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| author | marcost2 <52476474+marcost2@users.noreply.github.com> | 2022-04-04 04:47:09 -0300 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-04-04 09:47:09 +0200 |
| commit | 21cb859b4fedd548fe9c15e8a82cf8b4b189b9e1 (patch) | |
| tree | 9559bc12827a90726a74f58559ba948d492f6f2d /var | |
| parent | dc7fbafdb2556e0cda423a3f4fc26138cb1d5478 (diff) | |
| download | spack-21cb859b4fedd548fe9c15e8a82cf8b4b189b9e1.tar.gz spack-21cb859b4fedd548fe9c15e8a82cf8b4b189b9e1.tar.bz2 spack-21cb859b4fedd548fe9c15e8a82cf8b4b189b9e1.tar.xz spack-21cb859b4fedd548fe9c15e8a82cf8b4b189b9e1.zip | |
amber20 + ambertools21: fix build issues (#29809)
* Amber: fix must be declared before the namelist is declared
[1]: http://archive.ambermd.org/202105/0098.html
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/amber/package.py | 13 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/amber/sebomd_fix.patch | 78 |
2 files changed, 91 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/amber/package.py b/var/spack/repos/builtin/packages/amber/package.py index 9447060525..26ceba87dc 100644 --- a/var/spack/repos/builtin/packages/amber/package.py +++ b/var/spack/repos/builtin/packages/amber/package.py @@ -104,6 +104,10 @@ class Amber(Package, CudaPackage): patch(patch_url_str.format(ver, num), sha256=checksum, level=0, when='@{0}'.format(ver)) + # Patch to move the namelist sebomd after the variable declarations + # Taken from http://archive.ambermd.org/202105/0098.html + patch('sebomd_fix.patch', when='@20') + # Patch to add ppc64le in config.guess patch('ppc64le.patch', when='@18: target=ppc64le:') @@ -132,6 +136,7 @@ class Amber(Package, CudaPackage): depends_on('bison', type='build') depends_on('netcdf-fortran') depends_on('parallel-netcdf', when='@20:') # when='AmberTools@21:' + depends_on('tcsh', type=('build'), when='@20') # when='AmberTools@21:' # Potential issues with openmpi 4 # (http://archive.ambermd.org/201908/0105.html) depends_on('mpi', when='+mpi') @@ -152,6 +157,10 @@ class Amber(Package, CudaPackage): conflicts('+openmp', when='%pgi', msg='OpenMP not available for the pgi compiler') + def url_for_version(self, version): + url = "file://{0}/Amber{1}.tar.bz2".format(os.getcwd(), version) + return url + def setup_build_environment(self, env): amber_src = self.stage.source_path env.set('AMBERHOME', amber_src) @@ -189,6 +198,10 @@ class Amber(Package, CudaPackage): else: raise InstallError('Unknown compiler, exiting!!!') + # Alternative way to make csh/tcsh detection work with modules + filter_file(r'-x /bin/csh', 'command -v csh &> /dev/null/', + 'AmberTools/src/configure2', string=True) + # Base configuration conf = Executable('./configure') base_args = ['--skip-python', diff --git a/var/spack/repos/builtin/packages/amber/sebomd_fix.patch b/var/spack/repos/builtin/packages/amber/sebomd_fix.patch new file mode 100644 index 0000000000..c2ee04a0b0 --- /dev/null +++ b/var/spack/repos/builtin/packages/amber/sebomd_fix.patch @@ -0,0 +1,78 @@ +--- a/ambertools_tmpdir/AmberTools/src/sander/sebomd_module.F90 2019-08-01 09:29:43.000000000 -0300 ++++ b/ambertools_tmpdir/AmberTools/src/sander/sebomd_module.F90 2022-03-30 09:07:07.635303955 -0300 +@@ -121,37 +121,6 @@ + implicit none + integer :: stat + +- namelist /sebomd/ hamiltonian, & +- modif, & +- ncore, & +- dbuff1, & +- dbuff2, & +- charge_out, & +- bond_order_out, & +- lambda, & +- peptk, & +- method, & +- charge, & +- longrange, & +- fullscf, & +- ntwc, & +- ntwb, & +- chtype, & +- chewald, & +- screen, & +- guess, & +- pdump, & +- ipolyn, & +- nresidue, & +- ntwh, & +- iprec, & +- peptcorr, & +- debugmsg, & +- debugforces, & +- diag_routine, & +- dpmax, & +- bocut +- + character(10) :: hamiltonian + character(10) :: modif + integer :: method +@@ -183,6 +152,37 @@ + integer :: debugforces + integer :: diag_routine + ++ namelist /sebomd/ hamiltonian, & ++ modif, & ++ ncore, & ++ dbuff1, & ++ dbuff2, & ++ charge_out, & ++ bond_order_out, & ++ lambda, & ++ peptk, & ++ method, & ++ charge, & ++ longrange, & ++ fullscf, & ++ ntwc, & ++ ntwb, & ++ chtype, & ++ chewald, & ++ screen, & ++ guess, & ++ pdump, & ++ ipolyn, & ++ nresidue, & ++ ntwh, & ++ iprec, & ++ peptcorr, & ++ debugmsg, & ++ debugforces, & ++ diag_routine, & ++ dpmax, & ++ bocut ++ + hamiltonian = sebomd_obj%hamiltonian + modif = sebomd_obj%modif + method = sebomd_obj%method |