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Synthcity #357

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laraPPr opened this issue Jul 1, 2024 · 15 comments · Fixed by easybuilders/easybuild-easyconfigs#21140, easybuilders/easybuild-easyconfigs#21141 or easybuilders/easybuild-easyconfigs#21211 · May be fixed by easybuilders/easybuild-easyconfigs#21845
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Synthcity #357

laraPPr opened this issue Jul 1, 2024 · 15 comments · Fixed by easybuilders/easybuild-easyconfigs#21140, easybuilders/easybuild-easyconfigs#21141 or easybuilders/easybuild-easyconfigs#21211 · May be fixed by easybuilders/easybuild-easyconfigs#21845
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@pavelToman
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difficulty: medium software that likely require a fair amount of effort to support easyconfig Easyconfig is available priority: medium site:ugent Software installation request for UGent Tier-2 update

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@laraPPr
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laraPPr commented Jul 1, 2024 •
edited by pavelToman
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@laraPPr laraPPr added difficulty: easy software that should be easy to support priority: medium update site:ugent Software installation request for UGent Tier-2 easyconfig Easyconfig is available labels Jul 1, 2024
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laraPPr commented Jul 1, 2024

https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb

@pavelToman pavelToman self-assigned this Jul 2, 2024
pavelToman added a commit that referenced this issue Jul 3, 2024
@pavelToman
#357 to update lifelines
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#357 add lifelines.eb
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#357 build ok + decaf + fastai
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#357 synthcity test deps added
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#357 tests not working
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#357 synthcity tests working + testlog
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#357 synthcity with wotking test cmd + fix unnecessary deps
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#357 add xgboost v1.7.2 and debug pytest errors
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#357 debug ERROR7 after pytest
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pavelToman commented Jul 23, 2024 •
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There is a problem with version of PyTorch:

  • synthcity need PyTorch v1.x but for foss/2023a there is only v2.x which is not compatible
  • I can try to create PyTorch v1.x for foss/2023a but I have to either create MONAI with this version of PyTorch
  • sythcity is not compatible with XGBoost v2.x neither PyTorch-Lightning v2.x

Synthcity v0.2.10 needs be-great >= 0.0.5 and it needs numpy>=1.24.2 and pandas>=1.4.4 so it can not be created for foss/2022a.

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pavelToman commented Jul 23, 2024 •
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Part of log from pytest with errors for Synthcity-0.2.10-foss-2023a:

# ============================================== short test summary info ===============================================
        # FAILED tests/plugins/core/test_schema.py::test_schema_fail - AttributeError: module 'pydantic' has no attribute 'py...
            # -> move fix prom preinstallopts to runtest cmd - should fix this
            
            # def test_schema_fail() -> None:
            #     if pydantic.__version__ < "2":
            #         with pytest.raises(pydantic.error_wrappers.ValidationError):
            #             Schema(data="sdfsfs")
            #     else:
            #         with pytest.raises(pydantic.pydantic_core._pydantic_core.ValidationError):
            # tests/plugins/core/test_schema.py:17: 
            # _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/__init__.
            # py:363: in __getattr__
            #     return _getattr_migration(attr_name)
            # _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
            # > raise AttributeError(f'module {module!r} has no attribute {name!r}')
            # E AttributeError: module 'pydantic' has no attribute 'pydantic_core'
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/_migration.py:306: AttributeError

        # FAILED tests/plugins/privacy/test_decaf.py::test_plugin_generate[test_plugin0] - RuntimeError: Training with multip...
            # -> https://stackoverflow.com/questions/75907443/pytorch-lightning-works-on-cuda-but-throws-training-with-multiple-optimizers-is
            # -> probably skip this test or create PyTorch-Lightning-1.8.4.foss-2023a -> pytorch-lighning v1.8.4 created
            
