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

Terwilliger, Thomas C terwilliger at lanl.gov
Wed Jul 11 16:17:38 PDT 2012

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:

workdir AutoBuild_run_8_/TEMP0
outputdir AutoBuild_run_8_
hklin aniso_data_PHX.mtz
labin FP=F120 SIGFP=SIGF120
hklout exptl_phases_and_amplitudes_for_density_modification_aniso.mtz
solvent_content 0.52
mask_cycles 1
minor_cycles 0
ha_file NONE
database 5
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
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

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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

phenixbb mailing list
phenixbb at phenix-online.org

More information about the phenixbb mailing list