Virtual Fugaku V1.1

README_build_procedure.txt

@@ -0,0 +1,25 @@
+# The steps to create "virtual_fugaku" environment are as follows:
+# 
+# First
+# Build the GCC environment
+spack install gcc@14.1.0+binutils
+spack load gcc
+spack compiler find
+
+# Second,
+# Create environment for python.
+cd spack
+spack env create virtual_fugaku_python etc/spack/spack_python.yaml
+spack -e virtual_fugaku_python concretize
+spack -e virtual_fugaku_python install
+
+# Third,
+# Create environment for application including "virtual_fugaku_python".
+spack env create --include-concrete virtual_fugaku_python virtual_fugaku etc/spack/spack.yaml
+spack -e virtual_fugaku concretize
+spack -e virtual_fugaku install
+
+# You can use the spack in one of the following ways.
+# "spack env activate virtual_fugaku"
+#   or
+# "spack load [spec]"

etc/spack/mirrors.yaml

@@ -0,0 +1,4 @@
+mirrors:
+  build_cache_https:
+    url: https://spack-mirror.r-ccs.riken.jp
+    signed: false

etc/spack/packages.yaml

@@ -15,7 +15,7 @@
 # -------------------------------------------------------------------------
 packages:
   all:
-    compiler: [gcc, intel, pgi, clang, xl, nag, fj, aocc]
+    compiler: [gcc@14.1.0, gcc, intel, pgi, clang, xl, nag, fj, aocc]
     providers:
       awk: [gawk]
       blas: [openblas, amdblis]
@@ -68,4 +68,5 @@ packages:
     externals:
     - spec: "openmpi@4.1.5"
       prefix: /opt/amazon/openmpi
-
+  python:
+    require: "@3.11"

etc/spack/spack.yaml

@@ -12,19 +12,13 @@ spack:
   - tmux
   - petsc ^openblas~ilp64
   - openbabel
-  - paraview+python~qt
-    #  - gcc +binutils
   - gnuplot
   - lammps
   - julia ^openblas+ilp64
-  - py-scipy
-  - py-numpy
-  - py-mpi4py
-  - py-matplotlib
-  - py-ase
-  - py-toml
-  - py-scikit-learn
-  - py-pandas
+  - cp2k
+  - cpmd+omp+mpi
+  - frontistr
+  - autodock-vina
   concretizer:
     unify: when_possible
   view:

etc/spack/spack_AI2.yaml

@@ -0,0 +1,14 @@
+spack:
+  specs:
+  - py-tensorflow-hub%gcc@14.1.0
+  - py-tensorflow-metadata%gcc@14.1.0
+  - py-tensorflow-datasets%gcc@14.1.0 ^py-numpy@1.24.3
+  concretizer:
+    unify: when_possible
+  view:
+    default:
+      root: .spack-env/view
+      projections:
+        all: "{name}-{version}-{hash:7}"
+  config:
+    build_jobs: 1

etc/spack/spack_python.yaml

@@ -0,0 +1,45 @@
+spack:
+  specs:
+  - paraview+python~qt
+  - py-tensorflow~cuda+mpi
+  - py-tensorflow-estimator
+  - py-tensorflow-probability@0.22 ^py-dm-tree@0.1.8%gcc@8.5.0
+  - py-torch~cuda
+  - py-botorch
+  - py-efficientnet-pytorch
+  - py-gpytorch
+  - py-pytorch-gradual-warmup-lr
+  - py-pytorch-lightning
+  - py-pytorch-sphinx-theme
+  - py-segmentation-models-pytorch
+  - py-torch-cluster
+  - py-torchdata
+  - py-torchdiffeq
+  - py-torchfile
+  - py-torch-geometric
+  - py-torchmetrics
+  - py-torch-nvidia-apex~cuda
+  - py-torch-scatter
+  - py-torch-sparse
+  - py-torch-spline-conv
+  - py-torchsummary
+  - py-torchtext
+  - py-torchvision
+  - py-vector-quantize-pytorch
+  - py-torchgeo
+  - py-torchaudio
+  - py-scipy
+  - py-numpy
+  - py-mpi4py
+  - py-matplotlib
+  - py-ase
+  - py-toml
+  - py-scikit-learn
+  - py-pandas
+  concretizer:
+    unify: when_possible
+  view:
+    default:
+      root: .spack-env/view
+      projections:
+        all: "{name}-{version}-{hash:7}"

