.6-GCCcore-7.3.0 Tk/8.6.5-foss-2016b GCCcore/6.4.0 libxml2/2.9.4-GCCcore-6.4.0 Tk/8.6.8-GCCcore-7.3.0 GCCcore/7.3.0 libxml2/2.9.7-GCCcore-6.4.0 Tk/8.6.8-iomkl-2018a gcccuda/2018b libxml2/2.9.8-GCCcore-7.3.0 UDUNITS/2.2.26-intel-2018b GDAL/2.2.3-foss-2018a-Python-2.7.14 libyaml/0.1.7 util-linux/2.31.1-GCCcore-6.4.0 GDAL/2.2.3-intel-2018b-Python-3.6.6 libyaml/0.1.7-GCCcore-6.4.0 util-linux/2.32-GCCcore-7.3.0 GDAL/2.2.3-iomkl-2018a-Python-3.6.4 libyaml/0.2.1-GCCcore-7.3.0 Wannier90/2.1.0-intel-2017b GEOS/3.6.2-foss-2018a-Python-2.7.14 LLVM/5.0.1-GCCcore-6.4.0 wheel/0.31.0-foss-2018a-Python-3.6.4 GEOS/3.6.2-intel-2018b-Python-3.6.6 LLVM/6.0.0-GCCcore-7.3.0 wheel/0.31.1-foss-2018b-Python-3.6.6 GEOS/3.6.2-iomkl-2018a-Python-3.6.4 M4/1.4.17 X11/20180131-GCCcore-6.4.0 gettext/0.19.8.1 M4/1.4.17-foss-2016b X11/20180604-GCCcore-7.3.0 gettext/0.19.8.1-GCCcore-6.4.0 M4/1.4.17-GCC-4.9.3-binutils-2.25 XML-Parser/2.44_01-GCCcore-6.4.0-Perl-5.26.1 gettext/0.19.8.1-GCCcore-6.4.0-libxml2-2.9.7 M4/1.4.17-GCC-5.4.0-2.26 XML-Parser/2.44_01-GCCcore-7.3.0-Perl-5.28.0 gettext/0.19.8.1-GCCcore-7.3.0 M4/1.4.17-GCCcore-5.4.0 xorg-macros/1.19.1-GCCcore-6.4.0 Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12 M4/1.4.18 xorg-macros/1.19.2-GCCcore-7.3.0 GLib/2.54.3-GCCcore-6.4.0 M4/1.4.18-GCCcore-6.4.0 XZ/5.2.3-GCCcore-6.4.0 GLib/2.54.3-GCCcore-7.3.0 M4/1.4.18-GCCcore-7.3.0 XZ/5.2.4-GCCcore-7.3.0 GMP/6.1.1-foss-2016b magma/2.5.0-fosscuda-2018b zlib/1.2.11 GMP/6.1.2-GCCcore-6.4.0 Mako/1.0.7-intel-2018b-Python-2.7.15 zlib/1.2.11-GCCcore-6.4.0 GMP/6.1.2-GCCcore-7.3.0 Mako/1.0.7-iomkl-2018a-Python-2.7.14 zlib/1.2.11-GCCcore-7.3.0 GMT/5.4.3-foss-2018a Mesa/17.3.6-iomkl-2018a zlib/1.2.8 GNU/4.9.3-2.25 Mesa/18.1.1-intel-2018b zlib/1.2.8-GCC-4.9.3-binutils-2.25 gompi/2016b mkl-dnn/0.13-intel-2018a zlib/1.2.8-GCCcore-5.4.0 gompi/2018a NASM/2.13.03-GCCcore-6.4.0 zlib/1.2.8-intel-2015b gompi/2018b NASM/2.13.03-GCCcore-7.3.0
- module load [nazwa_modułu] - ładuje moduł [nazwa_modułu]
$ module load intel/12.1 binutils/2.25 load complete. intel/12.1 load complete.
- module list - wyświetla załadowane moduły
$ module list Currently Loaded Modulefiles: 1) binutils/2.25(default) 2) intel/12.1
- module rm [nazwa_modułu] - usuwa załadowany moduł
$ module rm binutils binutils/2.25 unload complete $ module list Currently Loaded Modulefiles: 1) intel/12.1
- module purge - usuwa wszystkie moduły