[GAMBIT] Understanding memory (ram) limits

ghost82 · September 2, 2013, 09:16

Hi all!
I want to be sure about my thoughts memory limits in gambit vs operating systems.

I'm using gambit, and, as I know these are available versions:

- 32 bit gambit for windows
- 32 bit gambit for linux
- 64 bit gambit for linux (found several threads in this forum saying it exists, but never seen it)

I was using gambit on my laptop, with windows 7 64 bit and 4gb of ram.
Sometimes, when meshing, I have the memory error, which I ever solved by splitting my domain into more subvolumes; with this method I was able to mesh domains of about 3 - 3,5 million cells without problems.

Now, I'm waiting for a new workstation with windows 7 64 bit and 64gb of ram.

My questions are:
1- if for example in the configuration "win7 64 bit + 4gb ram" the limit in meshing a single volume at one time is 1 million cells (I don't know/remember the exact limit), due to 4gb of ram, will am I able to mesh a single volume with more than 1 million cells in the new workstation, or the limit is in the 32bit version of gambit?

2- I read an old thread, saying that a user couldn't save the .msh file if the domain contained about 19 million cells ore more: anyone can confirm this?

Thank you,
have a good day!

Daniele

-mAx- · September 3, 2013, 01:40

Hello Daniele,
I confirm that there is a linux 64 bit version (lnamd64)
With your new machine, I assume you will be still limited for meshing one volume (memory for one operation), but you should be able to write the entire mesh (*.msh). I also had problem while writing mesh file about 4-9 millions cells
So as you mentionned if you want to mesh a geometry with 4 millions cells, you cannot doing it on the fly since you are limited by the 32bit version. But you can split your model and mesh subvolumes. And at the end you can write the entire mesh (*.msh). This last operation doesn't seem to be limited by the 32bit version, but by the hardware.
They are my own presumptions

ghost82 · September 3, 2013, 05:54

Thank you Max,
since the same gambit license file can be installed independently on win or linux, could the lnamd64 version be installed on linux64 with Intel Xeon e5 processors?I read lnamd64 should be installed with AMD processors, but I'm not sure.

In case it can be installed, which linux distribution do you recommend?
I'm not linux expert, so an easy distribution such as ubuntu/kubuntu would be an optimal solution.

Thanks

Daniele

-mAx- · September 3, 2013, 07:17

I don't know if lnadm64 could be installed on your Intel Xeon 5, but it doesn't cost anything to try.
I am also not a linux expert, and I am satisfied with caelinux distribution (you have lots of opensource cae softwares preinstalled)

ghost82 · September 5, 2013, 11:32

Hi all,
just for reference, I tried to install the 64 bit of gambit on my laptop (macbook pro early 2008, with an intel T9300 core due duo processor).
I created a virtual machine and installed latest kubuntu version 64 bit, then I installed lnamd64 gambit.
It works, so I'm just planning to use on my workstation a similar setup, by creating in windows 7 a kubuntu 64 bit virtual machine with gambit 64 bit and by setting this virtual machine to use 32 gb ram (half of the total) and 1 processor (6 cores): this should have enough power for my needs..

PS: just for reference (2), I saw on our server at university an "ultra" release of gambit (142 mb); maybe this is another 64 bit release, base on Sun Ultra, but I'm not sure.

Daniele

ghost82 · September 9, 2013, 12:54

I also noticed that by default gambit won't start if started with command:

Code:

sudo ./gambit

it returns a series of errors such as:

Code:

