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

Terwilliger, Thomas C terwilliger at lanl.gov
Thu Jul 12 09:17:16 PDT 2012


Hi Phil,
Hmm...sounds bad!  In this case might it be possible to send me the required inputs off-list so that I can track down the problem?
Thanks very much!
-Tom T

________________________________________
From: Phil Jeffrey [pjeffrey at princeton.edu]
Sent: Thursday, July 12, 2012 10:15 AM
To: PHENIX user mailing list
Cc: Terwilliger, Thomas C
Subject: 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: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Phil Jeffrey [pjeffrey at princeton.edu]
> 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 Jeffrey<pjeffrey at princeton.edu
>> <mailto:pjeffrey at princeton.edu>>  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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>
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