Messages

1

General Questions and Answers / Re: Problem running QuantumATK X-2025.06 in parallel with SLURM

« on: September 1, 2025, 15:48 »

Hi Pshinyeong, QuantumATK ships it's own version of Intel MPI. The version shipped with QuantumATK X-2025.06 is Intel MPI 2021.15 which comes with Intel oneAPI 2024.2 (I believe), which is newer than the one you load in your job script. Newer versions of Intel MPI are not necessarily compatible with older versions, so that could be why it fails.

I suggest that you do not use a custom Intel MPI version unless you really, REALLY know what you're doing. So instead of loading oneAPI or OpenMPI as you would maybe normally do for other academic software your simply don't. QuantumATK is a self-container plug-and-play solution that works as-is without any installed libraries or tools.

So I recommend you remove the module loads and simply have this line to launch your job:

Code

srun /path/to/atkpython $PYTHON_SCRIPT > $LOG_FILE

If in doubt - use the built in job manager GUI to set up submission scripts for Slurm.

2

General Questions and Answers / Re: MPI error

« on: May 15, 2025, 14:05 »

This appears to be problem with either the cluster configuration or Intel MPI. Contact your cluster admin and show them this error and/or submit a support question on the Intel oneAPI support forum: https://community.intel.com/t5/Intel-MPI-Library/bd-p/oneapi-hpc-toolkit

In both cases it can help them if you set the environment variable I_MPI_DEBUG=5 in your submission script and rerun and copy the debug output from Intel MPI when asking for help elsewhere.

3

Installation and License Questions / Re: can not start quantumatk in GUI mode

« on: May 13, 2025, 10:52 »

Vasilipe, if you search the internet for the error message "cannot execute: required file not found" you'll see that most of the times people report this problem it is due to errors with the shebang of scripts - either the program that the shebang points to doesn't exist or there is a typo or stray whitespace/newline characters. The 'atkpython' launcher script uses the same shebang as the 'quantumatk' launcher script, so if 'atkpython' works it would be weird if 'quantumatk' doesn't. Please check that the shebang (first line) of '/eng/tools/synopsys/atk/W-2024.09-SP1/atkpython/bin/quantumatk' is the same as in  '/eng/tools/synopsys/atk/W-2024.09-SP1/atkpython/bin/atkpython'. Also check that you can run the  '/eng/tools/synopsys/atk/W-2024.09-SP1/atkpython/bin/python3.11' executable.

If you're still having problems, it could be that the installation was somehow corrupted or that your system is not supported, see https://docs.quantumatk.com/intro/installation/technical_hardware.html#linux for system requirements. I recommend contacting your system administrator as the problem is most likely due to the installation or system configuration and not the software.

4

Installation and License Questions / Re: can not start quantumatk in GUI mode

« on: May 12, 2025, 10:49 »

Is it possible that the installation folder was moved after the program was installed?

Try to open the file '/eng/tools/synopsys/atk/W-2024.09-SP1/atkpython/bin/quantumatk' in a simple text editor (it's a simple text file). The first line has a "shebang" (which tells the OS which program to run the file with) and should be the full path the the actual python executable with the path: '/eng/tools/synopsys/atk/W-2024.09-SP1/atkpython/bin/python3.11'. If it points to a file that does not exist it means the installation directory was moved, and the launcher script will not work. You (or your sys admin) shouldn't move the installation folder, but you can try to fix the shebang to point to a valid path.

5

General Questions and Answers / Re: can someone help with log file update problem?

« on: April 22, 2025, 09:49 »

Can you share what kind of CPU, Operating System and network interface (ethernet/infiniband) these nodes have?

On another note: This level of parallelism is way overkill for this system and will probably make it run slower, not faster. You're trying to use 18 processes so find the eigenvalues of a 1004x1004 matrix, which is honestly not that big and can be done pretty quick on even a laptop CPU.

I suggest that you run on a single 48 core node with 16 MPI processes and 3 OpenMP threads. This will ensure that each MPI process get one k-point and three CPU cores are working on the matrices for that k-point.

6

General Questions and Answers / Re: Module "calculatePlasmaFrequency"

« on: April 8, 2025, 09:06 »

The function returns the plasma frequency, i.e. the square root of the expression in the documentation.

7

Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error

« on: March 6, 2025, 10:15 »

We have not looked into this yet, and it might take quite some time (months+) before it will happen, so if you need an urgent solution I recommend that you look for alternative ways to run QuantumATK. I have filed a ticket in our bug reporting system, so that the issue is not forgotten.

