All ATM tasks error out or have to be aborted

Message boards : Number crunching : All ATM tasks error out or have to be aborted

Author	Message
Greg _BE Send message Joined: 30 Jun 14 Posts: 135 Credit: 121,356,939 RAC: 23,416 Level Scientific publications	Message 60478 - Posted: 22 May 2023 \| 21:05:08 UTC
	I can't seem to get any ATM tasks to run. They either terminate on their own in a computation error or I abort them after they reach "100%" and stick in a endless loop until I kill them. For now I have suspended this project because its pointless to run stuff that doesn't work on my system. Here is a combination of BOINC tasks information (first section) and a run log (2nd section) Name p38_m2z_maa_3-QUICO_ATM_Sage_xTB_14-4-5-RND6656_0 Application ATMbeta: Free energy calculations of protein-ligand binding 1.09 (cuda1121) Workunit name p38_m2z_maa_3-QUICO_ATM_Sage_xTB_14-4-5-RND6656 State Running Received 5/20/2023 10:22:37 PM Report deadline 5/25/2023 10:22:36 PM Estimated app speed 32,450.25 GFLOPs/sec Estimated task size 1,000,000,000 GFLOPs Resources 0.988 CPUs + 1 NVIDIA GPU (device 0) CPU time at last checkpoint 00:00:00 CPU time 02:18:29 Elapsed time 00:51:04 Estimated time remaining 00:00:00 Fraction done 100.000% Virtual memory size 7,218.47 MB Working set size 2,101.48 MB Directory slots/0 Process ID 17800 Debug State: 2 - Scheduler: 2 This runs on a GTX 1080 and one virtual core. What does run.log show? Setup environment D:\data\slots\0>set HOMEPATH=D:\data\slots\0 D:\data\slots\0>set PATH=D:\data\slots\0;D:\data\slots\0\Library\usr\bin;D:\data\slots\0\Library\bin;C:\Windows\system32;C:\Windows D:\data\slots\0>set PYTHONPATH=D:\data\slots\0\Lib\python3.9\site-packages D:\data\slots\0>set SYSTEMROOT=C:\Windows Create a temporary directory D:\data\slots\0>set TEMP=D:\data\slots\0\tmp D:\data\slots\0>mkdir D:\data\slots\0\tmp Install AToM D:\data\slots\0>set REPO_URL=git+https://github.com/raimis/AToM-OpenMM.git@d7931b9a6217232d481731f7589d64b100a514ac D:\data\slots\0>python.exe -m pip install git+https://github.com/raimis/AToM-OpenMM.git@d7931b9a6217232d481731f7589d64b100a514ac \|\| exit 14 Collecting git+https://github.com/raimis/AToM-OpenMM.git@d7931b9a6217232d481731f7589d64b100a514ac Cloning https://github.com/raimis/AToM-OpenMM.git (to revision d7931b9a6217232d481731f7589d64b100a514ac) to d:\data\slots\0\tmp\pip-req-build-n4bnfm46 Resolved https://github.com/raimis/AToM-OpenMM.git to commit d7931b9a6217232d481731f7589d64b100a514ac Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Building wheels for collected packages: async-re Building wheel for async-re (setup.py): started Building wheel for async-re (setup.py): finished with status 'done' Created wheel for async-re: filename=async_re-3.3.0-py3-none-any.whl size=40735 sha256=b78cd7a2db0c0a4584d16c9a7967a2bdafe4f91754d0514cf1d4be7fd9e7038f Stored in directory: c:\users\greg\appdata\local\pip\cache\wheels\e3\94\02\5d2f795e8088e5cda09e48b0a167d6325c316862c02fa11467 Successfully built async-re Installing collected packages: async-re Successfully installed async-re-3.3.0 D:\data\slots\0>python.exe -m pip list Package Version ------------ ------- async-re 3.3.0 atmmetaforce 0.3 configobj 5.0.8 numpy 1.24.2 OpenMM 8.0.0 pip 23.0.1 setuptools 67.6.0 six 1.16.0 wheel 0.40.0 Configure AToM D:\data\slots\0>echo localhost,0:0,1,CUDA,,D:\data\slots\0\tmp 1>nodefile Extract restart D:\data\slots\0>tar.exe xjvf restart.tar.bz2 \|\| true r0/p38_m2z_maa_ckpt.xml r1/p38_m2z_maa_ckpt.xml r10/p38_m2z_maa_ckpt.xml r11/p38_m2z_maa_ckpt.xml r12/p38_m2z_maa_ckpt.xml r13/p38_m2z_maa_ckpt.xml r14/p38_m2z_maa_ckpt.xml r15/p38_m2z_maa_ckpt.xml r16/p38_m2z_maa_ckpt.xml r17/p38_m2z_maa_ckpt.xml r18/p38_m2z_maa_ckpt.xml r19/p38_m2z_maa_ckpt.xml r2/p38_m2z_maa_ckpt.xml r20/p38_m2z_maa_ckpt.xml r21/p38_m2z_maa_ckpt.xml r3/p38_m2z_maa_ckpt.xml r4/p38_m2z_maa_ckpt.xml r5/p38_m2z_maa_ckpt.xml r6/p38_m2z_maa_ckpt.xml r7/p38_m2z_maa_ckpt.xml r8/p38_m2z_maa_ckpt.xml r9/p38_m2z_maa_ckpt.xml Run AToM D:\data\slots\0>set CONFIG_FILE=p38_m2z_maa_asyncre.cntl D:\data\slots\0>python.exe Scripts\rbfe_explicit_sync.py p38_m2z_maa_asyncre.cntl \|\| exit 22 2023-05-21 12:44:43 - INFO - sync_re - Configuration: 2023-05-21 12:44:43 - INFO - sync_re - JOB_TRANSPORT: LOCAL_OPENMM 2023-05-21 12:44:43 - INFO - sync_re - BASENAME: p38_m2z_maa 2023-05-21 12:44:43 - INFO - sync_re - RE_SETUP: YES 2023-05-21 12:44:43 - INFO - sync_re - TEMPERATURES: 300 2023-05-21 12:44:43 - INFO - sync_re - LAMBDAS: 0.00, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, 0.50, 0.50, 0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 1.00 2023-05-21 12:44:43 - INFO - sync_re - DIRECTION: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 2023-05-21 12:44:43 - INFO - sync_re - INTERMEDIATE: 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 2023-05-21 12:44:43 - INFO - sync_re - LAMBDA1: 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.10, 0.20, 0.30, 0.40, 0.50, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00 2023-05-21 12:44:43 - INFO - sync_re - LAMBDA2: 0.00, 0.10, 0.20, 0.30, 0.40, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00 2023-05-21 12:44:43 - INFO - sync_re - ALPHA: 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10, 0.10 2023-05-21 12:44:43 - INFO - sync_re - U0: 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110., 110. 