            # tests/plugins/privacy/test_decaf.py:110: 
            # _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:55: in wrapper_function
            #     return vd.call(*args, **kwargs)
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:150: in call
            #     return self.execute(m)
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:222: in execute
            #     return self.raw_function(**d, **var_kwargs)
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/core/plugin.py:256: in fit
            #     output = self._fit(X, *args, **kwargs)
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/privacy/plugin_decaf.py:437: in _
            # fit
            #     trainer.fit(self.model, dm)
            # /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/PyTorch-Lightning/2.2.1-foss-2023a/lib/py
            # thon3.11/site-packages/pytorch_lightning/trainer/trainer.py:544: in fit
            #     call._call_and_handle_interrupt(
            # /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/PyTorch-Lightning/2.2.1-foss-2023a/lib/py
            # thon3.11/site-packages/pytorch_lightning/trainer/call.py:44: in _call_and_handle_interrupt
            #     return trainer_fn(*args, **kwargs)
            # /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/PyTorch-Lightning/2.2.1-foss-2023a/lib/py
            # thon3.11/site-packages/pytorch_lightning/trainer/trainer.py:580: in _fit_impl
            #     self._run(model, ckpt_path=ckpt_path)
            # /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/PyTorch-Lightning/2.2.1-foss-2023a/lib/py
            # thon3.11/site-packages/pytorch_lightning/trainer/trainer.py:963: in _run
            #     self.strategy.setup(self)
            # /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/PyTorch-Lightning/2.2.1-foss-2023a/lib/py
            # thon3.11/site-packages/pytorch_lightning/strategies/strategy.py:159: in setup
            #     self.setup_optimizers(trainer)
            # /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/PyTorch-Lightning/2.2.1-foss-2023a/lib/py
            # thon3.11/site-packages/pytorch_lightning/strategies/strategy.py:139: in setup_optimizers
            #     self.optimizers, self.lr_scheduler_configs = _init_optimizers_and_lr_schedulers(self.lightning_module)
            # /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/PyTorch-Lightning/2.2.1-foss-2023a/lib/py
            # thon3.11/site-packages/pytorch_lightning/core/optimizer.py:192: in _init_optimizers_and_lr_schedulers
            #     _validate_multiple_optimizers_support(optimizers, model)
            # _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
            # def _validate_multiple_optimizers_support(optimizers: List[Optimizer], model: "pl.LightningModule") -> None:
            #    if is_param_in_hook_signature(model.training_step, "optimizer_idx", explicit=True):
            #        raise RuntimeError(
            #             "Training with multiple optimizers is only supported with manual optimization. Remove the `optimizer_idx`"
            #             " argument from `training_step`, set `self.automatic_optimization = False` and access your optimizers"
            #             " in `training_step` with `opt1, opt2, ... = self.optimizers()`."
            #         )
            # E           RuntimeError: Training with multiple optimizers is only supported with manual optimization. 
            # Remove the `optimizer_idx` argument from `training_step`, set `self.automatic_optimization = False` and access your optimizers in `training_step` with `opt1, opt2, ... = self.optimizers()`.
            # /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/PyTorch-Lightning/2.2.1-foss-2023a/lib/python3.11/site-packages/pytorch_lightning/core/optimizer.py:351: RuntimeError
        # FAILED tests/plugins/privacy/test_decaf.py::test_plugin_generate[test_plugin1] - RuntimeError: Training with multip...
        # FAILED tests/plugins/privacy/test_decaf.py::test_plugin_generate[test_plugin2] - RuntimeError: Training with multip...
        
        # FAILED tests/plugins/privacy/test_dpgan.py::test_plugin_generate[True-test_plugin1] - AttributeError: 'DPOptimizer'...
            # -> seems DPOptimizer in Opacus do not have _optimizer_step_pre_hooks but Optimizer in Torch has -> problem -> can create PyTorch v1.13 but it is either in MONAI
            # -> DPOptimizer is in Opacus - but it gets the Torch Optimizer then and it has _optimizer_step_pre_hooks
            # ->https://github.com/pytorch/opacus/blob/v1.4.1/opacus/optimizers/optimizer.py
            # ->https://github.com/pytorch/pytorch/blob/v2.1.2/torch/optim/optimizer.py
            # maybe connected with this bug: https://github.com/pytorch/opacus/issues/649 or https://github.com/pytorch/opacus/issues/523
            
