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

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boegel merged 14 commits intoeasybuilders:developfrom
pavelToman:20251021134756_new_pr_dorado111
Feb 12, 2026
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{bio}[foss/2024a] dorado v1.1.1 w/ CUDA 12.6.0#24328
boegel merged 14 commits intoeasybuilders:developfrom
pavelToman:20251021134756_new_pr_dorado111

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@pavelToman pavelToman commented Oct 21, 2025 •
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github-actions bot commented Oct 21, 2025 •
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Updated software dorado-1.1.1-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-1.1.1-foss-2024a-CUDA-12.6.0.eb
index f1006a7765..eb876a41d6 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.9.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-1.1.1-foss-2024a-CUDA-12.6.0.eb
@@ -1,13 +1,13 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.9.1'
+version = '1.1.1'
 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-1.1.1.tar.xz': 'e3aad85ab5076bae19a679332b71215c3b10faa745e3b46b7a35fc8fdb14fed6'},
+    {'dorado-1.0.0_dont_install_external_libraries.patch':
+     '2db45a8b1d5360e743b96beb9ce61264a2b3d4a815bed10ee4978caa3fba3a3b'},
 ]
 
 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),
+    ('OpenSSL', '3', '', SYSTEM),
+    ('PyTorch', '2.7.1', versionsuffix),
+    ('HDF5', '1.14.5'),
+    ('zstd', '1.5.6'),
+    ('HTSlib', '1.21'),
+    ('kineto', '20250715', versionsuffix),
+    ('libaec', '1.1.3'),
 ]
 
 # don't link to OpenSSL static libraries
@@ -52,21 +52,36 @@ dependencies = [
 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 && "
+preconfigopts += r"sed -i 's/OpenSSL::SSL/ssl\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
 
 # don't use vendored HTSlib, use provided HTSlib dependency
 preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "
 preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && "
 preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && "
 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/utils/CMakeLists.txt && "
-preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
+# rename link target 'htslib' -> 'hts' only in CMake files, excluding kadayashi's cmake dir
+preconfigopts += r"find ../dorado -type f \( -name CMakeLists.txt -o -name '*.cmake' \) "
+preconfigopts += "-not -path '../dorado/dorado/3rdparty/kadayashi/cmake/*' -print0 | "
+preconfigopts += r"xargs -0 sed -i -E 's/\<htslib\>/hts/g' && "
+# keep kadayashi's find_package on 'htslib' and make it return -lhts via its finder
+preconfigopts += r"sed -i -E 's/find_package\(\s*hts\b/find_package(htslib/' "
+preconfigopts += "../dorado/dorado/3rdparty/kadayashi/CMakeLists.txt && "
+preconfigopts += r"sed -i -E 's/\bset\(HTSLIB_LIBRARIES\s+htslib(::hts)?\)/set(HTSLIB_LIBRARIES hts)/' "
+preconfigopts += "../dorado/dorado/3rdparty/kadayashi/cmake/Findhtslib.cmake && "
 
 # 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 += "../dorado/dorado/utils/CMakeLists.txt "
+preconfigopts += "../dorado/dorado/modbase/CMakeLists.txt "
+preconfigopts += "../dorado/dorado/torch_utils/CMakeLists.txt && "
+
+# skip including a nonexistant file
+preconfigopts += "TMPDIR=$(mktemp -d) && "
+preconfigopts += "head -442 ../dorado/cmake/Torch.cmake > $TMPDIR/cmake && "
+preconfigopts += "tail -31 ../dorado/cmake/Torch.cmake >> $TMPDIR/cmake && "
+preconfigopts += "mv $TMPDIR/cmake ../dorado/cmake/Torch.cmake && "
 
