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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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| 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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| theme | Emacs |
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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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First, we need a Spack recipe that takes a tar file from the current working directory rather than the Internet (note that this is a long command so next line won't display properly in a small window):
$ cp -r /software/setonix/2022.11/spack/var/spack/repos/builtin/packages/gromacs $MYSOFTWARE/setonix/spack_repo/packages
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Spack makes use of dynamic libraries and rpath when building software. The use of rpath means that executables contain the paths in which libraries are search searched for at runtime. The result of using rpath is that runtime are reproducible as executables will always point to the same library regardless of environment at runtime. A consequence of this is that if software has been built with not the desired version and build of library, it is not easy to have the executable use a different version. The package must be rebuilt with the different version of the library.
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