            # tests/plugins/privacy/test_dpgan.py:81: 
            # _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:55: in wrapper_function
            #     return vd.call(*args, **kwargs)
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:150: in call
            #     return self.execute(m)
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:222: in execute
            #     return self.raw_function(**d, **var_kwargs)
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/core/plugin.py:256: in fit
            #     output = self._fit(X, *args, **kwargs)
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/privacy/plugin_dpgan.py:287: in _
            # fit
            #     self.model.fit(X.dataframe(), cond=cond)
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:55: in wrapper_function
            #     return vd.call(*args, **kwargs)
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:150: in call
            #     return self.execute(m)
            # /apps/gent/RHEL8/cascadelake-ib/software/pydantic/2.5.3-GCCcore-12.3.0/lib/python3.11/site-packages/pydantic/deprecate
            # d/decorator.py:222: in execute
            #     return self.raw_function(**d, **var_kwargs)
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/core/models/tabular_gan.py:358: i
            # n fit
            #     self.model.fit(
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/core/models/gan.py:278: in fit
            #     self._train(
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/core/models/gan.py:616: in _train
            #     g_loss, d_loss = self._train_epoch(
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/core/models/gan.py:493: in _train
            # _epoch
            #     self._train_epoch_discriminator(
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/core/models/gan.py:462: in _train
            # _epoch_discriminator
            #     self.discriminator.optimizer.step()
            # ...
            # @functools.wraps(func)
            #     def wrapper(*args: _P.args, **kwargs: _P.kwargs) -> R:
                #     self, *_ = args
                #     self = cast(Optimizer, self)
                #     profile_name = f"Optimizer.step#{self.__class__.__name__}.step"
                #     with torch.autograd.profiler.record_function(profile_name):
                #         # call optimizer step pre hooks
            # >           for pre_hook in chain(_global_optimizer_pre_hooks.values(), self._optimizer_step_pre_hooks.values()):
            # E           AttributeError: 'DPOptimizer' object has no attribute '_optimizer_step_pre_hooks'
            # /apps/gent/RHEL8/cascadelake-ib/software/PyTorch/2.1.2-foss-2023a/lib/python3.11/site-packages/torch/optim/optimizer.py:363: AttributeError
        # FAILED tests/plugins/privacy/test_dpgan.py::test_plugin_generate[True-test_plugin2] - AttributeError: 'DPOptimizer'...
        # FAILED tests/plugins/privacy/test_dpgan.py::test_plugin_generate[False-test_plugin0] - AttributeError: 'DPOptimizer...
        # FAILED tests/plugins/privacy/test_dpgan.py::test_plugin_generate[False-test_plugin1] - AttributeError: 'DPOptimizer...
        # FAILED tests/plugins/privacy/test_dpgan.py::test_plugin_generate[False-test_plugin2] - AttributeError: 'DPOptimizer...
        # FAILED tests/plugins/privacy/test_dpgan.py::test_plugin_generate_constraints[test_plugin0] - AttributeError: 'DPOpt...
        # FAILED tests/plugins/privacy/test_dpgan.py::test_plugin_generate_constraints[test_plugin1] - AttributeError: 'DPOpt...
        # FAILED tests/plugins/privacy/test_dpgan.py::test_plugin_generate_constraints[test_plugin2] - AttributeError: 'DPOpt...
        
        # FAILED tests/plugins/time_series/test_timegan.py::test_plugin_generate_static_cond[source0] - ValueError: setting a...
            # -> should be solved: it was moved to prerunopts so should be ok
                # FROM: https://stackoverflow.com/questions/67183501/setting-an-array-element-with-a-sequence-requested-array-has-an-inhomogeneous-sh
                # With dtype="object" it works for me. -> variable2 = np.asarray(variable1, dtype="object")
            # tests/plugins/time_series/test_timegan.py:112:
            # def unpack(self, as_numpy: bool = False, pad: bool = False) -> Any:
            #     if pad:
            #         (
            #             static_data,
            #             temporal_data,
            #             observation_times,
            #             outcome,
            #         ) = TimeSeriesDataLoader.pad_and_mask(
            #             self.data["static_data"],
            #             self.data["temporal_data"],
            #             self.data["observation_times"],
            #             self.data["outcome"],
            #         )
            #     else:
            #         static_data, temporal_data, observation_times, outcome = (
            #             self.data["static_data"],
            #             self.data["temporal_data"],
            #             self.data["observation_times"],
            #             self.data["outcome"],
            #         )
            
            #     if as_numpy:
            #         longest_observation_seq = max([len(seq) for seq in temporal_data])
            #         return (
            #             np.asarray(static_data),
            #             np.asarray(
            #                 temporal_data
            #             ),  # TODO: check this works with time series benchmarks
            #             # masked array to handle variable length sequences
            #             ma.vstack(
            #                 [
            #                     ma.array(
            #                         np.resize(ot, longest_observation_seq),
            #                         mask=[True for i in range(len(ot))]
            #                         + [False for j in range(longest_observation_seq - len(ot))],
            #                     )
            #                     for ot in observation_times
            #                 ]
            #             ),
            #             np.asarray(outcome),
            #         )
            # E           ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after
            # 1 dimensions. The detected shape was (50,) + inhomogeneous part.
            # /tmp/vsc47063/eb-2r7nzoxm/tmps38qxu1i/lib/python3.11/site-packages/synthcity/plugins/core/dataloader.py:936: ValueError
        # FAILED tests/plugins/time_series/test_timegan.py::test_plugin_generate_static_cond[source1] - ValueError: setting a...
        # ======== 14 failed, 2145 passed, 13 skipped, 103 deselected, 2 xfailed, 2350 warnings in 15515.30s (4:18:35) ========

