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Messages - aziz.ogutlu

Pages: [1]
1
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« 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


2
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« on: January 28, 2025, 16:08 »
Ok filipr, thank you for your effort, we will wait for you.

3
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« 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)

4
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« 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

5
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« 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, |
|    reproduction, modification, or distribution of this software is strictly  |
|    prohibited. Licensed Products communicate with Synopsys servers for the   |
|      purpose of providing software updates, detecting software piracy and    |
|  verifying that customers are using Licensed products in conformity with the |
|      applicable License Key for such Licensed Products. Synopsys will use    |
|    information gathered in connection with this process to deliver software  |
|              updates and pursue software pirates and infringers.             |
|                                                                              |
|  Inclusivity & Diversity - Visit SolvNetPlus to read the "Synopsys Statement |
|        on Inclusivity and Diversity" (Refer to the article 000036315 at      |
|                       https://solvnetplus.synopsys.com)                      |
|                                                                              |
+------------------------------------------------------------------------------+
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]
---

6
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« 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.

7
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« 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
---

8
Installation and License Questions / QuantumATK 2024.09 PyQt5 error
« 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

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