Make package version names consistent.

.github/workflows/spack-mac.yml

@@ -23,5 +23,4 @@ jobs:
         . ./spack/share/spack/setup-env.sh      
         spack repo add .
         spack repo list
-        spack install hdf5-cmake
-        spack install hdf5-hpc-io
+        spack install hdf5-vol-tests+vol-cache

.github/workflows/spack.yml

@@ -21,9 +21,10 @@ jobs:
 
     - name: Run a multi-line script
       run: |
+        sudo apt-get update -y
+        sudo apt-get install -y libopenmpi-dev      
         . ./spack/share/spack/setup-env.sh
         spack repo add .
         spack repo list
-        spack install hdf5-cmake
-        spack install hdf5-hpc-io
+        spack install hdf5-vol-async
 

.github/workflows/vfd-gds.yml

@@ -0,0 +1,42 @@
+name: VFD GDS
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Install dependencies
+      run: |
+        sudo apt-get -y update
+        sudo apt-get -y install ninja-build automake autoconf cmake libtool libtool-bin libopenmpi-dev libpthread-stubs0-dev 
+    - name: Install GDS/CUDA
+      run: |
+        wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
+        sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
+        sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
+        sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
+        sudo apt-get -y update
+        sudo apt-get -y install cuda
+    - name: Checkout hdf-spack
+      uses: actions/checkout@v2
+    - name: Checkout spack
+      uses: actions/checkout@v2
+      with:
+        repository: spack/spack
+        path: ./spack
+    - name: Run a multi-line script
+      run: |
+        set
+        export PATH="/usr/local/cuda-11.5/bin:$PATH"
+        set
+        . ./spack/share/spack/setup-env.sh
+        spack repo add .
+        spack repo list
+        spack external find cuda                
+        spack install hdf5-vfd-gds@master ^[email protected] ^[email protected]

packages/hdf5-vfd-gds/package.py

@@ -0,0 +1,36 @@
+# Copyright 2013-2021 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 import *
+
+class Hdf5VfdGds(CMakePackage, CudaPackage):
+    """This pacakge enables GPU Direct Storage Virtual File Driver in HDF5."""
+
+    # Package info
+    homepage    = 'https://github.com/hpc-io/vfd-gds'
+    url = 'https://github.com/hpc-io/vfd-gds/archive/refs/tags/1.0.1.tar.gz'
+    git         = 'https://github.com/hpc-io/vfd-gds.git'
+    maintainers = ['hyoklee', 'lrknox']
+
+    # Versions
+    version('master', branch='master')
+    version('1.0.1', sha256='00e125fd149561be991f41e883824de826d8add604aebccf103a4fb82d5faac2', default=True)
+    version('1.0.0', sha256='6b16105c7c49f13fc05784ee69b78d45fb159270c78d760689f9cd21e230ddd2')
+
+    # Dependencies
+    depends_on('cuda')    
+    depends_on('[email protected]:')
+    depends_on('[email protected]:')    
+
+
+    def cmake_args(self):
+        spec = self.spec
+
+        # CMake options
+        args = [
+            self.define('BUILD_TESTING', self.run_tests),
+        ]
+
+        return args

packages/hdf5-vol-async/package.py

@@ -9,16 +9,20 @@ class Hdf5VolAsync(CMakePackage):
     """This package enables asynchronous IO in HDF5."""
 
     homepage = "https://sdm.lbl.gov/"
-    # hpc-io hasn't accepted the pull request for CMakeLists.txt yet.
-    # git      = "https://github.com/hpc-io/vol-async"
-    git      = "https://github.com/hyoklee/vol-async"
+    git      = "https://github.com/hpc-io/vol-async"
     maintainers = ['hyoklee']
 
-    version('develop', branch='develop')
+    version('develop', branch='develop', preferred=True)
+    version('hyoklee.develop',
+            branch='develop',
+            git='https://github.com/hyoklee/vol-async')
+    version('local.develop', branch='develop',
+            git='file:///scr/hyoklee/src/vol-async')
 
     depends_on('argobots@main')
-    # depends_on('hdf5-hpc-io')
-    depends_on('hdf5-cmake')
+    depends_on('hdf5-hpc-io')
+    # Use the following if you want to use HDFGroup/[email protected] instead.
+    # depends_on('[email protected]+mpi+threadsafe')
 
     def cmake_args(self):
         """Populate cmake arguments for HDF5 VOL."""
@@ -27,6 +31,16 @@ def cmake_args(self):
         args = [
             '-DBUILD_SHARED_LIBS:BOOL=ON',
             '-DBUILD_TESTING:BOOL=ON'
+            '-DCMAKE_C_COMPILER=mpicc',
+            '-DCMAKE_CXX_COMPILER=mpicxx',
         ]
 
