January 2019 Commit Log

Number of Commits:
135
Number of Active Developers:
4
sbu062 2019-01-31 22:49 Rev.: 7742

merged workaround against intel fortran 19 compiler bugs r7726:r7740 from HEDG2_06: crashes due to (a) loss of non-fixed log file unit while running and (b) loss of access to dynamic derived objects from other modules with O3 and -parallel optimisation flags

878 lines of code changed in 11 files:

sbu062 2019-01-31 20:51 Rev.: 7741

deleted work branch: fixed intel compiler bug workaround for FUCK_IFORT_WA1 block

0 lines of code changed in 3 files:

sbu062 2019-01-31 20:49 Rev.: 7740

minor: white space formatting

2 lines of code changed in 1 file:

sbu062 2019-01-31 20:43 Rev.: 7739

merged workaround against intel fortran 19 compiler bugs r7726:r7735: crashes due to (a) loss of non-fixed log file unit while running and (b) loss of access to dynamic derived objects from other modules with O3 and -parallel optimisation flags

174 lines of code changed in 2 files:

sbu062 2019-01-31 20:26 Rev.: 7738

deleted temporary work branches

0 lines of code changed in 2 files:

sbu062 2019-01-31 20:25 Rev.: 7737

merged xmpp notifications r7693 and r7736

42 lines of code changed in 6 files:

sbu062 2019-01-31 20:11 Rev.: 7736

fix notification on Windows

0 lines of code changed in 2 files:

sbu062 2019-01-31 16:18 Rev.: 7735

more info describing intel compiler bug with segmentation fault as workaround code in r7734

9 lines of code changed in 1 file:

sbu062 2019-01-31 16:09 Rev.: 7734

added workarounds against intel fortran compiler bugs that apear in optimised binary builds with O3, components of derived types and getters from different modules become unaccessible and result in segmentation crashes

22 lines of code changed in 1 file:

sbu062 2019-01-31 15:55 Rev.: 7733

print sanitiser bounds to log at start

2 lines of code changed in 1 file:

sbu062 2019-01-31 15:50 Rev.: 7732

doc: description for sanitiser bounds

5 lines of code changed in 1 file:

sbu062 2019-01-31 15:10 Rev.: 7731

global validation, low and high,parameters in (sanitise) and (do_sanitise)

7 lines of code changed in 1 file:

sbu062 2019-01-31 10:38 Rev.: 7730

refactored sanitise functions: (do_sanitise) and (sanitise), the former calling IEEE math modules

102 lines of code changed in 2 files:

sbu062 2019-01-30 23:16 Rev.: 7729

fix ifort crashes: LOG_FILEUNIT fixed parameter

dynamic log file unit proved problematic with ifort as it loses unit in complex code with multiple scope procedures, e.g. OO

16 lines of code changed in 1 file:

sbu062 2019-01-30 22:46 Rev.: 7728

fix ifort crashes: got rid of FILE_IO object as it breaks ifort; use array sanitizer in (generation_stats_record_write) to avoid crashes in csv file

When using a very long history, some perception object history stack values are broken/uninitialised/invalid which breaks output in CSV_IO call, hence use sanitiser added in r7727. Switched to raw CSV_IO calls instead of the FILE_IO wrapper because intel ifort breaks public file handle object rendering file unit and name unaccessible. Debugging did not succeed, perhaps it's a bug in Intel compiler. So, raw CSV_IO calls are used, but they are not verbose. Actually, FILE_IO may be oblivious...

0 lines of code changed in 2 files:

sbu062 2019-01-30 21:56 Rev.: 7727

fix ifort crashes: initial implementation of data sanitiser

0 lines of code changed in 2 files:

sbu062 2019-01-30 11:32 Rev.: 7725

(CSV_RECORD_APPEND): now pure function

20 lines of code changed in 1 file:

cje012 2019-01-30 11:23

Changed to be more memory efficient.

34 lines of code changed in 2 files:

sbu062 2019-01-30 07:47 Rev.: 7722

run: popsize 1000

Hopefully, with smaller popsize simulation is faster
but higher density of food make more agents growing,
easier to stat up the GA

1 lines of code changed in 1 file:

sbu062 2019-01-30 05:20 Rev.: 7721

fix typo

1 lines of code changed in 1 file:

sbu062 2019-01-30 05:17 Rev.: 7720

test shrinking planar area as in r7662 and r7719

3 lines of code changed in 1 file:

sbu062 2019-01-29 21:47 Rev.: 7719

reduced planar area to standard as in r7662
Testing for speed with popsize 10000, this will produce a
high food density, the same as in testing experiments with
models 01-05

3 lines of code changed in 1 file:

sbu062 2019-01-29 19:35 Rev.: 7718

refine and fix openmp instructions for benchmark

1 lines of code changed in 1 file:

nzlcj 2019-01-29 13:12 Rev.: 7717

Coded together. Added function for normal distribution. Added reproduction, inheritance, and density dependence (new cohort size).

