{bio}[foss/2024a] dorado v1.0.2 w/ CUDA 12.6.0 by jpecar · Pull Request #23436 · easybuilders/easybuild-easyconfigs

jpecar · 2025-07-17T09:15:19Z

(created using eb --new-pr)

github-actions · 2025-07-17T09:15:45Z

Updated software `dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb`

Diff against dorado-0.9.1-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/d/dorado/dorado-0.9.1-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.9.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb
index f1006a7765..be306183ce 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.9.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb
@@ -1,13 +1,13 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.9.1'
+version = '1.0.2'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/dorado'
 description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://github.com/nanoporetech/dorado/archive/']
@@ -21,30 +21,30 @@ sources = [{
     'filename': SOURCE_TAR_XZ,
 }]
 patches = [
-    '%(name)s-0.8.0_dont_install_external_libraries.patch',
+    '%(name)s-1.0.0_dont_install_external_libraries.patch',
 ]
 checksums = [
-    {'dorado-0.9.1.tar.xz':
-     '95fcbc822b0f31e0f670cafbd234ea639233e978d2fad745b0546b344974dff0'},
-    {'dorado-0.8.0_dont_install_external_libraries.patch':
-     '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1'},
+    {'dorado-1.0.2.tar.xz':
+     '6c07feb001de20f4d6bfc5b6199ecde159c836f67ac9e11002c89833a9d10bd6'},
+    {'dorado-1.0.0_dont_install_external_libraries.patch':
+     'feaaf0144e4e1c4fc2b6eff55254491b0d0da83833a8e72451b91a7df142f2dd'},
 ]
 
 builddependencies = [
-    ('binutils', '2.40'),
-    ('CMake', '3.26.3'),
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
     ('patchelf', '0.18.0'),
+    ('git', '2.45.1'),
 ]
 
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
-    ('OpenSSL', '1.1', '', SYSTEM),
-    ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'),
-    ('HDF5', '1.14.0'),
-    ('zstd', '1.5.5'),
-    ('HTSlib', '1.18'),
-    ('kineto', '0.4.0'),
-    ('libaec', '1.0.6'),
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('PyTorch', '2.6.0', '-CUDA-%(cudaver)s'),
+    ('HDF5', '1.14.5'),
+    ('zstd', '1.5.6'),
+    ('HTSlib', '1.21'),
+    ('kineto', '20250715'),
+    ('libaec', '1.1.3'),
 ]
 
 # don't link to OpenSSL static libraries
@@ -61,12 +61,22 @@ preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/
 preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
 # link with -lhts, not -lhtslib
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/secondary/CMakeLists.txt && "
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
 
 # disable treating warnings like errors by stripping out -Werror
 # cfr. https://github.com/nanoporetech/dorado/issues/779
 preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/modbase/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/torch_utils/CMakeLists.txt && "
+
+# skip including a nonexistant file
+preconfigopts += "head -442 ../dorado/cmake/Torch.cmake > /tmp/a && "
+preconfigopts += "tail -31 ../dorado/cmake/Torch.cmake >> /tmp/a && "
+preconfigopts += "mv /tmp/a ../dorado/cmake/Torch.cmake && "
 
 _copts = [
     "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
@@ -75,7 +85,7 @@ _copts = [
     "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib",
     # add -pthread flag (in addition to -lpthread) to avoid linking error:
     # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
-    '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+    '-DCMAKE_C_FLAGS="$CFLAGS -pthread -lcublas"',
 ]
 
 configopts = ' '.join(_copts) + ' '

Diff against dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/d/dorado/dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb
index 38a2abfe08..be306183ce 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb
@@ -1,13 +1,13 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.9.0'
+version = '1.0.2'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/dorado'
 description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://github.com/nanoporetech/dorado/archive/']
@@ -21,30 +21,30 @@ sources = [{
     'filename': SOURCE_TAR_XZ,
 }]
 patches = [
-    '%(name)s-0.8.0_dont_install_external_libraries.patch',
+    '%(name)s-1.0.0_dont_install_external_libraries.patch',
 ]
 checksums = [
-    {'dorado-0.9.0.tar.xz':
-     'f08ccbd047d16e20e1fbd71f3449c9b82cbe264aa07a0d0f9a637f957587d99a'},
-    {'dorado-0.8.0_dont_install_external_libraries.patch':
-     '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1'},
+    {'dorado-1.0.2.tar.xz':
+     '6c07feb001de20f4d6bfc5b6199ecde159c836f67ac9e11002c89833a9d10bd6'},
+    {'dorado-1.0.0_dont_install_external_libraries.patch':
+     'feaaf0144e4e1c4fc2b6eff55254491b0d0da83833a8e72451b91a7df142f2dd'},
 ]
 
 builddependencies = [
-    ('binutils', '2.40'),
-    ('CMake', '3.26.3'),
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
     ('patchelf', '0.18.0'),
+    ('git', '2.45.1'),
 ]
 
