From b081394713de226f4928ce36be319f092dcf9496 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 22 Nov 2023 15:41:23 +0100 Subject: [PATCH 1/4] {ai}[foss/2022a] pytorch-3dunet v1.6.0 w/ CUDA 11.7.0 --- ...rch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..30a11ee9960 --- /dev/null +++ b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,56 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonBundle' + +name = 'pytorch-3dunet' +version = '1.6.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/wolny/pytorch-3dunet' +description = """ +PyTorch implementation of 3D U-Net and its variants: + - UNet3D: Standard 3D U-Net based on 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation + - ResidualUNet3D: Residual 3D U-Net based on Superhuman Accuracy on the SNEMI3D + Connectomics Challenge + - ResidualUNetSE3D: Similar to ResidualUNet3D with the addition of Squeeze and + Excitation blocks based on Deep Learning Semantic Segmentation for High- + Resolution Medical Volumes. Original squeeze and excite paper: Squeeze-and- + Excitation Networks +The code allows for training the U-Net for both: semantic segmentation (binary +and multi-class) and regression problems (e.g. de-noising, learning +deconvolutions). +""" +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('cppy', '1.2.1') +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('CUDA', '11.7.0', '', SYSTEM), + ('h5py', '3.7.0'), + ('tensorboard', '2.10.0'), + ('scikit-image', '0.19.3') +] + +use_pip = True +sanity_pip_check = True + +github_account = 'wolny' +exts_list = [ + (name, version, { + 'modulename': 'pytorch3dunet', + 'source_urls': [GITHUB_SOURCE], + 'sources': '%(version)s.tar.gz', + 'checksums': ['5323eb8a31ad95c17a3e3d83e3de08b0d3cdd0841b28687aa41039355706b659'], + }), +] + +sanity_check_commands = [ + "train3dunet --help", + "predict3dunet --help" +] + +moduleclass = 'ai' From e24a81ac8a37aa5e64e4680b430bfc452c2af393 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 22 Nov 2023 16:01:05 +0100 Subject: [PATCH 2/4] fix src --- .../pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb index 30a11ee9960..e0ca7a4f166 100644 --- a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb @@ -43,7 +43,7 @@ exts_list = [ (name, version, { 'modulename': 'pytorch3dunet', 'source_urls': [GITHUB_SOURCE], - 'sources': '%(version)s.tar.gz', + 'sources': ['%(version)s.tar.gz'], 'checksums': ['5323eb8a31ad95c17a3e3d83e3de08b0d3cdd0841b28687aa41039355706b659'], }), ] From 18aa7ea9b5dc939dc465e59fadf226688ff1d128 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 8 Jan 2024 10:50:45 +0100 Subject: [PATCH 3/4] Update pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb add SciPy-bundle dependency --- .../pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb index e0ca7a4f166..4b306a76b67 100644 --- a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb @@ -32,7 +32,8 @@ dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), ('h5py', '3.7.0'), ('tensorboard', '2.10.0'), - ('scikit-image', '0.19.3') + ('scikit-image', '0.19.3'), + ('SciPy-bundle', '2022.05'), ] use_pip = True From 5bbd7a398b104aebd802905acd31f555c94431a0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 8 Jan 2024 12:45:12 +0100 Subject: [PATCH 4/4] Update pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb reorder dependencies --- .../pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb index 4b306a76b67..7e56318d66d 100644 --- a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb @@ -28,12 +28,12 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), - ('PyTorch', '1.12.0', versionsuffix), + ('SciPy-bundle', '2022.05'), ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), ('h5py', '3.7.0'), ('tensorboard', '2.10.0'), ('scikit-image', '0.19.3'), - ('SciPy-bundle', '2022.05'), ] use_pip = True