Re: [phenixbb] phenix.refine crash -- other error

Dear Peter, many thanks! Will try this -- I do not know about the FFT algorithm in phenix, but in CNS you could specify memory use and do calculations on a subgrid. Thi stakes more time but needs less memory. There is no cuh thing in phenix? many thanks again for your prompt help, Ulrich On Tue, 13 Mar 2007 20:07:46 +0100, Peter Zwart wrote:

Hi Ulrich,

You could try refining your structure in a primitive setting, this might alleviate memory usage a bit (not sure though).

try

phenix.python $MMTBX_DIST/mmtbx/examples/reindex.py data.file=mydata.mtz model.file=mymodel.pdb action=reindex standard_laws=niggli

You will get a new mtz file and a new pdb file. Unfortunately, the free flags are not copied over, so you would have to reindex those separately using iotbx.reflection_file_converter and read that file in separately in phenix.refine.

This might be a bit criptic, if so, let me know and I will post more details.

I am not sure this does the trick though, I hope Ralf or Pavel can give some suggestions.

Cheers

Peter

Ulrich Baumann wrote:

...

Hi there,

if you remove the ANISOU card from the input pdb file, phenix will run fine ....sometimes not.

phenix.refine ( Version: 2007_01_24_2154) crashed for me as well: we have a rather large unit cell and good resolution. The program crashes reproducibly (see below) when using resolution limits better than 3 A, although sometimes this only occurs in the 2nd macrocycle.

Working crystal symmetry after inspecting all inputs: Unit cell: (202.401, 202.401, 317.731, 90, 90, 120) Space group: R 3 :H (No. 146)

We have 2 GB memory and could stuff in more but maybe we can limit the memeory use in a different way?

Thanks a lot for your help,

Ulrich

============================= ml refinement start =============================

----------structure factors based statistics (before refinement)----------

Traceback (most recent call last): File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.p y", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_li ne.py", line 75, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py" , line 1108, in run log = log) File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies .py", line 174, in refinement_machine abcd = abcd) File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", line 185, in __init__ b_cart = b_cart) File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", line 466, in update_xray_structure f_mask = bulk_solvent_mask_obj.structure_factors(miller_set= self.f_obs) File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/masks.py", line 97, in structure_factors flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) MemoryError

---------------------------------------------------------- ------------------------------------------------------- Quoting Pavel Afonine :

...

Hi,

this is known problem and it will be fixed ASAP; sorry for this. This presumably happens because an atom selected to be refined as individual anisotropic is included into a TLS group. I will let you know once the fixed version of CCI Apps is available.

Pavel.

Jianghai Zhu wrote:

...

Hi,

I was using phenix.refine from the latest cci apps bundle to do tls+individual_sites+individual_adp refinement. The program crashed with the following error message.

----------Target weights (before refinement)----------

Traceback (most recent call last): File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 75, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1108, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 245, in refinement_machine log = log) File

"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py",

...

line 222, in __init__ compute_gradients = True) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", line 144, in energies_adp_aniso xray_structure = xray_structure, File "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", line 109, in __init__ self.check_flags(fl_i) File "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", line 177, in check_flags assert not fl.use_u_aniso() AssertionError

Anyone has any idea what is happening? Thanks.

Jianghai

+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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