Hello everyone! I have the following error when using phenix-1.3-final: /========================== Target weights: x-ray data ========================= Traceback (most recent call last): File "/usr/local/rossmann/phenix/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 89, in run File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/driver.py", line 1081, in run File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/strategies.py", line 472, in refinement_machine File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 264, in __init__ File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 307, in xyz_weights File "/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", line 196, in __init__ File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/__init__.py", line 72, in update_xray_structure force_update_f_mask = force_update_f_mask) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/f_model.py", line 675, in update_xray_structure force_update = force_update_f_mask) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 207, in f_mask return self.compute_f_mask() File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 222, in compute_f_mask miller_set = self.miller_array) File "/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 138, in structure_factors flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) MemoryError /I am running with defaults, i.e. the following command: phenix.refine se.water2.noano_001-2acetate-noH-coot-0.pdb cr2remote.cr3.1.8-2_scaleit1.mtz ray_data.r_free_flags.test_flag_value=1 output.prefix=se.noano2.acetate refinement.input.xray_data.labels="F_peak(+),SIGF_peak(+),F_peak(-),SIGF_peak(-),merged" I would greatly appreciate your help to resolve this issue and I can provide any additional information needed. Thank you, Anastasia
Hi Anastasia, sorry, but your jobs will only run on a machine with more memory. If your space group has lattice translations (e.g. C, I, F, R) you could try to transform the data and the model to a primitive setting, but since your job is crashing fairly early on I'm not sure how much it will help. Reducing phenix.refine's memory footprint is a long term development goal. Ralf
Thanks, Is there a way to find how much memory I need? I am running the job remotely on a machine that has 3.5 gig of memory free. Thanks once again, Anastasia Ralf W. Grosse-Kunstleve wrote:
Hi Anastasia, sorry, but your jobs will only run on a machine with more memory. If your space group has lattice translations (e.g. C, I, F, R) you could try to transform the data and the model to a primitive setting, but since your job is crashing fairly early on I'm not sure how much it will help. Reducing phenix.refine's memory footprint is a long term development goal. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Is there a way to find how much memory I need?
We don't have a "predictor". Memory is allocated as needed. If the allocation fails, there isn't an easy way to know how much more memory the process was trying to allocate. So sorry, the only way to easily find out how much you need is to find a machine that is big enough. You can add --show-process-info to get memory usage statistics. Ralf
participants (2)
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Anastasia A Aksyuk
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Ralf W. Grosse-Kunstleve