Hex 8.0.0 Failed to allocate memory

Question

[burkhart.joshua]

I'm using Hex 8.0.0 (hex8.0.0-nogui.x64) and every once in awhile see it failing to dock two models (pdb files). This occurs in perhaps 1 of 25 docking attempts and I'm only attempting one docking at a time. Is this a documented issue? Does anyone know how to avoid this?

The following error line is printed in the log.

*Error* Failed to allocate memory (-71Mb) [Cannot allocate memory]

My system has 16GB RAM so I'm not sure why it's having a memory issue. I'm running Ubuntu 16.04 LTS and don't think it's a stack size limit...

$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 64027
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 64027
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

An example of one of the log files produced is below.

*Warning* The environment variable HEX_ROOT is not set.
*Warning* Guessing HEX_ROOT = /home/burkhart/hex
Hex 8.0.0 starting at Fri Sep 30 19:08:03 2016 on host nyx.

Hostname:        nyx
Main memory:     16044 Mb
CPUs online:     8
GPUs online:     0
Compute threads: 4

Sizeof(short):   2
Sizeof(int):     4
Sizeof(long):    8
Sizeof(long int):8
Sizeof(float):   4
Sizeof(double):  8
Sizeof(octa):    8
Sizeof(int *):   8
Sizeof(long *):  8
Sizeof(void *):  8

Default path:    /media/burkhart/Media/Software/FIOncoNet
PATH:            /home/burkhart/hex/exe:/home/burkhart/hex/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/burkhart/anaconda/bin:/home/burkhart/.rvm/bin

Hex program:     /home/burkhart/hex/exe/hex8.0.0-nogui.x64
HEX_ROOT:        /home/burkhart/hex
HEX_STRIDE:      NULL
HEX_PDB:         NULL
HEX_DATA:        NULL
HEX_MACROS:      NULL
HEX_COLOURS:     NULL
HEX_STARTUP:     NULL
HEX_FONTFILE:    NULL
HEX_PIPE:        NULL
HEX_CACHE:       /home/burkhart/hex/cache
HEX_LOG:         NULL
HEX_CPUS:        NULL
HEX_GPUS:        NULL
HEX_FIRST_GPU:   NULL
HEX_GTO_SCALE:   NULL
HEX_ETO_SCALE:   NULL

CUDA enabled:    No



Running HEX_STARTUP file: /home/burkhart/hex/data/startup_v5.mac
Disc Cache enabled. Using directory: /home/burkhart/hex/cache


Reading commands from stdin ...
>> open_receptor /home/burkhart/Software/FIOncoNet/DockingServer/input/reaction_5672965/pdb/O14827-MDL-O14827.17-2ije_S.pdb
Assuming /home/burkhart/Software/FIOncoNet/DockingServer/input/reaction_5672965/pdb/O14827-MDL-O14827.17-2ije_S.pdb is a PDB file...

Opened PDB file: /home/burkhart/Software/FIOncoNet/DockingServer/input/reaction_5672965/pdb/O14827-MDL-O14827.17-2ije_S.pdb, ID = O14827-MDL-O14827.17-2ije_S
Loaded PDB file: /home/burkhart/Software/FIOncoNet/DockingServer/input/reaction_5672965/pdb/O14827-MDL-O14827.17-2ije_S.pdb, (233 residues, 2336 atoms, 1 models)
Counted 30 +ve and 29 -ve formal charged residues: Net formal charge: 1
>O14827-MDL-O14827.17-2ije_S A
SAMELAEQITLLDHVIFRSIPYEEFLGQGWMKLDKNERTPYIMKTSQHFNDMSNLVASQIMNYADVSSRANAIEKWVAVADICRCLHNYNGVLEITSALNRSAIYRLKKTWAKVSKQTKALMDKLQKTVSSEGRFKNLRETLKNCNPPAVPYLGMYLTDLAFIEEGTPNFTEEGLVNFSKMRMISHIIREIRQFQQTSYRIDHQPKVAQYLLDKDLIIDEDTLYELSLKIEPR
>> open_ligand /home/burkhart/Software/FIOncoNet/DockingServer/input/reaction_5672965/pdb/Q13554-MDL-Q13554.49-3soa_A.pdb
Assuming /home/burkhart/Software/FIOncoNet/DockingServer/input/reaction_5672966/pdb/Q13554-MDL-Q13554.49-3soa_A.pdb is a PDB file...

Opened PDB file: /home/burkhart/Software/FIOncoNet/DockingServer/input/reaction_5672965/pdb/Q13554-MDL-Q13554.49-3soa_A.pdb, ID = Q13554-MDL-Q13554.49-3soa_A
Loaded PDB file: /home/burkhart/Software/FIOncoNet/DockingServer/input/reaction_5672965/pdb/Q13554-MDL-Q13554.49-3soa_A.pdb, (655 residues, 6135 atoms, 1 models)
Counted 71 +ve and 73 -ve formal charged residues: Net formal charge: -2
>Q13554-MDL-Q13554.49-3soa_A A
TRFTDEYQLYEDIGKGAFSVVRRCVKLCTGHEYAAKIINTKKLSARDHQKLEREARICRLLKHSNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRDLKPENLLLASKCKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKEAYGKPVDIWACGVILYILLVGYPPFWDEDQHKLYQQIKAGAYDFPSPEWDTVTPEAKNLINQMLTINPAKRITAHEALKHPWVCQRSTVASMMHRQETVECLKKFNARRKLKGAILTTMLATRNFSVGRQTTAPATMSTAASGTTMGLVEQAKSLLNKKADGVKPQTNSTKNSAAATSPKGTLPPAALEPQTTVIHNPVDGIKESSDSANTTIEDEDAKAPRVPDILSSVRRGSGAPEAEGPLPCPSPAPFSPLPAPSPRISDILNSVRRGSGTPEAEGPLSAGPPPCLSPALLGPLSSPSPRISDILNSVRRGSGTPEAEGPSPVGPPPCPSPTIPGPLPTPSRKQEIIKTTEQLIEAVNNGDFEAYAKICDPGLTSFEPEALGNLVEGMDFHRFYFENLLAKNSKPIHTTILNPHVHVIGEDAACIAYIRLTQYIDGQGRPRTSQSEETRVWHRRDGKWQNVHFHCSGAP
>> activate_docking

Contouring surface for molecule O14827-MDL-O14827.17-2ije_S.
Polar probe = 1.40A, Apolar probe = 1.40A
Gaussian sampling over 1898 atoms done in 0.30 seconds.
Contoured 211652 triangles (105828 vertices) in 0.17 seconds.
Surface traversal done in 0.05 seconds - Found 1 surface segments.
Primary surface:   Area = 10601.59, Volume = 50840.88.
Culled 0 small segments in 0.06 seconds.
Total contouring time: 0.29 seconds.


Contouring surface for molecule Q13554-MDL-Q13554.49-3soa_A.
Polar probe = 1.40A, Apolar probe = 1.40A
Gaussian sampling over 5028 atoms done in 0.73 seconds.
Contoured 859368 triangles (429692 vertices) in 4.29 seconds.
Surface traversal done in 0.24 seconds - Found 6 surface segments.
Primary surface:   Area = 42905.82, Volume = 152163.53.
Secondary surface: Area = 191.33, Volume = 120.50.
Culled 3 small segments in 0.30 seconds.
Total contouring time: 4.82 seconds.

Sampling surface and interior volumes for molecule O14827-MDL-O14827.17-2ije_S.
*Error* Failed to allocate memory (-71Mb) [Cannot allocate memory]