119 lines of code changed in 2 files:

sbu062 2019-01-29 12:34 Rev.: 7716

gprof: reduce debug steps, valgrind is very slow (indeed veeerrrryyyyyyy sslloooowwwwwww)

1 lines of code changed in 1 file:

sbu062 2019-01-29 12:32 Rev.: 7715

gprof: restored profiling bransh from r7703 to valgrind

4 lines of code changed in 1 file:

sbu062 2019-01-29 11:55 Rev.: 7714

DEBUG_COMPILER_OPTIMISE: optimised IS_DEBUG as parameter for speed

5 lines of code changed in 1 file:

sbu062 2019-01-29 11:31 Rev.: 7713

run1: popsize 10000, evolution is unstable with smaller population size even if no complex migration of food.

1 lines of code changed in 1 file:

sbu062 2019-01-29 11:31 Rev.: 7712

(do_behave): returned to optimal predictive

1 lines of code changed in 1 file:

sbu062 2019-01-29 10:51 Rev.: 7711

send data to root directory of receiving server

1 lines of code changed in 1 file:

sbu062 2019-01-28 15:26 Rev.: 7710

intel fortran is also quite faster with openmp on windows

1 lines of code changed in 1 file:

sbu062 2019-01-28 15:21 Rev.: 7709

oracle fortran is faster with explicit openmp than -autopar

1 lines of code changed in 1 file:

sbu062 2019-01-28 15:16 Rev.: 7708

intel fortran is quite faster with explicit openmp than with automatic parallel -parallel

1 lines of code changed in 1 file:

sbu062 2019-01-28 15:10 Rev.: 7707

added openmp multithread benchmark

10 lines of code changed in 3 files:

sbu062 2019-01-28 15:09 Rev.: 7706

fix hedtools path

0 lines of code changed in 2 files:

sbu062 2019-01-28 11:49 Rev.: 7705

restored gprof branch for further testing and benchmarking

0 lines of code changed in 1 file:

sbu062 2019-01-27 18:25 Rev.: 7704

gprof: deleted profiling test branch after running

0 lines of code changed in 1 file:

sbu062 2019-01-27 16:37 Rev.: 7703

gprof: fix time steps for debug

1 lines of code changed in 1 file:

sbu062 2019-01-27 07:53 Rev.: 7702

gprof: IS_DEBUG unset as fixed parameter through DEBUG_COMPILER_OPTIMISE for profiling

4 lines of code changed in 1 file:

sbu062 2019-01-27 07:31 Rev.: 7701

gprof: profiling branch of model 6 with greatly reduced POPSIZE and GENERATIONS

0 lines of code changed in 2 files:

sbu062 2019-01-25 13:31 Rev.: 7700

SLM: reduced initial steps, this makes it even easier to start up with dumb agents

3 lines of code changed in 1 file:

cje012 2019-01-24 14:53 Rev.: 7699

Minor changes

9 lines of code changed in 1 file:

nzlcj 2019-01-24 14:08 Rev.: 7698

Coded together. Started on reproduction.

72 lines of code changed in 1 file:

lhi088 2019-01-24 13:04 Rev.: 7697

commented out

52 lines of code changed in 1 file:

sbu062 2019-01-24 10:43 Rev.: 7696

model run R2 on AF: GOS-linked non-predicted behaviour selection

0 lines of code changed in 2 files:

sbu062 2019-01-24 09:50 Rev.: 7695

prepare model run: big popsize is quite slow, alter (preevol_steps_adaptive) parameters to make earlier steps easier

This changeset makes earlier steps of the genetic algorithm easier for agents
by setting the first generation timnesteps to factor 0.1 rather than 0.3. This
would allow to reduce POPSIZE back to 1000 (from 2000). Also, time steps
increase slightly faster later in GA, (ordinate array 0.8 changed to 0.85).

