Comments (5)
The spack build logs:
spack-configure-args.txt
spack-build-out.txt
spack-build-env.txt
spack-build-env-mods.txt
spack-build-01-cmake-out.txt
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Eleni cross-checked for "official" EBRAINS collab builds that it also fails there when building without mpi: https://gitlab.ebrains.eu/technical-coordination/project-internal/devops/platform/ebrains-spack-builds/-/jobs/52502 (not-yet-public repo → @terhorstd again :))
from nest-simulator.
Eleni added link
dependency on hdf5
in the recipe and it seems to fix it…
i.e. depends_on('hdf5+cxx', when='@3.4.99:+sonata', type=('build', 'link', 'run'))
.
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During testing of #3112, it was deduced that the hdf5 variant influences this behavior.
If hdf5
wasn't built with mpi
enabled, the with/without
options works flawlessly — i.e. the bug can only be triggered if hdf5
is built with mpi
support, but nest
without.
from nest-simulator.
For the spack package I proposed to align nest
and its (sonata-feature-optional) dependency on hdf
, i.e. use hdf5
in an MPI version if NEST is to be built with MPI.
diff --git a/packages/nest/package.py b/packages/nest/package.py
index f88e8f3..ebd8484 100644
--- a/packages/nest/package.py
+++ b/packages/nest/package.py
@@ -93,7 +93,8 @@ class Nest(CMakePackage):
depends_on('boost', when="@2.16:+boost", type='build')
depends_on('py-setuptools@:44.99.99', when='@:2.15.99+python', type='build')
depends_on('py-h5py', when='@3.4.99:+sonata', type=('test', 'build', 'run'))
- depends_on('hdf5+cxx', when='@3.4.99:+sonata', type=('build', 'link', 'run'))
+ depends_on('hdf5+cxx+mpi', when='@3.4.99:+sonata+mpi', type=('build', 'link', 'run'))
+ depends_on('hdf5+cxx~mpi', when='@3.4.99:+sonata~mpi', type=('build', 'link', 'run'))
depends_on('py-pandas', when='@3.4.99:+sonata', type=('build', 'run'))
depends_on('py-nose', when='@:2.99.99+python+testsuite', type='test')
⇒ So technically, this avoids the issue for spack installs — it could be still reasonable to try within nest's cmake flow to detect this and fail with a "helpful" error message (e.g. if HDF5_ENABLE_PARALLEL
is ON
, but nest's ${with-mpi}
isn't ⇒ error).
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Related Issues (20)
- aeif-model documentation does not point out peculiarities
- Refactor handling of timers to achieve simpler code in place of use and increase coverage
- NEST hangs when setting connection weight in parallel simulations HOT 2
- Properly control validity of NodeCollections and SynapseCollections with hashes HOT 1
- ConnBuilder loop_over_targets() does not work as intended HOT 1
- NEST behaves incorrectly or fails when connecting sliced layers while using MPI
- Allow use of pairwise_bernoulli rule for connections to devices
- How do you run Potjans_2014 in full scale? HOT 4
- MPI initialization exits ungracefully HOT 1
- NEST fails to assert presence of required Boost libraries when Boost is configured HOT 2
- Connecting nodes with spatial positions fails in corner case HOT 1
- Nest-simulator 3.4 - installation on MAC - sli HOT 2
- Review use of types for number of processes and threads
- Refactor to use higher mathematical functions available per C++17 HOT 1
- Compiler warns about initializing reference with temporary in astrocyte_lr_1994
- Slow DumpLayerConnections() HOT 4
- Download NEST for working with Python HOT 4
- Displaying NodeCollection is very slow in IPython
- SelectNodesByMask() and DumpLayerConnections() combination problem HOT 1
- Failing MPI tests not properly detected HOT 1
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