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
-    ('OpenSSL', '1.1', '', SYSTEM),
-    ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'),
-    ('HDF5', '1.14.0'),
-    ('zstd', '1.5.5'),
-    ('HTSlib', '1.18'),
-    ('kineto', '0.4.0'),
-    ('libaec', '1.0.6'),
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('PyTorch', '2.6.0', '-CUDA-%(cudaver)s'),
+    ('HDF5', '1.14.5'),
+    ('zstd', '1.5.6'),
+    ('HTSlib', '1.21'),
+    ('kineto', '20250715'),
+    ('libaec', '1.1.3'),
 ]
 
 # don't link to OpenSSL static libraries
@@ -61,12 +61,22 @@ preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/
 preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
 # link with -lhts, not -lhtslib
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/secondary/CMakeLists.txt && "
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
 
 # disable treating warnings like errors by stripping out -Werror
 # cfr. https://github.com/nanoporetech/dorado/issues/779
 preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/modbase/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/torch_utils/CMakeLists.txt && "
+
+# skip including a nonexistant file
+preconfigopts += "head -442 ../dorado/cmake/Torch.cmake > /tmp/a && "
+preconfigopts += "tail -31 ../dorado/cmake/Torch.cmake >> /tmp/a && "
+preconfigopts += "mv /tmp/a ../dorado/cmake/Torch.cmake && "
 
 _copts = [
     "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
@@ -75,7 +85,7 @@ _copts = [
     "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib",
     # add -pthread flag (in addition to -lpthread) to avoid linking error:
     # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
-    '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+    '-DCMAKE_C_FLAGS="$CFLAGS -pthread -lcublas"',
 ]
 
 configopts = ' '.join(_copts) + ' '

Diff against dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb
index 263368b11c..be306183ce 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb
@@ -1,13 +1,13 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.8.3'
+version = '1.0.2'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/dorado'
 description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://github.com/nanoporetech/dorado/archive/']
@@ -21,30 +21,30 @@ sources = [{
     'filename': SOURCE_TAR_XZ,
 }]
 patches = [
-    '%(name)s-0.8.0_dont_install_external_libraries.patch',
+    '%(name)s-1.0.0_dont_install_external_libraries.patch',
 ]
 checksums = [
-    {'dorado-0.8.3.tar.xz':
-     'b33b259bf7cb6c7df8012b79c5373c588477d116bb59f563003e9453832c9532'},
-    {'dorado-0.8.0_dont_install_external_libraries.patch':
-     '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1'},
+    {'dorado-1.0.2.tar.xz':
+     '6c07feb001de20f4d6bfc5b6199ecde159c836f67ac9e11002c89833a9d10bd6'},
+    {'dorado-1.0.0_dont_install_external_libraries.patch':
+     'feaaf0144e4e1c4fc2b6eff55254491b0d0da83833a8e72451b91a7df142f2dd'},
 ]
 
 builddependencies = [
-    ('binutils', '2.40'),
-    ('CMake', '3.26.3'),
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
     ('patchelf', '0.18.0'),
+    ('git', '2.45.1'),
 ]
 
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
-    ('OpenSSL', '1.1', '', SYSTEM),
-    ('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'),
-    ('HDF5', '1.14.0'),
-    ('zstd', '1.5.5'),
-    ('HTSlib', '1.18'),
-    ('kineto', '0.4.0'),
-    ('libaec', '1.0.6'),
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('PyTorch', '2.6.0', '-CUDA-%(cudaver)s'),
+    ('HDF5', '1.14.5'),
+    ('zstd', '1.5.6'),
+    ('HTSlib', '1.21'),
+    ('kineto', '20250715'),
+    ('libaec', '1.1.3'),
 ]
 
 # don't link to OpenSSL static libraries
@@ -61,12 +61,22 @@ preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/
 preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
 # link with -lhts, not -lhtslib
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/secondary/CMakeLists.txt && "
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
 
 # disable treating warnings like errors by stripping out -Werror
 # cfr. https://github.com/nanoporetech/dorado/issues/779
 preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/modbase/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/torch_utils/CMakeLists.txt && "
+
+# skip including a nonexistant file
+preconfigopts += "head -442 ../dorado/cmake/Torch.cmake > /tmp/a && "
+preconfigopts += "tail -31 ../dorado/cmake/Torch.cmake >> /tmp/a && "
+preconfigopts += "mv /tmp/a ../dorado/cmake/Torch.cmake && "
 
