Which version of Numpy is preferred for Matminer install?

Matminer
1

Matminer is having trouble with the version of numpy (1.15.0) I have installed. The following messages are presented when import numpy:

import matminer

/usr/local/lib/python2.7/dist-packages/pandas/_libs/init.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime

/usr/local/lib/python2.7/dist-packages/pandas/init.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (hashtable as _hashtable,

/usr/local/lib/python2.7/dist-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos, lib

/usr/local/lib/python2.7/dist-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import hashing, tslib

/usr/local/lib/python2.7/dist-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (lib, index as libindex, tslib as libts,

/usr/local/lib/python2.7/dist-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.tslibs.offsets as liboffsets

/usr/local/lib/python2.7/dist-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos as libalgos, ops as libops

/usr/local/lib/python2.7/dist-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs.interval import (

/usr/local/lib/python2.7/dist-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import internals as libinternals

/usr/local/lib/python2.7/dist-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.sparse as splib

/usr/local/lib/python2.7/dist-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.window as _window

/usr/local/lib/python2.7/dist-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (lib, reduction,

/usr/local/lib/python2.7/dist-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos as _algos, reshape as _reshape

/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.parsers as parsers

/usr/local/lib/python2.7/dist-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos, lib, writers as libwriters

/usr/local/lib/python2.7/dist-packages/scipy/sparse/lil.py:19: RuntimeWarning:

numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

/usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/init.py:165: RuntimeWarning:

numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

Ideas? or the preferred version?

-Dennis

2

AFAIK numpy 1.15.0 should work. The error seems to be due to the installation of the pandas library which is separate from matminer and a pretty well-supported library. i.e. you will probably get the same error from typing “import pandas”

I would check / update your pandas installation

Most of us use anaconda to install pandas / etc. which is typically a pretty stable way to do it. Although perhaps the issue is also there with conda: https://github.com/ContinuumIO/anaconda-issues/issues/6678

There seem to be multiple discussions of this error on the web (e.g. https://stackoverflow.com/questions/40845304/runtimewarning-numpy-dtype-size-changed-may-indicate-binary-incompatibility/51587845) but none really seem related to matminer itself

Anubhav

···

On Friday, August 10, 2018 at 10:31:26 AM UTC-7, [email protected] wrote:

Matminer is having trouble with the version of numpy (1.15.0) I have installed. The following messages are presented when import numpy:

import matminer

/usr/local/lib/python2.7/dist-packages/pandas/_libs/init.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime

/usr/local/lib/python2.7/dist-packages/pandas/init.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (hashtable as _hashtable,

/usr/local/lib/python2.7/dist-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos, lib

/usr/local/lib/python2.7/dist-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import hashing, tslib

/usr/local/lib/python2.7/dist-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (lib, index as libindex, tslib as libts,

/usr/local/lib/python2.7/dist-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.tslibs.offsets as liboffsets

/usr/local/lib/python2.7/dist-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos as libalgos, ops as libops

/usr/local/lib/python2.7/dist-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs.interval import (

/usr/local/lib/python2.7/dist-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import internals as libinternals

/usr/local/lib/python2.7/dist-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.sparse as splib

/usr/local/lib/python2.7/dist-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.window as _window

/usr/local/lib/python2.7/dist-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (lib, reduction,

/usr/local/lib/python2.7/dist-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos as _algos, reshape as _reshape

/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.parsers as parsers

/usr/local/lib/python2.7/dist-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos, lib, writers as libwriters

/usr/local/lib/python2.7/dist-packages/scipy/sparse/lil.py:19: RuntimeWarning:

numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

/usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/init.py:165: RuntimeWarning:

numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

Ideas? or the preferred version?

-Dennis

3

The fix via the stackoverflow worked. The problem was with scipy install. Now I’m having issues with Pymatgen.

-Dennis

···

On Friday, August 10, 2018 at 9:27:28 PM UTC-6, Anubhav Jain wrote:

AFAIK numpy 1.15.0 should work. The error seems to be due to the installation of the pandas library which is separate from matminer and a pretty well-supported library. i.e. you will probably get the same error from typing “import pandas”

I would check / update your pandas installation

Most of us use anaconda to install pandas / etc. which is typically a pretty stable way to do it. Although perhaps the issue is also there with conda: https://github.com/ContinuumIO/anaconda-issues/issues/6678

There seem to be multiple discussions of this error on the web (e.g. https://stackoverflow.com/questions/40845304/runtimewarning-numpy-dtype-size-changed-may-indicate-binary-incompatibility/51587845) but none really seem related to matminer itself

Anubhav

On Friday, August 10, 2018 at 10:31:26 AM UTC-7, [email protected] wrote:

Matminer is having trouble with the version of numpy (1.15.0) I have installed. The following messages are presented when import numpy:

import matminer

/usr/local/lib/python2.7/dist-packages/pandas/_libs/init.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime

/usr/local/lib/python2.7/dist-packages/pandas/init.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (hashtable as _hashtable,

/usr/local/lib/python2.7/dist-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos, lib

/usr/local/lib/python2.7/dist-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import hashing, tslib

/usr/local/lib/python2.7/dist-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (lib, index as libindex, tslib as libts,

/usr/local/lib/python2.7/dist-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.tslibs.offsets as liboffsets

/usr/local/lib/python2.7/dist-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos as libalgos, ops as libops

/usr/local/lib/python2.7/dist-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs.interval import (

/usr/local/lib/python2.7/dist-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import internals as libinternals

/usr/local/lib/python2.7/dist-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.sparse as splib

/usr/local/lib/python2.7/dist-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.window as _window

/usr/local/lib/python2.7/dist-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import (lib, reduction,

/usr/local/lib/python2.7/dist-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos as _algos, reshape as _reshape

/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

import pandas._libs.parsers as parsers

/usr/local/lib/python2.7/dist-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

from pandas._libs import algos, lib, writers as libwriters

/usr/local/lib/python2.7/dist-packages/scipy/sparse/lil.py:19: RuntimeWarning:

numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

/usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/init.py:165: RuntimeWarning:

numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

Ideas? or the preferred version?

-Dennis