Merge pull request #165 from xylar/split-spack-software-and-libs

Split spack software and libs

deploy/bootstrap.py

@@ -400,13 +400,102 @@ def get_env_vars(machine, compiler, mpilib):
     return env_vars
 
 
-def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
-                    spack_env, spack_base, spack_template_path, env_vars,
-                    tmpdir, logger):
+def build_spack_soft_env(config, update_spack, machine, env_type,  # noqa: C901
+                         polaris_version, source_path, spack_base,
+                         spack_template_path, tmpdir):
+
+    if not config.has_option('deploy', 'software_compiler'):
+        return None
+
+    compiler = config.get('deploy', 'software_compiler')
+    if not config.has_option('deploy', f'mpi_{compiler}'):
+        raise ValueError(f'Machine config file for {machine} is missing '
+                         f'mpi_{compiler}, the MPI library for the software '
+                         f'compiler.')
+    mpi = config.get('deploy', f'mpi_{compiler}')
+
+    if machine is not None:
+        spack_base = get_spack_base(spack_base, config)
+
+    if spack_base is None:
+        return None
+
+    if env_type == 'dev':
+        ver = version.parse(polaris_version)
+        release_version = '.'.join(str(vr) for vr in ver.release)
+        spack_env = f'dev_polaris_soft_{release_version}'
+    elif env_type == 'test_release':
+        spack_env = f'test_polaris_soft_{polaris_version}'
+    else:
+        spack_env = f'polaris_soft_{polaris_version}'
+
+    spack_env = spack_env.replace('.', '_')
+
+    build_dir = f'deploy_tmp/build_soft_{machine}'
+
+    try:
+        shutil.rmtree(build_dir)
+    except OSError:
+        pass
+    try:
+        os.makedirs(build_dir)
+    except FileExistsError:
+        pass
+
+    os.chdir(build_dir)
+
+    esmf = config.get('deploy', 'esmf')
+
+    spack_branch_base = f'{spack_base}/{spack_env}'
+
+    specs = list()
+
+    e3sm_hdf5_netcdf = config.getboolean('deploy', 'use_e3sm_hdf5_netcdf')
+    if not e3sm_hdf5_netcdf:
+        hdf5 = config.get('deploy', 'hdf5')
+        netcdf_c = config.get('deploy', 'netcdf_c')
+        netcdf_fortran = config.get('deploy', 'netcdf_fortran')
+        specs.extend([
+            f'"hdf5@{hdf5}+cxx+fortran+hl+mpi+shared"',
+            f'"netcdf-c@{netcdf_c}+mpi~parallel-netcdf"',
+            f'"netcdf-fortran@{netcdf_fortran}"'])
+
+    if esmf != 'None':
+        specs.append(f'"esmf@{esmf}+mpi+netcdf~pnetcdf~external-parallelio"')
+
+    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, config_file=machine_config,
+                       include_e3sm_hdf5_netcdf=e3sm_hdf5_netcdf,
+                       yaml_template=yaml_template, tmpdir=tmpdir)
+
+    spack_view = f'{spack_branch_base}/var/spack/environments/' \
+                 f'{spack_env}/.spack-env/view'
+
+    os.chdir(source_path)
+
+    return spack_view
+
+
+def build_spack_libs_env(config, update_spack, machine, compiler,  # noqa: C901
+                         mpi, spack_env, spack_base, spack_template_path,
+                         env_vars, tmpdir, logger):
 
     albany = config.get('deploy', 'albany')
     cmake = config.get('deploy', 'cmake')
-    esmf = config.get('deploy', 'esmf')
     lapack = config.get('deploy', 'lapack')
     petsc = config.get('deploy', 'petsc')
     scorpio = config.get('deploy', 'scorpio')
@@ -430,8 +519,6 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
             f'"netcdf-fortran@{netcdf_fortran}"',
             f'"parallel-netcdf@{pnetcdf}+cxx+fortran"'])
 
