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adriverhoef
Master Cruncher
The Netherlands
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Post Count: 2219
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Error: Two atoms have the same XYZ coordinates!

Not a question, just an observation …

workunit 266691053
OPNG_0169376_00275_0  Linux Ubuntu  Invalid    2023-02-15T23:08:37  2023-02-16T06:03:02  0.24/0.72  58.6/0.0
OPNG_0169376_00275_1 Linux Ubuntu Invalid 2023-02-16T06:04:08 2023-02-16T06:58:49 0.28/0.90 58.6/0.0
OPNG_0169376_00275_2 Linux Ubuntu Invalid 2023-02-16T06:04:37 2023-02-16T06:53:45 0.26/0.80 58.6/0.0
OPNG_0169376_00275_3 Linux Ubuntu Invalid 2023-02-16T07:03:19 2023-02-16T07:50:11 0.24/0.78 58.6/0.0
OPNG_0169376_00275_4 Fedora Linux S.Aborted 2023-02-16T07:02:57 2023-02-16T07:56:09 0.00/0.00 0.0/0.0
OPNG_0169376_00275_5 Linux Debian Invalid 2023-02-16T07:08:08 2023-02-16T08:03:22 0.27/0.92 58.6/0.0
OPNG_0169376_00275_6 Linux Debian Invalid 2023-02-16T07:15:08 2023-02-16T08:46:06 0.04/1.51 58.6/0.0
---------------------------------------------------------------------------------------------------------------------------------------
Details:
OPNG_0169376_00275_0  Linux Ubuntu  Invalid    2023-02-15T23:08:37  2023-02-16T06:03:02  0.24/0.72  58.6/0.0
OS-Version: Ubuntu 22.04.1 LTS [5.15.0-58-generic|libc 2.35]
Logfile:
<core_client_version>7.20.5</core_client_version>
<stderr_txt>
../../projects/www.worldcommunitygrid.org/wcgrid_opng_autodockgpu_7.28_x86_64-pc-linux-gnu__opencl_intel_gpu_102 -jobs OPNG_0169376_00275.job -input OPNG_0169376_00275.zip -seed 473128886 -wcgruns 2100 -wcgdpf 42
INFO: Using gpu device from app init data 0
INFO:[06:19:42] Start AutoGrid...

autogrid4: Successful Completion.
INFO:[06:19:49] End AutoGrid...
... after 35 jobs ...
INFO:[06:55:32] Start AutoDock for OB37744998--8az9_B-001_cys_down--LYS125_inert.dpf(Job #35)...
OpenCL device: Intel(R) UHD Graphics 630 [0x3e9b]
Error: Two atoms have the same XYZ coordinates!
INFO:[06:55:34] End AutoDock...
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.dlg to wcg_autodock4.dlg. Error: 2
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.xml to wcg_ad4-result.xml. Error: 2

INFO:[06:55:34] Start AutoDock for OB37706299--8az9_B-001_cys_down--LYS125_inert.dpf(Job #36)...
OpenCL device: Intel(R) UHD Graphics 630 [0x3e9b]
INFO:[06:56:10] End AutoDock...
INFO:[06:56:10] Start AutoDock for OB37722962_1--8az9_B-001_cys_down--LYS125_inert.dpf(Job #37)...
OpenCL device: Intel(R) UHD Graphics 630 [0x3e9b]
INFO:[06:57:54] End AutoDock...
INFO:[06:57:55] Start AutoDock for OB37731161--8az9_B-001_cys_down--LYS125_inert.dpf(Job #38)...
OpenCL device: Intel(R) UHD Graphics 630 [0x3e9b]
INFO:[06:58:44] End AutoDock...
INFO:[06:58:44] Start AutoDock for OB37713914_4--8az9_B-001_cys_down--LYS125_inert.dpf(Job #39)...
OpenCL device: Intel(R) UHD Graphics 630 [0x3e9b]
INFO:[07:00:17] End AutoDock...
INFO:[07:00:17] Start AutoDock for OB37745752_2--8az9_B-001_cys_down--LYS125_inert.dpf(Job #40)...
OpenCL device: Intel(R) UHD Graphics 630 [0x3e9b]
INFO:[07:01:38] End AutoDock...
INFO:[07:01:38] Start AutoDock for OB37718995_4--8az9_B-001_cys_down--LYS125_inert.dpf(Job #41)...
OpenCL device: Intel(R) UHD Graphics 630 [0x3e9b]
INFO:[07:02:49] End AutoDock...
INFO:Cpu time = 858.656219
07:02:49 (63985): called boinc_finish(0)