         return args
+
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('HDF5_PLUGIN_PATH', self.build_directory+'/lib')
+        spack_env.set('HDF5_VOL_CONNECTOR',
+                         'async under_vol=0\;under_info={}')        
+        spack_env.set('LD_PRELOAD', self.spec['argobots'].prefix+'/lib/libabt.so')
+

packages/hdf5-vol-cache/package.py

@@ -14,12 +14,10 @@ class Hdf5VolCache(CMakePackage):
     maintainers = ['hyoklee']
 
     version('default', branch='develop')
-
-    # Set hdf5-cmake package option.
-    o_flt = '~zfp~mafisc~szip~zstd~blosc~bshuf~bitgroom'
-    o_vol = '~av~pv~cv'
-    o_par = '+mpi+threadsafe'
-    o = o_flt+o_vol+o_par
+    version('hyoklee.develop', branch='develop',
+            git='https://github.com/hyoklee/vol-cache.git', preferred=True)
+    version('local.develop', branch='develop',
+            git='file:///home/hyoklee/vol-cache')
 
     depends_on('hdf5-vol-async')
 

packages/hdf5-vol-external-passthrough/package.py

@@ -20,8 +20,6 @@ class Hdf5VolExternalPassthrough(CMakePackage):
 
     def cmake_args(self):
         """Populate cmake arguments for HDF5 DAOS."""
-        spec = self.spec
-
         args = [
             '-DBUILD_SHARED_LIBS:BOOL=ON',
             '-DBUILD_TESTING:BOOL=ON'

packages/hdf5-vol-tests/package.py

@@ -14,21 +14,34 @@ class Hdf5VolTests(CMakePackage):
 
     maintainers = ['hyoklee']
 
-    version('master', preferred=True)
-    variant('vol-async', default=True, description='Enable async VOL')
+    version('master', commit='9a147d3')
+    version('hyoklee.master',
+            git='https://github.com/hyoklee/vol-tests', preferred=True)
+    version('local.master', 
+            git='file:///Users/hyoklee/src/vol-tests')
+    variant('vol-async', default=False, description='Enable async VOL')
     variant('vol-cache', default=False, description='Enable cache VOL')
     variant('vol-external-passthrough', default=False, 
             description='Enable external pass-through VOL')
-
-    variant('async', default=True, description='Enable parallel tests.')
-    variant('parallel', default=True, description='Enable async API tests.')
+    variant('vol-log', default=False, 
+            description='Enable log-based VOL')
+    variant('vol-adios2', default=False, 
+            description='Enable ADIOS2 VOL')
+    variant('vol-rest', default=False, 
+            description='Enable REST VOL')
+
+    variant('async', default=True, description='Enable async API tests.')
+    variant('parallel', default=True, description='Enable parallel tests.')
     variant('part', default=True, 
             description='Enable building the main test executable.')
-    depends_on('szip', when='+parallel')
+    depends_on('szip')
     depends_on('hdf5-vol-async', when='+vol-async')
     depends_on('hdf5-vol-cache', when='+vol-cache')
     depends_on('hdf5-vol-external-passthrough', 
                when='+vol-external-passthrough')
+    depends_on('hdf5-vol-log', when='+vol-log')
+    depends_on('adios2+shared+hdf5 ^[email protected]', when='+vol-adios2')
+    depends_on('hdf5-vol-rest', when='+vol-rest')    
 
     def cmake_args(self):
         args = []

packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch

@@ -14,4 +14,3 @@ index dd2b171..629418a 100644
    EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER)
    EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL)
    EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE)
-

packages/hdf5/h5public-skip-mpicxx.patch

@@ -9,4 +9,3 @@
  #   include <mpi.h>
  #ifndef MPI_FILE_NULL		/*MPIO may be defined in mpi.h already       */
  #   include <mpio.h>
-

packages/hdf5/package.py

@@ -24,6 +24,8 @@ class Hdf5(CMakePackage):
     maintainers = ['lrknox', 'brtnfld', 'byrnHDF', 'ChristopherHogan', 'epourmal',
                    'gheber', 'hyoklee', 'lkurz', 'soumagne']
 
+    tags = ['e4s']
+
     test_requires_compiler = True
 
     # The 'develop' version is renamed so that we could uninstall (or patch) it
@@ -91,13 +93,13 @@ class Hdf5(CMakePackage):
     # The compiler wrappers (h5cc, h5fc, etc.) run 'pkg-config'.
     depends_on('pkgconfig', type='run')
 
