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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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| title | Installing Python and R packages |
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The Spack setup at Pawsey is capable of handling both system-wide and user package installations. However, the current implementation does not properly generate user modulefiles for interpreted languages such as Python and R. For Python package installations, we recommend using pip or setuptools, see: Installing Python Packages For R package installations, we recommend using the R package manager, see: Installing R Packages |
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| title | Installing GPU applications |
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The 0.17.0 version of Spack currently deployed on Setonix does not support installations of applications depending on ROCm, the AMD GPU computing platform. We will soon deploy a new software stack with a more recent version of Spack. |
Using Spack
First, the Spack module has to be loaded:
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| language | bash |
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| theme | Emacs |
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| title | Terminal 5: spack install with variants and dependencies |
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| $ # 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
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namd@2.12~cuda fftw=3 interface=python
^fftw@3.3.4+mpi+openmp+pfft_patches
Concretized
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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' |
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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: | Column |
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| language | bash |
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| title | Terminal 6: namd install issue |
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| $ 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.
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This can be addressed by first manually downloading the source tarball into your current directory where spack will detect it. |
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Install a package for the entire project team
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