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Old 03-19-2009, 10:38 PM
AlexVader AlexVader is offline
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Default Engineering applications in PC BSD
Hi Forum

Does anyone in this forum has any experience running Engineering/Scientific applications in PC BSD...?

I mean applications like OpenFOAM, Fluent, or CD Adapco for Computational Fluid Dynamics, or Abaqus, Ansys or Adina for Finite Elements Analysis, or PointWise, GrigGen, GMSH or NetGen for finite element/volume mesh generation, or Matlab, Scilab, Maxima for generic Math analysis or numeric equation solving.

If anyone ever acheived running/installing anyone of these kinds of apps in PC BSD, I would like to know...

Currently a Ubuntu user, I would like to test PC BSD for speed and performance when running apps like these...


Is there a neat gain in performance when running these in PC BSD compared to running these in Linux...?

The default binary to run in PC BSD can be a linux compiled one or must it be a Mac compiled one...? ( ...probably the most noobish question in this forum, but who cares... :-)... If I ask is out of my own ignorance about BSD ;-p )

Thanks in advance

Alex
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Old 03-20-2009, 04:56 AM
Oko Oko is offline
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Default Re: Engineering applications in PC BSD
Originally Posted by AlexVader
Hi Forum

Does anyone in this forum has any experience running Engineering/Scientific applications in PC BSD...?

I mean applications like OpenFOAM, Fluent, or CD Adapco for Computational Fluid Dynamics, or Abaqus, Ansys or Adina for Finite Elements Analysis, or PointWise, GrigGen, GMSH or NetGen for finite element/volume mesh generation, or Matlab, Scilab, Maxima for generic Math analysis or numeric equation solving.
From the top of my head I know that Abaqus, Scilab, and Maxima are ported to
FreeBSD. MathLab is written for Linux so it can only be run through Linux compatibility layer. Installing Maple, MatLab, and Mathematic is bit tricky. I am not familiar with other applications.


http://www.freebsd.org/ports/
http://www.freebsd.org/doc/en/books/handbook/


./configure, make, make install in principle should work if the application
is correctly written with portability in mind. In reality I would be shocked
that it works without patches. That is really porting question.
There is about 20000 peaces of software ported to FreeBSD. If something is not ported I would not expect that can be easily ported by a person without deep knowledge of the FreeBSD and compiler itself. Check for yourself.

http://www.freebsd.org/doc/en/books/porters-handbook/


I noticed your post earlier. On standard hardware PC hardware (P4-2 Cores) I would not expect any performance gains. I do not know if the particular processes you want to run can make a use of multiprocessors. If that is the case I would expect FreeBSD kernel to slightly out preform Linux kernel if you have 6-12 cores. For instance if you need 15-20 days of up time to preform particular computation you might be able to save a day or two. If the application is linear (must be executed on the single processor) I would not
expect any significant difference between Linux and FreeBSD.

I do not know if you are aware of the fact that you are actually penalized
in performance for using amd unless the application is truly written for 64
bits processor. I would run i386 if I was you unless I am 100% sure that
application is written for 64 bits.



I honestly do not see you benefiting on the short run from moving from Ubuntu/Debian to PC-BSD/FreeBSD. Quite on the contrary it might slow you down significantly since you are not familiar with BSD. Linux is much more System V like so that is really a big deal.

On the long run the question is more difficult.
If you do know that you will be running applications which are ported or can be ported to FreeBSD (or you are writing them on the FreeBSD) you will benefit great deal from clean FreeBSD kernel and userland. I personally would not run applications written for Linux as MatLab via Linux compatibility layer on FreeBSD. I would not run them on Ubuntu either but that is another story. I would run them on the system which they are certified for which is RedHat ( CentOS or Scientific Linux).

I would strongly discourage you from using "user friendly" desktop distros like
PC-BSD or Ubuntu for that matter. If you decide to run BSD (in your case) FreeBSD then run vanilla FreeBSD. In Linux world situation is much more easy. I would not run anything else but RedHat.

Obviously, above statements are subjective and reflect my personal philosophy.
For the record I run OpenBSD but I would not run above applications on it
for any serious purposes due to poor scalability of OpenBSD (security it has its price). They are buy the way mostly ported to OpenBSD.
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Old 03-20-2009, 03:19 PM
AlexVader AlexVader is offline
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Default Re: Engineering applications in PC BSD
Hi OKO

Thanx for your hints...

Most of my system uptimes are in the hours range ( I am talking about my Lappy , a HP DV5 1170 ), as I do moderate to light workload engineering analysis in FEA and CFD as well as Genetic structural optimization with applications that i myself designed, built around Open source finite element or finite volume solvers like Calculix or OpenFOAM.