 _copts = [
     "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
@@ -75,7 +85,7 @@ _copts = [
     "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib",
     # add -pthread flag (in addition to -lpthread) to avoid linking error:
     # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
-    '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+    '-DCMAKE_C_FLAGS="$CFLAGS -pthread -lcublas"',
 ]
 
 configopts = ' '.join(_copts) + ' '

Updated software `kineto-20250715-GCC-13.3.0.eb`

Diff against kineto-0.4.0-GCC-12.3.0.eb

easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-20250715-GCC-13.3.0.eb
index 8bbd957c43..ff3bbac347 100644
--- a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/k/kineto/kineto-20250715-GCC-13.3.0.eb
@@ -1,28 +1,30 @@
 easyblock = 'CMakeMake'
 
 name = 'kineto'
-version = '0.4.0'
+version = '20250715'
+local_commit = '16e2a56'
 
 homepage = 'https://github.com/pytorch/kineto'
 description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters"
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
 source_urls = ['https://github.com/pytorch/kineto/archive/']
 sources = [{
     'git_config': {
         'url': 'https://github.com/pytorch',
         'repo_name': name,
-        'tag': 'v%(version)s',
+        'commit': local_commit,
         'recursive': True,
     },
     'filename': SOURCE_TAR_XZ,
 }]
-checksums = ['5f1c744d57fdc40878b0ff87400097b04ed3027757bcccf6d4f8ceecc8e29855']
+checksums = ['65e986bfc7664257b09563dceddb1dd0f4c0857af4696597d73b3bf970728db4']
 
 builddependencies = [
-    ('CMake', '3.26.3'),
-    ('Python', '3.11.3'),
+    ('CMake', '3.29.3'),
+    ('Python', '3.12.3'),
+    ('CUDA', '12.6.0', '', SYSTEM),
 ]
 
 start_dir = 'libkineto'

Diff against kineto-0.4.0-GCC-11.3.0.eb

easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-20250715-GCC-13.3.0.eb
index 37a633e728..ff3bbac347 100644
--- a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/k/kineto/kineto-20250715-GCC-13.3.0.eb
@@ -1,28 +1,30 @@
 easyblock = 'CMakeMake'
 
 name = 'kineto'
-version = '0.4.0'
+version = '20250715'
+local_commit = '16e2a56'
 
 homepage = 'https://github.com/pytorch/kineto'
 description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters"
 
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
 source_urls = ['https://github.com/pytorch/kineto/archive/']
 sources = [{
     'git_config': {
         'url': 'https://github.com/pytorch',
         'repo_name': name,
-        'tag': 'v%(version)s',
+        'commit': local_commit,
         'recursive': True,
     },
     'filename': SOURCE_TAR_XZ,
 }]
-checksums = ['5f1c744d57fdc40878b0ff87400097b04ed3027757bcccf6d4f8ceecc8e29855']
+checksums = ['65e986bfc7664257b09563dceddb1dd0f4c0857af4696597d73b3bf970728db4']
 
 builddependencies = [
-    ('CMake', '3.24.3'),
-    ('Python', '3.10.4', '-bare'),
+    ('CMake', '3.29.3'),
+    ('Python', '3.12.3'),
+    ('CUDA', '12.6.0', '', SYSTEM),
 ]
 
 start_dir = 'libkineto'

jpecar · 2025-07-17T09:16:27Z

Needs PyTorch from #23433 (which needs magma from #23432), untested, but builds. Waiting for feedback from our users.

fizwit · 2025-07-23T20:04:39Z

Can you please upload dorado-1.0.0_dont_install_external_libraries.patch, I created my own but....

I had to add this one line to builddependencies

    ('pkgconf', '2.2.0'),

and had to remove this one line: # preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "
NONE of the checksums matched, including the checksum for kineto-20250715-GCC-13.3.0.eb

thanks for the PR, with these few changed it built with EB 5.1.1 on Ubuntu 24.04

fizwit · 2025-07-28T17:07:12Z

The maintaners will ask you to add a comment to your patch file. Then don't forget to update the checksums.

Don't install external libraries in Dorado's lib directory.
Simon Branford (University of Birmingham)
updated Jure Pečar (EMBL)

pavelToman · 2025-10-20T12:13:31Z

easybuild/easyconfigs/k/kineto/kineto-20250715-GCC-13.3.0.eb

+    },
+    'filename': SOURCE_TAR_XZ,
+}]
+checksums = ['65e986bfc7664257b09563dceddb1dd0f4c0857af4696597d73b3bf970728db4']