2023-05-21 12:44:43 - INFO - sync_re - W0COEFF: 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 2023-05-21 12:44:43 - INFO - sync_re - DISPLACEMENT: 22.0, 22.0, 22.0 2023-05-21 12:44:43 - INFO - sync_re - WALL_TIME: 9999 2023-05-21 12:44:43 - INFO - sync_re - CYCLE_TIME: 60 2023-05-21 12:44:43 - INFO - sync_re - CHECKPOINT_TIME: 300 2023-05-21 12:44:43 - INFO - sync_re - NODEFILE: nodefile 2023-05-21 12:44:43 - INFO - sync_re - SUBJOBS_BUFFER_SIZE: 0 2023-05-21 12:44:43 - INFO - sync_re - PRODUCTION_STEPS: 2000 2023-05-21 12:44:43 - INFO - sync_re - PRNT_FREQUENCY: 2000 2023-05-21 12:44:43 - INFO - sync_re - TRJ_FREQUENCY: 40000 2023-05-21 12:44:43 - INFO - sync_re - LIGAND1_ATOMS: ['5596', '5597', '5598', '5599', '5600', '5601', '5602', '5603', '5604', '5605', '5606', '5607', '5608', '5609', '5610', '5611', '5612', '5613', '5614', '5615', '5616', '5617', '5618', '5619', '5620', '5621', '5622', '5623', '5624', '5625', '5626', '5627', '5628', '5629', '5630', '5631', '5632', '5633', '5634', '5635', '5636', '5637', '5638', '5639', '5640'] 2023-05-21 12:44:43 - INFO - sync_re - LIGAND2_ATOMS: ['5641', '5642', '5643', '5644', '5645', '5646', '5647', '5648', '5649', '5650', '5651', '5652', '5653', '5654', '5655', '5656', '5657', '5658', '5659', '5660', '5661', '5662', '5663', '5664', '5665', '5666', '5667', '5668', '5669', '5670', '5671', '5672', '5673', '5674', '5675', '5676', '5677', '5678', '5679', '5680', '5681', '5682', '5683'] 2023-05-21 12:44:43 - INFO - sync_re - LIGAND1_CM_ATOMS: 5601 2023-05-21 12:44:43 - INFO - sync_re - LIGAND2_CM_ATOMS: 5646 2023-05-21 12:44:43 - INFO - sync_re - RCPT_CM_ATOMS: ['460', '483', '494', '501', '550', '745', '755', '771', '1178', '1337', '1363', '1654', '1673', '1689', '1703', '1720', '1739', '1756', '1763', '1773', '2532', '2685'] 2023-05-21 12:44:43 - INFO - sync_re - CM_KF: 25.00 2023-05-21 12:44:43 - INFO - sync_re - CM_TOL: 10 2023-05-21 12:44:43 - INFO - sync_re - POS_RESTRAINED_ATOMS: ['4', '19', '51', '57', '71', '91', '112', '136', '153', '168', '187', '201', '223', '237', '256', '280', '295', '319', '325', '340', '364', '385', '402', '416', '435', '454', '460', '476', '483', '494', '501', '511', '532', '539', '550', '566', '577', '587', '597', '617', '629', '643', '665', '679', '686', '705', '729', '745', '755', '771', '793', '815', '834', '845', '877', '883', '903', '920', '931', '950', '969', '986', '996', '1018', '1042', '1056', '1077', '1101', '1116', '1135', '1159', '1178', '1197', '1219', '1236', '1253', '1275', '1292', '1307', '1321', '1337', '1356', '1363', '1382', '1401', '1413', '1429', '1449', '1471', '1477', '1487', '1511', '1522', '1541', '1556', '1571', '1591', '1605', '1617', '1633', '1654', '1673', '1689', '1703', '1720', '1739', '1756', '1763', '1773', '1785', '1804', '1818', '1832', '1851', '1867', '1889', '1900', '1917', '1939', '1958', '1972', '1984', '1996', '2013', '2029', '2046', '2066', '2085', '2104', '2125', '2142', '2161', '2180', '2204', '2211', '2230', '2252', '2273', '2292', '2309', '2320', '2330', '2342', '2361', '2380', '2397', '2421', '2433', '2452', '2482', '2488', '2499', '2513', '2532', '2542', '2558', '2572', '2587', '2599', '2610', '2625', '2644', '2666', '2685', '2704', '2716', '2736', '2743', '2765', '2782', '2796', '2808', '2820', '2835', '2852', '2866', '2873', '2894', '2910', '2920', '2934', '2958', '2982', '3003', '3027', '3045', '3051', '3066', '3085', '3102', '3121', '3135', '3159', '3176', '3193', '3214', '3228', '3245', '3259', '3275', '3287', '3306', '3330', '3341', '3357', '3364', '3375', '3394', '3411', '3421', '3436', '3455', '3474', '3488', '3495', '3519', '3533', '3552', '3580', '3586', '3593', '3607', '3619', '3636', '3655', '3667', '3684', '3703', '3725', '3744', '3763', '3782', '3806', '3825', '3841', '3848', '3870', '3876', '3883', '3893', '3908', '3927', '3946', '3968', '3990', '4009', '4020', '4031', '4046', '4057', '4067', '4091', '4105', '4126', '4145', '4162', '4173', '4192', '4206', '4223', '4248', '4254', '4276', '4293', '4307', '4327', '4337', '4351', '4367', '4387', '4406', '4413', '4423', '4445', '4451', '4470', '4480', '4496', '4508', '4527', '4546', '4561', '4583', '4600', '4619', '4635', '4654', '4666', '4677', '4689', '4711', '4735', '4754', '4768', '4778', '4788', '4805', '4815', '4834', '4844', '4861', '4871', '4892', '4912', '4922', '4939', '4960', '4977', '4997', '5003', '5015', '5027', '5050', '5056', '5072', '5082', '5102', '5108', '5129', '5141', '5158', '5169', '5189', '5204', '5215', '5239', '5251', '5270', '5289', '5308', '5320', '5335', '5359', '5381', '5392', '5411', '5425', '5446', '5458', '5473', '5489', '5508', '5519', '5539', '5563', '5577', '5591'] 2023-05-21 12:44:43 - INFO - sync_re - POSRE_FORCE_CONSTANT: 25.0 2023-05-21 12:44:43 - INFO - sync_re - POSRE_TOLERANCE: 1.5 2023-05-21 12:44:43 - INFO - sync_re - ALIGN_LIGAND1_REF_ATOMS: ['5', '1', '20'] 2023-05-21 12:44:43 - INFO - sync_re - ALIGN_LIGAND2_REF_ATOMS: ['5', '1', '20'] 2023-05-21 12:44:43 - INFO - sync_re - ALIGN_KF_SEP: 2.5 2023-05-21 12:44:43 - INFO - sync_re - ALIGN_K_THETA: 25.0 2023-05-21 12:44:43 - INFO - sync_re - ALIGN_K_PSI: 25.0 2023-05-21 12:44:43 - INFO - sync_re - UMAX: 200.00 2023-05-21 12:44:43 - INFO - sync_re - ACORE: 0.062500 2023-05-21 12:44:43 - INFO - sync_re - UBCORE: 100.0 2023-05-21 12:44:43 - INFO - sync_re - FRICTION_COEFF: 0.100000 2023-05-21 12:44:43 - INFO - sync_re - TIME_STEP: 0.004 2023-05-21 12:44:43 - INFO - sync_re - OPENMM_PLATFORM: CUDA 2023-05-21 12:44:43 - INFO - sync_re - VERBOSE: no 2023-05-21 12:44:43 - INFO - sync_re - HMASS: 1.5 2023-05-21 12:44:43 - INFO - sync_re - MAX_SAMPLES: +70 2023-05-21 12:44:43 - INFO - sync_re - State parameters 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.0, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.0, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.05, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.1, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.1, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.2, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.15, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.3, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.2, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.4, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.25, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.3, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.1, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.35, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.2, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.4, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.3, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.45, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.4, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.5, 'atmdirection': 1.0, 'atmintermediate': 1.0, 'lambda1': 0.5, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=1.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.5, 'atmdirection': -1.0, 'atmintermediate': 1.0, 'lambda1': 0.5, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=1.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.55, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.4, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.6, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.3, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.65, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.2, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.7, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.1, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.75, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.8, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.4, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.85, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.3, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.9, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.2, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 0.95, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.1, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - State: {'lambda': 1.0, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.0, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'u0': Quantity(value=110.0, unit=kilocalorie/mole), 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=300.0, unit=kelvin)} 2023-05-21 12:44:43 - INFO - sync_re - Started: ATM setup 2023-05-21 12:44:43 - INFO - sync_re - Started: create system warning: AddRestraintForce() is deprecated. Use addVsiteRestraintForceCMCM() warning: AddRestraintForce() is deprecated. Use addVsiteRestraintForceCMCM() 2023-05-21 12:44:46 - INFO - sync_re - Running with a 4.000000 fs time-step with bonded forces integrated 4 times per time-step 2023-05-21 12:44:46 - INFO - sync_re - Finished: create system (duration: 3.515999999999849 s) 2023-05-21 12:44:46 - INFO - sync_re - Started: create worker 2023-05-21 12:44:46 - INFO - sync_re - Device: CUDA 0 2023-05-21 12:45:24 - INFO - sync_re - Finished: create worker (duration: 37.702999999999975 s) 2023-05-21 12:45:24 - INFO - sync_re - Started: create replicas 2023-05-21 12:45:24 - INFO - sync_re - Loading checkpointfile r0/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:27 - INFO - sync_re - Loading checkpointfile r1/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:29 - INFO - sync_re - Loading checkpointfile r2/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:32 - INFO - sync_re - Loading checkpointfile r3/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:34 - INFO - sync_re - Loading checkpointfile r4/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:37 - INFO - sync_re - Loading checkpointfile