var/spack/repos/local/packages/autodock-vina/package.py

@@ -0,0 +1,63 @@
+# 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)
+
+
+import sys
+
+from spack.package import *
+
+
+class AutodockVina(MakefilePackage):
+    """AutoDock Vina is an open-source program for doing molecular docking"""
+
+    homepage = "http://vina.scripps.edu/"
+    url = "https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.2.3.tar.gz"
+
+    license("Apache-2.0")
+
+    version("1.2.3", sha256="22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0")
+    version("1.2.2", sha256="b9c28df478f90d64dbbb5f4a53972bddffffb017b7bb58581a1a0034fff1b400")
+    version("1.2.1", sha256="2d8d9871a5a95265c03c621c0584d9f06b202303116e6c87e23c935f7b694f74")
+    version("1.2.0", sha256="9c9a85766b4d124d7c1d92e767aa8b4580c6175836b8aa2c28f88a9c40a5b90e")
+    version(
+        "1.1.2",
+        sha256="65422b2240c75d40417872a48e98043e7a7c435300dc8490af0c1f752f1ca4a2",
+        url="https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.1.2-boost-new.tar.gz",
+    )
+
+    depends_on(
+        "boost@1.50.0:1.75.0 +filesystem +program_options +serialization +system +thread",
+        when="@1.1.2",
+    )
+    depends_on(
+        "boost@1.54.0: +filesystem +program_options +serialization +system +thread", when="@1.2.0:"
+    )
+
+    @property
+    def build_directory(self):
+        if sys.platform == "darwin":
+            return join_path("build", "mac", "release")
+        else:
+            return join_path("build", "linux", "release")
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            makefile = FileFilter("Makefile")
+            makefile.filter(
+                "BOOST_INCLUDE = .*", f"BOOST_INCLUDE = {self.spec['boost'].prefix.include}"
+            )
+            makefile.filter("C_PLATFORM=.*", "C_PLATFORM=-pthread")
+            makefile.filter("GPP=.*", f"GPP={spack_cxx}")
+            makefile.filter("-DNDEBUG", "-DNDEBUG -DBOOST_TIMER_ENABLE_DEPRECATED")
+
+    def build(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make()
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdirp(prefix.bin)
+            install("vina", prefix.bin)
+            install("vina_split", prefix.bin)

var/spack/repos/local/packages/cpmd/package.py

@@ -0,0 +1,101 @@
+# 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 Cpmd(MakefilePackage):
+    """The CPMD code is a parallelized plane wave / pseudopotential
+    implementation of Density Functional Theory, particularly
+    designed for ab-initio molecular dynamics."""
+
+    homepage = "https://www.cpmd.org/wordpress/"
+    url = "https://github.com/CPMD-code/CPMD/archive/refs/tags/4.3.tar.gz"
+
+    license("MIT")
+
+    version("4.3", sha256="e0290f9da0d255f90a612e60662b14a97ca53003f89073c6af84fa7bc8739f65")
+
+    variant("omp", description="Enables the use of OMP instructions", default=False)
+    variant("mpi", description="Build with MPI support", default=False)
+
+    depends_on("lapack")
+    depends_on("mpi", when="+mpi")
+
+    conflicts("^openblas threads=none", when="+omp")
+    conflicts("^openblas threads=pthreads", when="+omp")
+
+    def edit(self, spec, prefix):
+        # patch configure file
+        cbase = "LINUX-GFORTRAN"
+        cp = FileFilter(join_path("configure", cbase))
+        # Compilers
+        if spec.satisfies("+mpi"):
+            fc = spec["mpi"].mpifc
+            cc = spec["mpi"].mpicc
+        else:
+            fc = spack_fc
+            cc = spack_cc
+            cp.filter(r"FFLAGS='([^']*)'", "FFLAGS='\\1 -fallow-argument-mismatch'")
+
+        cp.filter("FC=.+", "FC='{0}'".format(fc))
+        cp.filter("CC=.+", "CC='{0}'".format(cc))
+        cp.filter("LD=.+", "LD='{0}'".format(fc))
+
+        # MPI flag
+        if spec.satisfies("+mpi"):
+            cp.filter("-D__Linux", "-D__Linux -D__PARALLEL")
+
+        # OMP flag
+        if spec.satisfies("+omp"):
+            cp.filter("-fopenmp", self.compiler.openmp_flag)
+
+        # lapack
+        cp.filter("LIBS=.+", "LIBS='{0}'".format(spec["lapack"].libs.ld_flags))
+
+        # LFLAGS
+        cp.filter("'-static '", "")
+
+        # Compiler specific
+        if spec.satisfies("%gcc@=14.1.0"):
+            cp.filter(r"FFLAGS='([^']*)'", "FFLAGS='\\1 -fallow-argument-mismatch'")
+            cp.filter(r"CFLAGS='([^']*)'", "CFLAGS='\\1 -Wno-int-conversion'")
+
+        if spec.satisfies("%fj"):
+            cp.filter("-ffixed-form", "-Fixed")
+            cp.filter("-ffree-line-length-none", "")
+            cp.filter("-falign-commons", "-Kalign_commons")
+
+        # create Makefile
+        bash = which("bash")
+        if spec.satisfies("+omp"):
+            bash("./configure.sh", "-omp", cbase)
+        else:
+            bash("./configure.sh", cbase)
+
+    def install(self, spec, prefix):
+        install_tree(".", prefix)
+
+    def test_cpmd(self):
+        test_dir = self.test_suite.current_test_data_dir
+        test_file = join_path(test_dir, "1-h2o-pbc-geoopt.inp")
+        opts = []
+        if self.spec.satisfies("+mpi"):
+            exe_name = self.spec["mpi"].prefix.bin.mpirun
+            opts.extend(["-n", "2"])
+            opts.append(join_path(self.prefix.bin, "cpmd.x"))
+        else:
+            exe_name = "cpmd.x"
+        opts.append(test_file)
+        opts.append(test_dir)
+        cpmd = which(exe_name)
+        out = cpmd(*opts, output=str.split, error=str.split)
+
+        expected = [
+            "2       1        H        O              1.84444     0.97604",
+            "3       1        H        O              1.84444     0.97604",
+            "2   1   3         H     O     H              103.8663",
+        ]
+        check_outputs(expected, out)

