Re: [phenixbb] v1.8 bug ? memory allocation crash - apparently also in AutoBuild

Hi Tom, Even setting the high resolution limit in the Other Options form to 6.0, and with filled_2fofc_maps=false, it dies in the same place and interestingly with the same mmap memory allocation request - this seems invariant with the resolution parameter: Python(12184) malloc: *** mmap(size=283115520) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug The memory on the machine is not filling up while the process is running. Phil On 7/11/12 7:17 PM, Terwilliger, Thomas C wrote:

Hi Phil,

Usually that error message means literally that the required resolve size is too big. In that space group it could be so even if the cell is not huge. Sometimes there is some other error however. You can probably tell by cutting the resolution way back and then if there is an error it is coming from something else (In that case please let me know!)

All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of Phil Jeffrey [[email protected]] Sent: Wednesday, July 11, 2012 5:05 PM To: PHENIX user mailing list Subject: Re: [phenixbb] v1.8 bug ? memory allocation crash - apparently also in AutoBuild

I find that parameter under the model building GUI and verify its setting under View All Settings but it makes no difference. Don't see any other parameters involving "fill" set to True.

Potentially informative last part of log:

Possibly cresolve size 96 was too big for this machine ---------------------------------- TRIED SIZE OF 48 ...but not OK Last log file in AutoBuild_run_8_/LAST.LOG Last 20 lines of logfile: ---------------------------------- *************ERROR ENDING *******************

******************************************************************************** Failed to carry out AutoBuild_multiple_models:

COMMANDS USED: workdir AutoBuild_run_8_/TEMP0 outputdir AutoBuild_run_8_ freer_if_present hklin aniso_data_PHX.mtz labin FP=F120 SIGFP=SIGF120 hklout exptl_phases_and_amplitudes_for_density_modification_aniso.mtz solvent_content 0.52 no_build mask_cycles 1 minor_cycles 0 ha_file NONE keep_missing use_wang no_ha database 5 no_optimize_ncs spg_name_use F 4 3 2 min_z_value_rho -3.0 start_chain 1 8 start_chain 2 10 start_chain 3 105 start_chain 4 105 no_create_free use_all_for_test delta_phi 20.00 group_ca_length 1 group_length 2 n_random_frag 0

See overall log file and also resolve log file (in /Users/phil/Structures/Cog5-Cog7/native/from_Jun/phenix-tests/AutoBuild_run_8_/LAST.LOG)

Note: It is possible that the required size of resolve needs more memory than is available ********************************************************************************

*************ERROR ENDING *******************

On 7/11/12 6:30 PM, Nathaniel Echols wrote:

...

On Wed, Jul 11, 2012 at 3:24 PM, Phil Jeffreymailto:[email protected]> wrote:

I think phenix is not particularly fond of F432, because in AutoBuild I get:

Python(6992) malloc: *** mmap(size=283115520) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug

While a larger unit cell, the asymmetric unit is not huge, nor is the # of reflections.

You might be able to circumvent this crash by setting this parameter:

filled_2fofc_maps=False

(which I hope does the same thing as my previous advice.)

-Nat

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