 _copts = [
     "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
@@ -76,6 +91,11 @@ _copts = [
     # add -pthread flag (in addition to -lpthread) to avoid linking error:
     # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
     '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+    '-DCMAKE_CXX_FLAGS="$CXXFLAGS -pthread"',
+    # "-DHTSLIB_INCLUDE_DIR=$EBROOTHTSLIB/include",
+    # "-DHTSLIB_LIBRARIES=$EBROOTHTSLIB/lib/libhts.so",
+    '-DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -lcublas"',
+    '-DCMAKE_SHARED_LINKER_FLAGS="$LDFLAGS -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-1.1.1-foss-2024a-CUDA-12.6.0.eb
index 38a2abfe08..eb876a41d6 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.9.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-1.1.1-foss-2024a-CUDA-12.6.0.eb
@@ -1,13 +1,13 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.9.0'
+version = '1.1.1'
 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-1.1.1.tar.xz': 'e3aad85ab5076bae19a679332b71215c3b10faa745e3b46b7a35fc8fdb14fed6'},
+    {'dorado-1.0.0_dont_install_external_libraries.patch':
+     '2db45a8b1d5360e743b96beb9ce61264a2b3d4a815bed10ee4978caa3fba3a3b'},
 ]
 
 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),
+    ('OpenSSL', '3', '', SYSTEM),
+    ('PyTorch', '2.7.1', versionsuffix),
+    ('HDF5', '1.14.5'),
+    ('zstd', '1.5.6'),
+    ('HTSlib', '1.21'),
+    ('kineto', '20250715', versionsuffix),
+    ('libaec', '1.1.3'),
 ]
 
 # don't link to OpenSSL static libraries
@@ -52,21 +52,36 @@ dependencies = [
 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 && "
+preconfigopts += r"sed -i 's/OpenSSL::SSL/ssl\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
 
 # don't use vendored HTSlib, use provided HTSlib dependency
 preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "
 preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && "
 preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && "
 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/utils/CMakeLists.txt && "
-preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
+# rename link target 'htslib' -> 'hts' only in CMake files, excluding kadayashi's cmake dir
+preconfigopts += r"find ../dorado -type f \( -name CMakeLists.txt -o -name '*.cmake' \) "
+preconfigopts += "-not -path '../dorado/dorado/3rdparty/kadayashi/cmake/*' -print0 | "
+preconfigopts += r"xargs -0 sed -i -E 's/\<htslib\>/hts/g' && "
+# keep kadayashi's find_package on 'htslib' and make it return -lhts via its finder
+preconfigopts += r"sed -i -E 's/find_package\(\s*hts\b/find_package(htslib/' "
+preconfigopts += "../dorado/dorado/3rdparty/kadayashi/CMakeLists.txt && "
+preconfigopts += r"sed -i -E 's/\bset\(HTSLIB_LIBRARIES\s+htslib(::hts)?\)/set(HTSLIB_LIBRARIES hts)/' "
+preconfigopts += "../dorado/dorado/3rdparty/kadayashi/cmake/Findhtslib.cmake && "
 
 # 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 += "../dorado/dorado/utils/CMakeLists.txt "
+preconfigopts += "../dorado/dorado/modbase/CMakeLists.txt "
+preconfigopts += "../dorado/dorado/torch_utils/CMakeLists.txt && "
+
+# skip including a nonexistant file
+preconfigopts += "TMPDIR=$(mktemp -d) && "
+preconfigopts += "head -442 ../dorado/cmake/Torch.cmake > $TMPDIR/cmake && "
+preconfigopts += "tail -31 ../dorado/cmake/Torch.cmake >> $TMPDIR/cmake && "
+preconfigopts += "mv $TMPDIR/cmake ../dorado/cmake/Torch.cmake && "
 
 _copts = [
     "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
@@ -76,6 +91,11 @@ _copts = [
     # add -pthread flag (in addition to -lpthread) to avoid linking error:
     # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
     '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+    '-DCMAKE_CXX_FLAGS="$CXXFLAGS -pthread"',
+    # "-DHTSLIB_INCLUDE_DIR=$EBROOTHTSLIB/include",
+    # "-DHTSLIB_LIBRARIES=$EBROOTHTSLIB/lib/libhts.so",
+    '-DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -lcublas"',
+    '-DCMAKE_SHARED_LINKER_FLAGS="$LDFLAGS -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-1.1.1-foss-2024a-CUDA-12.6.0.eb
index 263368b11c..eb876a41d6 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-1.1.1-foss-2024a-CUDA-12.6.0.eb
@@ -1,13 +1,13 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.8.3'
+version = '1.1.1'
 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-1.1.1.tar.xz': 'e3aad85ab5076bae19a679332b71215c3b10faa745e3b46b7a35fc8fdb14fed6'},
+    {'dorado-1.0.0_dont_install_external_libraries.patch':
+     '2db45a8b1d5360e743b96beb9ce61264a2b3d4a815bed10ee4978caa3fba3a3b'},
 ]
 
