如何在SLURM中分配memory？

Question

我是 Slurm 的新手。 下面，我要执行一个 Python 文件，它需要 92.3GiB。 我分配了 120GB，但我的代码仍然返回 memory 错误。

submit_venv.sh

#/bin/bash

#SBATCH --account=melchua
#SBATCH --mem=120GB
#SBATCH --time=2`:00:00

module load python/3.8.2
python3 1.methylation_data_processing.py

使用./submit_venv.sh运行脚本

追溯：

  File "1.methylation_data_processing.py", line 49, in <module>
    meth_clin = pd.concat([gene_symbol, meth_clin])  # add gene_symbol to dataframe
  File "/scg/apps/software/python/3.8.2/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/scg/apps/software/python/3.8.2/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 307, in concat
    return op.get_result()
  File "/scg/apps/software/python/3.8.2/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 532, in get_result
    new_data = concatenate_managers(
  File "/scg/apps/software/python/3.8.2/lib/python3.8/site-packages/pandas/core/internals/concat.py", line 222, in concatenate_managers
    values = _concatenate_join_units(join_units, concat_axis, copy=copy)
  File "/scg/apps/software/python/3.8.2/lib/python3.8/site-packages/pandas/core/internals/concat.py", line 486, in _concatenate_join_units
    to_concat = [
  File "/scg/apps/software/python/3.8.2/lib/python3.8/site-packages/pandas/core/internals/concat.py", line 487, in <listcomp>
    ju.get_reindexed_values(empty_dtype=empty_dtype, upcasted_na=upcasted_na)
  File "/scg/apps/software/python/3.8.2/lib/python3.8/site-packages/pandas/core/internals/concat.py", line 441, in get_reindexed_values
    missing_arr = np.empty(self.shape, dtype=empty_dtype)
numpy.core._exceptions.MemoryError: Unable to allocate 92.3 GiB for an array with shape (111331, 111332) and data type object

Answer 1

假设您的 slurm.conf 文件正确地将 RAM 列为消耗性资源（例如，SelectTypeParameters=CR_CPU_Memory），问题可能与 Slurm 无关，很可能与您的操作系统不希望将那么多 memory 分配给单个任务。 这里有一个类似的问题： Unable to allocate array with shape and data type 。