Task 38581612
| Name | JNK1_A19_A12_r0_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-2-5-RND4114_1 |
| Workunit | 31546105 |
| Created | 12 Dec 2025, 11:18:20 UTC |
| Sent | 12 Dec 2025, 11:18:25 UTC |
| Report deadline | 17 Dec 2025, 11:18:25 UTC |
| Received | 12 Dec 2025, 17:03:57 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 610128 |
| Run time | 4 hours 6 min 55 sec |
| CPU time | 3 hours 57 min 48 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 35,587.29 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 670.41 MB |
| Peak swap size | 5.49 GB |
| Peak disk usage | 4.68 GB |
Stderr output
<core_client_version>7.22.2</core_client_version>
<![CDATA[
<stderr_txt>
06:49:59 (11916): wrapper (7.9.26016): starting
06:49:59 (11916): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A19_A12_0.pdb
QB_A19_A12_0.xml
QB_A19_A12_equil.pdb
QB_A19_A12.inpcrd
QB_A19_A12_input.yaml
QB_A19_A12_mdlambda.pdb
QB_A19_A12_min.pdb
QB_A19_A12_npt.pdb
QB_A19_A12_out_merged_nowater.pdb
QB_A19_A12.pdb
QB_A19_A12.prmtop
QB_A19_A12_sys.xml
QB_A19_A12_therm.pdb
run.bat
run.sh
06:50:01 (11916): Library/usr/bin/tar.exe exited; CPU time 0.000000
06:50:01 (11916): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
WARNING: The script pyaml.exe is installed in 'C:\ProgramData\BOINC\slots\6\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Running command pip subprocess to install build dependencies
Using pip 24.3.1 from C:\ProgramData\BOINC\slots\6\Lib\site-packages\pip (python 3.11)
Collecting setuptools
Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl.metadata
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Collecting setuptools-scm>=8
Obtaining dependency information for setuptools-scm>=8 from https://files.pythonhosted.org/packages/3d/ea/ac2bf868899d0d2e82ef72d350d97a846110c709bacf2d968431576ca915/setuptools_scm-9.2.2-py3-none-any.whl.metadata
Downloading setuptools_scm-9.2.2-py3-none-any.whl.metadata (7.7 kB)
Collecting packaging>=20 (from setuptools-scm>=8)
Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl.metadata
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
Using cached packaging-25.0-py3-none-any.whl (66 kB)
Installing collected packages: setuptools, packaging, setuptools-scm
Creating C:\ProgramData\BOINC\slots\6\pip-build-env-nnocucvi\overlay\Scripts
Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
Running command Getting requirements to build wheel
C:\ProgramData\BOINC\slots\6\pip-build-env-nnocucvi\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
warnings.warn(self.message)
running egg_info
writing atom_openmm.egg-info\PKG-INFO
writing dependency_links to atom_openmm.egg-info\dependency_links.txt
writing entry points to atom_openmm.egg-info\entry_points.txt
writing requirements to atom_openmm.egg-info\requires.txt
writing top-level names to atom_openmm.egg-info\top_level.txt
listing git files failed - pretending there aren't any
reading manifest file 'atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'atom_openmm.egg-info\SOURCES.txt'
Running command Preparing metadata (pyproject.toml)
C:\ProgramData\BOINC\slots\6\pip-build-env-nnocucvi\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
warnings.warn(self.message)
running dist_info
creating C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info
writing C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info\entry_points.txt
writing requirements to C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info\requires.txt
writing top-level names to C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\6\pip-modern-metadata-o6tl988j\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
C:\ProgramData\BOINC\slots\6\pip-build-env-nnocucvi\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
warnings.warn(self.message)
running bdist_wheel
running build
running build_py
creating build\lib\atom_openmm
copying atom_openmm\abfe_explicit.py -> build\lib\atom_openmm
