QuantumATK Forum

QuantumATK => Installation and License Questions => Topic started by: aziz.ogutlu on January 23, 2025, 09:53

Title: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on January 23, 2025, 09:53
Hi there all,
We are trying to install QuantumATK 2024.09 (also SP1) on Centos 7.9 HPC system. It's giving glibc 2.28 error because centos 7.9 supports 2.17 version max. Then we try to install on singularity image with Rocky Linux 8. But this time we get PyQt5 mismatch error with atkpython (which is 5.15.12 and it is only for macos on pypi.org) and system wide. Do you have PyQt5 5.15.12 downloadable version for x64 linux system? Also do you have any suggestion for using QuantumATK 2024.09 on our HPC system?
Best regards,
Aziz
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: filipr 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)

Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on January 23, 2025, 14:47
Hi filipr,
We run quantumatk command inside the singularity container like this:

---
[root@celestia singularity]# singularity shell --cleanenv --env DISPLAY=$DISPLAY --env XDG_SESSION_ID=$XDG_SESSION_ID --network bridge  --bind /run/munge:/run/munge --bind /opt/ohpc/pub:/opt/ohpc/pub qatk-2024.09-test.sif
Singularity> quantumatk
Traceback (most recent call last):
  File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
    sys.exit(start_quantumatk())
             ^^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
  File "zipdir/NL/__init__.py", line 9, in <module>
  File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
  File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
    raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
---
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: filipr 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.
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on January 28, 2025, 00:49
Hi filipr,
Thank you for your response.
We are installing almost all desktop packages with singularity definition file like below:
---
  dnf -y install libXft libXft-devel libXScrnSaver && \
  dnf -y install https://repos.openhpc.community/OpenHPC/2/CentOS_8/x86_64/ohpc-release-2-1.el8.x86_64.rpm && \
  dnf -y --enablerepo=powertools install lua-filesystem lua-posix && \
  dnf -y install ohpc-filesystem cairo libXext pixman lmod-ohpc && \
  dnf -y install mesa-libGL mesa-dri-drivers libglvnd libfabric && \
  dnf -y install qt5-qtbase.x86_64 python3-qt5.x86_64 python3-qt5-base.x86_64 lm_sensors-libs && \
---
When we run ld debug and qt debug command on page that you mention, we get these errors:
---
[root@celestia singularity]# singularity shell --cleanenv --env DISPLAY=$DISPLAY --env XDG_SESSION_ID=$XDG_SESSION_ID --network bridge  --bind /run/munge:/run/munge --bind /opt/ohpc/pub:/opt/ohpc/pub qatk-2024.09-test.sif
Singularity> LD_DEBUG=files /opt/ohpc/pub/apps/qatk/2024.09/bin/quantumatk > ld_debug.out 2>&1
Singularity> grep -i error ld_debug.out
    raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found


Singularity> QT_DEBUG_PLUGINS=3 /opt/ohpc/pub/apps/qatk/2024.09/bin/quantumatk
Traceback (most recent call last):
  File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
    sys.exit(start_quantumatk())
             ^^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
  File "zipdir/NL/__init__.py", line 9, in <module>
  File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
  File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
    raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
---
We want to update our systems OS to Rocky Linux 8, it is training for us to run QuantumATK 2024.09 on singularity.
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: filipr 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'.
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on January 28, 2025, 10:22
filipr, there is no variable name QT_API:
---
Code
[root@celestia singularity]# singularity shell --cleanenv --env DISPLAY=$DISPLAY --env XDG_SESSION_ID=$XDG_SESSION_ID --network bridge  --bind /run/munge:/run/munge --bind /opt/ohpc/pub:/opt/ohpc/pub qatk-2024.09-test.sif
Singularity> echo $QT_API

