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Apply workaround in CI for NMODL change #143

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d17b2bd
Apply workaround in CI for NMODL change
JCGoran Mar 10, 2025
326b1a4
Reenable test
JCGoran Mar 10, 2025
bd4f2e6
Update NEURON_COMMIT_ID
JCGoran Mar 12, 2025
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12 changes: 11 additions & 1 deletion .github/workflows/simulation_test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ on:
required: false

env:
NEURON_COMMIT_ID: 'c48d7d5'
NEURON_COMMIT_ID: '0e7570e50'
RDMAV_FORK_SAFE: '1'

jobs:
Expand Down Expand Up @@ -147,6 +147,16 @@ jobs:
else
git clone --branch=${{ env.NEURON_BRANCH }} https://github.com/neuronsimulator/nrn.git --depth=1
fi
if [[ -d ${PWD}/nrn/external/nmodl ]]; then
git -C ${PWD}/nrn submodule update --init --recursive --depth=1 external/nmodl
# apply temp workaround for https://github.com/openbraininstitute/neurodamus/issues/3
patch="${PWD}/ci/0001-Revert-Use-aligned_alloc-as-we-do-in-CoreNEURON-too-.patch"
if git -C ${PWD}/nrn/external/nmodl apply "${patch}" >& /dev/null; then
echo "Successfully applied patch ${patch}"
else
echo "Failed to apply patch ${patch}; CI will continue as-is"
fi
fi
python -m pip install --upgrade pip -r nrn/nrn_requirements.txt
cmake -B nrn/build -S nrn -G Ninja \
-DPYTHON_EXECUTABLE=$(which python) \
Expand Down
34 changes: 34 additions & 0 deletions ci/0001-Revert-Use-aligned_alloc-as-we-do-in-CoreNEURON-too-.patch
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@@ -0,0 +1,34 @@
From 66791fc353535abe0a45ff00e0049e740962fa18 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <[email protected]>
Date: Mon, 10 Mar 2025 13:37:09 +0100
Subject: [PATCH] Revert "Use aligned_alloc as we do in CoreNEURON too (#933)"

This reverts commit 3eab851dd4a31e6f8e082faf79d83d69b6482e2b.
---
src/codegen/codegen_coreneuron_cpp_visitor.cpp | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/codegen/codegen_coreneuron_cpp_visitor.cpp b/src/codegen/codegen_coreneuron_cpp_visitor.cpp
index c46ad2e..38e3f08 100644
--- a/src/codegen/codegen_coreneuron_cpp_visitor.cpp
+++ b/src/codegen/codegen_coreneuron_cpp_visitor.cpp
@@ -297,12 +297,11 @@ bool CodegenCoreneuronCppVisitor::optimize_ion_variable_copies() const {

void CodegenCoreneuronCppVisitor::print_memory_allocation_routine() const {
printer->add_newline(2);
- auto args = "size_t num, size_t size, size_t alignment = 64";
+ auto args = "size_t num, size_t size, size_t alignment = 16";
printer->fmt_push_block("static inline void* mem_alloc({})", args);
- printer->add_line(
- "size_t aligned_size = ((num*size + alignment - 1) / alignment) * alignment;");
- printer->add_line("void* ptr = aligned_alloc(alignment, aligned_size);");
- printer->add_line("memset(ptr, 0, aligned_size);");
+ printer->add_line("void* ptr;");
+ printer->add_line("posix_memalign(&ptr, alignment, num*size);");
+ printer->add_line("memset(ptr, 0, size);");
printer->add_line("return ptr;");
printer->pop_block();

--
2.39.3 (Apple Git-145)

10 changes: 4 additions & 6 deletions tests/scientific/test_lfp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -188,13 +188,11 @@ def test_v5_sonata_lfp(test_file, tmp_path):
nd.run()

# compare results with refs
# t3_data = np.array([0.00027065672, -0.00086610153, 0.0014563566, -0.0046603414])
# t7_data = np.array([0.00029265403, -0.0009364929, 0.001548515, -0.004955248])
t3_data = np.array([0.00027065672, -0.00086610153, 0.0014563566, -0.0046603414])
t7_data = np.array([0.00029265403, -0.0009364929, 0.001548515, -0.004955248])
node_ids = np.array([0, 4])
result_ids, result_data = _read_sonata_lfp_file(Path(output_dir) / "lfp.h5")

# TODO: reenable after: https://github.com/openbraininstitute/neurodamus/issues/3
# is solved
# npt.assert_allclose(result_data.data[3], t3_data)
# npt.assert_allclose(result_data.data[7], t7_data)
npt.assert_allclose(result_data.data[3], t3_data)
npt.assert_allclose(result_data.data[7], t7_data)
npt.assert_allclose(result_ids, node_ids)
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