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Updates to Isambard-3 spack env and purify benchmark #356

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merged 9 commits into from
Jan 17, 2025
Merged

Updates to Isambard-3 spack env and purify benchmark #356

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1141060
Update purify to run with changes I'm working on
tkoskela Nov 8, 2024
34dac41
Fix algorithm in FB
tkoskela Nov 8, 2024
9d704c5
Add FB Onnx benchmark
tkoskela Dec 12, 2024
c35480f
Merge branch 'main' into tk/update-purify
tkoskela Dec 12, 2024
7b4aee6
Isambard-3 env update
tkoskela Jan 17, 2025
efe8c2d
Use latest release and add some checks
tkoskela Jan 17, 2025
29bf30e
remove private python package
tkoskela Jan 17, 2025
124bf16
add python version dependency to specs to avoid version clashes
tkoskela Jan 17, 2025
38c1506
remove buildable:false to simplify environment resolution
tkoskela Jan 17, 2025
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64 changes: 58 additions & 6 deletions benchmarks/apps/purify/purify.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ class PurifyBase(SpackTest):
valid_systems = ['*']
valid_prog_environs = ['default']

spack_spec = 'purify@4.2.0+benchmarks'
spack_spec = 'purify@5.0.0+mpi+openmp+benchmarks ^fftw'
executable_opts = ['--benchmark_format=csv',
'--benchmark_out=purify_benchmark.out',
'--benchmark_out_format=csv']
Expand Down Expand Up @@ -104,7 +104,7 @@ def filter_benchmarks(self):
self.env_vars['OMP_NUM_THREADS'] = f'{self.threads}'
self.num_tasks = self.tasks
self.num_cpus_per_task = self.threads
self.num_tasks_per_node = 1
self.num_tasks_per_node = max(1,self.current_partition.processor.num_sockets)

@rfm.simple_test
class PurifyPADMMBenchmark_PratleyEtAl(PurifyBase):
Expand All @@ -114,19 +114,71 @@ class PurifyPADMMBenchmark_PratleyEtAl(PurifyBase):
threads = 16
tasks = parameter([1,2,3,4,8,12])

executable = 'mpi_benchmark_PADMM'
executable = 'mpi_benchmark_algorithms'
time_limit = '60m'

algorithm = parameter(["PadmmDistributeImage", "PadmmDistributeGrid"])
numberOfVisibilities = parameter([10**6, 10**7])
imgsize = parameter([1024])

@run_after('setup')
def filter_benchmarks(self):
self.executable_opts.append(f'--benchmark_filter=AlgoFixtureMPI/'
f'{self.algorithm}'
f'/{self.imgsize}/{self.numberOfVisibilities}/')
self.env_vars['OMP_NUM_THREADS'] = f'{self.threads}'
self.num_tasks = self.tasks
self.num_cpus_per_task = self.threads
self.num_tasks_per_node = max(1,self.current_partition.processor.num_sockets)

@rfm.simple_test
class PurifyForwardBackwardBenchmark(PurifyBase):
"""
This benchmark uses the Forward Backward algorithm, otherwise it's similar to PurifyPADMMBenchmark.
"""
threads = 16
tasks = parameter([1,2,4,8,16])

executable = 'mpi_benchmark_algorithms'
time_limit = '60m'

algorithm = parameter([1,3])
algorithm = parameter(["FbDistributeImage", "FbDistributeGrid"])
numberOfVisibilities = parameter([10**6, 10**7])
imgsize = parameter([1024])

@run_after('setup')
def filter_benchmarks(self):
self.executable_opts.append(f'--benchmark_filter=PadmmFixtureMPI/'
f'ApplyAlgo{self.algorithm}'
self.executable_opts.append(f'--benchmark_filter=AlgoFixtureMPI/'
f'{self.algorithm}'
f'/{self.imgsize}/{self.numberOfVisibilities}/')
self.env_vars['OMP_NUM_THREADS'] = f'{self.threads}'
self.num_tasks = self.tasks
self.num_cpus_per_task = self.threads
self.num_tasks_per_node = 1