---
I run atkpython commands and return values are below:
---
Code
Singularity> /opt/ohpc/pub/apps/qatk/2024.09/bin/atkpython -c "from PyQt5 import QtCore"
MPI startup(): FI_PSM3_UUID was not generated, please set it to avoid possible resources ownership conflicts between MPI processes
+------------------------------------------------------------------------------+
|                                                                              |
|                                  QuantumATK®                                 |
|                                                                              |
|          Version: W-2024.09 for Windows and Linux [Build fe68a9810a2]        |
|                                                                              |
|                      Copyright © 2004-2025 Synopsys, Inc.                    |
|                                                                              |
|  This software and the associated documentation are proprietary to Synopsys, |
|      Inc. This software may only be used in accordance with the terms and    |
|  conditions of a written license agreement with Synopsys Inc. All other use, |
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|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 769, in __run_atkpython
  File "<string>", line 1, in <module>
  File "zipdir/QuantumATK.py", line 48, in <module>
  File "zipdir/NL/CommonConcepts/Configurations/SQSTools.py", line 17, in <module>
  File "zipdir/NL/Dynamics/CrystalStructurePrediction/CrystalStructurePrediction.py", line 11, in <module>
  File "zipdir/NL/Calculators/Interfaces/BulkCalculatorInterface.py", line 13, in <module>
  File "zipdir/NL/Calculators/CalculatorSettings.py", line 21, in <module>
  File "zipdir/NL/Calculators/GenericParameters/AlgorithmParameters.py", line 12, in <module>
  File "zipdir/NL/CommonConcepts/DensityMatrixMethods/IterativeEigensolvers/GeneralizedDavidsonSolver.py", line 10, in <module>
  File "zipdir/NL/CommonConcepts/DensityMatrixMethods/IterativeEigensolvers/IterativeEigensolver.py", line 6, in <module>
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/BaseLCAOCalculator.py", line 16, in <module>
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/SolvationModel/CosmoSolvationParameters.py", line 3, in <module>
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/SolvationModel/CosmoSolventSurface.py", line 46, in <module>
  File "zipdir/NL/GUI/Store/LIB.py", line 7, in <module>
  File "zipdir/NL/GUI/Store/Store.py", line 9, in <module>
  File "zipdir/qtbindings.py", line 7, in <module>
  File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
    raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
---
---
Code
Singularity> LD_DEBUG=files /opt/ohpc/pub/apps/qatk/2024.09/bin/atkpython -c "from PyQt5 import QtCore" > pyqt5_ld_debug.out 2>&1
Singularity> grep -i error pyqt5_ld_debug.out
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/lib/libpetsc.so.3.21: error: symbol lookup error: undefined symbol: ompi_mpi_init (fatal)
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/lib/libpetsc_real.so.3.21: error: symbol lookup error: undefined symbol: ompi_mpi_init (fatal)
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/lib/libiomp5.so: error: symbol lookup error: undefined symbol: ompt_start_tool (fatal)
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/atkpython/bin/python3.11: error: symbol lookup error: undefined symbol: scalable_malloc (fatal)
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/lib/libiomp5.so: error: symbol lookup error: undefined symbol: omp_target_alloc_host (fatal)
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/lib/libiomp5.so: error: symbol lookup error: undefined symbol: omp_target_alloc_shared (fatal)
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/lib/libiomp5.so: error: symbol lookup error: undefined symbol: omp_target_alloc_device (fatal)
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/lib/libiomp5.so: error: symbol lookup error: undefined symbol: omp_target_free (fatal)
    177214:    /opt/ohpc/pub/apps/qatk/2024.09/lib/libiomp5.so: error: symbol lookup error: undefined symbol: __tgt_register_ptask_services (fatal)
    177214:    file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/h5py/_errors.cpython-311-x86_64-linux-gnu.so [0];  dynamically loaded by /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/libpython3.11.so.1.0 [0]
    177214:    file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/h5py/_errors.cpython-311-x86_64-linux-gnu.so [0];  generating link map
    177214:    file=libhdf5_hl.so.10 [0];  needed by /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/h5py/_errors.cpython-311-x86_64-linux-gnu.so [0]
    177214:    calling init: /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/h5py/_errors.cpython-311-x86_64-linux-gnu.so
