{bio}[foss/2023a] RELION v5.0.0 w/ CUDA 12.1.1

easybuild/easyconfigs/r/RELION/RELION-5.0.0-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,218 @@
+# Author: Jasper Grimm (UoY)
+easyblock = 'CMakeMake'
+
+name = 'RELION'
+version = '5.0.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page'
+description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer
+ program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class
+ averages in electron cryo-microscopy (cryo-EM).
+ """
+
+build_info_msg = """To install RELION, it's recommended to change the defaults in this easyconfig,
+ to something suitable for your site. Recommended changes:
+   * Set '_torch_home' to the location where the model weights are downloaded (~12GB). The weights
+     can be downloaded manually by setting 'TORCH_HOME' and running 'relion_python_fetch_weights'.
+
+   * RELION has various optional dependencies. The following have been enaled by default, since they
+     only add extra functionality, but can be commented out to build without:
+       - X11 and FLTK (GUI)
+       - Ghostscript (PDF)
+       - xpdf (PDF viewer)
+       - XZ, zstd, PBZIP2 (compression libraries)
+       - tcsh
+       - gnuplot
+     Other dependencies that are not enabled by default:
+       - evince (alternate PDF viewer)
+       - ctffind or GCTF
+       - MotionCor2/MotionCor3
+       - AreTomo2
+       - ResMap
+     these can be enabled by uncommenting the corresponding entry in the dependencies list.
+
+   * Set additional 'RELION_*' variables, such as 'RELION_SCRATCH_DIR'. See:
+     https://relion.readthedocs.io/en/release-5.0/Installation.html#edit-the-environment-set-up
+     These variables should be added to 'modextrapaths' or 'modextravars' as appropriate.
+
+   * Add a job submission template for queue submission. See:
+     https://relion.readthedocs.io/en/release-5.0/Installation.html#set-up-queue-job-submission
+"""
+
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'opt': True}
+
+source_urls = ['https://github.com/3dem/relion/archive']
+sources = ['%(version)s.tar.gz']
+patches = ['%(name)s-5.0.0_target-all-cuda-compute-capabilities.patch']
+checksums = [
+    {'5.0.0.tar.gz': '5d02d529bfdb396204310b35963f35e5ec40ed9fd10bc88c901119ae7d7739fc'},
+    {'RELION-5.0.0_target-all-cuda-compute-capabilities.patch':
+     'd53ca4873278ebf8d297f062218c7096679531b1289b76d8bd4b35152a6c1543'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('poetry', '1.7.1'),  # use poetry compatible with build 1.x
+    ('meson-python', '0.15.0'),  # pandas 2.1.4 needs meson >= 1.2.1
+]
+
+dependencies = [
+    # required dependencies #
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('LibTIFF', '4.5.0'),
+    ('tbb', '2021.11.0'),
+    ('libpng', '1.6.39'),
+    ('morphosamplers', '0.0.10'),   # required for: src/tomography_python_programs/get_particle_poses/filaments.py
+
+    # optional dependencies #
+    ('tcsh', '6.24.10'),
+    ('gnuplot', '5.4.8'),
+    ('FLTK', '1.3.8'),            # for GUI
+    ('X11', '20230603'),          # for GUI
+    ('PBZIP2', '1.1.13'),         # for compression
+    ('zstd', '1.5.5'),            # for compression
+    ('XZ', '5.4.2'),              # for compression
+    ('Ghostscript', '10.01.2'),   # for PDF files
+    ('xpdf', '4.04'),             # pdf viewer
+    # ('evince', '45.0'),         # pdf viewer
+    # ('ctffind', '4.1.14'),      # lens defocus estimation
+    # ('AreTomo2', '1.0.0', versionsuffix),     # alternative movie alignment
+    # ('MotionCor2', '1.5.0'),                  # alternative movie alignment
+    # ('MotionCor3', '1.0.1', versionsuffix),   # alternative movie alignment
+    # ('ResMap', '1.1.4'),        # alternative local resolution estimation
+
+    # dependencies from conda environment.yaml file #
+    ('Python', '3.11.3'),
+    ('PyTorch-bundle', '2.1.2', versionsuffix),
+    ('SciPy-bundle', '2023.07'),
+    ('tqdm', '4.66.1'),
+    ('scikit-learn', '1.3.1'),
+    ('matplotlib', '3.7.2'),
+    ('PyQt5', '5.15.10'),
+    ('Biopython', '1.83'),
+    ('Seaborn', '0.13.2'),
+    ('dill', '0.3.7'),
+    ('umap-learn', '0.5.5'),
+    ('einops', '0.7.0'),
+    ('mrcfile', '1.5.0'),
+    ('t-SNE-CUDA', '3.0.1', versionsuffix),
+    ('ESM-2', '2.0.0', versionsuffix),
+    ('topaz', '0.2.5.20231120', versionsuffix),
+    ('dask', '2023.9.2'),
+    ('imageio', '2.33.1'),
+    ('napari', '0.4.19.post1'),
+    ('tensorboard', '2.15.1'),
