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bigdft : add v1.9.5 (#45270)

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This commit is contained in:
Fernando Ayats
2024-08-13 18:25:34 +02:00
committed by GitHub
parent 645c8eeaeb
commit df8507f470
14 changed files with 183 additions and 14 deletions
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3
var/spack/repos/builtin/packages/bigdft-atlab/package.py
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@@ -14,6 +14,7 @@ class BigdftAtlab(AutotoolsPackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489")
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
@@ -38,7 +39,7 @@ class BigdftAtlab(AutotoolsPackage):
depends_on("mpi", when="+mpi")
depends_on("openbabel", when="+openbabel")
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.3", "1.9.4", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.3", "1.9.4", "1.9.5", "develop"]:
depends_on(f"bigdft-futile@{vers}", when=f"@{vers}")
configure_directory = "atlab"

13
var/spack/repos/builtin/packages/bigdft-chess/package.py
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@@ -15,6 +15,9 @@ class BigdftChess(AutotoolsPackage, CudaPackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489")
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
@@ -26,7 +29,7 @@ class BigdftChess(AutotoolsPackage, CudaPackage):
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
variant("scalapack", default=True, description="Enable SCALAPACK support")
variant("ntpoly", default=False, description="Option to use NTPoly")
variant("ntpoly", default=True, description="Option to use NTPoly")
variant(
"shared", default=True, description="Build shared libraries"
) # Not default in bigdft, but is typically the default expectation
@@ -35,6 +38,7 @@ class BigdftChess(AutotoolsPackage, CudaPackage):
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("pkg-config", type="build")
depends_on("python@3.0:", type=("build", "run"))
@@ -43,10 +47,11 @@ class BigdftChess(AutotoolsPackage, CudaPackage):
depends_on("py-pyyaml")
depends_on("mpi", when="+mpi")
depends_on("scalapack", when="+scalapack")
depends_on("ntpoly", when="+ntpoly")
# depends_on('netlib-minpack', when='+minpack')
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("ntpoly@:2", when="@:1.9.3")
depends_on("ntpoly@3:", when="@1.9.4:")
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.3", "1.9.4", "1.9.5", "develop"]:
depends_on(f"bigdft-futile@{vers}", when=f"@{vers}")
depends_on(f"bigdft-atlab@{vers}", when=f"@{vers}")

9
var/spack/repos/builtin/packages/bigdft-core/package.py
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@@ -15,6 +15,9 @@ class BigdftCore(AutotoolsPackage, CudaPackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
# version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489") # broken
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
@@ -34,6 +37,7 @@ class BigdftCore(AutotoolsPackage, CudaPackage):
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("pkg-config", type="build")
depends_on("python@3.0:", type=("build", "run"))
@@ -48,12 +52,15 @@ class BigdftCore(AutotoolsPackage, CudaPackage):
depends_on("libxc@:4.3.4", when="@1.9.2:")
depends_on("libxc@:4.3.4", when="@develop")
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.4", "1.9.5", "develop"]:
depends_on(f"bigdft-futile@{vers}", when=f"@{vers}")
depends_on(f"bigdft-chess@{vers}", when=f"@{vers}")
depends_on(f"bigdft-psolver@{vers}", when=f"@{vers}")
depends_on(f"bigdft-libabinit@{vers}", when=f"@{vers}")
for vers in ["1.9.3", "1.9.4", "1.9.5", "develop"]:
depends_on(f"bigdft-liborbs@{vers}", when=f"@{vers}")
configure_directory = "bigdft"
def configure_args(self):

1
var/spack/repos/builtin/packages/bigdft-futile/package.py
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@@ -18,6 +18,7 @@ class BigdftFutile(AutotoolsPackage, CudaPackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489")
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")

5
var/spack/repos/builtin/packages/bigdft-libabinit/package.py
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@@ -17,6 +17,9 @@ class BigdftLibabinit(AutotoolsPackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489")
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
@@ -40,7 +43,7 @@ class BigdftLibabinit(AutotoolsPackage):
depends_on("libxc@:2.2.2", when="@:1.9.1")
depends_on("libxc@:4.3.4", when="@1.9.1:")
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.3", "1.9.4", "1.9.5", "develop"]:
depends_on(f"bigdft-futile@{vers}", when=f"@{vers}")
configure_directory = "libABINIT"