daniele@ubuntu:~/Desktop/gambit/Fluent.Inc/bin$ sudo ./gambit
LANG en_US.UTF-8 changed temporarily to en_US for gambit use.
Starting /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit ...
Gambit build SP2007051420.
Warning: locale not supported by C library, locale unchanged
Locking assertion failure.  Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb26ab767]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_unlock+0x31) [0xb26ab8b1]
#2 /usr/lib/libX11.so.6(_XReply+0xfd) [0xb29651bd]
#3 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit [0x9affcc9]
#4 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit [0x9b0009a]
#5 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit [0x9afe807]
#6 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit [0x9afeecb]
#7 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit(vgl_OpenGLDevBestVisualX+0x1f7) [0x9a51f25]
#8 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/BX.so(vgl_visual+0x2a6) [0xb6a9111e]
#9 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/G.so(_Z16cpp_teleuse_mainiPPc+0x31a) [0xb60e6c76]
#10 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/G.so(teleuse_main+0x1e) [0xb606a2ea]
#11 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/BX.so(motif_init+0xfb) [0xb6a90c07]
#12 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit(_Z17local_gambit_mainiPPc+0x2a6) [0x808d94e]
#13 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit [0x808e8b0]
#14 /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0) [0xb26e8460]
#15 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit(XMapRaised+0x31) [0x8073271]
Locking assertion failure.  Backtrace:
#0 /usr/lib/libxcb-xlib.so.0 [0xb26ab767]
#1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0xb26ab81e]
#2 /usr/lib/libX11.so.6 [0xb2964518]
#3 /usr/lib/libX11.so.6(XGetVisualInfo+0x26) [0xb295b0a6]
#4 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit [0x9aff40f]
#5 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit(vgl_OpenGLDevBestVisualX+0x1f7) [0x9a51f25]
#6 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/BX.so(vgl_visual+0x2a6) [0xb6a9111e]
#7 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/G.so(_Z16cpp_teleuse_mainiPPc+0x31a) [0xb60e6c76]
#8 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/G.so(teleuse_main+0x1e) [0xb606a2ea]
#9 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/BX.so(motif_init+0xfb) [0xb6a90c07]
#10 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit(_Z17local_gambit_mainiPPc+0x2a6) [0x808d94e]
#11 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit [0x808e8b0]
#12 /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0) [0xb26e8460]
#13 /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit(XMapRa
gambit: ../../src/xcb_lock.c:77: _XGetXCBBuffer: Assertion `((int) ((xcb_req) -

Received exception: SIGABRT (abort signal)

Please send the GAMBIT.5573/jou and GAMBIT.5573/trn files to your local
Fluent office or distributor.  Also send a message including any
relevant errors or warnings you see above in this window.  You may
wish to delete the temporary directory GAMBIT.5573 after sending the
above files.
ERROR: Please retain a copy of the GAMBIT.5573/jou, GAMBIT.5573/trn, and
GAMBIT.5573/*.dbs files, any imported geometry and any relevant
errors or warnings you see above in this window and contact
support at your local Fluent office or distributor.
Aborted

Possibile solution is to start gambit with the -dev x11 option:

Code:

daniele@ubuntu:~/Desktop/gambit/Fluent.Inc/bin$ sudo ./gambit -dev x11
[sudo] password for daniele:
LANG en_US.UTF-8 changed temporarily to en_US for gambit use.
Starting /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit -device x11...
Gambit build SP2007051420.
Warning: locale not supported by C library, locale unchanged
        Using X_DEVICE_DRIVER with standard visual.

This command will start gambit with standard visual, as you can read in the terminal;

However, if you want to use opengl as driver, I found the solution:
1- download old libx11 lib:
for linux 32 bit (debian like):
http://rghost.net/48660906

for linux 64 bit (debian like):
http://rghost.net/48660943

Install lib with following command (linux 32 bit (debian like)):

Code:

daniele@ubuntu:~/Desktop$ sudo dpkg -i libx11-6_1.1.1-1ubuntu4_i386.deb
[sudo] password for daniele:
dpkg - warning: downgrading libx11-6 from 2:1.1.3-1ubuntu2 to 2:1.1.1-1ubuntu4.
(Reading database ... 91515 files and directories currently installed.)
Preparing to replace libx11-6 2:1.1.3-1ubuntu2 (using libx11-6_1.1.1-1ubuntu4_i3                                                                                                                          86.deb) ...
Unpacking replacement libx11-6 ...
Setting up libx11-6 (2:1.1.1-1ubuntu4) ...

Processing triggers for libc6 ...
ldconfig deferred processing now taking place

Now you can start gambit and it will use opengl drivers:

Code:

daniele@ubuntu:~/Desktop/gambit/Fluent.Inc/bin$ sudo ./gambit
LANG en_US.UTF-8 changed temporarily to en_US for gambit use.
Starting /home/daniele/Desktop/gambit/Fluent.Inc/gambit2.4.6/lnx86/gambit ...
Gambit build SP2007051420.
Warning: locale not supported by C library, locale unchanged
        Using default visual with OPENGL_DEVICE_DRIVER.

PS: I tested, for now, with linux 32bit, as soon as I have my new 64 bit workstation I will test with 64 bit and if it will work I will delete this PS.

