{bio}[foss/2023a] relion-classranker v0.0.1.20230822 w/ CUDA 12.1.1

easybuild/easyconfigs/r/relion-classranker/relion-classranker-0.0.1.20230822.b6e751e-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,82 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+easyblock = 'PythonBundle'
+
+name = 'relion-classranker'
+_v = '0.0.1'
+_sha = 'b6e751e5cb4205d8e9b36d0ae38c3687b3395acb'
+_date = '20230822'
+version = '%s.%s.%s' % (_v, _date, _sha[:7])
+
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/3dem/%(name)s'
+description = """The class ranker is part of the cryogenic electron microscopy (cryo-EM) dataset 
+processing pipeline in RELION. It is used to automatically select suitable      
+particles (EM images) assigned to 2D class averages for further downstream      
+processing.
+
+This model comprises two main components: a CNN responsible for extracting image
+features, and an MLP that combines the image features with additional statistics
+to assigns a score ranging from zero to one for each 2D class average.
+
+The selection is subsequently done in RELION through a user defined cutoff for  
+the predicted score.
+
+For training, a supervised approach is adopted, where pairs of 2D classes and   
+corresponding human-assigned scores are used to teach the model.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+patches = []
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('relion-classranker_data', '1.0', '', SYSTEM),
+]
+
+use_pip = True
+
+exts_list = [
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    ('relion_classranker', '0.0.1.20230822', {
+        'patches': [
+            'relion-classranker-0.0.1_relax_requirements.patch',
+            'relion-classranker-0.0.1_multi_torch_home.patch',
+            'relion-classranker-0.0.1_add_script.patch',
+        ],
+        'source_urls': ['https://github.com/3dem/relion-classranker/archive/'],
+        'sources': [{
+            'download_filename': 'b6e751e5cb4205d8e9b36d0ae38c3687b3395acb.tar.gz',
+            'filename': '%(name)s-%(version)s.tar.gz'
+        }],
+        'checksums': [
+            {'relion_classranker-0.0.1.20230822.tar.gz':
+             'f5fa204831a47155a6a509d7dc427ee216eef7c391784eb8844006d5dce6f014'},
+            {'relion-classranker-0.0.1_relax_requirements.patch':
+             '943728e60498ff154f65b29a73cccf759018f56f90970ed728d94f1a2f4b1958'},
+            {'relion-classranker-0.0.1_multi_torch_home.patch':
+             '2b1c612b687d6a552492da75dc05003c04ed677862514dfa7317941f500c9033'},
+            {'relion-classranker-0.0.1_add_script.patch':
+             'cb2c9c362f79faa25527f58fad3bdaaed4090b791c46aca70447587742600907'},
+        ],
+    }),
+]
+
+fix_python_shebang_for = ['bin/command_line.py']
+
+postinstallcmds = ['mv %(installdir)s/bin/{command_line.py,relion_classranker}']
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/relion_classranker'],
+}
+sanity_check_commands = ['relion_classranker -h']
+
+moduleclass = 'bio'

easybuild/easyconfigs/r/relion-classranker/relion-classranker-0.0.1_add_script.patch

@@ -0,0 +1,17 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+# install command_line.py to bin. (to be renamed later by postinstall) 
+diff -ru relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb/setup.py relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb_add_script.patch/setup.py
+--- relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb/setup.py	2023-08-22 19:15:52.000000000 +0200
++++ relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb_add_script.patch/setup.py	2023-11-16 18:28:25.274552072 +0100
+@@ -35,8 +35,9 @@
+     packages=find_packages(),
+     install_requires=install_requires,
+     python_requires=">=3.5",
++    scripts = ["relion_classranker/command_line.py"]
+ )
+
+ # Download, install and load model
+ # import relion_classranker
+-# relion_classranker.install_and_load_model("v1.0")
+\ No newline at end of file
++# relion_classranker.install_and_load_model("v1.0")

easybuild/easyconfigs/r/relion-classranker/relion-classranker-0.0.1_multi_torch_home.patch