For me it is failing on checksums check and --inject-checksums gives me other checksum: bc44d710104b879f6982ffd4d79a8ba6c97c8aa5fefbcfd85c317d541ed1094d

pavelToman · 2025-10-22T14:50:57Z

I create a newer version of dorado based on your PR: #24328
There are few things to fix:

use mktemp -d not /tmp: {bio}[foss/2024a] dorado v1.1.1 w/ CUDA 12.6.0 #24328 (comment)
add OpenSSL as a dependency: {bio}[foss/2024a] dorado v1.1.1 w/ CUDA 12.6.0 #24328 (comment)
maybe update the sed command: {bio}[foss/2024a] dorado v1.1.1 w/ CUDA 12.6.0 #24328 (comment)

pavelToman · 2025-10-22T14:53:25Z

easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb

+preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && "
+# link in the ssl and crypto libs, to fix:
+# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
+preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "


Suggested change

preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "

preconfigopts += r"sed -i 's/OpenSSL::SSL/ssl\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "

pavelToman · 2025-10-22T15:04:09Z

easybuild/easyconfigs/d/dorado/dorado-1.0.0_dont_install_external_libraries.patch

@@ -0,0 +1,11 @@
+--- cmake/InstallRedistLibs.cmake.orig	2025-06-03 10:40:42.830160000 +0200


a patch should have a description

Suggested change

--- cmake/InstallRedistLibs.cmake.orig 2025-06-03 10:40:42.830160000 +0200

Use installed modules instead of external libraries

Author: Jure Pečar (EMBL)

--- cmake/InstallRedistLibs.cmake.orig 2025-06-03 10:40:42.830160000 +0200

pavelToman · 2026-01-26T09:57:41Z

I extracted kineto easyconfig from this PR:

{perf}[GCC/13.3.0] kineto v20250715 w/ CUDA 12.6.0 #25146

boegel · 2026-01-27T12:33:12Z

easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb

+
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('PyTorch', '2.6.0', '-CUDA-%(cudaver)s'),


Can we bump this to 2.7.1?
See:

{ai}[foss/2024a] PyTorch v2.7.1 w/ CUDA 12.6.0 #23923

If memory serves, yes. But needs to be tested.

pavelToman · 2026-02-04T12:39:05Z

Is the CUDA in builddependencies really necessary for kineto?
In other kineto easyconfigs there is no CUDA.
If it is needed it should be renamed with versionsuffix = '-CUDA-%(cudaver)s'

EDIT: Yes the CUDA should be in dependencies now (not builddeps): #25146

laraPPr · 2026-02-04T12:39:15Z

easybuild/easyconfigs/k/kineto/kineto-20250715-GCC-13.3.0.eb

+
+name = 'kineto'
+version = '20250715'
+local_commit = '16e2a56'


Suggested change

local_commit = '16e2a56'

local_commit = '16e2a56'

versionsuffix = '-CUDA-%(cudaver)s'

Should we add the version suffix because CUDA is a build dependency? For easybuild-easyconfigs/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.4.0-GCC-13.3.0-CUDA-12.6.0.eb we did.

That's being dealt with in:

{perf}[GCC/13.3.0] kineto v20250715 w/ CUDA 12.6.0 #25146

boegel · 2026-02-12T16:38:21Z

@jpecar I think we should just go ahead with:

{bio}[foss/2024a] dorado v1.1.1 w/ CUDA 12.6.0 #24328
And close this one, what do you think?

jpecar · 2026-02-13T10:10:58Z

Fine with me.

adding easyconfigs: dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb

84b0f06

github-actions bot added the update label Jul 17, 2025

jpecar added 2 commits July 17, 2025 14:53

forgot to add kineto dependency

6b83295

fix kineto sha256

915eb62

add missing patch

c23941f

pavelToman mentioned this pull request Jul 30, 2025

Dorado 1.0.2 or newer vscentrum/vsc-software-stack#584

Closed

2 tasks

boegel added this to the 5.x milestone Jul 31, 2025

Thyre added the 2024a issues & PRs related to 2024a common toolchains label Aug 18, 2025

pavelToman reviewed Oct 20, 2025

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pavelToman mentioned this pull request Oct 21, 2025

{bio}[foss/2024a] dorado v1.1.1 w/ CUDA 12.6.0 #24328

Merged

pavelToman reviewed Oct 22, 2025

View reviewed changes

pavelToman mentioned this pull request Jan 26, 2026

{perf}[GCC/13.3.0] kineto v20250715 w/ CUDA 12.6.0 #25146

Merged

boegel reviewed Jan 27, 2026

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laraPPr reviewed Feb 4, 2026

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jpecar closed this Feb 13, 2026

	preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
	preconfigopts += r"sed -i 's/OpenSSL::SSL/ssl\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "

		@@ -0,0 +1,11 @@
		--- cmake/InstallRedistLibs.cmake.orig 2025-06-03 10:40:42.830160000 +0200

	local_commit = '16e2a56'
	local_commit = '16e2a56'
	versionsuffix = '-CUDA-%(cudaver)s'

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Updated software `dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb`

Updated software `kineto-20250715-GCC-13.3.0.eb`

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