Merge pull request #103 from xylar/update-to-0.2.0

Update to v0.2.0

deploy/albany_supported.txt

@@ -5,3 +5,4 @@ chicoma-cpu, gnu, mpich
 chrysalis, gnu, openmpi
 compy, gnu, openmpi
 pm-cpu, gnu, mpich
+morpheus, gnu, openmpi

deploy/bootstrap.py

@@ -6,16 +6,17 @@
 import os
 import platform
 import shutil
+import socket
 import stat
 import subprocess
 from configparser import ConfigParser
 from typing import Dict
 
 import progressbar
 from jinja2 import Template
-from mache import MachineInfo, discover_machine
+from mache import MachineInfo
+from mache import discover_machine as mache_discover_machine
 from mache.spack import get_spack_script, make_spack_env
-from mache.version import __version__ as mache_version
 from shared import (
     check_call,
     get_conda_base,
@@ -186,18 +187,14 @@ def get_env_setup(args, config, machine, compiler, mpi, env_type, source_path,
     else:
         config.set('deploy', 'albany', 'None')
 
-    if args.with_netlib_lapack:
-        lib_suffix = f'{lib_suffix}_netlib_lapack'
-    else:
-        config.set('deploy', 'lapack', 'None')
-
     if args.with_petsc:
         lib_suffix = f'{lib_suffix}_petsc'
         logger.info('Turning off OpenMP because it doesn\'t work well '
                     'with  PETSc')
         args.without_openmp = True
     else:
         config.set('deploy', 'petsc', 'None')
+        config.set('deploy', 'lapack', 'None')
 
     activ_suffix = f'{activ_suffix}{lib_suffix}'
 
@@ -290,7 +287,7 @@ def build_conda_env(config, env_type, recreate, mpi, conda_mpi, version,
 
         for package in ['esmf', 'geometric_features', 'jigsaw', 'jigsawpy',
                         'mache', 'mpas_tools', 'netcdf_c', 'netcdf_fortran',
-                        'otps', 'pnetcdf', 'scorpio']:
+                        'otps', 'parallelio', 'pnetcdf']:
             replacements[package] = config.get('deploy', package)
 
         spec_file = template.render(**replacements)
@@ -366,6 +363,12 @@ def get_env_vars(machine, compiler, mpilib):
                    f'export I_MPI_F77=ifort\n' \
                    f'export I_MPI_F90=ifort\n'
 
+    if machine.startswith('conda'):
+        # we're using parallelio so we don't have ADIOS support
+        env_vars = \
+            f'{env_vars}' \
+            f'export HAVE_ADIOS=false\n'
+
     if platform.system() == 'Linux' and machine.startswith('conda'):
         env_vars = \
             f'{env_vars}' \
@@ -392,8 +395,9 @@ def get_env_vars(machine, compiler, mpilib):
     return env_vars
 
 
-def build_spack_env(config, update_spack, machine, compiler, mpi, spack_env,
-                    spack_base, spack_template_path, env_vars, tmpdir, logger):
+def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
+                    spack_env, spack_base, spack_template_path, env_vars,
+                    tmpdir, logger):
 
     albany = config.get('deploy', 'albany')
     cmake = config.get('deploy', 'cmake')
@@ -402,12 +406,12 @@ def build_spack_env(config, update_spack, machine, compiler, mpi, spack_env,
     petsc = config.get('deploy', 'petsc')
     scorpio = config.get('deploy', 'scorpio')
 
-    spack_branch_base = f'{spack_base}/spack_for_mache_{mache_version}'
+    spack_branch_base = f'{spack_base}/{spack_env}'
 
     specs = list()
 
     if cmake != 'None':
-        specs.append(f'cmake "@{cmake}"')
+        specs.append(f'"cmake@{cmake}"')
 
     e3sm_hdf5_netcdf = config.getboolean('deploy', 'use_e3sm_hdf5_netcdf')
     if not e3sm_hdf5_netcdf:
@@ -416,39 +420,58 @@ def build_spack_env(config, update_spack, machine, compiler, mpi, spack_env,
         netcdf_fortran = config.get('deploy', 'netcdf_fortran')
         pnetcdf = config.get('deploy', 'pnetcdf')
         specs.extend([
-            f'hdf5@{hdf5}+cxx+fortran+hl+mpi+shared',
-            f'netcdf-c@{netcdf_c}+mpi~parallel-netcdf',
-            f'netcdf-fortran@{netcdf_fortran}',
-            f'parallel-netcdf@{pnetcdf}+cxx+fortran'])
+            f'"hdf5@{hdf5}+cxx+fortran+hl+mpi+shared"',
+            f'"netcdf-c@{netcdf_c}+mpi~parallel-netcdf"',
+            f'"netcdf-fortran@{netcdf_fortran}"',
+            f'"parallel-netcdf@{pnetcdf}+cxx+fortran"'])
 
     if esmf != 'None':
-        specs.append(f'esmf@{esmf}+mpi+netcdf~pio+pnetcdf')
+        specs.append(f'"esmf@{esmf}+mpi+netcdf~pnetcdf~external-parallelio"')
     if lapack != 'None':
-        specs.append(f'netlib-lapack@{lapack}')
+        specs.append(f'"netlib-lapack@{lapack}"')
         include_e3sm_lapack = False
     else:
         include_e3sm_lapack = True
     if petsc != 'None':
-        specs.append(f'petsc@{petsc}+mpi+batch')
+        specs.append(f'"petsc@{petsc}+mpi+batch"')
 