r5/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:39 - INFO - sync_re - Loading checkpointfile r6/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:42 - INFO - sync_re - Loading checkpointfile r7/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:44 - INFO - sync_re - Loading checkpointfile r8/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:47 - INFO - sync_re - Loading checkpointfile r9/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:49 - INFO - sync_re - Loading checkpointfile r10/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:52 - INFO - sync_re - Loading checkpointfile r11/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:54 - INFO - sync_re - Loading checkpointfile r12/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:57 - INFO - sync_re - Loading checkpointfile r13/p38_m2z_maa_ckpt.xml 2023-05-21 12:45:59 - INFO - sync_re - Loading checkpointfile r14/p38_m2z_maa_ckpt.xml 2023-05-21 12:46:02 - INFO - sync_re - Loading checkpointfile r15/p38_m2z_maa_ckpt.xml 2023-05-21 12:46:04 - INFO - sync_re - Loading checkpointfile r16/p38_m2z_maa_ckpt.xml 2023-05-21 12:46:07 - INFO - sync_re - Loading checkpointfile r17/p38_m2z_maa_ckpt.xml 2023-05-21 12:46:09 - INFO - sync_re - Loading checkpointfile r18/p38_m2z_maa_ckpt.xml 2023-05-21 12:46:12 - INFO - sync_re - Loading checkpointfile r19/p38_m2z_maa_ckpt.xml 2023-05-21 12:46:14 - INFO - sync_re - Loading checkpointfile r20/p38_m2z_maa_ckpt.xml 2023-05-21 12:46:17 - INFO - sync_re - Loading checkpointfile r21/p38_m2z_maa_ckpt.xml 2023-05-21 12:46:19 - INFO - sync_re - Replica 0: cycle 211, state 5 2023-05-21 12:46:19 - INFO - sync_re - Replica 1: cycle 211, state 2 2023-05-21 12:46:19 - INFO - sync_re - Replica 2: cycle 211, state 3 2023-05-21 12:46:19 - INFO - sync_re - Replica 3: cycle 211, state 11 2023-05-21 12:46:19 - INFO - sync_re - Replica 4: cycle 211, state 1 2023-05-21 12:46:19 - INFO - sync_re - Replica 5: cycle 211, state 6 2023-05-21 12:46:19 - INFO - sync_re - Replica 6: cycle 211, state 1 2023-05-21 12:46:19 - INFO - sync_re - Replica 7: cycle 211, state 10 2023-05-21 12:46:19 - INFO - sync_re - Replica 8: cycle 211, state 4 2023-05-21 12:46:19 - INFO - sync_re - Replica 9: cycle 211, state 8 2023-05-21 12:46:19 - INFO - sync_re - Replica 10: cycle 211, state 7 2023-05-21 12:46:19 - INFO - sync_re - Replica 11: cycle 211, state 20 2023-05-21 12:46:19 - INFO - sync_re - Replica 12: cycle 211, state 12 2023-05-21 12:46:19 - INFO - sync_re - Replica 13: cycle 211, state 14 2023-05-21 12:46:19 - INFO - sync_re - Replica 14: cycle 211, state 9 2023-05-21 12:46:19 - INFO - sync_re - Replica 15: cycle 211, state 13 2023-05-21 12:46:19 - INFO - sync_re - Replica 16: cycle 211, state 19 2023-05-21 12:46:19 - INFO - sync_re - Replica 17: cycle 211, state 15 2023-05-21 12:46:19 - INFO - sync_re - Replica 18: cycle 211, state 17 2023-05-21 12:46:19 - INFO - sync_re - Replica 19: cycle 211, state 16 2023-05-21 12:46:19 - INFO - sync_re - Replica 20: cycle 211, state 18 2023-05-21 12:46:19 - INFO - sync_re - Replica 21: cycle 211, state 21 2023-05-21 12:46:19 - INFO - sync_re - Finished: create replicas (duration: 55.406000000000176 s) 2023-05-21 12:46:19 - INFO - sync_re - Started: update replicas 2023-05-21 12:46:28 - INFO - sync_re - Finished: update replicas (duration: 9.1099999999999 s) 2023-05-21 12:46:28 - INFO - sync_re - Finished: ATM setup (duration: 105.7349999999999 s) 2023-05-21 12:46:28 - INFO - sync_re - Started: ATM simulations 2023-05-21 12:46:28 - INFO - sync_re - Additional number of samples: 70 2023-05-21 12:46:28 - INFO - sync_re - Started: sample 211 2023-05-21 12:46:28 - INFO - sync_re - Started: sample 211, replica 0 2023-05-21 12:47:05 - INFO - sync_re - Finished: sample 211, replica 0 (duration: 36.125 s) 2023-05-21 12:47:05 - INFO - sync_re - Started: sample 211, replica 1 2023-05-21 12:47:35 - INFO - sync_re - Finished: sample 211, replica 1 (duration: 30.8900000000001 s) 2023-05-21 12:47:35 - INFO - sync_re - Started: sample 211, replica 2 2023-05-21 12:48:07 - INFO - sync_re - Finished: sample 211, replica 2 (duration: 31.9849999999999 s) 2023-05-21 12:48:07 - INFO - sync_re - Started: sample 211, replica 3 2023-05-21 12:48:38 - INFO - sync_re - Finished: sample 211, replica 3 (duration: 30.54600000000005 s) 2023-05-21 12:48:38 - INFO - sync_re - Started: sample 211, replica 4 2023-05-21 12:49:09 - INFO - sync_re - Finished: sample 211, replica 4 (duration: 31.297000000000025 s) 2023-05-21 12:49:09 - INFO - sync_re - Started: sample 211, replica 5 2023-05-21 12:49:41 - INFO - sync_re - Finished: sample 211, replica 5 (duration: 31.375 s) 2023-05-21 12:49:41 - INFO - sync_re - Started: sample 211, replica 6 2023-05-21 12:50:11 - INFO - sync_re - Finished: sample 211, replica 6 (duration: 30.672000000000025 s) 2023-05-21 12:50:11 - INFO - sync_re - Started: sample 211, replica 7 2023-05-21 12:50:43 - INFO - sync_re - Finished: sample 211, replica 7 (duration: 31.6099999999999 s) 2023-05-21 12:50:43 - INFO - sync_re - Started: sample 211, replica 