+    ('PyHMMER', '0.10.6'),
+]
+
+# set this to the path to the Blush model weight database
+# workaround until we merged the "Dataset" easyblock:
+#   https://github.com/easybuilders/easybuild-easyblocks/pull/3246
+#   https://github.com/easybuilders/easybuild-framework/pull/4474
+_torch_home = ''
+
+_copts = [
+    '-DCMAKE_SHARED_LINKER="$LIBS"',
+    '-DMPI_INCLUDE_PATH="$MPI_INC_DIR"',
+    '-DCUDA_NVCC_FLAGS="--std=c++14"',
+    '-DCUDA_ARCH="%(cuda_cc_semicolon_sep)s"',
+    '-DCUDA_TEXTURE=ON',
+    '-DDoublePrec_CPU=OFF',
+    '-DFETCH_WEIGHTS=OFF',
+    '-DTORCH_HOME="%s"' % _torch_home,
+]
+
+configopts = ' '.join(_copts)
+
+install_cmd = 'make -j %(parallel)s install'
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+}
+
+exts_list = [
+    # starfile 0.5.4 needs pandas>=2.1.1
+    ('pandas', '2.1.4', {
+        'checksums': ['fcb68203c833cc735321512e13861358079a96c174a61f5116a1de89c58c0ef7'],
+    }),
+    ('starfile', '0.5.4', {
+        'checksums': ['4e7cea4f871f5aeeff6829b2cd95efc0c2212ca7a3a583f5fc8ff53329bc4417'],
+    }),
+    ('loguru', '0.7.2', {
+        'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'],
+    }),
+    ('typer', '0.9.0', {
+        'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'],
+    }),
+    ('fastcluster', '1.2.6', {
+        'checksums': ['aab886efa7b6bba7ac124f4498153d053e5a08b822d2254926b7206cdf5a8aa6'],
+    }),
+    ('relion-classranker', '0.0.1_20230822', {
+        'sources': [{
+            'filename': '%(name)s-%(version)s.tar.gz',
+            'git_config': {
+                'url': 'https://github.com/3dem',
+                'repo_name': '%(name)s',
+                'commit': 'b6e751e5cb4205d8e9b36d0ae38c3687b3395acb',
+                'keep_git_dir': True,
+            },
+        }],
+        'checksums': [None],
+    }),
+    ('relion-blush', '0.0.1_20231105', {
+        'sources': [{
+            'filename': '%(name)s-%(version)s.tar.gz',
+            'git_config': {
+                'url': 'https://github.com/3dem',
+                'repo_name': '%(name)s',
+                'commit': '3148869de884fc01cff6c51a047b1413fc0b62cb',
+                'keep_git_dir': True,
+            },
+        }],
+        'checksums': [None],
+    }),
+    ('DynaMight', '0.0.1_20240319', {
+        'sources': [{
+            'filename': '%(name)s-%(version)s.tar.gz',
+            'git_config': {
+                'url': 'https://github.com/3dem',
+                'repo_name': '%(name)s',
+                'commit': 'eef4aa673af6cc908042b38646ae489ee8f2fde9',
+                'keep_git_dir': True,
+            },
+        }],
+        'checksums': [None],
+    }),
+    ('model-angelo', '1.0.12_20240226', {
+        'sources': [{
+            'filename': '%(name)s-%(version)s.tar.gz',
+            'git_config': {
+                'url': 'https://github.com/3dem',
+                'repo_name': '%(name)s',
+                'commit': '6fdad9b47a0a2abb86990803f243ef028197a04d',
+                'keep_git_dir': True,
+            },
+        }],
+        'checksums': [None],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/relion%s' % x for x in ['', '_autopick', '_batchrun', '_batchrun_mpi']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['relion --help', 'relion --version']
+
+modextravars = {
+    'TORCH_HOME': _torch_home,
+    'RELION_PDFVIEWER_EXECUTABLE': '$EBROOTXPDF/bin/xpdf',
+    # 'RELION_SHELL': '$EBROOTTCSH/bin/tcsh',
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/r/RELION/RELION-5.0.0_target-all-cuda-compute-capabilities.patch

@@ -0,0 +1,60 @@
+Description: enhance the cmake build scripts to:
+ - allow targetting of multiple CUDA architectures (with -gencode=)
+ - introduce DEFAULT_CUDA_ARCH to set the default CUDA arch target (-arch=)
+Original Author: Jasper Grimm <jasper.grimm@york.ac.uk>
+Updated by:
+ - Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+     Modified to correctly set NVCC build flags and allow externally setting --std=xxx flag.
+ - Jasper Grimm <jasper.grimm@york.ac.uk>
+    Update for relion 5.0.0 beta
+
+diff -Nru relion.orig/cmake/BuildTypes.cmake relion/cmake/BuildTypes.cmake
+--- relion.orig/cmake/BuildTypes.cmake	2024-01-12 16:34:35.601247994 +0000
++++ relion/cmake/BuildTypes.cmake	2024-01-12 16:36:40.744752894 +0000
+@@ -4,8 +4,8 @@
+ # So -D__INTEL_COMPILER just manages to avoid compiling float128-targets (see fftw3.h, for instance).