+    custom_spack = ''
     if scorpio != 'None':
         specs.append(
-            f'scorpio@{scorpio}+pnetcdf~timing+internal-timing~tools+malloc')
+            f'"scorpio'
+            f'@{scorpio}+pnetcdf~timing+internal-timing~tools+malloc"')
+        # make sure scorpio, not esmf, libraries are linked
+        lib_path = f'{spack_branch_base}/var/spack/environments/' \
+                   f'{spack_env}/.spack-env/view/lib'
+        scorpio_lib_path = '$(spack find --format "{prefix}" scorpio)'
+        custom_spack = \
+            f'{custom_spack}' \
+            f'ln -sfn {scorpio_lib_path}/lib/libpioc.a {lib_path}\n' \
+            f'ln -sfn {scorpio_lib_path}/lib/libpiof.a {lib_path}\n'
 
     if albany != 'None':
-        specs.append(f'albany@{albany}+mpas')
+        specs.append(f'"albany@{albany}+mpas"')
 
     yaml_template: str | None = None
     template_path = f'{spack_template_path}/{machine}_{compiler}_{mpi}.yaml'
     if os.path.exists(template_path):
         yaml_template = template_path
+
+    if machine is not None:
+        here = os.path.abspath(os.path.dirname(__file__))
+        machine_config = os.path.join(here, '..', 'polaris', 'machines',
+                                      f'{machine}.cfg')
+    else:
+        machine_config = None
+
     if update_spack:
         make_spack_env(spack_path=spack_branch_base, env_name=spack_env,
                        spack_specs=specs, compiler=compiler, mpi=mpi,
-                       machine=machine,
+                       machine=machine, config_file=machine_config,
                        include_e3sm_lapack=include_e3sm_lapack,
                        include_e3sm_hdf5_netcdf=e3sm_hdf5_netcdf,
-                       yaml_template=yaml_template, tmpdir=tmpdir)
+                       yaml_template=yaml_template, tmpdir=tmpdir,
+                       custom_spack=custom_spack)
 
         # remove ESMC/ESMF include files that interfere with MPAS time keeping
         include_path = f'{spack_branch_base}/var/spack/environments/' \
@@ -461,7 +484,7 @@ def build_spack_env(config, update_spack, machine, compiler, mpi, spack_env,
 
     spack_script = get_spack_script(
         spack_path=spack_branch_base, env_name=spack_env, compiler=compiler,
-        mpi=mpi, shell='sh', machine=machine,
+        mpi=mpi, shell='sh', machine=machine, config_file=machine_config,
         include_e3sm_lapack=include_e3sm_lapack,
         include_e3sm_hdf5_netcdf=e3sm_hdf5_netcdf,
         yaml_template=yaml_template)
@@ -804,6 +827,57 @@ def check_supported(library, machine, compiler, mpi, source_path):
                      f'on {machine}')
 
 
+def safe_rmtree(path):
+    try:
+        shutil.rmtree(path)
+    except OSError:
+        pass
+
+
+def discover_machine(quiet=False):
+    """
+    Figure out the machine from the host name
+
+    Parameters
+    ----------
+    quiet : bool, optional
+        Whether to print warnings if the machine name is ambiguous
+
+    Returns
+    -------
+    machine : str
+        The name of the current machine
+    """
+    machine = mache_discover_machine(quiet=quiet)
+    if machine is None:
+        possible_hosts = get_possible_hosts()
+        hostname = socket.gethostname()
+        for possible_machine, hostname_contains in possible_hosts.items():
+            if hostname_contains in hostname:
+                machine = possible_machine
+                break
+    return machine
+
+
+def get_possible_hosts():
+    here = os.path.abspath(os.path.dirname(__file__))
+    files = sorted(glob.glob(os.path.join(
+        here, '..', 'polaris', 'machines', '*.cfg')))
+
+    possible_hosts = dict()
+    for filename in files:
+        machine = os.path.splitext(os.path.split(filename)[1])[0]
+        config = ConfigParser()
+        config.read(filename)
+        if config.has_section('discovery') and \
+                config.has_option('discovery', 'hostname_contains'):
+            hostname_contains = config.get('discovery',
+                                           'hostname_contains')
+            possible_hosts[machine] = hostname_contains
+
+    return possible_hosts
+
+
 def main():  # noqa: C901
     args = parse_args(bootstrap=True)
 
@@ -828,7 +902,7 @@ def main():  # noqa: C901
         else:
             machine = args.machine
 