93
var/spack/repos/builtin/packages/bigdft-liborbs/package.py Normal file
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@@ -0,0 +1,93 @@
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class BigdftLiborbs(AutotoolsPackage, CudaPackage):
"""BigDFT-liborbs: a library for orbital treatments in DFT."""
homepage = "https://bigdft.org/"
url = "https://gitlab.com/l_sim/bigdft-suite/-/archive/1.9.5/bigdft-suite-1.9.5.tar.gz"
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489")
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
variant("scalapack", default=True, description="Enable SCALAPACK support")
variant(
"shared", default=True, description="Build shared libraries"
) # Not default in bigdft, but is typically the default expectation
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("blas")
depends_on("lapack")
depends_on("mpi", when="+mpi")
depends_on("scalapack", when="+scalapack")
for vers in ["1.9.3", "1.9.4", "1.9.5", "develop"]:
depends_on(f"bigdft-futile@{vers}", when=f"@{vers}")
depends_on(f"bigdft-atlab@{vers}", when=f"@{vers}")
configure_directory = "liborbs"
def configure_args(self):
spec = self.spec
prefix = self.prefix
openmp_flag = []
if "+openmp" in spec:
openmp_flag.append(self.compiler.openmp_flag)
linalg = []
if "+scalapack" in spec:
linalg.append(spec["scalapack"].libs.ld_flags)
linalg.append(spec["lapack"].libs.ld_flags)
linalg.append(spec["blas"].libs.ld_flags)
args = [
f"FCFLAGS={' '.join(openmp_flag)}",
f"--with-ext-linalg={' '.join(linalg)}",
f"--with-moduledir={prefix.include}",
f"--prefix={prefix}",
]
if spec.satisfies("+shared"):
args.append("--enable-dynamic-libraries")
if "+mpi" in spec:
args.append(f"CC={spec['mpi'].mpicc}")
args.append(f"CXX={spec['mpi'].mpicxx}")
args.append(f"FC={spec['mpi'].mpifc}")
args.append(f"F90={spec['mpi'].mpifc}")
args.append(f"F77={spec['mpi'].mpif77}")
else:
args.append("--disable-mpi")
if "+openmp" in spec:
args.append("--with-openmp")
else:
args.append("--without-openmp")
if "+cuda" in spec:
args.append("--enable-opencl")
args.append(f"--with-ocl-path={spec['cuda'].prefix}")
args.append("--enable-cuda-gpu")
args.append(f"--with-cuda-path={spec['cuda'].prefix}")
args.append(f"--with-cuda-libs={spec['cuda'].libs.link_flags}")
return args
@property
def libs(self):
shared = "+shared" in self.spec
return find_libraries("libbigdft-*", root=self.prefix, shared=shared, recursive=True)

4
var/spack/repos/builtin/packages/bigdft-psolver/package.py
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@@ -16,6 +16,7 @@ class BigdftPsolver(AutotoolsPackage, CudaPackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489")
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
@@ -36,6 +37,7 @@ class BigdftPsolver(AutotoolsPackage, CudaPackage):
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("pkg-config", type="build")
depends_on("python@3.0:", type=("build", "run"))
@@ -45,7 +47,7 @@ class BigdftPsolver(AutotoolsPackage, CudaPackage):
depends_on("mpi", when="+mpi")
depends_on("scalapack", when="+scalapack")
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.3", "1.9.4", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.3", "1.9.4", "1.9.5", "develop"]:
depends_on(f"bigdft-futile@{vers}", when=f"@{vers}")
depends_on(f"bigdft-atlab@{vers}", when=f"@{vers}")

6
var/spack/repos/builtin/packages/bigdft-spred/package.py
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@@ -15,6 +15,9 @@ class BigdftSpred(AutotoolsPackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
# version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489") # bigdft-core broken
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
@@ -26,6 +29,7 @@ class BigdftSpred(AutotoolsPackage):
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("pkg-config", type="build")
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
@@ -42,7 +46,7 @@ class BigdftSpred(AutotoolsPackage):
depends_on("mpi", when="+mpi")
depends_on("scalapack", when="+scalapack")
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.4", "1.9.5", "develop"]:
depends_on(f"bigdft-futile@{vers}", when=f"@{vers}")
depends_on(f"bigdft-psolver@{vers}", when=f"@{vers}")
depends_on(f"bigdft-core@{vers}", when=f"@{vers}")