    177214:    opening file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/h5py/_errors.cpython-311-x86_64-linux-gnu.so [0]; direct_opencount=1
    177214:    file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/errors.cpython-311-x86_64-linux-gnu.so [0];  dynamically loaded by /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/libpython3.11.so.1.0 [0]
    177214:    file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/errors.cpython-311-x86_64-linux-gnu.so [0];  generating link map
    177214:    calling init: /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/errors.cpython-311-x86_64-linux-gnu.so
    177214:    opening file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/errors.cpython-311-x86_64-linux-gnu.so [0]; direct_opencount=1
    177214:    file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/error_wrappers.cpython-311-x86_64-linux-gnu.so [0];  dynamically loaded by /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/libpython3.11.so.1.0 [0]
    177214:    file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/error_wrappers.cpython-311-x86_64-linux-gnu.so [0];  generating link map
    177214:    calling init: /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/error_wrappers.cpython-311-x86_64-linux-gnu.so
    177214:    opening file=/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/error_wrappers.cpython-311-x86_64-linux-gnu.so [0]; direct_opencount=1
    raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
    177214:    calling fini: /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/h5py/_errors.cpython-311-x86_64-linux-gnu.so [0]
    177214:    calling fini: /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/errors.cpython-311-x86_64-linux-gnu.so [0]
    177214:    calling fini: /opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/pydantic/error_wrappers.cpython-311-x86_64-linux-gnu.so [0]
---
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: filipr 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"
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on January 28, 2025, 12:03
Code
Singularity> /opt/ohpc/pub/apps/qatk/2024.09/atkpython/bin/python -c "from PyQt5 import QtCore"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: libQt5Core.so.5: cannot open shared object file: No such file or directory
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: filipr 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'?
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on January 28, 2025, 13:31
There is no 5.15.14 version of that file but 5.15.12 version of it:
Code
Singularity> ls /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5
libQt5Core.so.5        libQt5Core.so.5.15     libQt5Core.so.5.15.12
Singularity> ls /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5 -l
lrwxrwxrwx 1 root root 21 Aug 16 15:30 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5 -> libQt5Core.so.5.15.12
Singularity> ldd /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.12
    linux-vdso.so.1 (0x00007ffdee7e1000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b47e2fae000)
    libz.so.1 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libz.so.1 (0x00002b47e27e2000)
    libdouble-conversion.so.3 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libdouble-conversion.so.3 (0x00002b47e2801000)
    libicutest.so.74 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libicutest.so.74 (0x00002b47e2814000)
    libicutu.so.74 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libicutu.so.74 (0x00002b47e28b0000)
    libicuio.so.74 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libicuio.so.74 (0x00002b47e2922000)
    libicui18n.so.74 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libicui18n.so.74 (0x00002b47e31ce000)
    libicuuc.so.74 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libicuuc.so.74 (0x00002b47e35bb000)
    libicudata.so.74 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libicudata.so.74 (0x00002b47e380c000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00002b47e556b000)
    libpcre2-16.so.0 => /opt/ohpc/pub/apps/qatk/2024.09/lib/libpcre2-16.so.0 (0x00002b47e2937000)
    libstdc++.so.6 => /opt/ohpc/pub/apps/qatk/2024.09/lib/pinned-libs/libstdc++.so.6 (0x00002b47e576f000)
    libm.so.6 => /lib64/libm.so.6 (0x00002b47e59eb000)
    libgcc_s.so.1 => /opt/ohpc/pub/apps/qatk/2024.09/lib/pinned-libs/libgcc_s.so.1 (0x00002b47e2994000)
    libc.so.6 => /lib64/libc.so.6 (0x00002b47e5d6d000)
    /lib64/ld-linux-x86-64.so.2 (0x00002b47e27a7000)
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: filipr 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.
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on January 28, 2025, 16:08
Ok filipr, thank you for your effort, we will wait for you.
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: Anders Blom on January 29, 2025, 00:07
Could it be something simple as file permissions not being right...?

