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{bio}[foss/2023a] ESM3 v3.1.2 w/ CUDA 12.1.1 #22075

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{bio}[foss/2023a] ESM3 v3.1.2 w/ CUDA 12.1.1 #22075

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@smoors smoors commented Dec 20, 2024 •
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@smoors smoors added the update label Dec 20, 2024
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Updated software ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb

Diff against ESM3-3.1.2-foss-2023a.eb

easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb
index 39cf45e353..f3dbb7192f 100644
--- a/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb
@@ -2,6 +2,7 @@ easyblock = 'PythonBundle'
 
 name = 'ESM3'
 version = '3.1.2'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.evolutionaryscale.ai/'
 description = """ESM3 is a frontier generative model for biology, able to jointly reason across
@@ -16,15 +17,14 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 
 builddependencies = [
     ('hatch', '1.9.7'),  # for biotite
-    # ('Ninja', '1.11.1'),
 ]
 
 dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
-    ('PyTorch-bundle', '2.3.0'),
+    ('PyTorch-bundle', '2.3.0', versionsuffix),
     ('Transformers', '4.39.3'),
     ('Biopython', '1.83'),
-    # ('Biotite', '0.41.0'),
     ('Brotli-python', '1.0.9'),
     ('einops', '0.7.0'),
     ('IPython', '8.14.0'),
Diff against ESM3-3.0.0.post2-foss-2023a.eb

easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb
index 60125c1af4..f3dbb7192f 100644
--- a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb
+++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,8 @@
 easyblock = 'PythonBundle'
 
 name = 'ESM3'
-version = '3.0.0.post2'
+version = '3.1.2'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.evolutionaryscale.ai/'
 description = """ESM3 is a frontier generative model for biology, able to jointly reason across
@@ -14,30 +15,45 @@ predictions for all the tracks.
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('hatch', '1.9.7'),  # for biotite
+]
+
 dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
-    ('PyTorch-bundle', '2.1.2'),
+    ('PyTorch-bundle', '2.3.0', versionsuffix),
     ('Transformers', '4.39.3'),
     ('Biopython', '1.83'),
-    ('Biotite', '0.41.0'),
     ('Brotli-python', '1.0.9'),
     ('einops', '0.7.0'),
     ('IPython', '8.14.0'),
     ('scikit-learn', '1.3.1'),
+    ('Cython', '3.0.8'),  # for biotite
+    ('zstd', '1.5.5'),
 ]
 
 use_pip = True
 
 exts_list = [
+    ('biotite', '0.41.2', {
+        'checksums': ['f4ebca8071fade51103c9e8534d60fff2021c22e6af85058a53ed6a3d96b6ad4'],
+    }),
     ('msgpack-numpy', '0.4.8', {
         'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'],
     }),
     ('cloudpathlib', '0.16.0', {
         'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'],
     }),
+    ('zstd', '1.5.5.1', {
+        'checksums': ['1ef980abf0e1e072b028d2d76ef95b476632651c96225cf30b619c6eef625672'],
+    }),
+    ('tenacity', '8.5.0', {
+        'checksums': ['8bc6c0c8a09b31e6cad13c47afbed1a567518250a9a171418582ed8d9c20ca78'],
+    }),
     ('esm', version, {
-        'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'],
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['0c5ba0e12c28a1ddcad8a1e3fe152e476f2d24d412a8a04085b057f72759ba46'],
     }),
 ]
 
@@ -46,6 +62,7 @@ sanity_pip_check = True
 sanity_check_commands = [
     "python -c 'import esm'",
     "python -c 'from esm.models.esm3 import ESM3'",
+    "python -c 'from esm.models.esmc import ESMC'",
 ]
 