5
var/spack/repos/builtin/packages/bigdft-suite/package.py
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@@ -15,13 +15,16 @@ class BigdftSuite(BundlePackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5")
version("1.9.4")
# version("1.9.3") # bigdft-core broken
version("1.9.2")
version("1.9.1")
version("1.9.0")
depends_on("python@3.0:", type=("run"))
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.4", "1.9.5", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-psolver@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-libabinit@{0}".format(vers), when="@{0}".format(vers))

4
var/spack/repos/builtin/packages/libgain/package.py
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@@ -24,6 +24,10 @@ class Libgain(AutotoolsPackage):
depends_on("fortran", type="build") # generated
def flag_handler(self, name, flags):
flags.append(self.compiler.fc_pic_flag)
return (None, None, flags)
@property
def libs(self):
shared = "+shared" in self.spec

1
var/spack/repos/builtin/packages/ntpoly/package.py
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@@ -21,6 +21,7 @@ class Ntpoly(CMakePackage):
license("MIT")
version("3.1.0", sha256="71cd6827f20c68e384555dbcfc85422d0690e21d21d7b5d4f7375544a2755271")
version("2.7.2", sha256="968571a42e93827617c40c4ceefd29be52447c176309f801bb5a454527fe5f49")
version("2.3.1", sha256="af8c7690321607fbdee9671b9cb3acbed945148014e0541435858cf82bfd887e")
depends_on("cxx", type="build") # generated

22
var/spack/repos/builtin/packages/py-bigdft/bad_string.patch Normal file
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@@ -0,0 +1,22 @@
From e12f8694bb40ef4f0d984df67bf2c6e7c6d0a81b Mon Sep 17 00:00:00 2001
From: Luigi Genovese <luigi.genovese@cea.fr>
Date: Wed, 19 Jun 2024 13:51:33 +0200
Subject: [PATCH] type corrected
---
PyBigDFT/BigDFT/BioQM.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/PyBigDFT/BigDFT/BioQM.py b/PyBigDFT/BigDFT/BioQM.py
index 6bb2985fc..20323c535 100644
--- a/PyBigDFT/BigDFT/BioQM.py
+++ b/PyBigDFT/BigDFT/BioQM.py
@@ -1,4 +1,4 @@
-long_ra"""A module to define typical operations that can be done on biological systems
+"""A module to define typical operations that can be done on biological systems
"""
from BigDFT.Systems import System
--
2.45.1

22
var/spack/repos/builtin/packages/py-bigdft/package.py
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@@ -15,6 +15,9 @@ class PyBigdft(PythonPackage):
git = "https://gitlab.com/l_sim/bigdft-suite.git"
version("develop", branch="devel")
version("1.9.5", sha256="5fe51e92bb746569207295feebbcd154ce4f1b364a3981bace75c45e983b2741")
version("1.9.4", sha256="fa22115e6353e553d2277bf054eb73a4710e92dfeb1ed9c5bf245337187f393d")
version("1.9.3", sha256="f5f3da95d7552219f94366b4d2a524b2beac988fb2921673a65a128f9a8f0489")
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
@@ -23,11 +26,22 @@ class PyBigdft(PythonPackage):
depends_on("cxx", type="build") # generated
depends_on("fortran", type="build") # generated
depends_on("python@3.0:", type=("build", "run"))
depends_on("py-numpy")
depends_on("py-setuptools")
depends_on("python@3.0:", type=("build", "run"), when="@:1.9.3")
depends_on("python@3.6:", type=("build", "run"), when="@1.9.4:")
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("py-setuptools")
depends_on("py-hatchling")
depends_on("py-numpy", type=("run"))
depends_on("py-ase", when="@1.9.3", type=("run"))
depends_on("py-matplotlib", when="@1.9.3", type=("run"))
depends_on("py-scipy", when="@1.9.4:", type=("run"))
for vers in ["1.9.0", "1.9.1", "1.9.2", "1.9.3", "1.9.4", "1.9.5", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), type="run", when="@{0}".format(vers))
build_directory = "PyBigDFT"
patch("pyproject_fix.patch", when="@1.9.4") # based on cb66dd0c4
patch("bad_string.patch", when="@1.9.5")

9
var/spack/repos/builtin/packages/py-bigdft/pyproject_fix.patch Normal file
View File

@@ -0,0 +1,9 @@
--- a/PyBigDFT/pyproject.toml
+++ b/PyBigDFT/pyproject.toml
@@ -33,3 +33,6 @@ viz = ["py3dmol", "matplotlib"]
[tool.hatch.build]
artifacts = ["*.xyz", "psppar*.yaml", "postprocess.yaml"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["BigDFT"]