Fix overconstrained HDF5 variants (#29132)

* hdf5: mark +fortran+shared conflict for older version

This version was only activated unintentionally by silo's conflict
statement, but `@1.8.15+shared+fortran+cxx` errors out in configure:

```
CMake Error at CMakeLists.txt:814 (message):
   **** Shared FORTRAN libraries are unsupported ****
```

* silo: refine hdf5 conflicts to avoid building old version

Before this, `silo+hdf5` concretized to 1.10.7 or sometimes 1.8.15. Now
I've verified it works for the following configurations:
```
silo@4.10.2 patches=7b5a1dc,952d3c9
^   hdf5@1.10.7 api=default

silo@4.10.2 patches=7b5a1dc,952d3c9,eb2a3a0
^   hdf5@1.10.8 api=v18

silo@4.10.2 patches=7b5a1dc,952d3c9,eb2a3a0
^   hdf5@1.12.1 api=v110

silo@4.11-bsd patches=eb2a3a0
^   hdf5@1.12.1 api=v110

silo@4.11-bsd patches=eb2a3a0
^   hdf5@1.10.8 api=default

silo@4.11-bsd patches=eb2a3a0
^   hdf5@1.12.1 api=default
```

and verified that the following fail:
```
silo@4.10.2 ^hdf5@1.12.1 api=default
silo@4.11 ^hdf5 api=v18
silo@4.11-bsd ^hdf5@1.13.0 api=v12
silo@4.11-bsd ^hdf5@1.13.0 api=default
```

and have updated the constraints to match. Hdf5 no longer has to be
downgraded to work with Silo.

* silo: fix dependency conflicts

* py-h5py: shorten and add comments to py-h5py hdf5 dependencies

* e4s: remove slightly outdated hdf5 requirement

* e4s: remove excessive hdf5 variant constraints

These I think are holdovers from the old concretizer.

- `hdf5_compat` can be expressed as `+hdf5 ^hdf5@1.8`
- The extra variants on hdf5 shouldn't break conduit
- axom unnecessarily restricts hdf5 version

* conduit: restore hdf5_compat flag

share/spack/gitlab/cloud_pipelines/stacks/e4s/spack.yaml

@@ -33,8 +33,6 @@ spack:
       variants: +bzip2 ~nls +xz
     hdf5:
       variants: +fortran +hl +shared
-      version:
-        - 1.10.7
     libfabric:
       variants: fabrics=sockets,tcp,udp,rxm
     libunwind:

var/spack/repos/builtin/packages/axom/package.py

@@ -98,9 +98,6 @@ class Axom(CachedCMakePackage, CudaPackage):
     depends_on("conduit+hdf5", when="+hdf5")
     depends_on("conduit~hdf5", when="~hdf5")
 
-    # HDF5 needs to be the same as Conduit's
-    depends_on("hdf5@1.8.19:1.8~cxx~fortran", when="+hdf5")
-
     depends_on("lua", when="+lua")
 
     depends_on("scr", when="+scr")

var/spack/repos/builtin/packages/conduit/package.py

@@ -77,6 +77,8 @@ class Conduit(CMakePackage):
     # set to false for systems that implicitly link mpi
     variant('blt_find_mpi', default=True, description='Use BLT CMake Find MPI logic')
     variant("hdf5", default=True, description="Build Conduit HDF5 support")
+    # TODO: remove 'compat' variant when VisIt starts distributing HDF5
+    # binaries
     variant("hdf5_compat", default=True, when='+hdf5',
             description="Build Conduit with HDF5 1.8.x (compatibility mode)")
     variant("silo", default=False, description="Build Conduit Silo support")
@@ -117,26 +119,18 @@ class Conduit(CMakePackage):
     ###############
     # HDF5
     ###############
-    # Note: cxx variant is disabled due to build issue Cyrus
-    # experienced on BGQ. When on, the static build tries
-    # to link against shared libs.
-    #
-    # Use HDF5 1.8, for wider output compatibly
-    # variants reflect we are not using hdf5's mpi or fortran features.
-    depends_on("hdf5~cxx", when="+hdf5")
-    depends_on("hdf5~shared", when="+hdf5~shared")
-    depends_on("hdf5@1.8.19:1.8", when="+hdf5+hdf5_compat")
 
-    # we need to hand this to conduit so it can properly
+    depends_on("hdf5", when="+hdf5")
-    # handle downstream linking of zlib reqed by hdf5
+    depends_on("hdf5~shared", when="+hdf5~shared")
-    depends_on("zlib", when="+hdf5")
+    # Require older HDF5 to ensure compatibility with VisIt: see #29132
+    depends_on("hdf5@1.8.0:1.8", when="+hdf5+hdf5_compat")
 