-    conflicts('api=v114', when='@1.6:1.12.99',
+    conflicts('api=v114', when='@1.6:1.12',
               msg='v114 is not compatible with this release')
-    conflicts('api=v112', when='@1.6:1.10.99',
+    conflicts('api=v112', when='@1.6:1.10',
               msg='v112 is not compatible with this release')
-    conflicts('api=v110', when='@1.6:1.8.99',
+    conflicts('api=v110', when='@1.6:1.8',
               msg='v110 is not compatible with this release')
-    conflicts('api=v18', when='@1.6:1.6.99',
+    conflicts('api=v18', when='@1.6.0:1.6',
               msg='v18 is not compatible with this release')
 
     # The Java wrappers and associated libhdf5_java library
@@ -172,6 +174,13 @@ def patch(self):
             'INTEGER(SIZE_T), INTENT(OUT) :: buf_size',
             'fortran/src/H5Fff_F03.f90',
             string=True, ignore_absent=True)
+        if self.run_tests:
+            # hdf5 has ~2200 CPU-intensive tests, some of them have races:
+            # Often, these loop endless(at least on one Xeon and one EPYC).
+            # testphdf5 fails indeterministic. This fixes finishing the tests
+            filter_file('REMOVE_ITEM H5P_TESTS',
+                        'REMOVE_ITEM H5P_TESTS t_bigio t_shapesame testphdf5',
+                        'testpar/CMakeTests.cmake')
 
     # The parallel compiler wrappers (i.e. h5pcc, h5pfc, etc.) reference MPI
     # compiler wrappers and do not need to be changed.
@@ -185,26 +194,33 @@ def url_for_version(self, version):
         return url.format(version.up_to(2), version)
 
     def flag_handler(self, name, flags):
+        spec = self.spec
         cmake_flags = []
 
         if name == "cflags":
-            cc_name = os.path.basename(self.compiler.cc)
-            if "clang" in cc_name or "gcc" in cc_name:
+            if spec.compiler.name in ['gcc', 'clang', 'apple-clang']:
                 # Quiet warnings/errors about implicit declaration of functions
                 # in C99:
                 cmake_flags.append("-Wno-implicit-function-declaration")
-            if self.spec.satisfies('@:1.8.12~shared'):
+                # Note that this flag will cause an error if building %nvhpc.
+            if spec.satisfies('@:1.8.12~shared'):
                 # More recent versions set CMAKE_POSITION_INDEPENDENT_CODE to
                 # True and build with PIC flags.
                 cmake_flags.append(self.compiler.cc_pic_flag)
         elif name == 'cxxflags':
-            if self.spec.satisfies('@:1.8.12+cxx~shared'):
+            if spec.satisfies('@:1.8.12+cxx~shared'):
                 cmake_flags.append(self.compiler.cxx_pic_flag)
         elif name == "fflags":
-            if self.spec.satisfies('@:1.8.12+fortran~shared'):
+            if spec.satisfies('%cce+fortran'):
+                # Cray compiler generates module files with uppercase names by
+                # default, which is not handled by the CMake scripts. The
+                # following flag forces the compiler to produce module files
+                # with lowercase names.
+                cmake_flags.append('-ef')
+            if spec.satisfies('@:1.8.12+fortran~shared'):
                 cmake_flags.append(self.compiler.fc_pic_flag)
         elif name == "ldlibs":
-            if '+fortran %fj' in self.spec:
+            if '+fortran %fj' in spec:
                 cmake_flags.extend(['-lfj90i', '-lfj90f',
                                     '-lfjsrcinfo', '-lelf'])
 
@@ -386,9 +402,9 @@ def ensure_parallel_compiler_wrappers(self):
         # 1.10.6 and 1.12.0. The current develop versions do not produce 'h5pfc'
         # at all. Here, we make sure that 'h5pfc' is available when Fortran and
         # MPI support are enabled (only for versions that generate 'h5fc').
-        if self.spec.satisfies('@1.8.22:1.8.999,'
-                               '1.10.6:1.10.999,'
-                               '1.12.0:1.12.999,'
+        if self.spec.satisfies('@1.8.22:1.8,'
+                               '1.10.6:1.10,'
+                               '1.12.0:1.12,'
                                'develop:'
                                '+fortran+mpi'):
             with working_dir(self.prefix.bin):

packages/hdf5/pre-c99-comments.patch

@@ -41,4 +41,3 @@ index 9ce3524..3b4e5e7 100644
  }
 
  /*-------------------------------------------------------------------------
-