8 2023-05-21 12:51:14 - INFO - sync_re - Finished: sample 211, replica 8 (duration: 30.843000000000075 s) 2023-05-21 12:51:14 - INFO - sync_re - Started: sample 211, replica 9 2023-05-21 12:51:42 - INFO - sync_re - Finished: sample 211, replica 9 (duration: 28.672000000000025 s) 2023-05-21 12:51:42 - INFO - sync_re - Started: sample 211, replica 10 2023-05-21 12:52:13 - INFO - sync_re - Finished: sample 211, replica 10 (duration: 30.5 s) 2023-05-21 12:52:13 - INFO - sync_re - Started: sample 211, replica 11 2023-05-21 12:52:43 - INFO - sync_re - Finished: sample 211, replica 11 (duration: 30.312999999999874 s) 2023-05-21 12:52:43 - INFO - sync_re - Started: sample 211, replica 12 2023-05-21 12:53:15 - INFO - sync_re - Finished: sample 211, replica 12 (duration: 31.797000000000025 s) 2023-05-21 12:53:15 - INFO - sync_re - Started: sample 211, replica 13 2023-05-21 12:53:48 - INFO - sync_re - Finished: sample 211, replica 13 (duration: 32.5 s) 2023-05-21 12:53:48 - INFO - sync_re - Started: sample 211, replica 14 2023-05-21 12:54:20 - INFO - sync_re - Finished: sample 211, replica 14 (duration: 32.53099999999995 s) 2023-05-21 12:54:20 - INFO - sync_re - Started: sample 211, replica 15 2023-05-21 12:54:52 - INFO - sync_re - Finished: sample 211, replica 15 (duration: 32.34400000000005 s) 2023-05-21 12:54:52 - INFO - sync_re - Started: sample 211, replica 16 2023-05-21 12:55:24 - INFO - sync_re - Finished: sample 211, replica 16 (duration: 31.75 s) 2023-05-21 12:55:24 - INFO - sync_re - Started: sample 211, replica 17 2023-05-21 12:55:56 - INFO - sync_re - Finished: sample 211, replica 17 (duration: 31.875 s) 2023-05-21 12:55:56 - INFO - sync_re - Started: sample 211, replica 18 2023-05-21 12:56:29 - INFO - sync_re - Finished: sample 211, replica 18 (duration: 32.4849999999999 s) 2023-05-21 12:56:29 - INFO - sync_re - Started: sample 211, replica 19 2023-05-21 12:56:59 - INFO - sync_re - Finished: sample 211, replica 19 (duration: 30.077999999999975 s) 2023-05-21 12:56:59 - INFO - sync_re - Started: sample 211, replica 20 2023-05-21 12:57:30 - INFO - sync_re - Finished: sample 211, replica 20 (duration: 31.2650000000001 s) 2023-05-21 12:57:30 - INFO - sync_re - Started: sample 211, replica 21 2023-05-21 12:58:00 - INFO - sync_re - Finished: sample 211, replica 21 (duration: 30.593999999999824 s) 2023-05-21 12:58:00 - INFO - sync_re - Started: exchange replicas 2023-05-21 12:58:00 - INFO - sync_re - Replica 18: 17 --> 18 2023-05-21 12:58:00 - INFO - sync_re - Replica 20: 18 --> 17 2023-05-21 12:58:00 - INFO - sync_re - Finished: exchange replicas (duration: 0.047000000000025466 s) 2023-05-21 12:58:00 - INFO - sync_re - Started: update replicas 2023-05-21 12:58:09 - INFO - sync_re - Finished: update replicas (duration: 8.812000000000126 s) 2023-05-21 12:58:09 - INFO - sync_re - Started: write replicas samples and trajectories 2023-05-21 12:58:09 - INFO - sync_re - Finished: write replicas samples and trajectories (duration: 0.015999999999849024 s) 2023-05-21 12:58:09 - INFO - sync_re - Started: checkpointing 2023-05-21 12:58:59 - INFO - sync_re - Finished: checkpointing (duration: 50.031000000000176 s) 2023-05-21 12:58:59 - INFO - sync_re - Finished: sample 211 (duration: 750.9680000000001 s) 2023-05-21 12:58:59 - INFO - sync_re - Started: sample 212 2023-05-21 12:58:59 - INFO - sync_re - Started: sample 212, replica 0 2023-05-21 12:59:30 - INFO - sync_re - Finished: sample 212, replica 0 (duration: 30.687999999999874 s) 2023-05-21 12:59:30 - INFO - sync_re - Started: sample 212, replica 1 2023-05-21 13:00:00 - INFO - sync_re - Finished: sample 212, replica 1 (duration: 30.25 s) 2023-05-21 13:00:00 - INFO - sync_re - Started: sample 212, replica 2 2023-05-21 13:00:31 - INFO - sync_re - Finished: sample 212, replica 2 (duration: 30.797000000000025 s) 2023-05-21 13:00:31 - INFO - sync_re - Started: sample 212, replica 3 2023-05-21 13:01:02 - INFO - sync_re - Finished: sample 212, replica 3 (duration: 30.467999999999847 s) 2023-05-21 13:01:02 - INFO - sync_re - Started: sample 212, replica 4 2023-05-21 13:01:31 - INFO - sync_re - Finished: sample 212, replica 4 (duration: 29.71900000000005 s) 2023-05-21 13:01:31 - INFO - sync_re - Started: sample 212, replica 5 2023-05-21 13:02:02 - INFO - sync_re - Finished: sample 212, replica 5 (duration: 30.90599999999995 s) 2023-05-21 13:02:02 - INFO - sync_re - Started: sample 212, replica 6 2023-05-21 13:02:32 - INFO - sync_re - Finished: sample 212, replica 6 (duration: 29.96900000000005 s) 2023-05-21 13:02:32 - INFO - sync_re - Started: sample 212, replica 7 2023-05-21 13:03:03 - INFO - sync_re - Finished: sample 212, replica 7 (duration: 30.391000000000076 s) 2023-05-21 13:03:03 - INFO - sync_re - Started: sample 212, replica 8 2023-05-21 13:03:33 - INFO - sync_re - Finished: sample 212, replica 8 (duration: 30.34400000000005 s) 2023-05-21 13:03:33 - INFO - sync_re - Started: sample 212, replica 9 2023-05-21 13:04:04 - INFO - sync_re - Finished: sample 212, replica 9 (duration: 30.79599999999982 s) 