pavelToman added a commit that referenced this issue Jul 23, 2024
@pavelToman
#357 debug ERROR7 + pyTorch-lightning v1.x
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@pavelToman
#357 debug error8
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@pavelToman
#357 add Synthcity-0.2.10-foss-2022b + all deps
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#357 add torchtext-2022b
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pavelToman added a commit that referenced this issue Aug 1, 2024
@pavelToman
#357 synthcity-2022b build ok
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#357 2022b - ERROR3
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#357 added test_log for 2022b
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#357 added numpy 1.23.5 to 2022b - ok
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#357 working synthcity-2022b
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For now Synthcity-0.2.10 can be installed with a toolchain foss/2022b, but not with foss/2023a, because of PyTorch and NumPy version.
As soon as Synthcity will support PyTorch v2 and newer Numpy it will be possible to install it with newer toolchain.

pavelToman added a commit that referenced this issue Aug 6, 2024
@pavelToman
#357 updates sources
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#357 synthcity-2022b PR version
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Problem to build ITK 5.4.0 for Synthcity-0.2.11-foss-2023b reported here:

* [Compilation error of v5.4.0 with GCC-13.2.0 - CastXML problem? InsightSoftwareConsortium/ITK#4911](https://github.com/InsightSoftwareConsortium/ITK/issues/4911)

@pavelToman How did you deal with this issue in the end? You should definitely also follow up there, so they at least know how you worked around it...

I used MONAI-minimum to avoid use ITK as its dependency. Seems synthcity does not need it as a part of MONAI.

pavelToman added a commit that referenced this issue Nov 25, 2024
@pavelToman
#357 Monai-full + ITK-5.4.0 debug
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#357 ITK make failed - log
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#357 Monai-full debug ITK-5.4.0
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#357 Monai-full deps
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#357 Monai-full deps
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#357 ITK reorganization + CastXML-0.6.10
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#357 working ITK-5.4.0 with new CastXML + SWIG
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#357 imagecodecs pre-PR
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#357 imagecodecs PR version
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#357 monai-full - onnx dep
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#357 monai-full - ITK-5.4.0 PR
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#357 monai-full deps
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#357 monai-full PR version
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Problem to build ITK 5.4.0 for Synthcity-0.2.11-foss-2023b reported here:

* [Compilation error of v5.4.0 with GCC-13.2.0 - CastXML problem? InsightSoftwareConsortium/ITK#4911](https://github.com/InsightSoftwareConsortium/ITK/issues/4911)

@pavelToman How did you deal with this issue in the end? You should definitely also follow up there, so they at least know how you worked around it...

They fix it! Now the ITK-5.4.0 works with CastXML-0.6.10.
See easybuilders/easybuild-easyconfigs#21937

pavelToman added a commit that referenced this issue Dec 17, 2024
@pavelToman
#357 synthcity-2023b with monai-full
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pavelToman added a commit that referenced this issue Dec 18, 2024
@pavelToman
#357 synthcity-monai-full pretestopts update
f510731
pavelToman added a commit that referenced this issue Dec 19, 2024
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#357 debug pytests synthcity_monai_full
88356d3
pavelToman added a commit that referenced this issue Dec 20, 2024
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#357 debug failing tests - synthcity monai_full
1149738
pavelToman added a commit that referenced this issue Jan 2, 2025
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#357 synthcity_monai_full passed tests
83cf9f4
pavelToman added a commit that referenced this issue Jan 2, 2025
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#357 synthcity_monai_full PR version
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@boegel boegel closed this as completed Jan 7, 2025
@pavelToman pavelToman reopened this Jan 7, 2025
@laraPPr
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laraPPr commented Jan 16, 2025

It is this one that needs be reviewed, https://github.com/easybuilders/easybuild-easyconfigs/pull/21937/files? That one does not include synthcity so than another pr for that would also be needed?

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The PR for Synthcity is there and yes, MONAI is in its deps and needs to be merged first easybuilders/easybuild-easyconfigs#21937

pavelToman added a commit that referenced this issue Jan 22, 2025
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#357 fix OpenSlide - patch-fix-poison
3455b6d
pavelToman added a commit that referenced this issue Jan 22, 2025
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#357 OpenSlide + patch PR version
81f623c
pavelToman added a commit that referenced this issue Jan 22, 2025
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#357 fix MOANI sources
36576b2
pavelToman added a commit that referenced this issue Jan 24, 2025
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#357 fix slurm_ntasks in decaf tests
fce5d36
pavelToman added a commit that referenced this issue Jan 28, 2025
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#357 fix teast_decaf.py slurm problem
384b15a
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difficulty: medium software that likely require a fair amount of effort to support easyconfig Easyconfig is available priority: medium site:ugent Software installation request for UGent Tier-2 update
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