 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),
+    ('OpenSSL', '3', '', SYSTEM),
+    ('PyTorch', '2.7.1', versionsuffix),
+    ('HDF5', '1.14.5'),
+    ('zstd', '1.5.6'),
+    ('HTSlib', '1.21'),
+    ('kineto', '20250715', versionsuffix),
+    ('libaec', '1.1.3'),
 ]
 
 # don't link to OpenSSL static libraries
@@ -52,21 +52,36 @@ dependencies = [
 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 && "
+preconfigopts += r"sed -i 's/OpenSSL::SSL/ssl\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
 
 # don't use vendored HTSlib, use provided HTSlib dependency
 preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "
 preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && "
 preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && "
 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/utils/CMakeLists.txt && "
-preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
+# rename link target 'htslib' -> 'hts' only in CMake files, excluding kadayashi's cmake dir
+preconfigopts += r"find ../dorado -type f \( -name CMakeLists.txt -o -name '*.cmake' \) "
+preconfigopts += "-not -path '../dorado/dorado/3rdparty/kadayashi/cmake/*' -print0 | "
+preconfigopts += r"xargs -0 sed -i -E 's/\<htslib\>/hts/g' && "
+# keep kadayashi's find_package on 'htslib' and make it return -lhts via its finder
+preconfigopts += r"sed -i -E 's/find_package\(\s*hts\b/find_package(htslib/' "
+preconfigopts += "../dorado/dorado/3rdparty/kadayashi/CMakeLists.txt && "
+preconfigopts += r"sed -i -E 's/\bset\(HTSLIB_LIBRARIES\s+htslib(::hts)?\)/set(HTSLIB_LIBRARIES hts)/' "
+preconfigopts += "../dorado/dorado/3rdparty/kadayashi/cmake/Findhtslib.cmake && "
 
 # 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 += "../dorado/dorado/utils/CMakeLists.txt "
+preconfigopts += "../dorado/dorado/modbase/CMakeLists.txt "
+preconfigopts += "../dorado/dorado/torch_utils/CMakeLists.txt && "
+
+# skip including a nonexistant file
+preconfigopts += "TMPDIR=$(mktemp -d) && "
+preconfigopts += "head -442 ../dorado/cmake/Torch.cmake > $TMPDIR/cmake && "
+preconfigopts += "tail -31 ../dorado/cmake/Torch.cmake >> $TMPDIR/cmake && "
+preconfigopts += "mv $TMPDIR/cmake ../dorado/cmake/Torch.cmake && "
 
 _copts = [
     "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
@@ -76,6 +91,11 @@ _copts = [
     # add -pthread flag (in addition to -lpthread) to avoid linking error:
     # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
     '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+    '-DCMAKE_CXX_FLAGS="$CXXFLAGS -pthread"',
+    # "-DHTSLIB_INCLUDE_DIR=$EBROOTHTSLIB/include",
+    # "-DHTSLIB_LIBRARIES=$EBROOTHTSLIB/lib/libhts.so",
+    '-DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -lcublas"',
+    '-DCMAKE_SHARED_LINKER_FLAGS="$LDFLAGS -lcublas"',
 ]
 
 configopts = ' '.join(_copts) + ' '