2023-05-21 13:04:04 - INFO - sync_re - Started: sample 212, replica 10 2023-05-21 13:04:34 - INFO - sync_re - Finished: sample 212, replica 10 (duration: 30.375 s) 2023-05-21 13:04:34 - INFO - sync_re - Started: sample 212, replica 11 2023-05-21 13:05:04 - INFO - sync_re - Finished: sample 212, replica 11 (duration: 30.063000000000102 s) 2023-05-21 13:05:04 - INFO - sync_re - Started: sample 212, replica 12 2023-05-21 13:05:34 - INFO - sync_re - Finished: sample 212, replica 12 (duration: 29.827999999999975 s) 2023-05-21 13:05:34 - INFO - sync_re - Started: sample 212, replica 13 2023-05-21 13:06:05 - INFO - sync_re - Finished: sample 212, replica 13 (duration: 30.952999999999975 s) 2023-05-21 13:06:05 - INFO - sync_re - Started: sample 212, replica 14 2023-05-21 13:06:35 - INFO - sync_re - Finished: sample 212, replica 14 (duration: 30.264999999999873 s) 2023-05-21 13:06:35 - INFO - sync_re - Started: sample 212, replica 15 2023-05-21 13:07:04 - INFO - sync_re - Finished: sample 212, replica 15 (duration: 28.563000000000102 s) 2023-05-21 13:07:04 - INFO - sync_re - Started: sample 212, replica 16 2023-05-21 13:07:16 - INFO - sync_re - Finished: sample 212, replica 16 (duration: 12.0 s) 2023-05-21 13:07:16 - INFO - sync_re - Started: sample 212, replica 17 2023-05-21 13:07:27 - INFO - sync_re - Finished: sample 212, replica 17 (duration: 11.530999999999949 s) 2023-05-21 13:07:27 - INFO - sync_re - Started: sample 212, replica 18 2023-05-21 13:07:39 - INFO - sync_re - Finished: sample 212, replica 18 (duration: 11.938000000000102 s) 2023-05-21 13:07:39 - INFO - sync_re - Started: sample 212, replica 19 2023-05-21 13:07:51 - INFO - sync_re - Finished: sample 212, replica 19 (duration: 11.5 s) 2023-05-21 13:07:51 - INFO - sync_re - Started: sample 212, replica 20 2023-05-21 13:08:03 - INFO - sync_re - Finished: sample 212, replica 20 (duration: 11.967999999999847 s) 2023-05-21 13:08:03 - INFO - sync_re - Started: sample 212, replica 21 2023-05-21 13:08:14 - INFO - sync_re - Finished: sample 212, replica 21 (duration: 11.672000000000025 s) 2023-05-21 13:08:14 - INFO - sync_re - Started: exchange replicas 2023-05-21 13:08:14 - INFO - sync_re - Replica 4: 1 --> 1 2023-05-21 13:08:14 - INFO - sync_re - Replica 6: 1 --> 1 2023-05-21 13:08:14 - INFO - sync_re - Replica 7: 10 --> 11 2023-05-21 13:08:14 - INFO - sync_re - Replica 3: 11 --> 10 2023-05-21 13:08:14 - INFO - sync_re - Finished: exchange replicas (duration: 0.06300000000010186 s) 2023-05-21 13:08:14 - INFO - sync_re - Started: update replicas 2023-05-21 13:08:23 - INFO - sync_re - Finished: update replicas (duration: 8.827999999999975 s) 2023-05-21 13:08:23 - INFO - sync_re - Started: write replicas samples and trajectories 2023-05-21 13:08:23 - INFO - sync_re - Finished: write replicas samples and trajectories (duration: 0.0 s) 2023-05-21 13:08:23 - INFO - sync_re - Started: checkpointing 2023-05-21 13:09:12 - INFO - sync_re - Finished: checkpointing (duration: 49.266000000000076 s) 2023-05-21 13:09:13 - INFO - sync_re - Finished: sample 212 (duration: 613.1569999999999 s) 2023-05-21 13:09:13 - INFO - sync_re - Started: sample 213 2023-05-21 13:09:13 - INFO - sync_re - Started: sample 213, replica 0 2023-05-21 13:09:59 - INFO - sync_re - Finished: sample 213, replica 0 (duration: 46.4369999999999 s) 2023-05-21 13:09:59 - INFO - sync_re - Started: sample 213, replica 1 2023-05-21 13:10:45 - INFO - sync_re - Finished: sample 213, replica 1 (duration: 45.733999999999924 s) 2023-05-21 13:10:45 - INFO - sync_re - Started: sample 213, replica 2 2023-05-21 13:11:33 - INFO - sync_re - Finished: sample 213, replica 2 (duration: 48.28200000000015 s) 2023-05-21 13:11:33 - INFO - sync_re - Started: sample 213, replica 3 2023-05-21 13:12:24 - INFO - sync_re - Finished: sample 213, replica 3 (duration: 51.3119999999999 s) 2023-05-21 13:12:24 - INFO - sync_re - Started: sample 213, replica 4 2023-05-21 13:13:16 - INFO - sync_re - Finished: sample 213, replica 4 (duration: 51.922000000000025 s) 2023-05-21 13:13:16 - INFO - sync_re - Started: sample 213, replica 5 2023-05-21 13:14:08 - INFO - sync_re - Finished: sample 213, replica 5 (duration: 51.375 s) 2023-05-21 13:14:08 - INFO - sync_re - Started: sample 213, replica 6 2023-05-21 13:14:59 - INFO - sync_re - Finished: sample 213, replica 6 (duration: 51.53099999999995 s) 2023-05-21 13:14:59 - INFO - sync_re - Started: sample 213, replica 7 2023-05-21 13:15:51 - INFO - sync_re - Finished: sample 213, replica 7 (duration: 51.8130000000001 s) 2023-05-21 13:15:51 - INFO - sync_re - Started: sample 213, replica 8 2023-05-21 13:16:42 - INFO - sync_re - Finished: sample 213, replica 8 (duration: 51.0619999999999 s) 2023-05-21 13:16:42 - INFO - sync_re - Started: sample 213, replica 9 2023-05-21 13:17:34 - INFO - sync_re - Finished: sample 213, replica 9 (duration: 51.98500000000013 s) 2023-05-21 13:17:34 - INFO - sync_re - Started: sample 213, replica 10 2023-05-21 13:18:26 - INFO - sync_re - Finished: sample 213, replica 10 (duration: 52.0 s) 2023-05-21 13:18:26 - INFO - sync_re - Started: sample 213, replica 11 2023-05-21 13:19:18 - INFO - sync_re - Finished: sample 213, replica 11 (duration: 52.28099999999995 s) 2023-05-21 13:19:18 - INFO - sync_re - Started: sample 213, replica 12 2023-05-21 13:20:10 - INFO - sync_re - Finished: sample 213, replica 12 (duration: 51.266000000000076 s) 2023-05-21 13:20:10 - INFO - sync_re - Started: sample 213, replica 13 2023-05-21 13:21:03 - INFO - sync_re - Finished: sample 213, replica 13 (duration: 53.233999999999924 s) 2023-05-21 13:21:03 - INFO - sync_re - Started: sample 213, replica 14 2023-05-21 13:21:55 - INFO - sync_re - Finished: sample 213, replica 14 (duration: 52.03099999999995 s) 2023-05-21 13:21:55 - INFO - sync_re - Started: sample 213, replica 15 2023-05-21 13:22:49 - INFO - sync_re - Finished: sample 213, replica 15 (duration: 53.75 s) 2023-05-21 13:22:49 - INFO - sync_re - Started: sample 213, replica 16 2023-05-21 13:23:42 - INFO - sync_re - Finished: sample 213, replica 16 (duration: 53.077999999999975 s) 2023-05-21 13:23:42 - INFO - sync_re - Started: sample 213, replica 17 2023-05-21 13:24:34 - INFO - sync_re - Finished: sample 213, replica 17 (duration: 52.327999999999975 s) 2023-05-21 13:24:34 - INFO - sync_re - Started: sample 213, replica 18 2023-05-21 13:25:27 - INFO - sync_re - Finished: sample 213, replica 18 (duration: 52.82900000000018 s) 2023-05-21 13:25:27 - INFO - sync_re - Started: sample 213, replica 19 2023-05-21 13:26:20 - INFO - sync_re - Finished: sample 213, replica 19 (duration: 52.92099999999982 s) 2023-05-21 13:26:20 - INFO - sync_re - Started: sample 213, replica 20 2023-05-21 13:27:13 - INFO - sync_re - Finished: sample 213, replica 20 (duration: 53.40700000000015 s) 2023-05-21 13:27:13 - INFO - sync_re - Started: sample 213, replica 21 2023-05-21 13:28:05 - INFO - sync_re - Finished: sample 213, replica 21 (duration: 52.28099999999995 s) 2023-05-21 13:28:05 - INFO - sync_re - Started: exchange replicas 2023-05-21 13:28:05 - INFO - sync_re - Finished: exchange replicas (duration: 0.047000000000025466 s) 2023-05-21 13:28:05 - INFO - sync_re - Started: update replicas 2023-05-21 13:28:14 - INFO - sync_re - Finished: update replicas (duration: 9.030999999999949 s) 2023-05-21 13:28:14 - INFO - sync_re - Started: write replicas samples and trajectories 2023-05-21 13:28:14 - INFO - sync_re - Finished: write replicas samples and trajectories (duration: 0.0 s) 2023-05-21 13:28:14 - INFO - sync_re - Started: checkpointing 2023-05-21 13:29:04 - INFO - sync_re - Finished: checkpointing (duration: 50.016000000000076 s) 2023-05-21 13:29:04 - INFO - sync_re - Finished: sample 213 (duration: 1191.953 s) 2023-05-21 13:29:04 - INFO - sync_re - Started: sample 214 2023-05-21 13:29:04 - INFO - sync_re - Started: sample 214, replica 0 2023-05-21 13:29:58 - INFO - sync_re - Finished: sample 214, replica 0 (duration: 53.28099999999995 s) 2023-05-21 13:29:58 - INFO - sync_re - Started: sample 214, replica 1 2023-05-21 13:30:50 - INFO - sync_re - Finished: sample 214, replica 1 (duration: 52.483999999999924 s) 2023-05-21 13:30:50 - INFO - sync_re - Started: sample 214, replica 2 2023-05-21 13:31:43 - INFO - sync_re - Finished: sample 214, replica 2 (duration: 53.172000000000025 s) 2023-05-21 13:31:43 - INFO - sync_re - Started: sample 214, replica 3 2023-05-21 13:32:37 - INFO - sync_re - Finished: sample 214, replica 3 (duration: 53.141000000000076 s) 2023-05-21 13:32:37 - INFO - sync_re - Started: sample 214, replica 4 2023-05-21 13:33:30 - INFO - sync_re - Finished: sample 214, replica 4 (duration: 53.63999999999987 s) 2023-05-21 13:33:30 - INFO - sync_re - Started: sample 214, replica 5 2023-05-21 13:34:22 - INFO - sync_re - Finished: sample 214, replica 5 (duration: 51.98500000000013 s) 2023-05-21 13:34:22 - INFO - sync_re - Started: sample 214, replica 6 2023-05-21 13:35:07 - INFO - sync_re - Finished: sample 214, replica 6 (duration: 44.85900000000038 s) 2023-05-21 13:35:07 - INFO - sync_re - Started: sample 214, replica 7 2023-05-21 13:35:51 - INFO - sync_re - Finished: sample 214, replica 7 (duration: 44.35999999999967 s) 2023-05-21 13:35:51 - INFO - sync_re - Started: sample 214, replica 8 The common message in the stderr file contains this: Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. Detected memory leaks! Dumping objects -> ..\api\boinc_api.cpp(309) : {3078512} normal block at 0x000002153E930FD0, 8 bytes long. Data: < 6@ > 00 00 36 40 15 02 00 00 ..\lib\diagnostics_win.cpp(417) : {3077232} normal block at 0x000002153E919030, 1080 bytes long. Data: <8> h > 38 3E 00 00 CD CD CD CD 68 01 00 00 00 00 00 00 ..\zip\boinc_zip.cpp(122) : {278} normal block at 0x000002153E92E7F0, 260 bytes long. Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 Object dump complete. This depreciated item seems to be the cause. I have no memory leaks, thats just a stupid line. I run primegrid,LHC, SiDock and others just fine. Anyone know what the cause of this depricated whatever is? I saw something in github but didn't really understand it.