Update: I'm using a virtual machine to test opengl and gambit; the trick seems to work on the 32 bit kubuntu 8.04; even if glxinfo shows no direct rendering gambit can start with opengl. Same version of kubuntu but 64 bit, gambit only starts with X11....I don't know why.
I also installed old gutsy version, but I'm not able to make opengl to work...I think 64 bit doesn't support opengl...(?).
Also, newer versions of linux (32 and 64 bit) don't allow to downgrade libx11-6

Hope this helps,

Daniele

September 2, 2013, 09:16	Understanding memory (ram) limits	#1
ghost82 Senior Member Rick Join Date: Oct 2010 Posts: 1,016 Rep Power: 26	Hi all! I want to be sure about my thoughts memory limits in gambit vs operating systems. I'm using gambit, and, as I know these are available versions: - 32 bit gambit for windows - 32 bit gambit for linux - 64 bit gambit for linux (found several threads in this forum saying it exists, but never seen it) I was using gambit on my laptop, with windows 7 64 bit and 4gb of ram. Sometimes, when meshing, I have the memory error, which I ever solved by splitting my domain into more subvolumes; with this method I was able to mesh domains of about 3 - 3,5 million cells without problems. Now, I'm waiting for a new workstation with windows 7 64 bit and 64gb of ram. My questions are: 1- if for example in the configuration "win7 64 bit + 4gb ram" the limit in meshing a single volume at one time is 1 million cells (I don't know/remember the exact limit), due to 4gb of ram, will am I able to mesh a single volume with more than 1 million cells in the new workstation, or the limit is in the 32bit version of gambit? 2- I read an old thread, saying that a user couldn't save the .msh file if the domain contained about 19 million cells ore more: anyone can confirm this? Thank you, have a good day! Daniele Last edited by ghost82; September 5, 2013 at 11:41.

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September 3, 2013, 01:40		#2
-mAx- Super Moderator Maxime Perelli Join Date: Mar 2009 Location: Switzerland Posts: 3,297 Rep Power: 41	Hello Daniele, I confirm that there is a linux 64 bit version (lnamd64) With your new machine, I assume you will be still limited for meshing one volume (memory for one operation), but you should be able to write the entire mesh (.msh). I also had problem while writing mesh file about 4-9 millions cells So as you mentionned if you want to mesh a geometry with 4 millions cells, you cannot doing it on the fly since you are limited by the 32bit version. But you can split your model and mesh subvolumes. And at the end you can write the entire mesh (.msh). This last operation doesn't seem to be limited by the 32bit version, but by the hardware. They are my own presumptions ghost82 likes this. __________________ In memory of my friend Hervé: CFD engineer & freerider

September 3, 2013, 05:54		#3
ghost82 Senior Member Rick Join Date: Oct 2010 Posts: 1,016 Rep Power: 26	Thank you Max, since the same gambit license file can be installed independently on win or linux, could the lnamd64 version be installed on linux64 with Intel Xeon e5 processors?I read lnamd64 should be installed with AMD processors, but I'm not sure. In case it can be installed, which linux distribution do you recommend? I'm not linux expert, so an easy distribution such as ubuntu/kubuntu would be an optimal solution. Thanks Daniele

September 3, 2013, 07:17		#4
-mAx- Super Moderator Maxime Perelli Join Date: Mar 2009 Location: Switzerland Posts: 3,297 Rep Power: 41	I don't know if lnadm64 could be installed on your Intel Xeon 5, but it doesn't cost anything to try. I am also not a linux expert, and I am satisfied with caelinux distribution (you have lots of opensource cae softwares preinstalled) ghost82 likes this. __________________ In memory of my friend Hervé: CFD engineer & freerider

September 5, 2013, 11:32		#5
ghost82 Senior Member Rick Join Date: Oct 2010 Posts: 1,016 Rep Power: 26	Hi all, just for reference, I tried to install the 64 bit of gambit on my laptop (macbook pro early 2008, with an intel T9300 core due duo processor). I created a virtual machine and installed latest kubuntu version 64 bit, then I installed lnamd64 gambit. It works, so I'm just planning to use on my workstation a similar setup, by creating in windows 7 a kubuntu 64 bit virtual machine with gambit 64 bit and by setting this virtual machine to use 32 gb ram (half of the total) and 1 processor (6 cores): this should have enough power for my needs.. PS: just for reference (2), I saw on our server at university an "ultra" release of gambit (142 mb); maybe this is another 64 bit release, base on Sun Ultra, but I'm not sure. Daniele -mAx- likes this.