var/spack/repos/local/packages/cpmd/test/1-h2o-pbc-geoopt.inp

@@ -0,0 +1,51 @@
+&INFO
+single water molecule with pbc.
+default geometry optimization
+&END
+
+&CPMD
+  OPTIMIZE GEOMETRY XYZ
+  HESSIAN UNITY
+  CONVERGENCE ORBITALS
+   1.0d-7  
+  CONVERGENCE GEOMETRY
+   3.0d-4
+  ODIIS
+   5
+  MAXSTEP
+   100 
+  MAXCPUTIME
+   1500
+
+  STRUCTURE BONDS ANGLES
+&END
+
+&DFT
+  FUNCTIONAL BLYP
+  GC-CUTOFF
+   1.0d-06
+&END
+
+&SYSTEM
+  SYMMETRY
+   1
+  CELL
+   20.0   1.0   1.0  0.0  0.0  0.0  
+  CUTOFF
+   70.0
+&END
+
+&ATOMS
+
+*O_MT_BLYP.psp KLEINMAN-BYLANDER
+   LMAX=P
+   1
+   10.0    10.0    10.0
+
+*H_CVB_BLYP.psp
+   LMAX=S
+    2
+    8.5     9.0    10.0
+   11.5     9.0    10.0
+
+&END

var/spack/repos/local/packages/cpmd/test/H_CVB_BLYP.psp

@@ -0,0 +1,28 @@
+&ATOM
+ Z  =    1 
+ ZV =    1 
+ XC = 1312        .666667
+ TYPE = NORMCONSERVING CAR
+&END
+&INFO
+    ============================================================
+    |  hydrogen pseudopotential with                           |
+    |  Exchange-Correlation Functional :                       |
+    |     Slater exchange :   .6667                            |
+    |     LDA correlation : Lee-Yang-Parr                      |
+    |     Exchange GC     : Becke (1988)                       |
+    |     Correlation GC  : Lee-Yang-Parr                      |
+    |  Von Barth-Car normconserving PP after P. Giannozzi      |
+    |  ALPHA(CORE):     .25                                    | 
+    |     .2829559     -1.961599       .4051810                | 
+    |  Note this is the PP used by Michiel Sprik               |
+    ============================================================
+&END
+&POTENTIAL
+    CAR
+              0.25000
+    0.2829559  -1.9615990  0.405181
+    0.2829559  -1.9615990  0.405181
+    0.2829559  -1.9615990  0.405181
+&END
+