8

General Questions and Answers / Re: I need help on bader charge analysis

« on: February 24, 2025, 17:35 »

You should use the PAW method instead of normconserving pseudopotentials. See also documentation and notes in the manual: https://docs.quantumatk.com/manual/Types/BaderCharges/BaderCharges.html

9

Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error

« on: January 28, 2025, 15:37 »

Hmm it seems to be something different than just missing system libraries - probably some deeper problem related to how these containers work. I don't have a solution for you right now - we will have to try to get our hands on our own singularity container and that can take a while.

I suggest that you install QuantumATK on bare metal or in a VM. Do note that QuantumATK ships all needed dependencies and does not require that the cluster has anything installed as long as it lives up to our stated requirements, most notably a Linux distro that has glibc version 2.28 or newer (no RHEL/CentOS 7). For that reason there is little utility in using containers for QuantumATK.

10

Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error

« on: January 28, 2025, 12:59 »

Is the file 'libQt5Core.so.5' in the directory '/opt/ohpc/pub/apps/qatk/2024.09/lib'? i.e. does the symlink ''/opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5' exist and point to the file '/opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.14'?

If it exists, what it the output of 'ldd /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.14'?

11

Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error

« on: January 28, 2025, 11:48 »

Hmm, try to run

Code

/opt/ohpc/pub/apps/qatk/2024.09/atkpython/bin/python -c "from PyQt5 import QtCore"

12

Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error

« on: January 28, 2025, 09:54 »

Ok, as you can see the error comes from within the loading of the 'QtPy' Python package in the file (which you can open yourself to see): "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py" on line 259. It appears that QtPy tries to load PySide but fails. QuantumATK uses PyQt5, not PySide. So something causes it to try to load PySide instead. This can either be because an environment variable 'QT_API' is set or because PyQt5 cannot be loaded for some reason (most likely missing system libraries).

So first check if there's an environment variable 'QT_API' set before running 'quantumatk'? If there is, be sure to unset this before running quantumatk: 'unset QT_API'.

If there's no such variable, try to run: `/opt/ohpc/pub/apps/qatk/2024.09/bin/atkpython -c "from PyQt5 import QtCore"' and see what comes out. If it fail, but doesn't mention any reason, try to run:

Code

LD_DEBUG=files /opt/ohpc/pub/apps/qatk/2024.09/bin/atkpython -c "from PyQt5 import QtCore" > pyqt5_ld_debug.out 2>&1

and then grep for errors in the generated file 'pyqt5_ld_debug.out'.

13

Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error

« on: January 27, 2025, 11:20 »

It could be that the Rocky Linux Singularity image is rather minimal and does not come by default with basic libraries for graphics applications (X window system). Our installation guide and system requirements assumes a default consumer Linux distribution.

It might be that you have to install some X related system libraries, check out: https://docs.quantumatk.com/intro/installation/technical_hardware.html#distribution-specific-installation-steps and https://docs.quantumatk.com/faq/faq_technical_hardware_for_v2023_12.html#distribution-specific-installation-steps

If installing the mentioned libraries (libxcb-xinerama0 and perhaps libXScrnSaver) does not fix it, you can check if more libraries are missing by running

Code

$> LD_DEBUG=files path/to/quantumatk > ld_debug.out 2>&1

then look in the generated file 'ld_debug.out' for errors, e.g. 'grep -i error ld_debug.out' and see if it fails to find any .so files. If it does, then find out what system packages (typically some X/xcb related ones) are missing and install those. You can look for which packages that ship library files here: https://pkgs.org/ (filter by Rocky8 and x86_64)

If you cannot install/use graphical applications in the Singularity container, you need to create a container that allows for this. We do not officially support Singularity containers, but we hope to get some time to look into this if this becomes a frequent user request.

14

Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error

« on: January 23, 2025, 14:02 »

Hi Aziz,

QuantumATK ships it's own version of Qt and PyQt - it does not depend, nor use the one installed on the system. When you say "But this time we get PyQt5 mismatch error with atkpython" what do you mean by this? How do you get this error? How do you attempt to run atkpython or quantumatk? And what is the full error message? (please copy and paste verbatim)

15

General Questions and Answers / Re: linear response optimization of Hubbard U value for non-metallic kagome graphene

« on: January 13, 2025, 13:49 »

Not in 2018.06, but in the newest version 2024.09 you can calculate U from linear response: https://docs.quantumatk.com/manual/Types/calculateFiniteDifferenceLinearResponseHubbardU/calculateFiniteDifferenceLinearResponseHubbardU.html