copying atom_openmm\abfe_production.py -> build\lib\atom_openmm
copying atom_openmm\abfe_structprep.py -> build\lib\atom_openmm
copying atom_openmm\async_re.py -> build\lib\atom_openmm
copying atom_openmm\gibbs_sampling.py -> build\lib\atom_openmm
copying atom_openmm\local_openmm_transport.py -> build\lib\atom_openmm
copying atom_openmm\make_atm_system_from_amber.py -> build\lib\atom_openmm
copying atom_openmm\make_atm_system_from_pdb.py -> build\lib\atom_openmm
copying atom_openmm\make_atm_system_from_rcpt_lig.py -> build\lib\atom_openmm
copying atom_openmm\ommreplica.py -> build\lib\atom_openmm
copying atom_openmm\ommsystem.py -> build\lib\atom_openmm
copying atom_openmm\ommworker.py -> build\lib\atom_openmm
copying atom_openmm\openmm_async_re.py -> build\lib\atom_openmm
copying atom_openmm\rbfe_explicit.py -> build\lib\atom_openmm
copying atom_openmm\rbfe_production.py -> build\lib\atom_openmm
copying atom_openmm\rbfe_structprep.py -> build\lib\atom_openmm
copying atom_openmm\temperatureRE_explicit.py -> build\lib\atom_openmm
copying atom_openmm\transport.py -> build\lib\atom_openmm
copying atom_openmm\uwham.py -> build\lib\atom_openmm
copying atom_openmm\__init__.py -> build\lib\atom_openmm
creating build\lib\atom_openmm\utils
copying atom_openmm\utils\AtomUtils.py -> build\lib\atom_openmm\utils
copying atom_openmm\utils\config.py -> build\lib\atom_openmm\utils
copying atom_openmm\utils\singal_guard.py -> build\lib\atom_openmm\utils
copying atom_openmm\utils\timer.py -> build\lib\atom_openmm\utils
copying atom_openmm\utils\__init__.py -> build\lib\atom_openmm\utils
running egg_info
writing atom_openmm.egg-info\PKG-INFO
writing dependency_links to atom_openmm.egg-info\dependency_links.txt
writing entry points to atom_openmm.egg-info\entry_points.txt
writing requirements to atom_openmm.egg-info\requires.txt
writing top-level names to atom_openmm.egg-info\top_level.txt
listing git files failed - pretending there aren't any
reading manifest file 'atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'atom_openmm.egg-info\SOURCES.txt'
copying atom_openmm\utils\logging.conf -> build\lib\atom_openmm\utils
installing to build\bdist.win-amd64\wheel
running install
running install_lib
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\atom_openmm
copying build\lib\atom_openmm\abfe_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\abfe_production.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\abfe_structprep.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\async_re.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\gibbs_sampling.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\local_openmm_transport.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\make_atm_system_from_amber.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\make_atm_system_from_pdb.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\make_atm_system_from_rcpt_lig.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\ommreplica.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\ommsystem.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\ommworker.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\openmm_async_re.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\rbfe_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\rbfe_production.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\rbfe_structprep.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\temperatureRE_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\transport.py -> build\bdist.win-amd64\wheel\.\atom_openmm
creating build\bdist.win-amd64\wheel\atom_openmm\utils
copying build\lib\atom_openmm\utils\AtomUtils.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
copying build\lib\atom_openmm\utils\config.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
copying build\lib\atom_openmm\utils\logging.conf -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
copying build\lib\atom_openmm\utils\singal_guard.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