@pavelToman pavelToman mentioned this pull request Oct 21, 2025
Closed
2 tasks
@Thyre Thyre added the 2024a issues & PRs related to 2024a common toolchains label Oct 21, 2025
jfgrimm
jfgrimm previously requested changes Oct 22, 2025
View reviewed changes
pavelToman and others added 5 commits October 22, 2025 16:36
@pavelToman
Update dorado-1.1.1-foss-2024a-CUDA-12.6.0.eb - fix TMP dir
de23381
@pavelToman @jfgrimm
Update dorado-1.1.1-foss-2024a-CUDA-12.6.0.eb - raw strings
a0be393 
Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com>
@pavelToman
Update dorado-1.1.1-foss-2024a-CUDA-12.6.0.eb - add SSL
14df9ae
@pavelToman @jfgrimm
Update dorado-1.1.1-foss-2024a-CUDA-12.6.0.eb - update sed cmd
94b2630 
Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com>
@pavelToman @jfgrimm
Update dorado-1.1.1-foss-2024a-CUDA-12.6.0.eb - another raw string fix
1594ac5 
Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com>
@pavelToman pavelToman mentioned this pull request Oct 22, 2025
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pavelToman commented Oct 22, 2025 •
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@jfgrimm thanks for review, should be fixed

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pavelToman commented Oct 22, 2025

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4011.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/a2f850db7e874dda27d9325b4936de5e for a full test report.

@boegel boegel added this to the 5.x milestone Jan 24, 2026
@pavelToman pavelToman mentioned this pull request Jan 26, 2026
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pavelToman commented Feb 10, 2026

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (total: 9 mins 36 secs) (1 easyconfigs in total)
node4016.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/ea8169c621b7b909c2b23c270c51ccaa for a full test report.

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pavelToman commented Feb 10, 2026

Test report by @pavelToman
SUCCESS
Build succeeded for 2 out of 2 (total: 9 mins 35 secs) (1 easyconfigs in total)
node3309.joltik.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz, 1 x NVIDIA Tesla V100-SXM2-32GB, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/eb86d1535547713f1c912804fd40ab7c for a full test report.

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pavelToman commented Feb 10, 2026

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (total: 9 mins 38 secs) (1 easyconfigs in total)
node4016.donphan.os - Linux RHEL 9.6, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 580.95.05, Python 3.9.21
See https://gist.github.com/pavelToman/54de07732b20c6c16b837ddddefb633f for a full test report.

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pavelToman commented Feb 10, 2026

@boegelbot please test @ jsc-zen3-a100

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boegelbot commented Feb 10, 2026

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=24328 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_24328 --ntasks=8 --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9621

Test results coming soon (I hope)...

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- notification for comment with ID 3879479552 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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boegelbot commented Feb 12, 2026

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 2 (total: 33 hours 49 mins 24 secs) (1 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 590.44.01, Python 3.9.23
See https://gist.github.com/boegelbot/4361d9288ba15a3cec0203abf6b8f5af for a full test report.

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pavelToman commented Feb 12, 2026

Test report by @boegelbot FAILED Build succeeded for 0 out of 2 (total: 33 hours 49 mins 24 secs) (1 easyconfigs in total) jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 590.44.01, Python 3.9.23 See https://gist.github.com/boegelbot/4361d9288ba15a3cec0203abf6b8f5af for a full test report.

Failed on PyTorch-2.7.1-foss-2024a-CUDA-12.6.0.eb (not in this PR)

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boegel commented Feb 12, 2026

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (total: 18 mins 13 secs) (1 easyconfigs in total)
node3902.accelgor.os - Linux RHEL 9.6, x86_64, AMD EPYC 7413 24-Core Processor (zen3), 1 x NVIDIA NVIDIA A100-SXM4-80GB, 590.48.01, Python 3.9.21
See https://gist.github.com/boegel/6e152f0f406798bae1a89250f2e22441 for a full test report.

@boegel boegel dismissed jfgrimm’s stale review February 12, 2026 17:40

requested changes made

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lgtm

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boegel commented Feb 12, 2026

Going in, thanks @pavelToman!

@boegel boegel merged commit f98ee21 into easybuilders:develop Feb 12, 2026
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@boegel boegel modified the milestones: 5.x, next release (5.2.1) Feb 12, 2026
@pavelToman pavelToman deleted the 20251021134756_new_pr_dorado111 branch February 13, 2026 10:33
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