     ###############
     # Silo
     ###############
     # we are not using silo's fortran features
-    depends_on("silo~fortran", when="+silo+shared")
+    depends_on("silo+shared", when="+silo+shared")
-    depends_on("silo~shared~fortran", when="+silo~shared")
+    depends_on("silo~shared", when="+silo~shared")
 
     ###############
     # ADIOS
@@ -528,7 +522,9 @@ def hostconfig(self, spec, prefix):
 
         if "+hdf5" in spec:
             cfg.write(cmake_cache_entry("HDF5_DIR", spec['hdf5'].prefix))
-            cfg.write(cmake_cache_entry("ZLIB_DIR", spec['zlib'].prefix))
+            if 'zlib' in spec:
+                # HDF5 depends on zlib
+                cfg.write(cmake_cache_entry("ZLIB_DIR", spec['zlib'].prefix))
         else:
             cfg.write("# hdf5 not built by spack \n")
 

var/spack/repos/builtin/packages/hdf5/package.py

@@ -108,6 +108,8 @@ class Hdf5(CMakePackage):
     conflicts('+java', when='@:1.9')
     # The Java wrappers cannot be built without shared libs.
     conflicts('+java', when='~shared')
+    # Fortran cannot be built with shared
+    conflicts('+fortran', when='+shared@:1.8')
 
     # There are several officially unsupported combinations of the features:
     # 1. Thread safety is not guaranteed via high-level C-API but in some cases

var/spack/repos/builtin/packages/lbann/package.py

@@ -197,9 +197,12 @@ class Lbann(CMakePackage, CudaPackage, ROCmPackage):
     depends_on('cnpy', when='+numpy')
     depends_on('nccl', when='@0.94:0.98.2 +cuda')
 
-    depends_on('conduit@0.4.0: +hdf5~hdf5_compat ~python', when='@0.94:0 +conduit')
+    # Note that conduit defaults to +fortran +parmetis +python, none of which are
-    depends_on('conduit@0.5.0:0.6 +hdf5~hdf5_compat ~python', when='@0.100:0.101 +conduit')
+    # necessary by LBANN: you may want to disable those options in your
-    depends_on('conduit@0.6.0: +hdf5~hdf5_compat~fortran~parmetis ~python', when='@:0.90,0.99:')
+    # packages.yaml
+    depends_on('conduit@0.4.0: +hdf5', when='@0.94:0 +conduit')
+    depends_on('conduit@0.5.0:0.6 +hdf5', when='@0.100:0.101 +conduit')
+    depends_on('conduit@0.6.0: +hdf5', when='@:0.90,0.99:')
 
     # LBANN can use Python in two modes 1) as part of an extensible framework
     # and 2) to drive the front end model creation and launch

var/spack/repos/builtin/packages/py-h5py/package.py

@@ -36,38 +36,39 @@ class PyH5py(PythonPackage):
     variant('mpi', default=True, description='Build with MPI support')
 
     # Python versions
-    depends_on('python@3.6:', type=('build', 'run'), when='@3.0.0:3.1')
+    depends_on('python@3.6:', type=('build', 'run'), when='@3:3.1')
-    depends_on('python@3.7:', type=('build', 'run'), when='@3.2.0:')
+    depends_on('python@3.7:', type=('build', 'run'), when='@3.2:')
 
     # Build dependencies
     depends_on('py-cython@0.23:', type='build', when='@:2')
-    depends_on('py-cython@0.29:', type=('build'), when='@3.0.0:^python@:3.7')
+    depends_on('py-cython@0.29:', type=('build'), when='@3: ^python@:3.7')
-    depends_on('py-cython@0.29.14:', type=('build'), when='@3.0.0:^python@3.8.0:3.8')
+    depends_on('py-cython@0.29.14:', type=('build'), when='@3: ^python@3.8.0:3.8')
-    depends_on('py-cython@0.29.15:', type=('build'), when='@3.0.0:^python@3.9.0:')
+    depends_on('py-cython@0.29.15:', type=('build'), when='@3: ^python@3.9.0:')
     depends_on('py-pkgconfig', type='build')
     depends_on('py-setuptools', type='build')
-    depends_on('py-wheel', type='build', when='@3.0.0:')
+    depends_on('py-wheel', type='build', when='@3:')
 