copying build\lib\atom_openmm\utils\timer.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
copying build\lib\atom_openmm\utils\__init__.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
copying build\lib\atom_openmm\uwham.py -> build\bdist.win-amd64\wheel\.\atom_openmm
copying build\lib\atom_openmm\__init__.py -> build\bdist.win-amd64\wheel\.\atom_openmm
running install_egg_info
Copying atom_openmm.egg-info to build\bdist.win-amd64\wheel\.\atom_openmm-8.4.0-py3.11.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\atom_openmm-8.4.0.dist-info\WHEEL
creating 'C:\ProgramData\BOINC\slots\6\pip-wheel-0zoz3wc2\.tmp-zzvf02u1\atom_openmm-8.4.0-py3-none-any.whl' and adding 'build\bdist.win-amd64\wheel' to it
adding 'atom_openmm/__init__.py'
adding 'atom_openmm/abfe_explicit.py'
adding 'atom_openmm/abfe_production.py'
adding 'atom_openmm/abfe_structprep.py'
adding 'atom_openmm/async_re.py'
adding 'atom_openmm/gibbs_sampling.py'
adding 'atom_openmm/local_openmm_transport.py'
adding 'atom_openmm/make_atm_system_from_amber.py'
adding 'atom_openmm/make_atm_system_from_pdb.py'
adding 'atom_openmm/make_atm_system_from_rcpt_lig.py'
adding 'atom_openmm/ommreplica.py'
adding 'atom_openmm/ommsystem.py'
adding 'atom_openmm/ommworker.py'
adding 'atom_openmm/openmm_async_re.py'
adding 'atom_openmm/rbfe_explicit.py'
adding 'atom_openmm/rbfe_production.py'
adding 'atom_openmm/rbfe_structprep.py'
adding 'atom_openmm/temperatureRE_explicit.py'
adding 'atom_openmm/transport.py'
adding 'atom_openmm/uwham.py'
adding 'atom_openmm/utils/AtomUtils.py'
adding 'atom_openmm/utils/__init__.py'
adding 'atom_openmm/utils/config.py'
adding 'atom_openmm/utils/logging.conf'
adding 'atom_openmm/utils/singal_guard.py'
adding 'atom_openmm/utils/timer.py'
adding 'atom_openmm-8.4.0.dist-info/licenses/LICENSE'
adding 'atom_openmm-8.4.0.dist-info/METADATA'
adding 'atom_openmm-8.4.0.dist-info/WHEEL'
adding 'atom_openmm-8.4.0.dist-info/entry_points.txt'
adding 'atom_openmm-8.4.0.dist-info/top_level.txt'
adding 'atom_openmm-8.4.0.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
WARNING: The scripts abfe_production.exe, abfe_structprep.exe, make_atm_system_from_amber.exe, make_atm_system_from_pdb.exe, make_atm_system_from_rcpt_lig.exe, rbfe_production.exe and rbfe_structprep.exe are installed in 'C:\ProgramData\BOINC\slots\6\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835210} normal block at 0x0000020EC715EE10, 8 bytes long.
Data: < N > 00 00 4E C7 0E 02 00 00
..\lib\diagnostics_win.cpp(417) : {3833972} normal block at 0x0000020EC8B9E6B0, 1080 bytes long.
Data: < u > AC 75 00 00 CD CD CD CD A4 03 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {318} normal block at 0x0000020EC7156740, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
08:41:53 (21392): wrapper (7.9.26016): starting
08:41:53 (21392): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\6\tmp already exists.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3849893} normal block at 0x000001F1E62AE510, 8 bytes long.
Data: < i > 00 00 69 E6 F1 01 00 00
..\lib\diagnostics_win.cpp(417) : {3848655} normal block at 0x000001F1E629DD70, 1080 bytes long.
Data: < 3 > BC 33 00 00 CD CD CD CD 04 03 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {318} normal block at 0x000001F1E62A1CA0, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
08:55:48 (5272): wrapper (7.9.26016): starting
08:55:48 (5272): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
12:00:16 (5272): C:/Windows/system32/cmd.exe exited; CPU time 10727.656250
12:00:16 (5272): called boinc_finish(0)
0 bytes in 0 Free Blocks.
256 bytes in 6 Normal Blocks.
1144 bytes in 1 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 205141128 bytes.
Dumping objects ->
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Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{3849970} normal block at 0x0000021A6D8B9860, 48 bytes long.
Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{3849959} normal block at 0x0000021A6D8BA3C0, 48 bytes long.
Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61
{3849948} normal block at 0x0000021A6D8BA430, 48 bytes long.
Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{3849937} normal block at 0x0000021A6D8B9C50, 48 bytes long.
Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61
{3849906} normal block at 0x0000021A6F56B9C0, 64 bytes long.
Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
..\api\boinc_api.cpp(309) : {3849893} normal block at 0x0000021A6D88E1F0, 8 bytes long.
Data: < †m > 00 00 86 6D 1A 02 00 00
{3848656} normal block at 0x0000021A6D88E650, 8 bytes long.
Data: <p݇m > 70 DD 87 6D 1A 02 00 00
..\zip\boinc_zip.cpp(122) : {318} normal block at 0x0000021A6D881160, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
{303} normal block at 0x0000021A6D882640, 80 bytes long.
Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C
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Data: <ð ‰m > F0 1F 89 6D 1A 02 00 00 00 00 00 00 00 00 00 00
{269} normal block at 0x0000021A6D891FF0, 40 bytes long.
Data: < e‰m À¹Vo > A0 65 89 6D 1A 02 00 00 C0 B9 56 6F 1A 02 00 00
{268} normal block at 0x0000021A6D896C80, 16 bytes long.
Data: <àr‰m > E0 72 89 6D 1A 02 00 00 00 00 00 00 00 00 00 00
{267} normal block at 0x0000021A6D896A50, 16 bytes long.
Data: <¸r‰m > B8 72 89 6D 1A 02 00 00 00 00 00 00 00 00 00 00
{266} normal block at 0x0000021A6D890DE0, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{265} normal block at 0x0000021A6D896C30, 16 bytes long.
Data: < r‰m > 90 72 89 6D 1A 02 00 00 00 00 00 00 00 00 00 00
{264} normal block at 0x0000021A6D897290, 992 bytes long.
Data: <0l‰m à ‰m > 30 6C 89 6D 1A 02 00 00 E0 0D 89 6D 1A 02 00 00
{100} normal block at 0x0000021A6D8902A0, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{99} normal block at 0x0000021A6D88D9D0, 16 bytes long.
Data: <P$‰m > 50 24 89 6D 1A 02 00 00 00 00 00 00 00 00 00 00
{98} normal block at 0x0000021A6D892450, 40 bytes long.
Data: <ÐÙ m   ‰m > D0 D9 88 6D 1A 02 00 00 A0 02 89 6D 1A 02 00 00
{77} normal block at 0x0000021A6D88DC00, 16 bytes long.
Data: < êF`÷ > 80 EA 46 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{76} normal block at 0x0000021A6D88E060, 16 bytes long.
Data: <@éF`÷ > 40 E9 46 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{75} normal block at 0x0000021A6D88E600, 16 bytes long.
Data: <øWC`÷ > F8 57 43 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{74} normal block at 0x0000021A6D88DED0, 16 bytes long.
Data: <ØWC`÷ > D8 57 43 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{73} normal block at 0x0000021A6D88D8E0, 16 bytes long.
Data: <P C`÷ > 50 04 43 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{72} normal block at 0x0000021A6D88DE80, 16 bytes long.
Data: <0 C`÷ > 30 04 43 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{71} normal block at 0x0000021A6D88E4C0, 16 bytes long.
Data: <à C`÷ > E0 02 43 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{70} normal block at 0x0000021A6D88E010, 16 bytes long.
Data: < C`÷ > 10 04 43 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{69} normal block at 0x0000021A6D88DFC0, 16 bytes long.
Data: <p C`÷ > 70 04 43 60 F7 7F 00 00 00 00 00 00 00 00 00 00
{68} normal block at 0x0000021A6D88DE30, 16 bytes long.
Data: < ÀA`÷ > 18 C0 41 60 F7 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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