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Excerpt

Pawsey provides and maintains a number of prebuilt libraries and applications on Setonix, most of which are installed and managed through Spack. This page outlines how users can use Spack to install additional software or different builds of existing software that are not provided by Pawsey supported modules.  

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titleTerminal 5: spack install with variants and dependencies
$ # Before install, check the spec using specific version of fftw
$ spack spec namd@2.12 ~cuda fftw=3 interface=python ^fftw@3.3.4 +mpi +openmp +pfft_patches ^mpich@3.4.1
Input spec
--------------------------------
namd@2.12~cuda fftw=3 interface=python
    ^fftw@3.3.4+mpi+openmp+pfft_patches

Concretized
--------------------------------
namd@2.12%gcc@11.2.0~cuda cuda_arch=none fftw=3 interface=python arch=linux-sles15-zen3
    ^charmpp@6.7.1%gcc@11.2.0~cuda~omp~papi+production~pthreads+shared+smp~syncft~tcp~tracing backend=netlrts build-target=LIBS patches=92d507d8b72ac01f114f7772510049cc7656f93daeadef46e1f2b00ad8533d2b,e636c3f88a6944c87d910d4c8fdf25146b60f57e09228497a6cc01c7dbae9569 pmi=none arch=linux-sles15-zen3
    ^fftw@3.3.4%gcc@11.2.0+mpi+openmp+pfft_patches patches=4c813199aa39c0d2b23259ee3c3a58c9c96a3c0d09fe3485a33f299b95e0d9e7 precision=double,float arch=linux-sles15-zen3
        ^autoconf@2.69%gcc@11.2.0 arch=linux-sles15-zen3
        ^automake@1.15.1%gcc@11.2.0 arch=linux-sles15-zen3
        ^libtool@2.4.6%gcc@11.2.0 arch=linux-sles15-zen3
        ^mpich@3.4.1%gcc@11.2.0~argobots+fortran+hwloc+hydra+libxml2+pci+romio+slurm~verbs+wrapperrpath device=ch4 netmod=ofi pmi=pmi arch=linux-sles15-zen3
    ^python@3.6.13%gcc@11.2.0+bz2+ctypes+dbm~debug+libxml2+lzma+nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib arch=linux-sles15-zen3
    ^tcl@8.6.11%gcc@11.2.0 arch=linux-sles15-zen3
        ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-sles15-zen3
$ # the spec looks okay, let's install it
$ sg <projectcode> -c 'spack install namd@2.12 ~cuda fftw=3 interface=python ^fftw@3.3.4 +mpi +openmp +pfft_patches'


Note

Spack would normally download the source code for any packages that it needs to install. The source code for NAMD has a particular restriction that it cannot be downloaded by spack but must be obtained separately:

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titleTerminal 6: namd install issue
$ sg <projectcode> -c 'spack install namd@2.12 ~cuda fftw=3 interface=python ^fftw@3.3.4 +mpi +openmp +pfft_patches'
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==> Installing namd-2.12-tey6bdfijoegx3dkxfc553nckfecmhku
==> No binary for namd-2.12-tey6bdfijoegx3dkxfc553nckfecmhku found: installing from source
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==> Error: FetchError: Manual download is required for namd. Refer to http://www.ks.uiuc.edu/Research/namd/ for download instructions.


This can be addressed by first manually downloading the source tarball into your current directory where spack will detect it.


Install a package for the entire project team

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titleTerminal 8: spack module example
$ sg <projectcode> -c 'spack module lmod refresh --delete-tree -y'  # generate LUA modulefiles for Lmod
==> Regenerating lmod module files

$ # list the fftw modules available  
$ module avail fftw
fftw/3.3.7-aormek7
fftw/3.3.7-ibdoa45
fftw/3.3.8-ggtdo27
$ # load a particular fftw library 
$ module load fftw/3.3.7-aormek7
$ # to determine if this module is the correct variant one can examine the module file itself 
$ head -4 /software/projects/pawsey0xxx/user/setonix/modules/zen3/gcc/11.2.0/fftw/3.3.7-aormek7.lua | tail -1 
-- fftw@3.3.7%gcc@11.2.0~mpi~openmp~pfft_patches precision=double,float arch=linux-sles15-zen3/aormek7
$ # compare this to other 3.3.7 module 
$ head -4 /software/projects/pawsey000x/user/setonix/modules/zen3/gcc/11.2.0/fftw/3.3.7-ibdoa45.lua | tail -1 
-- fftw@3.3.7%gcc@11.2.0~mpi+openmp+pfft_patches patches=8132c27659f992311dcf3d1500056e0f9400aa22f6824124e3607dbaa8dfe3c0 precision=double,float arch=linux-sles15-zen3/ibdoa45



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Note
titleYour module not being listed with `module avail`

If your module is not being listed with module avail command, it is very possible that lmod is forcing the use of the cache instead of a real new search of installed modules. Then we recommend to remove the old cached list of modules, so that lmod search again for the currently installed modules including the recently created one. For that, users should simply delete the existing lmod cache with:

rm -rf ~/.cache/lmod


Installing a software package from a user-modified source code

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