[Gfs-users] live ubuntu gerris distribution
Stephane Popinet
I have just written instructions on how to boot a live Ubuntu
distribution with Gerris pre-installed. See:
http://gfs.sourceforge.net/wiki/index.php/Live_Ubuntu_Gerris_distribution
also linked on the installation summary page:
http://gfs.sourceforge.net/wiki/index.php/Installation_summary
I have tested it on the systems I have access to and it works fine.
It's meant to also work on Macs but it would be nice if mac users out
there tested it.
I would like to get a "statistical" feel of what proportion of systems
it supports, so it would be nice if people tried it on as many systems
as possible and reported their findings (both positive and negative).
cheers
Stephane
------------------------------------------------------------------------------
WhatsUp Gold - Download Free Network Management Software
The most intuitive, comprehensive, and cost-effective network
management toolset available today. Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd
_______________________________________________
Gfs-users mailing list
Gfs-...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gfs-users
cedric penard
I don't know if I am alone to have this problem, but I can't download the
totality of file : it's stop at 400Mo about...
Also you should put the md5sum file, so we could test if the file is not
corrupt.
Cedric
cedric penard
I already have a problem with the download.
With wget :
(sorry messages are in french...)
--12:00:53--
http://gerris.dalembert.upmc.fr/iso/ubuntu-gerris-10.04.2-desktop-i386.iso
=> `ubuntu-gerris-10.04.2-desktop-i386.iso'
Résolution de gerris.dalembert.upmc.fr... 134.157.69.22
Connexion vers gerris.dalembert.upmc.fr|134.157.69.22|:80... connecté.
requête HTTP transmise, en attente de la réponse... 200 OK
Longueur: 854 108 160 (815M) [application/x-iso9660-image]
77% [===========================> ] 659 752 915 1.05M/s ETA
02:56
12:10:54 (1.05 MB/s) - Fermeture de la connexion à l'octet 659752915.
Nouvel essai.
--12:10:55--
http://gerris.dalembert.upmc.fr/iso/ubuntu-gerris-10.04.2-desktop-i386.iso
(essai: 2) => `ubuntu-gerris-10.04.2-desktop-i386.iso'
Connexion vers gerris.dalembert.upmc.fr|134.157.69.22|:80... connecté.
requête HTTP transmise, en attente de la réponse... 200 OK
Longueur: 854 108 160 (815M) [application/x-iso9660-image]
43% [===============> ] 662 879 167 1.06M/s ETA
12:51
12:21:02 (1.05 MB/s) - Fermeture de la connexion à l'octet 662879167.
Nouvel essai.
--12:21:04--
http://gerris.dalembert.upmc.fr/iso/ubuntu-gerris-10.04.2-desktop-i386.iso
(essai: 3) => `ubuntu-gerris-10.04.2-desktop-i386.iso'
Connexion vers gerris.dalembert.upmc.fr|134.157.69.22|:80... connecté
etc...
Is there someone else with the same problem ?
Cheers
Cedric
------------------------------------------------------------------------------
Achieve unprecedented app performance and reliability
What every C/C++ and Fortran developer should know.
Learn how Intel has extended the reach of its next-generation tools
to help boost performance applications - inlcuding clusters.
http://p.sf.net/sfu/intel-dev2devmay
Kristjan Gudmundsson
I was able to download the ISO image without problems by just clicking on the link provided by Stephane. It was downloaded in under 2min via the connection at my uni.
Best,
Kristjan
Kristján Guðmundsson, Ph.D.
Physics of Fluids Group
Applied Physics Dept., Uni. of Twente
hermite.caltech.edu/kristjan
Arnaud Antkowiak
Yes, you are right, there is a timeout set to 10 minutes (sysadmins are picky). Unfortunately, for regular people who don't benefit the ultra-fast connection of Kristjan, "wget -c" requests won't be accepted by the server so partial downloads can't be resumed...
Arnaud
Institut d'Alembert - Université Pierre et Marie Curie
Tel : +33 (0)1 44 27 26 91 (office) or 7 27 05 (lab)
Wasy
Stephane Popinet
> Yes, you are right, there is a timeout set to 10 minutes (sysadmins are
> picky). Unfortunately, for regular people who don't benefit the ultra-fast
> connection of Kristjan, "wget -c" requests won't be accepted by the server
> so partial downloads can't be resumed...
The problem should be fixed now (the timeout has been reset to 100
minutes). Please confirm that this works for you. It would also be
good to know whether you are able to use the downloaded image to boot
the system (and whether anything is missing from the distribution).
cheers
Stephane
PS: Arnaud, could you please test whether Macs can also boot from this image?