-    if esmf != 'None':
-        specs.append(f'"esmf@{esmf}+mpi+netcdf~pnetcdf~external-parallelio"')
     if lapack != 'None':
         specs.append(f'"netlib-lapack@{lapack}"')
         include_e3sm_lapack = False
@@ -440,19 +527,10 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
     if petsc != 'None':
         specs.append(f'"petsc@{petsc}+mpi+batch"')
 
-    custom_spack = ''
     if scorpio != 'None':
         specs.append(
             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"')
@@ -475,16 +553,8 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
                        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,
-                       custom_spack=custom_spack)
-
-        # remove ESMC/ESMF include files that interfere with MPAS time keeping
-        include_path = f'{spack_branch_base}/var/spack/environments/' \
-                       f'{spack_env}/.spack-env/view/include'
-        for prefix in ['ESMC', 'esmf']:
-            files = glob.glob(os.path.join(include_path, f'{prefix}*'))
-            for filename in files:
-                os.remove(filename)
+                       yaml_template=yaml_template, tmpdir=tmpdir)
+
         set_ld_library_path(spack_branch_base, spack_env, logger)
 
     spack_script = get_spack_script(
@@ -531,7 +601,7 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
                    f'export PETSC={spack_view}\n' \
                    f'export USE_PETSC=true\n'
 
-    return spack_branch_base, spack_script, env_vars
+    return spack_script, env_vars
 
 
 def set_ld_library_path(spack_branch_base, spack_env, logger):
@@ -954,6 +1024,10 @@ def main():  # noqa: C901
     permissions_dirs = []
     activ_path = None
 
+    soft_spack_view = build_spack_soft_env(
+        config, args.update_spack, machine, env_type, polaris_version,
+        source_path, args.spack_base, spack_template_path, args.tmpdir)
+
     for compiler, mpi in zip(compilers, mpis):
 
         python, recreate, conda_mpi, activ_suffix, env_suffix, \
@@ -1011,7 +1085,8 @@ def main():  # noqa: C901
         if compiler is not None:
             env_vars = get_env_vars(machine, compiler, mpi)
             if spack_base is not None:
-                _, spack_script, env_vars = build_spack_env(
+
+                spack_script, env_vars = build_spack_libs_env(
                     config, args.update_spack, machine, compiler, mpi,
                     spack_env, spack_base, spack_template_path, env_vars,
                     args.tmpdir, logger)
@@ -1024,6 +1099,14 @@ def main():  # noqa: C901
                     f'{env_vars}' \
                     f'export PIO={conda_env_path}\n' \
                     f'export OPENMP_INCLUDE=-I"{conda_env_path}/include"\n'
+
+            if soft_spack_view is None:
+                raise ValueError('A software compiler or a spack base was not '
+                                 'defined so required software was not '
+                                 'installed with spack.')
+            env_vars = f'{env_vars}' \
+                       f'export PATH="{soft_spack_view}/bin:$PATH"\n'
+
         else:
             env_vars = ''
 
@@ -1067,6 +1150,7 @@ def main():  # noqa: C901
 
     if args.update_spack or env_type != 'dev':
         # we need to update permissions on shared stuff
+
         update_permissions(config, env_type, activ_path, permissions_dirs)
 
 

docs/developers_guide/deploying_spack.md

@@ -21,24 +21,38 @@ re-deploy shared spack environments on each supported machine.
 
