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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
--------------------------------
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'

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:

$ sg <projectcode> -c 'spack install namd@2.12 ~cuda fftw=3 interface=python ^fftw@3.3.4 +mpi +openmp +pfft_patches'
...
==> Installing namd-2.12-tey6bdfijoegx3dkxfc553nckfecmhku
==> No binary for namd-2.12-tey6bdfijoegx3dkxfc553nckfecmhku found: installing from source
...
==> 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.