 moduleclass = 'bio'
Diff against ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb
index 1382c12efc..f3dbb7192f 100644
--- a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'ESM3'
-version = '3.0.0.post2'
+version = '3.1.2'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.evolutionaryscale.ai/'
@@ -15,31 +15,45 @@ predictions for all the tracks.
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('hatch', '1.9.7'),  # for biotite
+]
+
 dependencies = [
     ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
-    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('PyTorch-bundle', '2.3.0', versionsuffix),
     ('Transformers', '4.39.3'),
     ('Biopython', '1.83'),
-    ('Biotite', '0.41.0'),
     ('Brotli-python', '1.0.9'),
     ('einops', '0.7.0'),
     ('IPython', '8.14.0'),
     ('scikit-learn', '1.3.1'),
+    ('Cython', '3.0.8'),  # for biotite
+    ('zstd', '1.5.5'),
 ]
 
 use_pip = True
 
 exts_list = [
+    ('biotite', '0.41.2', {
+        'checksums': ['f4ebca8071fade51103c9e8534d60fff2021c22e6af85058a53ed6a3d96b6ad4'],
+    }),
     ('msgpack-numpy', '0.4.8', {
         'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'],
     }),
     ('cloudpathlib', '0.16.0', {
         'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'],
     }),
+    ('zstd', '1.5.5.1', {
+        'checksums': ['1ef980abf0e1e072b028d2d76ef95b476632651c96225cf30b619c6eef625672'],
+    }),
+    ('tenacity', '8.5.0', {
+        'checksums': ['8bc6c0c8a09b31e6cad13c47afbed1a567518250a9a171418582ed8d9c20ca78'],
+    }),
     ('esm', version, {
-        'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'],
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['0c5ba0e12c28a1ddcad8a1e3fe152e476f2d24d412a8a04085b057f72759ba46'],
     }),
 ]
 
@@ -48,6 +62,7 @@ sanity_pip_check = True
 sanity_check_commands = [
     "python -c 'import esm'",
     "python -c 'from esm.models.esm3 import ESM3'",
+    "python -c 'from esm.models.esmc import ESMC'",
 ]
 
 moduleclass = 'bio'

Updated software ESM3-3.1.2-foss-2023a.eb

Diff against ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb
index f3dbb7192f..39cf45e353 100644
--- a/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb
@@ -2,7 +2,6 @@ easyblock = 'PythonBundle'
 
 name = 'ESM3'
 version = '3.1.2'
-versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://www.evolutionaryscale.ai/'
 description = """ESM3 is a frontier generative model for biology, able to jointly reason across
@@ -17,14 +16,15 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 
 builddependencies = [
     ('hatch', '1.9.7'),  # for biotite
+    # ('Ninja', '1.11.1'),
 ]
 
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
-    ('PyTorch-bundle', '2.3.0', versionsuffix),
+    ('PyTorch-bundle', '2.3.0'),
     ('Transformers', '4.39.3'),
     ('Biopython', '1.83'),
+    # ('Biotite', '0.41.0'),
     ('Brotli-python', '1.0.9'),
     ('einops', '0.7.0'),
     ('IPython', '8.14.0'),
Diff against ESM3-3.0.0.post2-foss-2023a.eb

easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb
index 60125c1af4..39cf45e353 100644
--- a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a.eb
+++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'ESM3'
-version = '3.0.0.post2'
+version = '3.1.2'
 
 homepage = 'https://www.evolutionaryscale.ai/'
 description = """ESM3 is a frontier generative model for biology, able to jointly reason across
@@ -14,30 +14,46 @@ predictions for all the tracks.
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('hatch', '1.9.7'),  # for biotite
+    # ('Ninja', '1.11.1'),
+]
+
 dependencies = [
     ('Python', '3.11.3'),
-    ('PyTorch-bundle', '2.1.2'),
+    ('PyTorch-bundle', '2.3.0'),
     ('Transformers', '4.39.3'),
     ('Biopython', '1.83'),
-    ('Biotite', '0.41.0'),
+    # ('Biotite', '0.41.0'),
     ('Brotli-python', '1.0.9'),
     ('einops', '0.7.0'),
     ('IPython', '8.14.0'),
     ('scikit-learn', '1.3.1'),
+    ('Cython', '3.0.8'),  # for biotite
+    ('zstd', '1.5.5'),
 ]
 