-    e3sm_machine = machine is not None
+    known_machine = machine is not None
 
     if machine is None and not args.conda_env_only:
         if platform.system() == 'Linux':
@@ -899,7 +973,7 @@ def main():  # noqa: C901
 
         if args.spack_base is not None:
             spack_base = args.spack_base
-        elif e3sm_machine and compiler is not None:
+        elif known_machine and compiler is not None:
             spack_base = get_spack_base(args.spack_base, config)
         else:
             spack_base = None
@@ -969,7 +1043,6 @@ def main():  # noqa: C901
             check_env(script_filename, conda_env_name, logger)
 
         if env_type == 'release' and not (args.with_albany or
-                                          args.with_netlib_lapack or
                                           args.with_petsc):
             # make a symlink to the activation script
             link = os.path.join(activ_path,

deploy/conda-dev-spec.template

@@ -31,7 +31,7 @@ otps={{ otps }}
 progressbar2
 pyamg>=4.2.2
 pyproj
-pyremap>=0.0.16,<0.1.0
+pyremap>=1.0.0,<2.0.0
 ruamel.yaml
 requests
 scipy>=1.8.0
@@ -59,7 +59,7 @@ fortran-compiler
 libnetcdf={{ netcdf_c }}={{ mpi_prefix }}_*
 netcdf-fortran={{ netcdf_fortran }}={{ mpi_prefix }}_*
 libpnetcdf={{ pnetcdf }}={{ mpi_prefix }}_*
-scorpio={{ scorpio }}={{ mpi_prefix }}_*
+parallelio={{ parallelio }}={{ mpi_prefix }}_*
 m4
 make
 {{ mpi }}
@@ -76,3 +76,6 @@ sphinx_rtd_theme
 myst-parser
 sphinx-multiversion
 rst-to-myst
+
+# Visualization
+ncview

deploy/default.cfg

@@ -14,30 +14,31 @@ recreate = False
 suffix =
 
 # the python version
-python = 3.10
+python = 3.11
 
 # the MPI version (nompi, mpich or openmpi)
 mpi = nompi
 
 # versions of conda packages
-geometric_features = 1.0.1
+geometric_features = 1.2.0
 jigsaw = 0.9.14
 jigsawpy = 0.3.3
-mache = 1.14.0
-mpas_tools = 0.18.0
+mache = 1.16.0
+mpas_tools = 0.21.0
 otps = 2021.10
+parallelio = 2.6.0
 
 # versions of conda or spack packages (depending on machine type)
-esmf = 8.2.0
-netcdf_c = 4.8.1
-netcdf_fortran = 4.6
-pnetcdf = 1.12.2
-scorpio = 1.3.2
+esmf = 8.4.2
+netcdf_c = 4.9.2
+netcdf_fortran = 4.6.1
+pnetcdf = 1.12.3
 
 # versions of spack packages
 albany = develop
 # cmake newer than 3.23.0 needed for Trilinos
 cmake = 3.23.0:
-hdf5 = 1.12.1
+hdf5 = 1.14.1
 lapack = 3.9.1
-petsc = 3.16.1
+petsc = 3.19.1
+scorpio = 1.4.1

deploy/petsc_supported.txt

@@ -7,5 +7,4 @@ chicoma-cpu, gnu, mpich
 chrysalis, intel, openmpi
 chrysalis, gnu, openmpi
 compy, intel, impi
-compy, gnu, openmpi
 pm-cpu, gnu, mpich

deploy/shared.py

@@ -58,14 +58,10 @@ def parse_args(bootstrap):
                         action='store_true',
                         help="Whether to include albany in the spack "
                              "environment.")
-    parser.add_argument("--with_netlib_lapack", dest="with_netlib_lapack",
-                        action='store_true',
-                        help="Whether to include Netlib-LAPACK in the spack "
-                             "environment.")
     parser.add_argument("--with_petsc", dest="with_petsc",
                         action='store_true',
-                        help="Whether to include PETSc in the spack "
-                             "environment.")
+                        help="Whether to include PETSc and Netlib-LAPACK in "
+                             "the spack environment.")
     parser.add_argument("--without_openmp", dest="without_openmp",
                         action='store_true',
                         help="If this flag is included, OPENMP=false will "
@@ -177,19 +173,16 @@ def install_mambaforge(conda_base, activate_base, logger):
         check_call(command, logger=logger)
         os.remove(mambaforge)
 
-    backup_bashrc()
-
     print('Doing initial setup\n')
     commands = f'{activate_base} && ' \
                f'conda config --add channels conda-forge && ' \
                f'conda config --set channel_priority strict && ' \
+               f'mamba update -y "mamba>1.3.1" "conda>=23.1.0" && ' \
                f'mamba update -y --all && ' \
-               f'mamba init'
+               f'mamba init --no-user'
 
     check_call(commands, logger=logger)
 
-    restore_bashrc()
-
 
 def backup_bashrc():
     home_dir = os.path.expanduser('~')