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This
is a copy of the manual included
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Manual for evolution@home
simulator S005 release 4 (Apr 28 2001)
International_Windows_Client
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=== QuickStart for evolution@home ====================
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Thank you for participating in evolution@home!
This simulator helps uncover potential genetic causes of
extinction of endangered and not-yet-endangered species
by investigating Muller's ratchet. Your help to improve
understanding of such genomic decay might one day be
used to fight it.
This simulator can not get tasks and return results
automatically. Therefore we ask you to do that. This gives
you maximal control over your Internet connections and
gives you most freedom to choose what you want to compute.
To get started quickly, do the following:
1. Make a new, empty folder (for example with the
name
"evolution@home" on your
desktop) and move this
simulator-program into that folder.
Move no unrelated
files to that folder.
2. Double-click the simulator just to generate a
quick,
anonymous preferences file and estimate
performance.
If you want to run complex simulations
or personalize
results then you have to customize
preferences. Just
answer the questions of the simulator
or edit the
preferences file to do that.
You can get the perfomance estimated
from the list of
values at the beginning of every log
file.
3. Goto the Simulator section of the website
http://www.evolutionary-research.net
and follow
the link to the run-files for S005
on that page.
4. Search the run-files-collections-index page for
a link
to a run-file with simulations that
demand less RAM and
uninterrupted time than you want to
commit. (Do not use
virtual memory and do not forget the
RAM you need for your
daily work!) Follow that link.
5. If you do not want to select certain simulations
from a
run-file, you may save that web page
from your browser
as a run-file (text-file under the
name "run" or "run.txt"
to your simulators folder). Currently
that is to
C:\WINDOWS\DESKTOP\evolution@home
6. If you want to select certain simulations only,
open an
ordinary text file from any editor
on your computer and
copy and paste as many simulations
as you want to compute
from the website to your text file.
Select only simulations
that need less computing time than
you can expect your
computer to work uninterruptedly. Compare
the perfomance
of your computer to the reference system
on the website
to avoid surprises. The simplest way
is to copy and paste
a whole range of simulate-commands
that fits your time
constraints.
How to select the right
simulation-complexity:
If your computer crashes
about 5 times a day then
select simulations with
estimated computing times of
1-2 hours at most,
smaller being better here. As
intermediate states of
a simulation can not be saved
currently, this may allow
a simulation to complete
before the next crash.
If your computer almost never
crashes (and has not to
be shut down regularily) or you
are about to leave for
holidays, then select simulations
with estimated computing
times of 5 days to many weeks,
larger being better here.
As probably few people have
such stable computing environments
such contributions
are very important: the
most interesting simulations
usually take the most RAM
and time. If a simulation
is interrupted occasionally
due to a crash, this is
no catastrophe, as intermediate
results are recorded
and will be evaluated too.
However, completed runs are
more interesting, where
they can be obtained.
Save that (unformatted ascii-) text
file under the name
"run" or "run.txt"
and move it to the simulators folder.
7. Now doubleclick the simulator to start computation.
The simulator will read the run-file,
compute results, and
collect them in a file called "
results.S005.txt".
Then it will quit. If you put an alias/link
to the
simulator in the startup/autostart-folder
of your operating
system, then simulations continue automatically
with the
next simulation after a crash. You
may want to switch of
screensavers and energy saving functions
to increase
performance. If you want to stop a
simulation without
aborting it, move a file with the name
"break.txt" to
the simulations folder. Then you can
use your computing
time for other intense tasks and
resume the original
simulation after completing the other
tasks.
8. When you want to submit results (after or during
computation),
just move the file called " results.S005.txt"
away from
the simulators folder and email it
to
simulator005@evolution-at-home.net
as an attachment. Then delete the file
or store it
elsewhere, but do not move it back
to the simulators folder
once you submitted it (to avoid submission
of duplicates).
9. For additional details read the manual.
But whatever you do, be part of the
adventure
and enjoy the evolutionary research
you are doing.
=======================================================
=== Online System Help ================================
=======================================================
Thank you for participating in evolution@home!
This simulator helps uncover potential genetic causes of
extinction of endangered and not-yet-endangered species
by investigating Muller's ratchet. Your help to improve
understanding of such genomic decay might one day be
used to fight it.
This simulator can not get tasks and return results
automatically. Therefore we ask you to do that. This gives
you maximal control over your Internet connections and
gives you most freedom to choose what you want to compute.
============================
For an overview and a simple start, read the QuickStart
part of the manual. Refer to this part for more details on
selected topics.
============================
When you submit results, do the following:
1. Open a new email to simulator005@evolution-at-home.net
2. While anything can be in subject or body of the
mail,
dont expect anybody to read it. (Please
send feedback or
questions etc... to info@evolution-at-home.net)
3. IMPORTANT: Move the results.S005.txt file from
this
folder to your desktop or any other
folder!
