我是Slurm的新手。下面,我想执行一个Python文件,它需要92.3GiB。我分配了120GB,但我的代码仍然返回内存错误。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
1条答案
按热度按时间0tdrvxhp1#
假设slurm.conf文件正确地将RAM列为可消耗资源(例如,SelectTypeParameters = CR_CPU_Memory),那么这个问题可能与Slurm无关,很可能与操作系统不想为单个任务分配那么多内存有关。Unable to allocate array with shape and data type.