+ # Add -G to allow cuda-gdb to break inside kernels.
+ if(CUDA)
+-    set(EXTRA_NVCC_FLAGS "-D__INTEL_COMPILER --default-stream per-thread --std=c++14")
+-    set(RELION_NVCC_FLAGS "${CUDARCH} ${WARN_DBL} ${EXTRA_NVCC_FLAGS}" CACHE STRING "" FORCE)
++    set(EXTRA_NVCC_FLAGS "-D__INTEL_COMPILER --default-stream per-thread")
++    set(RELION_NVCC_FLAGS "${WARN_DBL} ${EXTRA_NVCC_FLAGS}" CACHE STRING "" FORCE)
+ elseif (HIP)
+     if (${HIP_VERSION} VERSION_LESS "5.3" )
+         set(EXTRA_HIPCC_FLAGS "-fgpu-default-stream=legacy -fno-gpu-rdc -munsafe-fp-atomics")
+diff -Nru relion.orig/CMakeLists.txt relion/CMakeLists.txt
+--- relion.orig/CMakeLists.txt	2024-01-12 16:34:35.601247994 +0000
++++ relion/CMakeLists.txt	2024-01-12 16:41:34.615595884 +0000
+@@ -84,13 +84,20 @@
+
+ set(CUDA_ARCH "" CACHE STRING "CUDA architecture to use")
+ if (CUDA_ARCH STREQUAL "")
+-	message(STATUS "Setting fallback CUDA_ARCH=50")
+-	set(CUDARCH "-arch=sm_50")
++	message(STATUS "Setting fallback CUDA_ARCH=5.0")
++	set(CUDA_ARCH "5.0")
+ else ()
+ 	message(STATUS "Using provided CUDA_ARCH=${CUDA_ARCH}")
+-	set(CUDARCH "-arch=sm_${CUDA_ARCH}")
+ endif ()
+
++if(NOT DEFINED DEFAULT_CUDA_ARCH)
++    string(REGEX MATCH "[0-9]+\\.[0-9]+" DEFAULT_CUDA_ARCH "${CUDA_ARCH}")
++    message(STATUS "Setting fallback DEFAULT_CUDA_ARCH=${DEFAULT_CUDA_ARCH}")
++endif()
++
++string(REPLACE "." "" DEFAULT_CUDA_SM ${DEFAULT_CUDA_ARCH})
++set(CUDA_SM "-arch=sm_${DEFAULT_CUDA_SM}")
++
+ # -------------------------------------------------------------------FURTHER OPTIONS--
+
+ # CUDA on by default, so check for other GPU/CPU-accelration request and possible conflicting dual-requests
+@@ -204,6 +211,8 @@
+       if(CUDA)
+           add_definitions(-D_CUDA_ENABLED)
+       endif()
++      cuda_select_nvcc_arch_flags(CUDA_GENCODE "${CUDA_ARCH}")
++      list(APPEND CUDA_NVCC_FLAGS ${CUDA_SM} ${CUDA_GENCODE})
+     else(CUDA_FOUND)
+         message(FATAL_ERROR "CUDA enabled but unlable to locate packages...")
+     endif(CUDA_FOUND)

test/easyconfigs/easyconfigs.py

@@ -603,6 +603,8 @@ def check_dep_vars(self, gen, dep, dep_vars):
             'mpi4py': [(r'4\.0\.1', [r'OpenQP-1\.0'])],
             # FDMNES requires sequential variant of MUMPS
             'MUMPS': [(r'5\.6\.1; versionsuffix: -metis-seq', [r'FDMNES'])],
+            # RELION 5.0.0 requires fixes only in napari 0.4.19 and newer
+            'napari': [(r'0\.4\.19\.post1;', [r'RELION-5\.0\.0'])],
             # SRA-toolkit 3.0.0 requires ncbi-vdb 3.0.0, Finder requires SRA-Toolkit 3.0.0
             'ncbi-vdb': [(r'3\.0\.0', [r'SRA-Toolkit-3\.0\.0', r'finder-1\.1\.0'])],
             'OpenFOAM': [
@@ -661,7 +663,7 @@ def check_dep_vars(self, gen, dep, dep_vars):
             # (for 2021b, UCX was updated to v1.11.2)
             'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])],
             # Napari 0.4.19post1 requires VisPy >=0.14.1 <0.15
-            'VisPy': [('0.14.1;', ['napari-0.4.19.post1-'])],
+            'VisPy': [('0.14.1;', ['napari-0.4.19.post1-', r'RELION-5\.0\.0'])],
             # Visit-3.4.1 requires VTK 9.2.x
             'VTK': [('9.2.6;', ['Visit-3.4.1-'])],
             # wxPython 4.2.0 depends on wxWidgets 3.2.0