 ### Spack
 
-Spack is for libraries used by MPAS and tools that need system MPI:
+Spack is used to build libraries used by E3SM components and tools that need
+system MPI:
 
 - ESMF
+- MOAB
 - SCORPIO
+- Metis
+- Parmetis
+- Trilinos
 - Albany
 - PETSc
 - Netlib LAPACK
 
-When we update the versions of any of these libraries in Polaris, we also need
+We build one spack environment for tools (e.g. ESMF and MOAB) and another for
+libraries.  This allows us to build the tools with one set of compilers and
+MPI libraries adn the libraries with another.  This is sometimes necessary,
+since ESMF, MOAB and/or their dependencies can't always be built or don't
+run correctly with all compiler and MPI combinations.  For example, we have
+experienced problems running ESMF built with intel compilers on Perlmutter.
+We are also not able to build ESMF or the Eigen dependency of MOAB using
+`nvidiagpu` compilers.
+
+When we update the versions of any of these packages in Polaris, we also need
 to bump the Polaris version (typically either the major or the minor version)
 and then re-deploy shared spack environments on each supported machine.
 
 ### Conda
 
 Conda (via conda-forge) is used for python packages and related dependencies
 that don’t need system MPI. Conda environments aren’t shared between
-developers because the polaris you’re developing is part of the conda
-environment.
+developers because the polaris python package you’re developing is part of the
+conda environment.
 
 When we update the constraints on conda dependencies, we also need to bump the
 Polaris alpha, beta or rc version.  We do not need to re-deploy spack
@@ -67,6 +81,7 @@ These config options are shared across packages including:
 - E3SM_Diags
 - zppy
 - polaris
+- compass
 - E3SM-Unified
 
 Polaris uses these config options to know how to make a job script, where to

polaris/machines/anvil.cfg

@@ -15,6 +15,9 @@ polaris_envs = /lcrc/soft/climate/polaris/anvil/base
 # the compiler set to use for system libraries and MPAS builds
 compiler = intel
 
+# the compiler to use to build software (e.g. ESMF and MOAB) with spack
+software_compiler = intel
+
 # the system MPI library to use for intel compiler
 mpi_intel = impi
 

polaris/machines/chicoma-cpu.cfg

@@ -15,6 +15,9 @@ polaris_envs = /usr/projects/e3sm/polaris/chicoma-cpu/conda/base
 # the compiler set to use for system libraries and MPAS builds
 compiler = gnu
 
+# the compiler to use to build software (e.g. ESMF and MOAB) with spack
+software_compiler = gnu
+
 # the system MPI library to use for gnu compiler
 mpi_gnu = mpich
 

polaris/machines/chrysalis.cfg

@@ -15,6 +15,9 @@ polaris_envs = /lcrc/soft/climate/polaris/chrysalis/base
 # the compiler set to use for system libraries and MPAS builds
 compiler = intel
 
+# the compiler to use to build software (e.g. ESMF and MOAB) with spack
+software_compiler = intel
+
 # the system MPI library to use for intel compiler
 mpi_intel = openmpi
 

polaris/machines/compy.cfg

@@ -15,6 +15,9 @@ polaris_envs = /share/apps/E3SM/conda_envs/polaris/conda/base
 # the compiler set to use for system libraries and MPAS builds
 compiler = intel
 
+# the compiler to use to build software (e.g. ESMF and MOAB) with spack
+software_compiler = intel
+
 # the system MPI library to use for intel compiler
 mpi_intel = impi
 

polaris/machines/morpheus.cfg

@@ -42,6 +42,9 @@ polaris_envs = /home/xylar/data/polaris_envs
 # the compiler set to use for system libraries and MPAS builds
 compiler = gnu
 
+# the compiler to use to build software (e.g. ESMF and MOAB) with spack
+software_compiler = gnu
+
 # the system MPI library to use for gnu compiler
 mpi_gnu = openmpi
 

polaris/machines/pm-cpu.cfg

@@ -15,6 +15,9 @@ polaris_envs = /global/common/software/e3sm/polaris/pm-cpu/conda/base
 # the compiler set to use for system libraries and MPAS builds
 compiler = gnu
 
+# the compiler to use to build software (e.g. ESMF and MOAB) with spack
+software_compiler = gnu
+
 # the system MPI library to use for gnu compiler
 mpi_gnu = mpich