     # Build and runtime dependencies
     depends_on('py-cached-property@1.5:', type=('build', 'run'), when='^python@:3.7')
     depends_on('py-numpy@1.7:', type=('build', 'run'), when='@:2')
-    depends_on('py-numpy@1.12:', type=('build', 'run'), when='@3.0.0:^python@3.6.0:3.6')
+    depends_on('py-numpy@1.12:', type=('build', 'run'), when='@3: ^python@3.6.0:3.6')
-    depends_on('py-numpy@1.14.5:', type=('build', 'run'), when='@3.0.0:^python@3.7.0:3.7')
+    depends_on('py-numpy@1.14.5:', type=('build', 'run'), when='@3: ^python@3.7.0:3.7')
-    depends_on('py-numpy@1.17.5:', type=('build', 'run'), when='@3.0.0:^python@3.8.0:3.8')
+    depends_on('py-numpy@1.17.5:', type=('build', 'run'), when='@3: ^python@3.8.0:3.8')
-    depends_on('py-numpy@1.19.3:', type=('build', 'run'), when='@3.0.0:^python@3.9.0:')
+    depends_on('py-numpy@1.19.3:', type=('build', 'run'), when='@3: ^python@3.9.0:')
     depends_on('py-six', type=('build', 'run'), when='@:2')
 
-    # Link dependencies
+    # Link dependencies (py-h5py v2 cannot build against HDF5 1.12 regardless
-    depends_on('hdf5@1.8.4:1.11+hl', when='@:2')
+    # of API setting)
-    depends_on('hdf5@1.8.4:+hl', when='@3.0.0:')
+    depends_on('hdf5@1.8.4:1.11 +hl', when='@:2')
+    depends_on('hdf5@1.8.4: +hl', when='@3:')
 
     # MPI dependencies
     depends_on('hdf5+mpi', when='+mpi')
     depends_on('mpi', when='+mpi')
     depends_on('py-mpi4py', when='@:2 +mpi', type=('build', 'run'))
-    depends_on('py-mpi4py@3.0.0:', when='@3.0.0:3.2+mpi^python@3.0.0:3.7', type=('build', 'run'))
+    depends_on('py-mpi4py@3:', when='@3:3.2+mpi^python@3:3.7', type=('build', 'run'))
-    depends_on('py-mpi4py@3.0.2:', when='@3.3.0:+mpi^python@3.0.0:3.7', type=('build', 'run'))
+    depends_on('py-mpi4py@3.0.2:', when='@3.3.0:+mpi^python@3:3.7', type=('build', 'run'))
-    depends_on('py-mpi4py@3.0.3:', when='@3.0.0:+mpi^python@3.8.0:', type=('build', 'run'))
+    depends_on('py-mpi4py@3.0.3:', when='@3:+mpi^python@3.8.0:', type=('build', 'run'))
 
     def setup_build_environment(self, env):
         env.set('HDF5_DIR', self.spec['hdf5'].prefix)

var/spack/repos/builtin/packages/silo/package.py

@@ -33,7 +33,7 @@ class Silo(AutotoolsPackage):
     variant('mpi', default=True,
             description='Compile with MPI Compatibility')
     variant('hdf5', default=True,
-            description='Use the HDF5 for database')
+            description='Support HDF5 for database I/O')
     variant('hzip', default=True,
             description='Enable hzip support')
     variant('fpzip', default=True,
@@ -45,6 +45,7 @@ class Silo(AutotoolsPackage):
     depends_on('libtool', type='build', when='+shared')
     depends_on('mpi', when='+mpi')
     depends_on('hdf5', when='+hdf5')
+    depends_on('hdf5 api=v110', when='@:4.10 +hdf5 ^hdf5@1.12:')
     depends_on('qt+gui~framework@4.8:4.9', when='+silex')
     depends_on('libx11', when='+silex')
     # Xmu dependency is required on Ubuntu 18-20
@@ -55,11 +56,12 @@ class Silo(AutotoolsPackage):
     patch('remove-mpiposix.patch', when='@4.8:4.10.2')
     patch('H5FD_class_t-terminate.patch', when='@:4.10.2 ^hdf5@1.10.0:')
     # H5EPR_SEMI_COLON.patch should be applied only to silo@4.11 when building
-    # with hdf5@1.10.8 or later 1.10 or with hdf5@1.12.1 or later 1.12
+    # with hdf5@1.10.8 or later 1.10 or with hdf5@1.12.1 or later
-    patch('H5EPR_SEMI_COLON.patch', when='@:4.11 ^hdf5@1.10.8:1.10,1.12.1:1.12')
+    patch('H5EPR_SEMI_COLON.patch', when='@:4.11 ^hdf5@1.10.8:1.10,1.12.1:')
 
-    conflicts('hdf5@1.10.8:', when="@:4.10.2")
+    conflicts('^hdf5 api=v18', when="@4.11: +hdf5")
-    conflicts('hdf5@1.13.0:', when="@:4.11")
+    conflicts('^hdf5 api=v112', when="@:4.10 +hdf5")
+    conflicts('^hdf5@1.13:', when="+hdf5")
     conflicts('+hzip', when="@4.11-bsd")
     conflicts('+fpzip', when="@4.11-bsd")
     conflicts('+hzip', when="@4.10.2-bsd")