</stderr_txt>
OPNG_0169376_00275_1 Linux Ubuntu Invalid 2023-02-16T06:04:08 2023-02-16T06:58:49 0.28/0.90 58.6/0.0
OS-Version: Ubuntu 22.04.1 LTS [5.15.0-60-generic|libc 2.35]
Logfile:
<core_client_version>7.18.1</core_client_version>
<stderr_txt>
../../projects/www.worldcommunitygrid.org/wcgrid_opng_autodockgpu_7.28_x86_64-pc-linux-gnu__opencl_intel_gpu_102 -jobs OPNG_0169376_00275.job -input OPNG_0169376_00275.zip -seed 473128886 -wcgruns 2100 -wcgdpf 42
INFO: Using gpu device from app init data 0
INFO:[07:04:17] Start AutoGrid...

autogrid4: Successful Completion.
INFO:[07:04:19] End AutoGrid...
... Same problem ...
INFO:[07:50:44] Start AutoDock for OB37744998--8az9_B-001_cys_down--LYS125_inert.dpf(Job #35)...
OpenCL device: Intel(R) UHD Graphics 630 [0x3e92]
Error: Two atoms have the same XYZ coordinates!
INFO:[07:50:45] End AutoDock...
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.dlg to wcg_autodock4.dlg. Error: 2
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.xml to wcg_ad4-result.xml. Error: 2
...
INFO:Cpu time = 1015.900029
07:58:32 (4012728): called boinc_finish(0)

</stderr_txt>
OPNG_0169376_00275_2 Linux Ubuntu Invalid 2023-02-16T06:04:37 2023-02-16T06:53:45 0.26/0.80 58.6/0.0
OS-Version: Ubuntu 22.04.1 LTS [5.15.0-56-generic|libc 2.35]
Logfile:
<core_client_version>7.19.0</core_client_version>
<stderr_txt>
../../projects/www.worldcommunitygrid.org/wcgrid_opng_autodockgpu_7.28_x86_64-pc-linux-gnu__opencl_intel_gpu_102 -jobs OPNG_0169376_00275.job -input OPNG_0169376_00275.zip -seed 473128886 -wcgruns 2100 -wcgdpf 42
INFO: Using gpu device from app init data 0
INFO:[01:04:42] Start AutoGrid...

autogrid4: Successful Completion.
INFO:[01:04:47] End AutoGrid...
... Same problem ...
INFO:[01:45:06] Start AutoDock for OB37744998--8az9_B-001_cys_down--LYS125_inert.dpf(Job #35)...
OpenCL device: Intel(R) HD Graphics 630 [0x591b]
Error: Two atoms have the same XYZ coordinates!
INFO:[01:45:08] End AutoDock...
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.dlg to wcg_autodock4.dlg. Error: 2
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.xml to wcg_ad4-result.xml. Error: 2
...
INFO:Cpu time = 938.565609
01:52:53 (1041474): called boinc_finish(0)

</stderr_txt>
OPNG_0169376_00275_3 Linux Ubuntu Invalid 2023-02-16T07:03:19 2023-02-16T07:50:11 0.24/0.78 58.6/0.0
OS-Version: Ubuntu 22.04.1 LTS [5.15.0-60-generic|libc 2.35]
Logfile:
<core_client_version>7.18.1</core_client_version>
<stderr_txt>
../../projects/www.worldcommunitygrid.org/wcgrid_opng_autodockgpu_7.28_x86_64-pc-linux-gnu__opencl_intel_gpu_102 -jobs OPNG_0169376_00275.job -input OPNG_0169376_00275.zip -seed 473128886 -wcgruns 2100 -wcgdpf 42
INFO: Using gpu device from app init data 0
INFO:[16:03:26] Start AutoGrid...

autogrid4: Successful Completion.
INFO:[16:03:30] End AutoGrid...
... Same problem ...
INFO:[16:43:35] Start AutoDock for OB37744998--8az9_B-001_cys_down--LYS125_inert.dpf(Job #35)...
OpenCL device: Intel(R) UHD Graphics 630 [0x9bc5]
Error: Two atoms have the same XYZ coordinates!
INFO:[16:43:37] End AutoDock...
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.dlg to wcg_autodock4.dlg. Error: 2
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.xml to wcg_ad4-result.xml. Error: 2
...
INFO:Cpu time = 866.392068
16:49:55 (1388785): called boinc_finish(0)

</stderr_txt>
OPNG_0169376_00275_4 Fedora Linux S.Aborted 2023-02-16T07:02:57 2023-02-16T07:56:09 0.00/0.00 0.0/0.0
OS-Version: Fedora Linux 35 (Thirty Five) [5.18.5-100.fc35.x86_64|libc 2.34]
Logfile:
<core_client_version>7.20.2</core_client_version>