Or perhaps something more advanced like https://stackoverflow.com/questions/63627955/cant-load-shared-library-libqt5core-so-5 is needed.
It's a total guess from my side, but it does pop up in several online posts related to Docker images.
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on January 29, 2025, 01:45
I did on https://stackoverflow.com/questions/64588549/paraview-error-while-loading-shared-libraries-libqt5core-so-5-cannot-open-sha/64594256#64594256 solution but not lucky:
Code
Singularity> strip --remove-section=.note.ABI-tag /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5
Singularity> quantumatk
Traceback (most recent call last):
  File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
    sys.exit(start_quantumatk())
             ^^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
  File "zipdir/NL/__init__.py", line 9, in <module>
  File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
  File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
    raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
Singularity> find / -iname libstdc++.so.6
/opt/ohpc/pub/apps/qatk/2022.03/lib/pinned-libs/libstdc++.so.6
/opt/ohpc/pub/apps/qatk/2024.09/lib/pinned-libs/libstdc++.so.6
/opt/ohpc/pub/compiler/gcc/8.3.0/lib64/libstdc++.so.6
/opt/ohpc/pub/libs/singularity/3.10.4/var/singularity/mnt/session/root/qatk/singularity/qatk/usr/lib/pinned-libs/libstdc++.so.6
/opt/ohpc/pub/libs/singularity/3.10.4/var/singularity/mnt/session/root/qatk/singularity/qatk/usr/lib64/libstdc++.so.6
/opt/ohpc/pub/libs/singularity/3.10.4/var/singularity/mnt/session/rootfs/usr/lib64/libstdc++.so.6
/root/qatk/singularity/qatk/usr/lib/pinned-libs/libstdc++.so.6
/root/qatk/singularity/qatk/usr/lib64/libstdc++.so.6
/usr/lib64/libstdc++.so.6
Singularity> cp /usr/lib64/libstdc++.so.6 /opt/ohpc/pub/apps/qatk/2024.09/lib/pinned-libs/libstdc++.so.6
Singularity> quantumatk
Traceback (most recent call last):
  File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
    sys.exit(start_quantumatk())
             ^^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
  File "zipdir/NL/__init__.py", line 9, in <module>
  File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
  File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
    raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
And permission for file in and out of singularity is like this:
Code
Singularity> ls -la /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so*
lrwxrwxrwx 1 root root      21 Aug 16 15:30 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so -> libQt5Core.so.5.15.12
lrwxrwxrwx 1 root root      21 Aug 16 15:30 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5 -> libQt5Core.so.5.15.12
lrwxrwxrwx 1 root root      21 Aug 16 15:30 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15 -> libQt5Core.so.5.15.12
-rwxr-xr-x 1 root root 6095128 Jan 29 03:36 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.12
Singularity> exit
[root@celestia singularity]# ls -la /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so*
lrwxrwxrwx 1 root root      21 Aug 16 15:30 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so -> libQt5Core.so.5.15.12
lrwxrwxrwx 1 root root      21 Aug 16 15:30 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5 -> libQt5Core.so.5.15.12
lrwxrwxrwx 1 root root      21 Aug 16 15:30 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15 -> libQt5Core.so.5.15.12
-rwxr-xr-x 1 root root 6095128 Jan 29 03:36 /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.12

Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: Anders Blom on January 29, 2025, 22:02
I would imagine you need to "patch" the actual file, not the softlink. So
Code
strip --remove-section=.note.ABI-tag /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.12

might be worth trying
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on February 5, 2025, 03:05
Same error again:
Code
[root@celestia singularity]# singularity shell --cleanenv --env DISPLAY=$DISPLAY --env XDG_SESSION_ID=$XDG_SESSION_ID --network bridge  --bind /run/munge:/run/munge --bind /opt/ohpc/pub:/opt/ohpc/pub qatk-2024.09-test.sif
Code
Singularity> strip --remove-section=.note.ABI-tag /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.12
Code
Singularity> quantumatk
Traceback (most recent call last):
  File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
    sys.exit(start_quantumatk())
             ^^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
  File "zipdir/NL/__init__.py", line 9, in <module>
  File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
  File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
    raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: aziz.ogutlu on March 5, 2025, 14:08
Is there any progress about testing on singularity?
Title: Re: QuantumATK 2024.09 PyQt5 error
Post by: filipr 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.