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add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 #15874

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merged 2 commits into from
Aug 4, 2022
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add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 #15874

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b684ea7
patch for fixing jax0.3.9 nan problem
ThomasHoffmann77 Jul 19, 2022
fc8be77
fix jax version in filename and description of patch for AlphaFold 2.2.2
boegel Aug 4, 2022
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2 changes: 2 additions & 0 deletions easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,7 @@ components = [
'AlphaFold-2.0.0_n-cpu.patch',
'AlphaFold-2.1.0_fix-scp-path.patch',
'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
'AlphaFold-2.2.2_jax038_NaN.patch',
],
'checksums': [
'aa51dc4a1150b92310d20e63e9e4d9279b15b6a1f7e664360f52827f83256cdd', # v2.2.2.tar.gz
Expand All @@ -92,6 +93,7 @@ components = [
'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch
'5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch
'1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch
'0b040ba99208cd9ad79b7d17db5720f7a447a019ac0ca786b3b019a55d1544e0', # AlphaFold-2.2.2_jax038_NaN.patch
],
'start_dir': 'alphafold-%(version)s',
'use_pip': True,
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2 changes: 2 additions & 0 deletions easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb
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Expand Up @@ -78,6 +78,7 @@ components = [
'AlphaFold-2.0.0_n-cpu.patch',
'AlphaFold-2.1.0_fix-scp-path.patch',
'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
'AlphaFold-2.2.2_jax038_NaN.patch',
],
'checksums': [
'aa51dc4a1150b92310d20e63e9e4d9279b15b6a1f7e664360f52827f83256cdd', # v2.2.2.tar.gz
Expand All @@ -87,6 +88,7 @@ components = [
'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch
'5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch
'1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch
'0b040ba99208cd9ad79b7d17db5720f7a447a019ac0ca786b3b019a55d1544e0', # AlphaFold-2.2.2_jax038_NaN.patch
],
'start_dir': 'alphafold-%(version)s',
'use_pip': True,
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16 changes: 16 additions & 0 deletions easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax038_NaN.patch
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@@ -0,0 +1,16 @@
# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de
# Resulting pdb files contain NaNs because jax >= 0.3.8 is used.
# Fix according to https://github.com/deepmind/alphafold/issues/513 and
# https://jax.readthedocs.io/en/latest/changelog.html#jax-0-3-8-april-29-2022
diff -ru alphafold-2.2.2/alphafold/model/utils.py alphafold-2.2.2_jax38_NaN/alphafold/model/utils.py
--- alphafold-2.2.2/alphafold/model/utils.py 2022-06-13 17:49:22.000000000 +0200
+++ alphafold-2.2.2_jax38_NaN/alphafold/model/utils.py 2022-07-18 10:17:59.672423061 +0200
@@ -34,7 +34,7 @@

def batched_gather(params, indices, axis=0, batch_dims=0):
"""Implements a JAX equivalent of `tf.gather` with `axis` and `batch_dims`."""
- take_fn = lambda p, i: jnp.take(p, i, axis=axis)
+ take_fn = lambda p, i: jnp.take(p, i, axis=axis, mode="clip")
for _ in range(batch_dims):
take_fn = jax.vmap(take_fn)
return take_fn(params, indices)