OPNG_0169376_00275_5 Linux Debian Invalid 2023-02-16T07:08:08 2023-02-16T08:03:22 0.27/0.92 58.6/0.0
OS-Version: Debian GNU/Linux 11 (bullseye) [5.10.0-20-amd64|libc 2.31 (Debian GLIBC 2.31-13+deb11u5)]
Logfile:
<core_client_version>7.16.16</core_client_version>
<stderr_txt>
../../projects/www.worldcommunitygrid.org/wcgrid_opng_autodockgpu_7.28_x86_64-pc-linux-gnu__opencl_intel_gpu_102 -jobs OPNG_0169376_00275.job -input OPNG_0169376_00275.zip -seed 473128886 -wcgruns 2100 -wcgdpf 42
INFO: Using gpu device from app init data 0
INFO:[01:08:13] Start AutoGrid...

autogrid4: Successful Completion.
INFO:[01:08:15] End AutoGrid...
... Same problem ...
INFO:[01:56:35] Start AutoDock for OB37744998--8az9_B-001_cys_down--LYS125_inert.dpf(Job #35)...
OpenCL device: Intel(R) Graphics Gen9 [0x5912]
Error: Two atoms have the same XYZ coordinates!
INFO:[01:56:36] End AutoDock...
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.dlg to wcg_autodock4.dlg. Error: 2
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.xml to wcg_ad4-result.xml. Error: 2
...
INFO:Cpu time = 962.608294
02:03:10 (83029): called boinc_finish(0)

</stderr_txt>
OPNG_0169376_00275_6 Linux Debian Invalid 2023-02-16T07:15:08 2023-02-16T08:46:06 0.04/1.51 58.6/0.0
OS-Version: Debian GNU/Linux 11 (bullseye) [5.10.0-21-amd64|libc 2.31 (Debian GLIBC 2.31-13+deb11u5)]
Logfile:
<core_client_version>7.16.16</core_client_version>
<stderr_txt>
../../projects/www.worldcommunitygrid.org/wcgrid_opng_autodockgpu_7.28_x86_64-pc-linux-gnu__opencl_intel_gpu_102 -jobs OPNG_0169376_00275.job -input OPNG_0169376_00275.zip -seed 473128886 -wcgruns 2100 -wcgdpf 42
INFO: Using gpu device from app init data 0
INFO:[07:15:16] Start AutoGrid...

autogrid4: Successful Completion.
INFO:[07:15:19] End AutoGrid...
... Same problem ...
INFO:[08:34:51] Start AutoDock for OB37744998--8az9_B-001_cys_down--LYS125_inert.dpf(Job #35)...
OpenCL device: Intel(R) HD Graphics Haswell GT2 Desktop
Error: Two atoms have the same XYZ coordinates!
INFO:[08:34:54] End AutoDock...
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.dlg to wcg_autodock4.dlg. Error: 2
[ERROR] Failed to open either source or destination files while appending wcg_autodock4_sub.xml to wcg_ad4-result.xml. Error: 2
...
INFO:Cpu time = 160.900445
08:45:50 (1022167): called boinc_finish(0)

</stderr_txt>

[Feb 16, 2023 10:07:45 AM]   Link   Report threatening or abusive post: please login first  Go to top 
Grumpy Swede
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Re: Error: Two atoms have the same XYZ coordinates!

I hate it when Two atoms have the same XYZ coordinates. It's too much of Quantum mechanics for my taste, and goes against everything I feel about a too crowded space smile

But the problem is not unknown: Two atoms exist in the same coordinate position in the lattice?
[Feb 16, 2023 1:47:43 PM]   Link   Report threatening or abusive post: please login first  Go to top 
MarkH
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Re: Error: Two atoms have the same XYZ coordinates!

All this assumes our quantum theory is correct, became there is the distinct possibility that either the Heisenberg Uncertainty Principle applies, rendering our quantum theory the equivalent of dividing by zero, or in Transmogrification Space two objects can occupy the same space at the same time because neither is actually affected by the other's intrusion, being in different timeplanes.

I am available for consulting services to major technical and scientific organizations needing a fresh perspective, or a good laugh, but remember, they laughed at Wilbur and Orville also. "It's been a long road, gettin' from there to here..."
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"That science of the people, by the people, for the people, shall not perish from the Earth."
[Feb 19, 2023 2:15:02 AM]   Link   Report threatening or abusive post: please login first  Go to top 
NixChix
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Re: Error: Two atoms have the same XYZ coordinates!

Was that error generated when the inital data file was read by the application?

Cheers coffee
----------------------------------------

[Feb 24, 2023 8:39:05 PM]   Link   Report threatening or abusive post: please login first  Go to top 
NixChix
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Re: Error: Two atoms have the same XYZ coordinates!

Look what happened last time all of the atoms had the same XYZ coordinates!
----------------------------------------

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[Edit 1 times, last edit by NixChix at Feb 24, 2023 8:41:32 PM]
[Feb 24, 2023 8:41:11 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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