------------------------------------------------------------------------------
Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Discover what all the cheering's about.
Get your free trial download today.
http://p.sf.net/sfu/quest-dev2dev2
Geordie McBain
> Hi Arnaud, Cedric,
>
>> Yes, you are right, there is a timeout set to 10 minutes (sysadmins are
>> picky). Unfortunately, for regular people who don't benefit the ultra-fast
>> connection of Kristjan, "wget -c" requests won't be accepted by the server
>> so partial downloads can't be resumed...
>
> The problem should be fixed now (the timeout has been reset to 100
> minutes). Please confirm that this works for you.
I had another go at this and failed again. The first time, 16 May, I
only got 58M, today I got 512M, but I believe the full image is 850M.
(Is that right? The md5sum might be good to know; saves burning
corrupted images to disks.)
------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
cedric penard
The problem is fixed for me : the download is complete.
The image boots and works fine.
I tried some example with Gerris : it was running without problem.
cheers
Cedric
------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
cedric penard
I experiment a segmentation fault with Karamea example :
gerris2D -m karamea.gfs | gfsview flooding.gfv
step: 0 t: 0.00000000 dt: 3.846154e-01 cpu: 0.00000000
real: 0.00000100
Balance summary: 1 PE
domain min: 74614 avg: 74614 | 0 max: 74614
step: 10 t: 3.84615385 dt: 3.846154e-01 cpu: 1.74000000
real: 1.98678600
Balance summary: 1 PE
domain min: 16099 avg: 16099 | 0 max: 16099
step: 20 t: 7.69230769 dt: 3.846154e-01 cpu: 2.58000000
real: 2.83908800
Balance summary: 1 PE
domain min: 16132 avg: 16132 | 0 max: 16132
step: 30 t: 11.53846154 dt: 3.846154e-01 cpu: 3.40000000
real: 4.51521900
Balance summary: 1 PE
domain min: 16144 avg: 16144 | 0 max: 16144
step: 40 t: 15.38461539 dt: 3.846154e-01 cpu: 4.22000000
real: 5.35441400
Balance summary: 1 PE
domain min: 16192 avg: 16192 | 0 max: 16192
step: 50 t: 19.23076923 dt: 3.846154e-01 cpu: 5.03000000
real: 6.16519500
..................
Balance summary: 1 PE
domain min: 19819 avg: 19819 | 0 max: 19819
step: 5410 t: 2021.11111111 dt: 3.703704e-01 cpu: 529.12000000
real: 649.89508300
Balance summary: 1 PE
domain min: 19819 avg: 19819 | 0 max: 19819
step: 5420 t: 2024.81481482 dt: 3.703704e-01 cpu: 530.18000000
real: 650.96407100
Balance summary: 1 PE
domain min: 19807 avg: 19807 | 0 max: 19807
step: 5430 t: 2028.51851852 dt: 3.703704e-01 cpu: 531.21000000
real: 652.01198200
Balance summary: 1 PE
domain min: 19816 avg: 19816 | 0 max: 19816
[pc-penard:05579] *** Process received signal ***
[pc-penard:05579] Signal: Segmentation fault (11)
[pc-penard:05579] Signal code: (128)
[pc-penard:05579] Failing at address: (nil)
Inconsistency detected by ld.so: dl-open.c: 260: dl_open_worker: Assertion
`_dl_debug_initialize (0, args->nsid)->r_state == RT_CONSISTENT' failed!
gerris2D --version
gerris: using 2D libgfs version 1.3.2 (100701-064521)
compiled with flags: -I/no_save/opt2/netcdf-4.0.1/include
MPI: yes
pkg-config: yes
m4 and gawk: yes
The simulation file :
Define DRY 1e-3
1 0 GfsRiver GfsBox GfsGEdge { x = 0.5 y = 0.5 } {
PhysicalParams { L = 5600 g = 9.81 }
MapTransform { tx = 1523880 ty = 5430180 }
GModule terrain
Refine 8
VariableTerrain Zb { basename = topo }
Init {} {
Z0 = 0.01
}
SourceCoriolis 0 {
/* r = U/U^\star */
if (P < DRY || Z0 < 1e-6)
return 1e10;
double a = P/Z0;
double r = a > 2.718 ? 2.5*(log (a) - 1. + 1.359/a) :
0.46*a;
return sqrt(U*U+V*V)/(P*P*r*r);
}
Init {} {
P = MAX(-Zb, 0)
}
DischargeElevation E flow.cgd (y > 5431400 ? 0 : -1000)
AdaptFunction { istep = 1 } {
cmax = 0
minlevel = (t > 0 ? 0 : 8)
maxlevel = 10
} (P > DRY && Zbn > 1 ? MAX(Zbdmax - H, 0) : 0)
OutputTime { istep = 10 } stderr
OutputBalance { istep = 10 } stderr
OutputSimulation { step = 10 } stdout
OutputScalarSum { istep = 10 } volume { v = P }
OutputGRD { step = 600 } p-%g.asc { v = P }
} {
time_order = 1
dry = DRY
}
GfsBox {
right = Boundary {
BcDirichlet P (y > 5431400 ? MAX(E - Zb, 0) : -1000)
}
left = Boundary {
BcSubcritical U MAX(1.*sin(2.*M_PI*t/433512.) - Zb, 0)
}
top = Boundary
bottom = Boundary
}
It's difficult to reproduce this bug. I dont know if someone has already
have the same problem.