6 lines of code changed in 2 files:

sbu062 2019-01-24 09:50 Rev.: 7694

test fixed to agree with algo in (preevol_steps_adaptive)

1 lines of code changed in 1 file:

sbu062 2019-01-23 22:27 Rev.: 7693

added xmpp notification for exec status

8 lines of code changed in 1 file:

sbu062 2019-01-23 21:44 Rev.: 7692

prepare model run: popsize need larger to avoid sying out at start

1 lines of code changed in 1 file:

sbu062 2019-01-23 21:16 Rev.: 7691

prepare model run: increase history stack for acss and complexity

2 lines of code changed in 1 file:

sbu062 2019-01-23 14:00 Rev.: 7690

prepare model run: more agents reproducing due to smaller popsize, disable huge debug plotting

14 lines of code changed in 3 files:

sbu062 2019-01-23 13:01 Rev.: 7689

prepare model run: population size reduced to 1000, generations increased to 1000, preevol_steps larger 4 times

3 lines of code changed in 1 file:

sbu062 2019-01-23 12:01 Rev.: 7688

(food_resource_replenish_food_items_all): merged latest changes from model 06, r7676:r7687, tests pass

846 lines of code changed in 10 files:

sbu062 2019-01-23 10:15 Rev.: 7687

(food_resource_replenish_food_items_all): shrink functionality never used, deleted fully, tests pass

31 lines of code changed in 2 files:

sbu062 2019-01-22 22:39 Rev.: 7686

tests: added test suite for (replentish) method, shrink parameter not included so far

0 lines of code changed in 2 files:

sbu062 2019-01-22 15:50 Rev.: 7685

typo in text

1 lines of code changed in 1 file:

sbu062 2019-01-22 15:50 Rev.: 7684

added FOOD_REPLENISH_STEP_SAFE and FOOD_REPLENISH_STEP_DANGER parameters and included partial (replenish) in life cycle

20 lines of code changed in 2 files:

sbu062 2019-01-22 15:50 Rev.: 7683

(food_resource_replenish_food_items_all): shrink_to now intent in as no output is needed

4 lines of code changed in 1 file:

sbu062 2019-01-22 15:50 Rev.: 7682

(food_resource_replenish_food_items_all): replace intent in now, needn't to read or confirm it

5 lines of code changed in 1 file:

sbu062 2019-01-22 15:50 Rev.: 7681

(food_resource_replenish_food_items_all): named if constructs for visibility

7 lines of code changed in 1 file:

sbu062 2019-01-22 15:50 Rev.: 7680

(food_resource_replenish_food_items_all): reduce_to renamed to a better name shrink_to

11 lines of code changed in 1 file:

sbu062 2019-01-22 15:50 Rev.: 7679

(food_resource_replenish_food_items_all): edit explanations

10 lines of code changed in 1 file:

sbu062 2019-01-22 15:50 Rev.: 7678

(food_resource_replenish_food_items_all): new_number renamed to reduce_to because only reduction of food items can be done in (replenish) method

13 lines of code changed in 1 file:

sbu062 2019-01-22 15:50 Rev.: 7677

(food_resource_replenish_food_items_all): initial algorithm for partial food replentish replacement

52 lines of code changed in 1 file:

sbu062 2019-01-22 15:49 Rev.: 7676

(food_resource_replenish_food_items_all): better var name new_number because it changes the maximum

13 lines of code changed in 1 file:

sbu062 2019-01-21 12:55 Rev.: 7675

disable sinusoidal vertical migration of food items, they do random walk instead, merged change r6308 from MEDG2_03

6 lines of code changed in 1 file:

sbu062 2019-01-21 12:33 Rev.: 7674

model name fix

1 lines of code changed in 1 file:

sbu062 2019-01-21 11:30 Rev.: 7673

merged r7671, default vcs

15 lines of code changed in 5 files:

sbu062 2019-01-21 11:27 Rev.: 7672

model description set

1 lines of code changed in 1 file:

sbu062 2019-01-21 11:27 Rev.: 7671

set default version control system, therefore could never be undefined

3 lines of code changed in 1 file:

sbu062 2019-01-21 10:40 Rev.: 7670

merged r7669, version control info error fix

65 lines of code changed in 5 files:

sbu062 2019-01-21 10:34 Rev.: 7669

we use differen version control systems, get rid of error in non-svn

0 lines of code changed in 2 files:

lhi088 2019-01-21 09:51 Rev.: 7668

10 lines of code changed in 1 file:

sbu062 2019-01-18 18:53 Rev.: 7667

tests: debug parameter may modify (preevol_steps_adaptive), so tests should adapt to this case

