[Question]: I am not able to install gmxmmpbsa on ubuntu 2024.

[AKR845]

My Question is...

/tmp/pip-build-env-8i30r4s1/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h:139:62: note: in definition of macro ‘PyArray_GETPTR1’ 139 | (i)*PyArray_STRIDES(obj)[0])) | ^~~ /tmp/pip-build-env-8i30r4s1/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1526:38: note: expected ‘const PyArrayObject *’ {aka ‘const struct tagPyArrayObject_fields *’} but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 1526 | PyArray_STRIDES(const PyArrayObject *arr) | ~~~~~~~~~~~~~~~~~~~~~^~~ pandas/_libs/src/ujson/python/JSONtoObj.c:319:31: warning: passing argument 1 of ‘PyArray_SETITEM’ from incompatible pointer type [-Wincompatible-pointer-types] 319 | PyArray_SETITEM(npyarr->ret, item, value) == -1) { | ~~~~~~^~~~~ | | | PyObject * {aka struct _object *} /tmp/pip-build-env-8i30r4s1/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h:292:32: note: expected ‘PyArrayObject *’ {aka ‘struct tagPyArrayObject_fields *’} but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 292 | PyArray_SETITEM(PyArrayObject *arr, char *itemptr, PyObject *v) | ~~~~~~~~~~~~~~~^~~ error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pandas Failed to build pandas

[AKR845]

Please help me to solve this

[Valdes-Tresanco-MS]

What version of pandas are you trying to install?

[denizkavi]

I'm having the same problem:

Collecting pandas==1.2.2 (from gmx_MMPBSA)
  Using cached pandas-1.2.2.tar.gz (5.5 MB)

Was able to resolve by running
pip install pandas==2.2.2 gmx_MMPBSA

[Valdes-Tresanco-MS]

Probably this pandas version ends in an error. Please, try to install the 1.2.2

[AKR845]

Panda 1.2.2 still is not working. please give some way out of it.

…

On Fri, Jul 5, 2024 at 9:42 AM Mario Sergio Valdés Tresanco < ***@***.***> wrote: Probably this pandas version ends in an error. Please, try to install the 1.2.2 — Reply to this email directly, view it on GitHub <#517 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJVBG5NG6RVU3UQS6RXNQD3ZKYMLXAVCNFSM6AAAAABKLVBD26VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQGA4TQMJYG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Valdes-Tresanco-MS]

@denizkavi, @AKR845 I don't know why this is happening, but this configuration works for me

conda create -n gmxMMPBSA python=3.9 -y -q
conda activate gmxMMPBSA

conda install -c conda-forge "mpi4py<=3.1.5" "ambertools<=23.3" -y -q

python -m pip install "numpy==1.22.3" "pandas==1.2.2" "pyqt6<=6.6.1"

Please, let me know if this works for you

[vaghasiyautsav]

No this is not working. Still getting same error.

`pandas/_libs/src/ujson/python/JSONtoObj.c:319:31: warning: passing argument 1 of ‘PyArray_SETITEM’ from incompatible pointer type [-Wincompatible-pointer-types]
319 | PyArray_SETITEM(npyarr->ret, item, value) == -1) {
| ~~~~~~^~~~~
| |
| PyObject * {aka struct _object *}
/tmp/pip-build-env-r9ohf93i/overlay/lib/python3.10/site-packages/numpy/_core/include/numpy/ndarrayobject.h:292:32: note: expected ‘PyArrayObject *’ {aka ‘struct tagPyArrayObject_fields *’} but argument is of type ‘PyObject *’ {aka ‘struct _object *’}
292 | PyArray_SETITEM(PyArrayObject *arr, char *itemptr, PyObject *v)
| ~~~~~~~~~~~~~~~^~~
error: command '/usr/bin/gcc' failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pandas
Failed to build pandas
ERROR: Could not build wheels for pandas, which is required to install pyproject.toml-based projects
`

[Jameel9]

Hi all,

I installed gmx_MMPBSA on my laptop (Ubuntu) a month ago using the method of conda and the .yml file. It was smooth and successful. Yesterday, I tried to install the tool on my PC at work and I got the exact error reported in this issue. I tried the newly suggested method (above) and it didn't work.
It's very likely that the issue is caused by a third-party library/software that got updated recently.

[Valdes-Tresanco-MS]

Please, try to create a conda environment using Python 3.9 as the base.

[Jameel9]

Please, try to create a conda environment using Python 3.9 as the base.