@rfm.simple_test
class PurifyForwardBackwardOnnxBenchmark(PurifyBase):
"""
This benchmark uses the Forward Backward algorithm, otherwise it's similar to PurifyPADMMBenchmark.
"""
omp_threads = parameter([16])
ort_threads = parameter([16])
tasks = parameter([1,2,4,8,16])

executable = 'mpi_benchmark_algorithms'
time_limit = '60m'

algorithm = parameter(["FbOnnxDistributeImage", "FbOnnxDistributeGrid"])
numberOfVisibilities = parameter([10**6, 10**7])
imgsize = parameter([1024])

@run_after('setup')
def filter_benchmarks(self):
self.executable_opts.append(f'--benchmark_filter=AlgoFixtureMPI/'
f'{self.algorithm}/{self.imgsize}/{self.numberOfVisibilities}/')
self.env_vars['OMP_NUM_THREADS'] = f'{self.omp_threads}'
self.env_vars['ORT_NUM_THREADS'] = f'{self.ort_threads}'
self.num_tasks = self.tasks
self.num_cpus_per_task = max(self.omp_threads, self.ort_threads)
self.num_tasks_per_node = max(1,self.current_partition.processor.num_sockets)
self.spack_spec = '[email protected]+mpi+openmp+benchmarks+onnxrt ^fftw'
46 changes: 34 additions & 12 deletions benchmarks/spack/isambard3/grace/spack.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,6 @@
# configuration settings.
spack:
# add package specs to the `specs` list
specs:
- purify+mpi
view: false
include:
- ../../common.yaml
Expand All @@ -25,6 +23,18 @@ spack:
environment: {}
extra_rpaths: []
packages:
cmake:
externals:
- spec: [email protected]
prefix: /usr
python:
externals:
- spec: [email protected]+bz2+crypt+ctypes+dbm+lzma+pyexpat+pythoncmd+readline+sqlite3+ssl+tix+tkinter+uuid+zlib
prefix: /lfs1i3/home/lexci-i3/tkoskela.lexci-i3/python_envs/test
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- spec: [email protected]+bz2+crypt+ctypes+dbm+lzma+pyexpat+pythoncmd+readline+sqlite3+ssl+tix+tkinter+uuid+zlib
prefix: /opt/cray/pe/python/3.11.7
- spec: [email protected]+bz2+crypt+ctypes+dbm+lzma+pyexpat~pythoncmd+readline+sqlite3+ssl~tkinter+uuid+zlib
prefix: /usr
groff:
externals:
- spec: [email protected]
Expand Down Expand Up @@ -81,10 +91,6 @@ spack:
externals:
- spec: [email protected]
prefix: /usr
cmake:
externals:
- spec: [email protected]
prefix: /usr
pkg-config:
externals:
- spec: [email protected]
Expand Down Expand Up @@ -146,9 +152,25 @@ spack:
modules:
- craype-network-ofi
- cray-mpich/8.1.29
# cray-fftw:
# externals:
# - spec: [email protected]
# prefix: /opt/cray/pe/fftw/3.3.10.7/arm_grace/
# modules:
# - brics/cray-fftw/3.3.10.7
py-numpy:
externals:
- spec: [email protected]
modules:
- cray-python
prefix: /opt/cray/pe/python/3.11.7
buildable: false
py-scipy:
externals:
- spec: [email protected]
modules:
- cray-python
prefix: /opt/cray/pe/python/3.11.7
buildable: false
py-mpi4py:
externals:
- spec: [email protected]
modules:
- cray-python
prefix: /opt/cray/pe/python/3.11.7
buildable: false
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Any reason for using buildable: false for this packages? Also, I believe you want also to append ^ [email protected] to all these specs, to avoid making it match with other versions of python.

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I thought buildable: false guarantees that the external will always get used. Is it too strong requirement? Happy to remove it if you think that's better. Adding the python version to the spec

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buildable: false complicates environment resolution quite a bit whenever a package appears in the environment. I'd expect troubles for py-numpy and py-scipy because they're somewhat common, py-mpi4py less so and I'd hope spack links it to the right MPI library anyway.

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👍 thanks for explaining. My builds seem fine after removing it.

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For example, one problem could be the following: for some reason a package in the environment requires a specific version of python and that's not compatible with 3.11.7 (say 3.10 or 3.12), another package needs py-numpy, then you end up in the situation where you can't concretize the environment at all. We do use buildable: false for MPI, but we do really want to enforce using system MPI libraries only, I don't see that requirement being useful for python and python packages.

specs: []