Cheers
Cedric
cedric penard
When I tried these commands :
darcs get http://gerris.dalembert.upmc.fr/darcs/gfsview-stable/
darcs get http://gerris.dalembert.upmc.fr/darcs/gerris-stable/
I have these error message :
Invalid repository: http://gerris.dalembert.upmc.fr/darcs/gfsview-stable
darcs failed: Failed to download URL
http://gerris.dalembert.upmc.fr/darcs/gfsview-stable/_darcs/inventory :
HTTP error (404?)
Invalid repository: http://gerris.dalembert.upmc.fr/darcs/gerris-stable
darcs failed: Failed to download URL
http://gerris.dalembert.upmc.fr/darcs/gerris-stable/_darcs/inventory :
HTTP error (404?)
I need some help, with gts repository it's work well...
Thanks
Cedric
Stephane Popinet
> darcs get http://gerris.dalembert.upmc.fr/darcs/gfsview-stable/
> darcs get http://gerris.dalembert.upmc.fr/darcs/gerris-stable/
I just tried and it works fine for me. Maybe a temporary network problem?
cheers
Stephane
cedric penard
Perhaps a bug with darcs ?
I can explore the repository with firefox, but darcs doesn't work...
Strange !
Cheers
Cedric
Stephane Popinet
> I can explore the repository with firefox, but darcs doesn't work...
what version of darcs are you using?
darcs --version
make sure it's > 2
cedric penard
darcs --version
1.0.9
With 2.0.2 it works better.
Thanks
Cedric
Arnaud Antkowiak
Unfortunately I was not able to boot the live Ubuntu distribution on my MacBook Pro from the USB stick (created following the instructions from Ubuntu website).
Actually, I don't even see the USB stick at the boot. Following advices from Ubuntu and Mac forums I've installed the "rEFIt" boot loader, but the USB stick keeps not showing up.
Maybe this problem affects only unibody macbooks ? Here are some infos on my laptop:
version: MacBookPro5,5
processor: Intel Core 2 Duo (2,53 GHz)
OS: Mac OS X 10.6.7
Has anybody had some success in booting the Live Ubuntu from a USB stick on an Intel Mac?
Many thanks,
Arnaud
PS: I also tried the regular (gerris-free) Ubuntu distribution with the same result.
Kristjan Gudmundsson
> Actually, I don't even see the USB stick at the boot.
Same for me on a Macbook pro 5.3. Booting an intel-mac non-osx system
from usb seems to be a huge pain:
http://ubuntuforums.org/showthread.php?t=510030
I'll try this on a DVD and report back.
Cheers,
Kristjan
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> Gfs-users mailing list
> Gfs-...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gfs-users
>
>
--
Kristján Guðmundsson, Ph.D.
Physics of Fluids Group
Applied Physics Dept., Uni. of Twente
hermite.caltech.edu/kristjan
------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
Stephane Popinet
Hmm, sounds like Macs are even worse than I thought. At least
Microsoft cannot really prevent people from booting (and installing)
other OSes on PCs (yet). Sounds like Apple can (and does)...
>From my quick googling, it indeed sounds like burning a bootable CD
rather than a USB stick could work better.
Maybe a workaround would be to boot a virtual machine (e.g. Virtual
Box or VMware) from the .iso, all this from within MacOSX.
good luck
Stephane
Arnaud Antkowiak
I finally got it to work! Ouch, this wasn't easy.