4. Then attatch that results.S005.txt file to your
email
and send it to us.
5. You may delete the results.S005.txt file after
your mail
was actually sent (not only queued).
Or you may keep
results.S005.txt files anywhere,
BUT DO NOT MOVE THEM TO THEIR ORIGINAL
FOLDER:
If a file called " results.S005.txt"
is in this folder
then new results will be appended to
it.
This would make you submit the same
results more than
one time. This will *not* increase
your highscores, as
duplicates are removed from the results.
============================
To chose a good size for your results files, do the following:
1. Realize that one simulate-command in your run
file makes one
single-run of a simulated worldhistory.
2. To record all results from such a single-run
ca.
100 KB (or less) are needed, depending
on the simulation.
3. Go to http://www.evolutionary-research.net to
select the
simulations you want to compute, considering
RAM and
computing time.
4. Copy and paste the whole line with the simulate-command
from the browser to a text file.
Make sure you get the & #,
as these mark beginning and end of
a command. The rest of
the line is only for comment: remove
it or leave it.
5. Do that for all the simulations you want to compute
before
visiting the website again.
6. The number of these simulate-commands divided
by 10 will
give you an estimate of the maximal
result file size
in MegaBytes.
7. Check whether your harddisk has enough space
for that
and your Internet connection is fast
enough. 1MB makes ca.
>10 minutes with a 14.4kbps modem
or few seconds with
Ethernet.
8. Open a new ordinary (ascii-)text file with the
name "run"
or "run.txt" and store the
appropriate number of
simulate-commands in there.
9. Move that run-file to the simulators folder and
remove
any file with the name "position_in_run_file.info.txt",
if you interrupted batch execution
of another run-file.
10. Start the simulator
You can in principle accumulate huge results-files from many
small or few long run-files. However, we encourage you to send
us your results as soon as you have 10-20 results completed
or
the time since you downloaded the run-files is more than a
week or so. This keeps size of results files reasonable (1-2MB)
and allows us to update numbers indicating how often a certain
simulation has been calculated. As with all stochastic
simulations, ours have to be repeated too, so DO NOT WORRY
about computing the same run-file several times: This has to
be done in any case.
============================
To make the simulator start after booting, do the following:
1. Put an alias (or link) of (to) the executable
of the
simulator in the autostart (startup)
folder of your
operating system.
2. Don't worry about crashes. After rebooting, the
simulator
will use the next simulation in your
run-file. You just have
to click it to the background.
3. If you find the simulator *cause* operating system
crashes, then please report the exact
circumstances
(operating system, RAM installed, open
programs, RAM
requirements of the simulator as well
as the simulate-command
computed; in case of doubt send all
the files in the
simulators folder as attachment) via
email to
bugs@evolution-at-home.net.
Up to now, this has not been observed.
============================
To keep a complementary copy of the results you calculated,
do the following:
1. Edit the preferenes file before starting a new
run or
interrupt evolution and change the
StandardOutputToFile
parameter from 0 (default) to 1.
2. Make sure you have enough space on your harddisk,
as a
new log file will then be created with
each new start of
the simulator.
3. Adjust the upper limit for the size of a log-file
properly
============================
To watch speed of computation
Open the file called "eProgress.txt" and find estimates
of
current progress. It is not recommended to observe all clicks
of the Ratchet via life-reporting, as they are written to screen
and/or log-file. But if you want that, then do the following:
1. Interrupt evolution or edit the preferenes file before
starting a new run and change the ClicksAndGenerationsToScreen
parameter from 0 (default) to a *reasonable*
number.
(If you want a message every generation in
a small
population for example, you slow down computation
and fill
your hard disk with nonsense.)
2. Make sure you have enough space on your harddisk /
enough
RAM as all the output generated will
be written to RAM /
harddisk corresponding to your output preferences.
3. WARNING: This feature is not recommended if you do
not sit
there and actually watch. This function might
fill your
harddisk with garbage if you chose the wrong
parameters.
You get better informations by watching the
content of
"eProgress.txt" and "eLastParametersList.txt"
or by
interrupting evolution and printing ParametersList.
============================
To make your CPU as fast as possible, do the following:
1. *ALLWAYS* compute only simulations that need
less RAM
than you have left over. If your computations
ever need
virtual memory they slow down by a
factor of 100 - 1000.
2. Switch all life-reporting messages off to avoid
unnecessary output.
2. You may want to increase the interrupt intervalls
in the
preferences or during evolution. However,
be carefull,
as the application will be more difficult
to interrupt
the larger you make these values. (The
simulator will
only look for an interrupt after computation
of that
many individuals.)
