gmx_MMPBSA_ana - amber.python: relocation error -reg

[azbvenkat]

Dear All 

I performed test calculation of  gmx_MMPBSA using tutorial files, and now I tried to perform the analysis using gmx_MMPBSA_ana  got  error which related  libqxcb.so (libxcb-icccm.so.4: cannot open shared object file: No such file or directory)  and its  solved with help of  https://community.perforce.com/s/article/17363

followed by again I tried  gmx_MMPBSA_ana  -f  _GMXMMPBSA_info

got error like "amber.python: relocation error"

/opt/amber20/bin/amber.python: relocation error: /home/subbu/.local/lib/python3.8/site-packages/PyQt5/Qt5/lib/libQt5DBus.so.5: symbol dbus_message_get_allow_interactive_authorization, version LIBDBUS_1_3 not defined in file libdbus-1.so.3 with link time reference

kindly get the full log file from the  link https://drive.google.com/file/d/1QG1nap7REvGlfeICG0YXoq-ZzjTr64sD/view?usp=sharing

really don't have idea to further proceed  

Here I expecting your help to resolve their problem 

Thank you 

with regards 

venkat

[Mario Sergio Valdes]

Hi venkat and welcome.

I see that this error is very frequent in Archlinux and Ubuntu14.04 and is related to the dbus library.

Could you please, give me some information related to your OS?

[venkat]

sorry I forget to give  system information mine is Centos 7. 

Thank you 

--
You received this message because you are subscribed to a topic in the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/gmx_mmpbsa/j0aOhK7ApMw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/3cc8e2f2-66d8-4254-bad6-089c71778bf6n%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Mario Sergio Valdes]

This error is due to the fact that the dbus library (libdbus-1.so.3) is not compatible with the Qt libraries. It's probably because the library is too old. Apparently, there is no easy solution for this, you can check out a discussion about it here (https://forum.qt.io/topic/110272/5-12-x-offline-installer-fails-on-centos-7-could -not-load-xcb / 3)

You may also experience problems with pandas, mpi4py, and other python modules.

After an intensive search and several tests on the latest version of Centos 7 I managed to get it to work, however, it is extremely complicated, as there are too many incompatible libraries.

Unfortunately, I think the best solution is to use a more desktop-dedicated distribution. Centos, like Debian, are distributions dedicated to server, so they use the libraries that work (for example cmake available in the repository is 2.8 while ambertools needs at least version 3.8)

Since they are compatibility problems of various libraries, it is impossible for us to give them adequate support. I recommend using a distribution more dedicated to desktop, such as Ubuntu, Linux Mint, Manjaro, Fedora, OpenSuse, etc (There are many, choose the one that suits your needs)

In the case of an HPC, it is not necessary to install PyQt5 and gmx_MMPBSA should work correctly. To run gmx_MMPBSA on HPC you must define the -nogui option. Then you must download the results folder to your PC and do the analysis on it using gmx_MMPBSA_ana since it is a standalone application.

Best!

Mario

[azbvenkat]

Thank you very much for your help. 

I followed your given directions. I have tried with the computer which has Ubuntu OS (Ubuntu 20.04.2 LTS (Focal Fossa)).

next I have installed  AmberTools20 using conda 

python3.9 -m pip install PyQt5    # Checked for the amber.python command which is not available, so tried with python3.9

Collecting PyQt5
  Downloading PyQt5-5.15.4-cp36.cp37.cp38.cp39-abi3-manylinux2014_x86_64.whl (8.3 MB)
     |████████████████████████████████| 8.3 MB 6.2 MB/s
Collecting PyQt5-sip<13,>=12.8
  Downloading PyQt5_sip-12.8.1-cp39-cp39-manylinux1_x86_64.whl (286 kB)
     |████████████████████████████████| 286 kB 6.8 MB/s
Collecting PyQt5-Qt5>=5.15
  Downloading PyQt5_Qt5-5.15.2-py3-none-manylinux2014_x86_64.whl (59.9 MB)
     |████████████████████████████████| 59.9 MB 5.5 MB/s
Installing collected packages: PyQt5-sip, PyQt5-Qt5, PyQt5
Successfully installed PyQt5-5.15.4 PyQt5-Qt5-5.15.2 PyQt5-sip-12.8.1

Further, I have given the following command  

python3.9 -m pip install gmx_MMPBSA

but unfortunately ended up with an error https://drive.google.com/file/d/1q-wY2-CiXJeAs-XaZ5LFId1WeEB3fhK0/view?usp=sharing

please do needful in this regard 

Thank you  

[Mario Sergio Valdes]

amber.python corresponds to the python executable of the miniconda environment installed in Ambertools. If you use an existing Python environment and install ambertools from the conda repositories, use that then. Note that it is important that the python executable you use to install gmx_MMPBSA contains the Ambertools modules, otherwise you will get an error.

The error reported is due to the fact that the OpenMPI libraries are not installed.

Please try installing/reinstalling the OpenMPI library like this:

     sudo apt install openmpi-bin libopenmpi-dev openssh-client

or this way

    sudo apt install --reinstall openmpi-bin libopenmpi-dev openssh-client

Best!

Mario S.

[venkat]

Thank you very much for help 

I installed openmpi-bin libopenmpi-dev openssh-client 

Now, gmx_MMPBSA_anna working for me 

Happy and thank you 

  

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/868f9d84-6cf6-4ba4-b1ab-69010e68a467n%40googlegroups.com.

[Mario Sergio Valdes]

Excellent!

We are very happy to know that our tool is useful to you

Best!

Mario S.