MemoryError
Aplaus228 opened this issue · comments
Hello I just started study abinit and abipy and I am going through first base tutorial from abinit and when I wrote ( abiopen.py tbase1_1.out --expose) or something similar to it I will take memory error.
I have ubuntu 16.04 LTS also 8 gb RAW memory.
(base) vova@bobik:/Abinit/abinit-8.10.3/tests/tutorial/Input/work$ abiopen.py tbase1_1.out --expose/Abinit/abinit-8.10.3/tests/tutorial/Input/work$ abiopen.py tbase1_1.out --seaborn
Traceback (most recent call last):
File "/home/vova/miniconda3/bin/abiopen.py", line 15, in
from abipy import abilab
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/abilab.py", line 43, in
from abipy.electrons.ebands import (ElectronBands, ElectronBandsPlotter, ElectronDos, ElectronDosPlotter,
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/electrons/init.py", line 4, in
from .gsr import *
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/electrons/gsr.py", line 20, in
from abipy.tools.tensors import Stress
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/tools/tensors.py", line 9, in
from pymatgen.analysis.elasticity.elastic import ElasticTensor # flake8: noqa
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/init.py", line 5, in
from .elastic import *
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/elastic.py", line 20, in
import sympy as sp
File "/home/vova/miniconda3/lib/python3.7/site-packages/sympy/init.py", line 19, in
import mpmath
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/init.py", line 5, in
from .ctx_fp import FPContext
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/ctx_fp.py", line 1, in
from .ctx_base import StandardBaseContext
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/ctx_base.py", line 3, in
from .libmp.backend import xrange
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/init.py", line 17, in
from .libmpc import (mpc_one, mpc_zero, mpc_two, mpc_half,
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libmpc.py", line 23, in
from .libelefun import (
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libelefun.py", line 76, in
cache_prec_steps += [min(2k,LOG_TAYLOR_PREC)+20] * 2(k-1)
MemoryError
(base) vova@bobik:
Traceback (most recent call last):
File "/home/vova/miniconda3/bin/abiopen.py", line 15, in
from abipy import abilab
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/abilab.py", line 43, in
from abipy.electrons.ebands import (ElectronBands, ElectronBandsPlotter, ElectronDos, ElectronDosPlotter,
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/electrons/init.py", line 4, in
from .gsr import *
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/electrons/gsr.py", line 20, in
from abipy.tools.tensors import Stress
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/tools/tensors.py", line 9, in
from pymatgen.analysis.elasticity.elastic import ElasticTensor # flake8: noqa
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/init.py", line 5, in
from .elastic import *
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/elastic.py", line 20, in
import sympy as sp
File "/home/vova/miniconda3/lib/python3.7/site-packages/sympy/init.py", line 19, in
import mpmath
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/init.py", line 5, in
from .ctx_fp import FPContext
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/ctx_fp.py", line 1, in
from .ctx_base import StandardBaseContext
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/ctx_base.py", line 3, in
from .libmp.backend import xrange
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/init.py", line 17, in
from .libmpc import (mpc_one, mpc_zero, mpc_two, mpc_half,
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libmpc.py", line 23, in
from .libelefun import (
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libelefun.py", line 76, in
cache_prec_steps += [min(2k,LOG_TAYLOR_PREC)+20] * 2(k-1)
MemoryError
The MemoryError is raised inside one of the modules used by sympy thus it's not directly related to AbiPy.
Could you try to increase the stack size with the shell command:
ulimit -s unlimited
and rerun abiopen?
If ulimit does not fix the problem, you may want to remove the sympy import at
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/elastic.py", line 20, in
import sympy as sp
sympy is not a hard dependencies, only a small part of AbiPy requires this package.
I did what are you wrote and I have taken another mistake( File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/elastic.py", line 1061, in
v_diff = np.vectorize(sp.diff)
NameError: name 'sp' is not defined )
I understand that I can delete this line but I think it's not will solve this problem.
Thank you
yes, didn't work
Ok, try to remove also:
v_diff = np.vectorize(sp.diff)
in the pymatgen package as this statement is executed at the module level:
BTW: Can you print the length of cache_prec_steps and the value of k before this line?
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libelefun.py", line 76, in
cache_prec_steps += [min(2k,LOG_TAYLOR_PREC)+20] * 2(k-1)
I have deleted (v_diff = np.vectorize(sp.diff) this line and all work. Thank you a lot. You are the best.
also, the information that you asked.
LOG_TAYLOR_PREC = 2500
cache_prec_steps = [22,22]
for k in xrange(1, bitcount(LOG_TAYLOR_PREC)+1):