 use_pip = True
 
 exts_list = [
+    ('biotite', '0.41.2', {
+        'checksums': ['f4ebca8071fade51103c9e8534d60fff2021c22e6af85058a53ed6a3d96b6ad4'],
+    }),
     ('msgpack-numpy', '0.4.8', {
         'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'],
     }),
     ('cloudpathlib', '0.16.0', {
         'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'],
     }),
+    ('zstd', '1.5.5.1', {
+        'checksums': ['1ef980abf0e1e072b028d2d76ef95b476632651c96225cf30b619c6eef625672'],
+    }),
+    ('tenacity', '8.5.0', {
+        'checksums': ['8bc6c0c8a09b31e6cad13c47afbed1a567518250a9a171418582ed8d9c20ca78'],
+    }),
     ('esm', version, {
-        'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'],
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['0c5ba0e12c28a1ddcad8a1e3fe152e476f2d24d412a8a04085b057f72759ba46'],
     }),
 ]
 
@@ -46,6 +62,7 @@ sanity_pip_check = True
 sanity_check_commands = [
     "python -c 'import esm'",
     "python -c 'from esm.models.esm3 import ESM3'",
+    "python -c 'from esm.models.esmc import ESMC'",
 ]
 
 moduleclass = 'bio'
Diff against ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb
index 1382c12efc..39cf45e353 100644
--- a/easybuild/easyconfigs/e/ESM3/ESM3-3.0.0.post2-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/e/ESM3/ESM3-3.1.2-foss-2023a.eb
@@ -1,8 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'ESM3'
-version = '3.0.0.post2'
-versionsuffix = '-CUDA-%(cudaver)s'
+version = '3.1.2'
 
 homepage = 'https://www.evolutionaryscale.ai/'
 description = """ESM3 is a frontier generative model for biology, able to jointly reason across
@@ -15,31 +14,46 @@ predictions for all the tracks.
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('hatch', '1.9.7'),  # for biotite
+    # ('Ninja', '1.11.1'),
+]
+
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
-    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('PyTorch-bundle', '2.3.0'),
     ('Transformers', '4.39.3'),
     ('Biopython', '1.83'),
-    ('Biotite', '0.41.0'),
+    # ('Biotite', '0.41.0'),
     ('Brotli-python', '1.0.9'),
     ('einops', '0.7.0'),
     ('IPython', '8.14.0'),
     ('scikit-learn', '1.3.1'),
+    ('Cython', '3.0.8'),  # for biotite
+    ('zstd', '1.5.5'),
 ]
 
 use_pip = True
 
 exts_list = [
+    ('biotite', '0.41.2', {
+        'checksums': ['f4ebca8071fade51103c9e8534d60fff2021c22e6af85058a53ed6a3d96b6ad4'],
+    }),
     ('msgpack-numpy', '0.4.8', {
         'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'],
     }),
     ('cloudpathlib', '0.16.0', {
         'checksums': ['cdfcd35d46d529587d744154a0bdf962aca953b725c8784cd2ec478354ea63a3'],
     }),
+    ('zstd', '1.5.5.1', {
+        'checksums': ['1ef980abf0e1e072b028d2d76ef95b476632651c96225cf30b619c6eef625672'],
+    }),
+    ('tenacity', '8.5.0', {
+        'checksums': ['8bc6c0c8a09b31e6cad13c47afbed1a567518250a9a171418582ed8d9c20ca78'],
+    }),
     ('esm', version, {
-        'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['5544b6974945d791205226408100429c2ea6e49b30265aea1d359caabe20bb14'],
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['0c5ba0e12c28a1ddcad8a1e3fe152e476f2d24d412a8a04085b057f72759ba46'],
     }),
 ]
 
@@ -48,6 +62,7 @@ sanity_pip_check = True
 sanity_check_commands = [
     "python -c 'import esm'",
     "python -c 'from esm.models.esm3 import ESM3'",
+    "python -c 'from esm.models.esmc import ESMC'",
 ]
 
 moduleclass = 'bio'

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@smoors