@@ -0,0 +1,45 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+# allow to use TORCH_HOME with modextrapaths.
+# Automatic download of v1.0.ckpt is disabled for multi TORCH_HOME.
+diff -ru relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb/relion_classranker/command_line.py relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb_multi_torch_home/relion_classranker/command_line.py
+--- relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb/relion_classranker/command_line.py	2023-08-22 19:15:52.000000000 +0200
++++ relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb_multi_torch_home/relion_classranker/command_line.py	2023-11-16 18:57:48.509605576 +0100
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ import sys
+
+ if sys.version_info < (3, 0):
+@@ -42,9 +43,9 @@
+     model_path = os.path.join(dest_dir, f"{name}.ckpt")
+     model_path_gz = model_path + ".gz"
+     completed_check_path = os.path.join(dest_dir, f"{name}_installed.txt")
+-
++    is_torch_home_multi=False if os.getenv('TORCH_HOME')==None else len(os.getenv('TORCH_HOME').split(':'))>1
+     # Download file and install it if not already done
+-    if not os.path.isfile(completed_check_path):
++    if not os.path.isfile(completed_check_path) and not is_torch_home_multi:
+         if verbose:
+             print(f"Installing Classranker model ({name})...")
+         os.makedirs(dest_dir, exist_ok=True)
+@@ -63,8 +64,19 @@
+             print(f"Model ({name}) successfully installed in {dest_dir}")
+
+     # Load checkpoint file
+-    checkpoint = torch.load(model_path, map_location="cpu")
+-
++    checkpoint = None
++    if is_torch_home_multi:
++      for _p in os.getenv('TORCH_HOME').split(':'):
++          model_path = os.path.join(_p, "hub", "checkpoints", "relion_classranker",f"{name}.ckpt")
++          try: 
++              checkpoint = torch.load(model_path, map_location="cpu")
++          except:
++              if verbose: 
++                  print(f'Cannot load model {model_path}')
++          else:
++              break
++    else:
++        checkpoint = torch.load(model_path, map_location="cpu")
+     # Dynamically include model as a module
+     # Make sure to check download integrity for this, otherwise major security risk
+     model_module = types.ModuleType("classranker_model")

easybuild/easyconfigs/r/relion-classranker/relion-classranker-0.0.1_relax_requirements.patch

@@ -0,0 +1,14 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+# adapt versions to foss/2022a.
+# downgrading torch to 1.12.0 from 2.0.1 might be a problem.
+diff -ru relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb/requirements.txt relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb_relax_requirements/requirements.txt
+--- relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb/requirements.txt	2023-08-22 19:15:52.000000000 +0200
++++ relion-classranker-b6e751e5cb4205d8e9b36d0ae38c3687b3395acb_relax_requirements/requirements.txt	2023-11-16 18:21:03.394135835 +0100
+@@ -1,3 +1,3 @@
+-torch>=2.0.1
+-torchvision>=0.15.2
+-numpy>=1.24.4
+\ No newline at end of file
++torch>=1.12.0
++torchvision>=0.13.1
++numpy>=1.22.3

easybuild/easyconfigs/r/relion-classranker_data/relion-classranker_data-1.0.eb

@@ -0,0 +1,53 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+easyblock = 'Binary'
+# TODO: use generic data easyblock
+
+name = 'relion-classranker_data'
+version = '1.0'
+
+homepage = 'https://github.com/3dem/relion-classranker'
+description = """This file serves as the model weights for for the class ranking functionality of RELION.
+"""
+toolchain = SYSTEM
+
+_prepare = ''
+#  Uncomment and adapt to store data (10GB) elsewhere:
+# _common_data = '/easybuild/data'
+# _prepare = 'mkdir -p  %s/%%(name)s/%%(version)s/torch_home &&' % _common_data
+# _prepare += 'ln -s %s/%%(name)s/%%(version)s/torch_home %%(installdir)s/torch_home &&' % _common_data
+
+buildininstalldir = True
+
+_models = [
+    'relion_classranker_v%(version)s',
+]
+
+_torch_home = 'torch_home/'
+_checkpoints_rel = '%s/hub/checkpoints' % _torch_home
+_checkpoints = '%%(installdir)s/%s' % _checkpoints_rel
+
+
+source_urls = ['ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/']
+sources = ['classranker_v%(version)s.ckpt.gz']
+checksums = ['68a9855c16d7bab64b7e73e1e1442c7bf898f227ffd9a19c48ddfd2cf0646d73']
+
+skipsteps = ['configure', 'build', 'test']
+extract_sources = True
+
+
+preinstallopts = _prepare
+install_cmd = 'mkdir -p %s/relion_classranker/ &&' % _checkpoints
+install_cmd += 'cd %s/relion_classranker && ' % _checkpoints
+install_cmd += 'mv %(installdir)s/classranker_v%(version)s.ckpt v%(version)s.ckpt &&'
+install_cmd += 'echo Sucessfully downloaded model>v%(version)s_installed.txt'
+
+modextrapaths = {'TORCH_HOME': '%s' % _torch_home}
+
+sanity_check_paths = {
+    'files': [
+        '%s/relion_classranker/v%%(version)s.ckpt' % _checkpoints_rel,
+    ],
+    'dirs': [_checkpoints_rel]
+}
+
+moduleclass = 'data'