3. Turn of screen-saving, energy-saving and automated
system shut-down features, especially
if you leave for
home, weekend, holidays or whyever.
Obviously your
computer can not be fast while sleeping
...
============================
Known bugs:
If you find any bugs, please report the exact circumstances
(operating systen, RAM installed, open programs, RAM
requirements of the simulator as well as the simulate-command
computed; in case of doubt send all the files in the simulators
folder as attachment) via email to bugs@evolution-at-home.net
Currently no identifyable bugs are known for this
operating system.
============================
Finally, enjoy the evolutionary research you are doing,
and thank you again for computing with us.
Your evolutionary-research team.
=======================================================
=== Help on life-reporting system
=======================================================
Purpose of the life-reporting system is progress-tracking
in some rare occasions. For usual progress-infomation
open "Progress.txt". However, if you want a message
whenever the ratchet clicks (because you chose a simulation
with a very slow click-rate), and you want regular
messages to screen (say every 10 000 timesteps), then
the following is for you.
However, simulation will be interrupted, if it produces
more messages than can be stored in RAM or log-file.
If all messages are recorded on screen (= may be in RAM)
this may lead to out of memory problems. If all messages
are recorded in log-file (=on harddisk) this may cause
problems for your operating system if the last space on
your hard disk is filled . This does not happen if you
use default settings, have reasonable space on your disk
and do not accumulate huge results-files.
* Log-file size:
Maximum (single) log-file size before a simulation
terminates can range from 100KB to 2GB. One standard
simulation with no messages during evolution
(life-reporting off) needs ca. 10KB if you write
messages to log-file. Think about the number of
simulations you want to compute with one run-file.
Then estimate the number of bytes needed in the log file
if you want to record anything in the log-file and add
enough space for potential life-reports. Check whether
the harddisk with the simulators folder has enough free
space, also for results-files.
* Results-file:
What you can not switch off is the production of a
results-file that grows by ca. 100 KB (or less) with
each simulation you complete. IMPORTANT: Remove this
file
from the simulator directory as soon as you have sent
results to evolutionary-research via email.
* Life-reporting:
If you want a hi-I-am-still-busy message every more
than 0 timesteps, then clicks of the Ratchet are also
reported. If you choose 0 (safest choice), no messages
are written to screen at all. If you record too many
messages on screen (= may be in RAM) this may lead to
out
of memory problems. Therefore think about how much you
record, or use 0 which is the savest value (= default).
If the Ratchet clicks very often and you process many
small populations, 0 is recommended too. However, it
is
much better, to use progress files for monitoring progress
and not life-reporting.
* Progress-files:
If the a GUI is active (i.e. the file "eGUIactive.txt"
is in the simulators folder) then a progress-file
("eProgress.txt") and a copy of the parameterslist
is
("eLastParametersList.txt") written during
every timestep.
If the GUI is inactive the same files are written to
the
simulators folder, only less frequent to save computing
time.
If you open these, you find current progress estimations.
*** Savest settings = defaults:
Nothing is recorded on file or screen, 2 MB log-filesize
limit, no life-reporting (i.e. one message every 0 generations)
=======================================================
=== Commands from SController =========================
=======================================================
The following commands are available from
simulator S005 release 4 International_Windows_Client :
You may put them in a file called "run" in the programs
folder.
Then, starting the program, the commands in the run-file are
executed,
if you frame them with & # .
Everything outside &# is a comment.
Read S005_Preferences.txt for information on preferences parameters.
COMMANDS:
systemexplain
overall introduction into working with
this simulator system
licence
current licence: you are free to *use*
this programm
measureMINDS
measures e-performance in MINDS =
Million INDividuals per Second
remark
write everything after remark to screen and
log from run-file
quit
terminate the program session
=======================================================
=== Commands from EWorld ==============================
=======================================================
The following commands are available from
simulator S005 release 4 International_Windows_Client :
You may put them in a file called "run" in the programs
folder.
Then, starting the program, the commands in the run-file are
executed,
if you frame them with & # .
Everything outside &# is a comment.
COMMANDS:
simulate <parameters> runs a standard world history
with the
parameters given (formerly key<parameters>)
=======================================================
The following is a copy of the current preferences file
containing all explanations for meaningful editing.
=======================================================
READ THIS LINE FIRST: You may change preferences by editing
this file. But if you enter nonsense or destroy its structure,
this file is renamed as corrupt preferences. So: *Don't* change
the pattern (1 textline then 1 numberline except for this
line). *Don't* change the sequence of parameters. The computing
work counters for this machine are for your information only.
They are only valid if dont change them and preserve this
file in the directory of the simulator. You may change your
identity at any time or become anonymous again. The identity
you enter determines what account your contributions are added
to on the website.