I basically followed the instructions reported here : http://www.zebpedersen.co.uk/?p=962#more-962
In a nutshell, what I did is the following:
1) Download the Ubuntu-gerris iso cooked by Stéphane,
2) Download virtual box
3) Launch Ubuntu-gerris from within the virtual machine, as explained in the first link
4) Install Ubuntu-gerris on a USB stick
5) Install rEFIt on the macbook
6) Reboot
7) Reboot again
8) From rEFIt menu, choose to boot Ubuntu-gerris from USB stick
I quickly tested a few examples, and it perfectly works : gerris2D, gerris3D, PPM outputs from gfsview and... gfsview-batch ! This might be of some interest for Mac users.
On the dark side, I couldn't manage to make the wireless to work. And I had a few keyboard issues on my french keypad, but I bet this could be easily settled with a proper configuration.
I would be glad if anyone could confirm the reproducibility of the procedure,
Arnaud
Stephane Popinet
Thanks for the hard work. Just a few questions/comments:
1) Why didn't you just run within Virtual Box? Is it slow/not usable?
2) I think that what you did as described on
http://www.zebpedersen.co.uk/?p=962#more-962 was to do a full install
on a USB stick. It is quite different from booting the live USB stick.
The live distribution uses a compressed filesystem which allows to fit
the whole system in less than one GB. I guess your full install is
much bigger than this. How big is your USB stick?
3) Did you try to boot from the live USB stick (prepared as per the
MacOSX instructions on the Ubuntu site) using this rEFiTitTTT thing?
4) This complicated procedure sort of cancels the whole point of the
live USB stick: being able to boot any machine just with a USB stick
(i.e. on PCs, the only requirement is that the BIOS allows booting
from USB which is pretty much standard these days). From what you
write it seems that even once you have prepared your USB stick
"properly", you still require the Mac machine to have REffFFiTtt
installed before being able to boot?
cheers
Arnaud Antkowiak
1) Why didn't you just run within Virtual Box? Is it slow/not usable?
It perfectly works from within VirtualBox. But gerris seemed very slow... But I did not quantitatively checked that.
2) I think that what you did as described on
http://www.zebpedersen.co.uk/?p=962#more-962 was to do a full install
on a USB stick. It is quite different from booting the live USB stick.
The live distribution uses a compressed filesystem which allows to fit
the whole system in less than one GB. I guess your full install is
much bigger than this. How big is your USB stick?
You're right, the (late) key weighted something like 5 Gb.
3) Did you try to boot from the live USB stick (prepared as per the
MacOSX instructions on the Ubuntu site) using this rEFiTitTTT thing?
Actually, I asked my favourite gerris guru today to prepare me a live USB stick with its ubuntu, and no it didn't work.
rEFIt saw the key, but ended with a boot error.
So I tried to prepare my own USB key from Mac OS X, and it didn't work better. It was even worse, as the boot loader did not see the key.
Googling around, I ended up on this ubuntu page : https://help.ubuntu.com/community/Installation/FromUSBStick :
"There is an unresolved problem in that you cannot create a bootable USB flash drive from within Mac OS X. You must create the stick in Linux or Windows."
Ouch.
4) This complicated procedure sort of cancels the whole point of the
live USB stick: being able to boot any machine just with a USB stick
(i.e. on PCs, the only requirement is that the BIOS allows booting
from USB which is pretty much standard these days). From what you
write it seems that even once you have prepared your USB stick
"properly", you still require the Mac machine to have REffFFiTtt
installed before being able to boot?
And now the happy end. I finally found the definite answer allowing me to boot the live USB on my macbook pro on this page : http://www.devslashzero.com/node/160
Quoting: "The trick is to make the live USB stick with no partitions."
And it works perfectly well !! Even wireless is operational. If that's not a happy end... :)
I must say I'm impressed, turning my macbook into a fully functional Linux box running gerris with just a small USB key is kind of magical!
The only drawback is that yes, you'll need rEFIt to boot the key. But that's a little price to pay for this result IMHO (and you can have rEFIt on the stick if you want a standalone install on it).
Hope this helps,
Arnaud
Kristjan Gudmundsson
> And it works perfectly well !! Even wireless is operational. If that's not a
> happy end... :)
Great job, thanks for spending the time. I'll try this out, too. I'm
sure Stephane will buy a mac soon..
Kristjan
--
Kristján Guðmundsson, Ph.D.
Physics of Fluids Group
Applied Physics Dept., Uni. of Twente
hermite.caltech.edu/kristjan
------------------------------------------------------------------------------
Stephane Popinet
Thanks a lot for the hard work. I have added instructions for Mac users here:
http://gfs.sourceforge.net/wiki/index.php/Live_Ubuntu_Gerris_distribution
Stephane Popinet
> sure Stephane will buy a mac soon..
You bet. And I will switch to Fluent too while I am at it...
Stephane