Memory Error

0

Hello,
I am getting this "unable to allocate memory" error in R when trying to do this tutorial. What is the best way to avoid this memory issue? Should I increase memory limit()?

> mofa <- run_mofa(mofa)
Connecting to the mofapy2 python package using reticulate (use_basilisk = FALSE)... 
    Please make sure to manually specify the right python binary when loading R with reticulate::use_python(..., force=TRUE) or the right conda environment with reticulate::use_condaenv(..., force=TRUE)
    If you prefer to let us automatically install a conda environment with 'mofapy2' installed using the 'basilisk' package, please use the argument 'use_basilisk = TRUE'

    Error in py_call_impl(callable, dots$args, dots$keywords) : 
  MemoryError: Unable to allocate 2.43 GiB for an array with shape (11909, 27367) and data type float64

Detailed traceback: 
  File "C:UserscatheAppDataLocalbasilisk120584~1.1MOFA2-~1.1mofa_envlibsite-packagesmofapy2runentry_point.py", line 738, in build
    tmp = buildBiofam(self.data, self.data_opts, self.model_opts, self.dimensionalities, self.train_opts['seed'],  self.train_opts['weight_views'])
  File "C:UserscatheAppDataLocalbasilisk120584~1.1MOFA2-~1.1mofa_envlibsite-packagesmofapy2build_modelbuild_model.py", line 48, in __init__
    self.build_nodes()
  File "C:UserscatheAppDataLocalbasilisk120584~1.1MOFA2-~1.1mofa_envlibsite-packagesmofapy2build_modelbuild_model.py", line 57, in build_nodes
    self.build_Z()
  File "C:UserscatheAppDataLocalbasilisk120584~1.1MOFA2-~1.1mofa_envlibsite-packagesmofapy2build_modelbuild_model.py", line 91, in build_Z
    self.init_model.initZ(qmean="pca", Y=self.data, impute=True, weight_
In addition: Warning message:
In run_mofa(mofa) :
  No output filename provided. Using /tmp/mofa_20210430-004104.hdf5 to store the trained model.


R


Memory


MOFA

• 106 views

updated 52 minutes ago by

&utrif;

720

written 12 hours ago by

&utrif;

10


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