48 lines of code changed in 9 files:

sbu062 2019-01-18 18:37 Rev.: 7666

merged r7665: confusing UNIVERSE added _NOTUSE

30 lines of code changed in 5 files:

sbu062 2019-01-18 17:07 Rev.: 7665

doc: UNIVERSE parameters added _NOTUSE in doc

4 lines of code changed in 1 file:

sbu062 2019-01-18 15:52 Rev.: 7664

UNIVERSE parameters confusing, mark them with _NOTUSE tag

2 lines of code changed in 1 file:

sbu062 2019-01-18 15:52 Rev.: 7663

universe, one habitat, now square
* * *
decreased depth but greatly increased planar area

This commit increases real size of the universe as set by the
HABITAT_.._COORD parameters, rather then deprecated (and
apparently confusing UNIVERSE_...) parameters

4 lines of code changed in 1 file:

sbu062 2019-01-18 15:52 Rev.: 7662

decreased depth but greatly increased planar area

3 lines of code changed in 1 file:

sbu062 2019-01-18 14:49 Rev.: 7661

doc: wrong obsolete note remained, striped now

0 lines of code changed in 1 file:

sbu062 2019-01-17 21:04 Rev.: 7660

merged r7659 doc

7 lines of code changed in 1 file:

sbu062 2019-01-17 21:03 Rev.: 7659

doc: small addition on svn

7 lines of code changed in 1 file:

sbu062 2019-01-17 15:00 Rev.: 7658

merged latest HEDTOOLS doc r7657, LINK2005 issue workaround

19 lines of code changed in 1 file:

sbu062 2019-01-17 14:58 Rev.: 7657

main solution to LINK2005 is to use static runtime

19 lines of code changed in 1 file:

sbu062 2019-01-17 14:41 Rev.: 7656

do not need this test code, that was used to test Microsoft Visual Studio with HEDTOOLS, requires using non-DLL libraties

0 lines of code changed in 1 file:

sbu062 2019-01-17 10:28 Rev.: 7655

system: service commands deleted, ejabberdctl control should work better

4 lines of code changed in 1 file:

sbu062 2019-01-16 14:30 Rev.: 7654

backported r7653, intro doc on new stop file signal control

115 lines of code changed in 5 files:

sbu062 2019-01-16 14:19 Rev.: 7653

added subsection describing the stop file: (intro_overview_stopfile)

23 lines of code changed in 1 file:

sbu062 2019-01-16 13:54 Rev.: 7652

stop file code r7651 merged to other models

135 lines of code changed in 10 files:

sbu062 2019-01-16 13:40 Rev.: 7651

added stop file functionality to stop generation loop GENERATIONS_PREEVOL

0 lines of code changed in 4 files:

sbu062 2019-01-16 09:08 Rev.: 7650

system: add manual config commands because autoconfig still buggy

32 lines of code changed in 1 file:

sbu062 2019-01-16 08:37 Rev.: 7649

system: more fixes user create script, sleep between service commands

4 lines of code changed in 1 file:

sbu062 2019-01-16 08:15 Rev.: 7648

system: more fixes user create script

3 lines of code changed in 1 file:

sbu062 2019-01-15 08:22 Rev.: 7647

web: external repos are read-only

1 lines of code changed in 1 file:

sbu062 2019-01-14 17:16 Rev.: 7646

web: delete superfluous repo

0 lines of code changed in 1 file:

sbu062 2019-01-14 16:25 Rev.: 7645

doc: fix wrong doc statement on relative visual range in (predator_capture_risk_calculate_fish)

6 lines of code changed in 7 files:

sbu062 2019-01-10 21:48 Rev.: 7643

merged r7642 from model 04, libasan memory lean check disabled on Windows

24 lines of code changed in 4 files:

sbu062 2019-01-10 21:28 Rev.: 7642

memory leak check using libasan breaks debug build on most Windows installations, enable libasan only on non-Windows platforms

6 lines of code changed in 1 file:

sbu062 2019-01-09 14:43 Rev.: 7641

merged r7640

5 lines of code changed in 1 file:

sbu062 2019-01-09 14:41 Rev.: 7640

update on GUI tools, add link to AnkhSVN

5 lines of code changed in 1 file:

sbu062 2019-01-09 14:29 Rev.: 7639

another test change

1 lines of code changed in 1 file:

sbu062 2019-01-09 13:25 Rev.: 7638

testing how to do svn commit in AnkhSVN

0 lines of code changed in 2 files:

sbu062 2019-01-09 12:10 Rev.: 7636

merged r7635, reintegrate deleted

0 lines of code changed in 1 file:

sbu062 2019-01-09 12:08 Rev.: 7635

doc: reintegrate has never been used in our code and may be dangerous, deleted

0 lines of code changed in 1 file:

sbu062 2019-01-09 10:34 Rev.: 7634

merged doc r7633

23 lines of code changed in 1 file:

sbu062 2019-01-09 10:32 Rev.: 7633

doc: fix index terms

4 lines of code changed in 1 file:

sbu062 2019-01-09 10:27 Rev.: 7632

doc: small change in svn terms

6 lines of code changed in 1 file:

sbu062 2019-01-09 08:03 Rev.: 7631

doc: added svn intro terms

21 lines of code changed in 1 file:

sbu062 2019-01-09 07:37 Rev.: 7630

merged r7629 with LNK2005 workaround

2 lines of code changed in 1 file:

sbu062 2019-01-09 07:35 Rev.: 7629

doc: added more notes to workaround against LNK2005, see also r7627

2 lines of code changed in 1 file:

sbu062 2019-01-08 23:24 Rev.: 7628

merged doc on workaround against LNK2005 on Microsoft Studio 2015, static rather than dll runtime

12 lines of code changed in 3 files:

sbu062 2019-01-08 23:13 Rev.: 7627

doc: added workaround against LNK2005 build error on Windows Microsoft Developer Studio 2015

12 lines of code changed in 3 files:

cje012 2019-01-08 16:04 Rev.: 7626

Many changes from the last commit. Axis titles are changes, some figures have had minor tweaks while others have had major tweaks. Changes made according to figure meeting today.

138 lines of code changed in 1 file:

sbu062 2019-01-08 15:02 Rev.: 7625

web: make inverse xmpp client more conspicuous

64 lines of code changed in 1 file:

sbu062 2019-01-08 14:51 Rev.: 7624

Wellbeing paper 1.1, new rev

1 lines of code changed in 1 file:

sbu062 2019-01-08 14:49 Rev.: 7623

Wellbeing paper 1.0, Jarl's changes at Christmas time

231 lines of code changed in 2 files:

lhi088 2019-01-08 14:02 Rev.: 7622

added annotations

11 lines of code changed in 1 file:

nzlcj 2019-01-08 12:54 Rev.: 7621

Coded together, added small loop with individual physiology.

12 lines of code changed in 1 file:

lhi088 2019-01-08 12:12 Rev.: 7620

testing commit

1 lines of code changed in 1 file:

cje012 2019-01-08 07:16 Rev.: 7619

Added a way to calculate the different quantile individuals in the population based on when they finished growing up.

76 lines of code changed in 1 file:

nzlcj 2019-01-07 12:36 Rev.: 7618

...and the functions file.

62 lines of code changed in 1 file:

nzlcj 2019-01-07 12:35 Rev.: 7617

First commit of developing fortran code on sex evolution with Laura Hildesheim.

42 lines of code changed in 1 file:

sbu062 2019-01-06 10:12 Rev.: 7614

force exactly two arguments

1 lines of code changed in 1 file:

sbu062 2019-01-06 10:03 Rev.: 7613

set properties

3 lines of code changed in 1 file:

sbu062 2019-01-06 09:58 Rev.: 7612

compatibility of print across python 2 and 3

5 lines of code changed in 1 file:

sbu062 2019-01-05 19:08 Rev.: 7611

fix index, was excluding last element

1 lines of code changed in 1 file:

sbu062 2019-01-05 18:47 Rev.: 7610

cleanup tmp

0 lines of code changed in 1 file:

sbu062 2019-01-05 18:46 Rev.: 7609

get files from command line args

15 lines of code changed in 1 file:

sbu062 2019-01-05 18:25 Rev.: 7608

behaviour recode utility for acss

33 lines of code changed in 1 file:

sbu062 2019-01-05 18:22 Rev.: 7607

beautified quick & dirty code param keys and loop

22 lines of code changed in 1 file:

sbu062 2019-01-05 11:13 Rev.: 7606

small change, renames

6 lines of code changed in 1 file:

sbu062 2019-01-04 17:42 Rev.: 7605

added rudimentary behaviour string recode utility for acss

52 lines of code changed in 1 file:

cje012 2019-01-04 09:39

minor changes

9 lines of code changed in 2 files:

cje012 2019-01-03 13:55 Rev.: 7602

Added old figure B as figure F.

99 lines of code changed in 1 file:

cje012 2019-01-03 10:21 Rev.: 7601

Added mortality plots to figure B

44 lines of code changed in 1 file:

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