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