The notification,

Allocation of 5033164800 exceeds 10% of free system memor

… makes me think it’s asking to allocate an additional ~4G of RAM on top of what everything running on the machine is already using. That apparently generates the 10% of free memory warning, and then the system actually fails to allocate memory to run a new process.

If you are running other software applications that use appreciable system memory, then I would try not running anything else other than the mri_histo_atlas_segment_fireants command. If that still fails to allocate memory as the only running application, then I suggest switching to a machine with more memory.

- R.

On Mar 14, 2025, at 07:35, Payam Sadeghi Shabestari <payam.sadeghishabestari@uzh.ch> wrote:

        External Email - Use Caution

Hello FS Dev Team,
I'm attempting to run mri_histo_atlas_segment_fireants on Ubuntu 20.04.6, but I encountered a "Cannot allocate memory" error. Could this be due to insufficient RAM? I would appreciate your assistance.
Best regards,
Payam

Normalizing intensities
Subdividing brainstem into left and right halves, and cropping bottom if needed
   Running EasyReg
2025-03-14 10:50:24.182715: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2025-03-14 10:50:24.227568: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2025-03-14 10:50:24.228099: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2025-03-14 10:50:24.983225: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
UserWarning: int_downsize is deprecated, use the int_resolution parameter.
UserWarning: unet_half_res is deprecated, use the svf_resolution parameter.
2025-03-14 10:51:31.533186: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 5033164800 exceeds 10% of free system memory.
2025-03-14 10:54:04.568813: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 5033164800 exceeds 10% of free system memory.
  Creating and applying mask for left hemisphere
Reading in atlas
Traceback (most recent call last):
  File "/usr/local/freesurfer/8.0.0/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py", line 364, in <module>
  for n, (prior_indices, prior_values) in enumerate(label_loader):
  File "/usr/local/freesurfer/8.0.0/python/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 438, in __iter__
  return self._get_iterator()
  File "/usr/local/freesurfer/8.0.0/python/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 386, in _get_iterator
  return _MultiProcessingDataLoaderIter(self)
  File "/usr/local/freesurfer/8.0.0/python/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 1039, in __init__
  w.start()
  File "/usr/local/freesurfer/8.0.0/python/lib/python3.8/multiprocessing/process.py", line 121, in start
  self._popen = self._Popen(self)
  File "/usr/local/freesurfer/8.0.0/python/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
  return _default_context.get_context().Process._Popen(process_obj)
  File "/usr/local/freesurfer/8.0.0/python/lib/python3.8/multiprocessing/context.py", line 277, in _Popen
  return Popen(process_obj)
  File "/usr/local/freesurfer/8.0.0/python/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
  self._launch(process_obj)
  File "/usr/local/freesurfer/8.0.0/python/lib/python3.8/multiprocessing/popen_fork.py", line 70, in _launch
  self.pid = os.fork()
OSError: [Errno 12] Cannot allocate memory

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