Public family or group name (Enter name with up to 55 characters
or "anonymous". Will be published in highscores
at http://www.evolutionary-research.net. If this name is not
unique your results will be automatically added to the existing
group with this name. ) :
anonymous
Public personal or member name (Enter name with up to 55 characters
or "anonymous". Will be published in highscores
at http://www.evolutionary-research.net) :
anonymous
Not-published GroupNameCheckPIN (Enter "anonymous"
or a code with up to 20 numbers or letters, that is not similar
to any passwords you use on important occasions. This code
is neither published with the highscores, nor especially encrypted
while stored in the preferences file on your harddisk or transmitted
by email. Please store it also in some other place in case
you delete the preferences file.This string must not contain
spaces or tabs and is used for identification when calculating
the highscores: If you submit your first result, the NameCheckPIN
in there is remembered. If you then submit other results after
that, their NameCheckPIN is compared to the first one to make
sure that you submitted these results with the URL they promote.)
Now enter the code (up to 20 characters without space or tabs)
:
anonymous
Not-published PersonalNameCheckPIN (see explanation above
for GroupNameCheckPIN). This ID keeps other members of your
group from adding to your highscores, as all results submitted
under your group and personal name without this ID will be
anonymized. Now enter the code (up to 20 characters without
space or tabs) :
anonymous
Public PromotedURL (Your email or homepage that shall be used
as a link to allow people surfing the highscores, to be published
at http://www.evolutionary-research.net to visit your website
or email you. If your URL is not correct, people will not
find you. The email account used to send your results to evolutionary-research
will not be published whatsoever.) Use "anonymous"
or meaningful URL with up to 90 characters :
anonymous
Nation (enter name or "anonymous", may be published
in highscores at http://www.evolutionary-research.net) :
anonymous
ANSI CPU information (automatic) :
PENTIUM
ANSI OS information (automatic) :
Win32 on Windows 95 4.0
Systemdetails known (unknown or details like CPU type+speed,
Cache size+speed, RAM size+speed, up to 70 characters) :
unknown
EEPerformance of this system (MegaIndividualsPerSecond in
a 116508 individuals (= 10 MB) population):
0.0515750332004063
Total computing time (days) recorded in this preferences file
:
0
Total number of workunits (in GigaIndividuals) recorded in
this preferences file :
0
Worldhistory runs recorded in this preferences file :
0
InterruptFast: Call after so many individuals :
2578
InterruptSlow: Check for break-file after so many individuals
:
103150
ScreenActivity: Write a short message if the Ratchet clicks
or this number of Generations are over. This may lead to out
of memory errors, if RAM is short for long simulations, as
every message is recorded in memory! So use this feature with
caution:
0
StandardOutputToFile (default = 0): 1 = Batch-run output will
be written to log-file (uses diskspace) 0 = Batch-run output
will NOT be written to log-file (saves diskspace). (You may
get problems with a completely filled harddisk, if you request
too much output) :
0
StandardOutputToScreen (default = 1): 1 = Batch-run output
will be written to screen (uses RAM) 0 = Batch-run output
will NOT be written to screen (saves RAM, allows for simulation
of larger populations). (Simulator may terminate, if you request
too much output) :
0
Maximum log-file size before simulation stops can be from
100KB to 2GB (default = 10 000 000 bytes). One standardsimulation
with all reporting off needs ca. 10KB in log-file (+
ca. 100KB in separate results-file). Think about the number
of simulations you want to compute with one run-file. Then
estimate the number of bytes needed in the log file and add
space for extra reports.Check whether the harddisk with the
simulators folder has enough free space.Here is the current
maximal number of bytes a log-file is allowed to have:
2000000
Write-intervall for intermediate results to disk in minutes
(60 = default; this saves intermediate results so that they
can be added to the resultsfile after a systemcrash. The intermediate
result file is deleted automatically after adding its content
to the result file after starting the simulator the next time)
:
60
GetTimeSeriesRequestsFromFile (Shall the simulator evaluate
the file "TimeseriesRequests.txt" during every evolve-loop?
yes = 1, no = 0) :
0
WriteProgressFileIntervallSec (Write one "eProgress.txt"
file after how many seconds) :
120
WriteLastParametersListFileIntervallMin (write a new ParametersList
print out to file after how many minutes):
10
AcceptKeyRAMminimumMB (Reject keys that need less MB than)
:
0
AcceptKeyRAMmaximumMB (Reject keys that need more MB than)
:
10
AcceptKeyComputingTimeMinimumHours (Reject keys that need
less hours computing time than) :
0
AcceptKeyComputingTimeMaximumDays (Reject keys that need more
days computing time than) :
30
Last change : 2001Apr28_13h08m48
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