I did but still get this:

(gmxMMPBSA) jameel@users-Precision-3460:~$ python -m pip install "numpy==1.22.3" "pandas==1.2.2" "pyqt6<=6.6.1"
Collecting numpy==1.22.3
Using cached numpy-1.22.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
Collecting pandas==1.2.2
Using cached pandas-1.2.2-cp39-cp39-manylinux1_x86_64.whl.metadata (4.7 kB)
Collecting pyqt6<=6.6.1
Using cached PyQt6-6.6.1-cp38-abi3-manylinux_2_28_x86_64.whl.metadata (2.1 kB)
Requirement already satisfied: python-dateutil>=2.7.3 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from pandas==1.2.2) (2.9.0)
Requirement already satisfied: pytz>=2017.3 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from pandas==1.2.2) (2024.1)
Collecting PyQt6-sip<14,>=13.6 (from pyqt6<=6.6.1)
Using cached PyQt6_sip-13.8.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (420 bytes)
Collecting PyQt6-Qt6>=6.6.0 (from pyqt6<=6.6.1)
Using cached PyQt6_Qt6-6.7.2-py3-none-manylinux_2_28_x86_64.whl.metadata (534 bytes)
Requirement already satisfied: six>=1.5 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from python-dateutil>=2.7.3->pandas==1.2.2) (1.16.0)
Using cached numpy-1.22.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
Using cached pandas-1.2.2-cp39-cp39-manylinux1_x86_64.whl (9.7 MB)
Using cached PyQt6-6.6.1-cp38-abi3-manylinux_2_28_x86_64.whl (7.9 MB)
Using cached PyQt6_Qt6-6.7.2-py3-none-manylinux_2_28_x86_64.whl (74.3 MB)
Using cached PyQt6_sip-13.8.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (281 kB)
Installing collected packages: PyQt6-Qt6, PyQt6-sip, numpy, pyqt6, pandas
Attempting uninstall: numpy
Found existing installation: numpy 1.26.4
Uninstalling numpy-1.26.4:
Successfully uninstalled numpy-1.26.4
Attempting uninstall: pandas
Found existing installation: pandas 2.2.2
Uninstalling pandas-2.2.2:
Successfully uninstalled pandas-2.2.2
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
matplotlib 3.9.1 requires numpy>=1.23, but you have numpy 1.22.3 which is incompatible.
scipy 1.13.1 requires numpy<2.3,>=1.22.4, but you have numpy 1.22.3 which is incompatible.
Successfully installed PyQt6-Qt6-6.7.2 PyQt6-sip-13.8.0 numpy-1.22.3 pandas-1.2.2 pyqt6-6.6.1

[fgrcampos]

@denizkavi, @AKR845 I don't know why this is happening, but this configuration works for me

conda create -n gmxMMPBSA python=3.9 -y -q
conda activate gmxMMPBSA

conda install -c conda-forge "mpi4py<=3.1.5" "ambertools<=23.3" -y -q

python -m pip install "numpy==1.22.3" "pandas==1.2.2" "pyqt6<=6.6.1"

Please, let me know if this works for you

This solution has worked for me, with the exception of the numpy version being 1.23 for compatibility with other packages.

[Jameel9]

Hi @Valdes-Tresanco-MS,

Hi @fgrcampos, I did followed the steps and
python -m pip install gmx_MMPBSA
but when I ran
gmx_MMPBSA -h
I got this error

(gmxMMPBSA) shirehorse@shirehorse-Precision-3460:~/Downloads$ gmx_MMPBSA
Traceback (most recent call last):
File "/home/shirehorse/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 5, in
from GMXMMPBSA.app import gmxmmpbsa
File "/home/shirehorse/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 27, in
from GMXMMPBSA import main
File "/home/shirehorse/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 31, in
from GMXMMPBSA import utils, version
File "/home/shirehorse/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 43, in
import pandas as pd
File "/home/shirehorse/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/init.py", line 29, in
from pandas._libs import hashtable as _hashtable, lib as _lib, tslib as _tslib
File "/home/shirehorse/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/_libs/init.py", line 13, in
from pandas._libs.interval import Interval
File "pandas/_libs/interval.pyx", line 1, in init pandas._libs.interval
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

[Jameel9]

Hi everyone,

I just used the following commands, and I finally got an old version 1.5.0.3 (Feb. 2022). But it is working. I have just done MMGBSA calculations for a complex.

conda create -n gmxMMPBSA 
conda activate gmxMMPBSA
conda install -c conda-forge mpi4py ambertools -y -q
pip install PyQt5 
conda install conda-forge::gmx_mmpbsa

Even though the last command is supposed to install the 1.6.3 version (as the conda page claims), but it doesn't actually.

Don't try to update the tool via
pip install gmx-MMPBSA --upgrade

because you will end up with the error of which this issue was created for.