	ID: 60478 \| Rating: 0 \| rate: / Reply Quote

Keith Myers Send message Joined: 13 Dec 17 Posts: 1341 Credit: 7,684,871,308 RAC: 13,111,656 Level Scientific publications	Message 60479 - Posted: 22 May 2023 \| 23:05:54 UTC
	You do realize that most of the tasks with naming other than 0-5 jump right to 100% completion from the start. That is normal. You should let them run until they finish. Those tasks take around 10K seconds on my 2080 Ti. They are not stalled. If you view your disk activity you should see activity spiking every few minutes as the task writes out its progress in the slot files.
	ID: 60479 \| Rating: 0 \| rate: / Reply Quote

Greg _BE Send message Joined: 30 Jun 14 Posts: 135 Credit: 121,356,939 RAC: 23,416 Level Scientific publications	Message 60482 - Posted: 23 May 2023 \| 6:52:41 UTC - in response to Message 60479.
	You do realize that most of the tasks with naming other than 0-5 jump right to 100% completion from the start. That is normal. You should let them run until they finish. Those tasks take around 10K seconds on my 2080 Ti. They are not stalled. If you view your disk activity you should see activity spiking every few minutes as the task writes out its progress in the slot files. Interesting...ok...will restart them tonight and see what happens. BUT....the computation error tasks (look in my profile)....thats not normal.
	ID: 60482 \| Rating: 0 \| rate: / Reply Quote

Ian&Steve C. Send message Joined: 21 Feb 20 Posts: 1069 Credit: 40,231,533,983 RAC: 432 Level Scientific publications	Message 60485 - Posted: 23 May 2023 \| 11:57:21 UTC - in response to Message 60482. Last modified: 23 May 2023 \| 11:59:13 UTC
	these tasks are still in beta testing. some errors are normal. you will occasionally get errors if some tasks are sent out missing some files. you will occasionally get "energy is NaN" errors you will get errors if you suspend or interrupt the run of the task as they cannot be interrupted, will fail on restart because they don't resume from checkpoint properly. if you aren't willing to accept these kinds of situations, then I would recommend disabling beta testing in your project preferences and sticking to the non-beta tasks (PythonGPU and ACEMD3) when they are available. ____________
	ID: 60485 \| Rating: 0 \| rate: / Reply Quote

Greg _BE Send message Joined: 30 Jun 14 Posts: 135 Credit: 121,356,939 RAC: 23,416 Level Scientific publications	Message 60490 - Posted: 23 May 2023 \| 18:20:35 UTC - in response to Message 60485.
	these tasks are still in beta testing. some errors are normal. you will occasionally get errors if some tasks are sent out missing some files. you will occasionally get "energy is NaN" errors you will get errors if you suspend or interrupt the run of the task as they cannot be interrupted, will fail on restart because they don't resume from checkpoint properly. if you aren't willing to accept these kinds of situations, then I would recommend disabling beta testing in your project preferences and sticking to the non-beta tasks (PythonGPU and ACEMD3) when they are available. Thanks for the feedback. Question: what is a "normal" runtime to completion despite the status saying 100%?
	ID: 60490 \| Rating: 0 \| rate: / Reply Quote

Keith Myers Send message Joined: 13 Dec 17 Posts: 1341 Credit: 7,684,871,308 RAC: 13,111,656 Level Scientific publications	Message 60493 - Posted: 23 May 2023 \| 18:27:39 UTC - in response to Message 60490. Last modified: 23 May 2023 \| 18:28:56 UTC
	10,000 to 12,000 seconds typically on all my hosts. IOW 3 1/2 to 4 hours.
	ID: 60493 \| Rating: 0 \| rate: / Reply Quote

Richard Haselgrove Send message Joined: 11 Jul 09 Posts: 1620 Credit: 8,880,322,506 RAC: 19,946,201 Level Scientific publications	Message 60494 - Posted: 23 May 2023 \| 18:29:27 UTC - in response to Message 60493.
	10,000 to 12,000 seconds typically on all my hosts. It varies, depending on the GPU you're using.
	ID: 60494 \| Rating: 0 \| rate: / Reply Quote

Greg _BE Send message Joined: 30 Jun 14 Posts: 135 Credit: 121,356,939 RAC: 23,416 Level Scientific publications	Message 60496 - Posted: 23 May 2023 \| 21:26:32 UTC - in response to Message 60494. Last modified: 23 May 2023 \| 21:27:29 UTC
	10,000 to 12,000 seconds typically on all my hosts. It varies, depending on the GPU you're using. 1080 typically maybe my 1050 on occasion. I'll see if the 3-5 hour mark works the next time something is sent out. providing it doesn't error out on its own. Thanks guys
	ID: 60496 \| Rating: 0 \| rate: / Reply Quote

Post to thread

Message boards : Number crunching : All ATM tasks error out or have to be aborted

	About	Science	Volunteers	Performance	Forum	Join us	Donate