LImA2 error message
2023-07-13 21:49:23,148 |MX3.HWR|INFO | [LIMS] Searching for proposal: mx2429 2023-07-13 21:49:23,148 |MX3.HWR|INFO | [LIMS] Selecting proposal: mx2429 2023-07-13 21:49:23,148 |MX3.HWR|INFO | [LIMS] Proposal info: {'Proposal': {'code': 'mx', 'number': '2429', 'proposalId': '9227', 'title': 'Towards TR-SSX at ID29', 'type': 'MX', 'personId': '405446'}, 'Person': {'emailAddress': 'smarius@uwm.edu', 'familyName': 'SCHMIDT', 'givenName': 'Marius', 'login': 'marius1711', 'personId': '405446', 'personUUID': '0000000209629468', 'phoneNumber': '4146287998', 'siteId': '123899', 'title': 'Prof', 'laboratoryId': '314395'}, 'Laboratory': {'address': 'Kenwood Interdisciplinary Research Complex\nPhysics Department, Room 3087\n3135 North Maryland Avenue\n53211', 'city': 'MILWAUKEE', 'country': 'US', 'laboratoryExtPk': '228458', 'laboratoryId': '314395', 'name': 'University of Wisconsin-Milwaukee'}, 'Session': [{'beamlineName': 'ID29', 'beamlineOperator': 'BASU Shibom', 'endDate': '2023-07-14 08:00:00', 'expSessionPk': '141217', 'lastUpdate': '2023-07-14 08:00:00+02:00', 'nbShifts': '9', 'operatorSiteNumber': '333831', 'sessionId': '79100', 'sessionTitle': 'MX/2429 ID29 11-07-2023/14-07-2023', 'startDate': '2023-07-11 09:30:00', 'timeStamp': '2023-07-08 22:00:05+02:00', 'visit_number': '150', 'proposalId': '9227', 'proposalName': 'mx2429'}], 'status': {'code': 'ok'}} Creating Virtual Dataset (2000, 2164, 2068) on /data/visitor/mx2429/id29/20230713/RAW_DATA/PHYTO_MID/P2MY_tape_700ms/run_13/aggregated/master_PHYTO_MID-PHYTO_MID_dense_00149.h5 from ['../PHYTO_MID-PHYTO_MID_dense_0_00149.h5', '../PHYTO_MID-PHYTO_MID_dense_1_00149.h5'] Creating Virtual Dataset (2000, 2164, 2068) on /data/visitor/mx2429/id29/20230713/RAW_DATA/PHYTO_MID/P2MY_tape_700ms/run_13/aggregated/master_PHYTO_MID-PHYTO_MID_dense_00150.h5 from ['../PHYTO_MID-PHYTO_MID_dense_0_00150.h5', '../PHYTO_MID-PHYTO_MID_dense_1_00150.h5'] Master files saved: 150 Creating Virtual Dataset (300000, 2164, 2068) on /data/visitor/mx2429/id29/20230713/RAW_DATA/PHYTO_MID/P2MY_tape_700ms/run_13/aggregated/master_PHYTO_MID-PHYTO_MID_dense.h5 from ['master_PHYTO_MID-PHYTO_MID_dense_00000.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00001.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00002.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00003.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00004.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00005.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00006.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00007.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00008.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00009.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00010.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00011.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00012.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00013.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00014.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00015.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00016.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00017.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00018.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00019.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00020.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00021.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00022.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00023.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00024.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00025.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00026.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00027.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00028.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00029.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00030.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00031.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00032.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00033.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00034.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00035.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00036.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00037.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00038.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00039.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00040.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00041.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00042.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00043.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00044.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00045.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00046.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00047.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00048.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00049.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00050.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00051.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00052.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00053.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00054.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00055.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00056.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00057.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00058.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00059.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00060.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00061.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00062.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00063.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00064.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00065.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00066.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00067.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00068.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00069.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00070.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00071.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00072.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00073.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00074.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00075.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00076.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00077.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00078.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00079.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00080.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00081.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00082.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00083.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00084.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00085.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00086.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00087.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00088.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00089.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00090.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00091.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00092.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00093.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00094.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00095.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00096.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00097.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00098.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00099.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00100.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00101.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00102.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00103.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00104.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00105.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00106.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00107.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00108.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00109.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00110.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00111.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00112.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00113.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00114.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00115.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00116.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00117.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00118.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00119.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00120.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00121.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00122.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00123.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00124.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00125.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00126.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00127.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00128.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00129.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00130.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00131.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00132.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00133.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00134.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00135.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00136.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00137.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00138.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00139.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00140.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00141.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00142.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00143.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00144.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00145.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00146.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00147.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00148.h5', 'master_PHYTO_MID-PHYTO_MID_dense_00149.h5'] Traceback (most recent call last): File "src/gevent/greenlet.py", line 906, in gevent._gevent_cgreenlet.Greenlet.run File "/opt/bliss/src/sls_detectors/lima2-client/src/lima2/client/smx/aggregation.py", line 117, in dense_loop proc_info) File "/opt/bliss/src/sls_detectors/lima2-client/src/lima2/client/smx/aggregation.py", line 306, in create_virtual_dataset with h5.File(n, 'r') as f: File "/users/blissadm/conda/miniconda/envs/mxcubeweb/lib/python3.7/site-packages/h5py/_hl/files.py", line 533, in init fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr) File "/users/blissadm/conda/miniconda/envs/mxcubeweb/lib/python3.7/site-packages/h5py/_hl/files.py", line 226, in make_fid fid = h5f.open(name, flags, fapl=fapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 106, in h5py.h5f.open OSError: Unable to open file (truncated file: eof = 395532674, sblock->base_addr = 0, stored_eof = 8510821098) 2023-07-13T19:49:36Z <BlissGreenlet at 0x7f8281f86050: <bound method Writer.dense_loop of <lima2.client.smx.aggregation.Writer object at 0x7f82821ba950>>> failed with OSError