Of course when I work in a "cooperative" environment I must port my work to a less "geekish" environment, this is when I use Pro Engineer instead of BRL CAD, Fluent instead of OpenFOAM, and Abaqus instead of Calculix.

The "nuclear style" High power computing is made in a cluster or 4 workstations, and it can take one whole month to run, But it is used to solve "weird" problems with an "exotic" physics, like shock wave driven implosions in layered condensed matter, Deflagration to Detonation Transition in complex geometries, standing detonation waves in hypersonic reacting flows... real "Hard Core" numerics...

But this is not for a lappy...

Anyway, Thx for yr hints... :-)

Alex
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Old 03-23-2009, 02:34 PM
AlexVader AlexVader is offline
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Default Re: Engineering applications in PC BSD
Hi OKO

One thing puzzles me though...

You said that you woudn't use "user friendly" distros for high performance computing...

I myself used to be a Red Hat guy... started RHEL 4 x64, I must admit it was rock stable... but the "user unfriendliness" used to be a pain in the ass each time I had to install new software... resolve library dependencies and all...

This is the main reason that made me shift to Fedora Core 4 x64, then OpenSuse 10.2, 10.3 finally 11.0 and at last Ubuntu.

All these last distros are User Friendly as you tag them...

Does this mean that they are lest stable, or less customizable...?

What is your opinion on this...?

BRGDS

Alex
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Old 03-23-2009, 07:47 PM
Oko Oko is offline
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Default Re: Engineering applications in PC BSD
Originally Posted by AlexVader
Hi OKO

One thing puzzles me though...

You said that you woudn't use "user friendly" distros for high performance computing...

I myself used to be a Red Hat guy... started RHEL 4 x64, I must admit it was rock stable... but the "user unfriendliness" used to be a pain in the ass each time I had to install new software... resolve library dependencies and all...
I heard that RedHat Hell is the thing of the past with Yum. I remember those times. Back then I used Solaris on SUN hardware Bottom line. RedHat is the most stable Linux distribution with a HUGE corporations behind itself. When something reads Linux certified that usually means it is certified to run on RedHat.

Originally Posted by AlexVader
This is the main reason that made me shift to Fedora Core 4 x64, then OpenSuse 10.2, 10.3 finally 11.0 and at last Ubuntu.
Honestly a bit strange choices for a developer. Fedora is bleeding edge. OpenSuSE I do not know. I live in U.S. It is very hard to find SuSE i OpenSuSE in U.S. Ubuntu, sure if you want something like Windows but do not want to pay for it.

Originally Posted by AlexVader
All these last distros are User Friendly as you tag them...
Yes, all of them are "user friendly" in my book with RedHat being the least "user friendly". Unfriendly Linux distros are Slackware, Debian, and Gentoo(based on other people stories). I might have missed some but those are major unfriendly distros.

Originally Posted by AlexVader
Does this mean that they are lest stable, or less customizable...?
I am not the right guy really to answer those kinds of questions. I use Linux only if you point the gun into my head but here is my personal experience of what little I used Linux.

RedHat (CentOS, ScientificLinux) rock stable almost in par with BSDs (Linux guys will probably correct me and say BSDs almost in par with RedHat).
It obviously suffers as most commercial product from proprietary legacy. It has to keep support customers and they can not that easily break compatibility with older code (that is the most annoying thing about Solaris too). In BSDs bad things will go quickly through the Window as there are no paid customers to complain about it. RedHat is less customizable. Actually too many decisions in my mind are made for you by installer and somebody in North Carolina. I am sure that qualified RedHat administrators (which I am not) can deal with it easily but it sucks when the OS works against you instead for you.Never the less as we said earlier. If the proprietary application is certified to run on Linux that means RedHat.

Fedora really doesn't deserve much discussion. It is testing bed for RedHat and too unstable for me at least but I am VERY conservative. If you want a new RedHat based desktop you might be forced to use Fedora because of new hardware drivers. Other than that I really see nothing that Fedora could offer to RedHat users.

OpenSuSE probably goes under the same category as Fedora as it is testing bad for SuSE. Honestly, I lived most of my adult life in U.S (I am European by birth and deeply in my heart). I have seen no more than 2-3 OpenSuSE or SuSE installations in my entire life. I just do not know what to tell you about it.

I am very familiar with Ubuntu. I think of it as Windows except that I do know
Ubuntu's internals quite a bit while for me Windows is just a GUI on the top of mysterious black box. Let me put this straight to you. I am not a fan of Debian but if you use something Debian based then vanilla Debian is the way to go.

I have never used Gentoo in my life. I have never even install it once. To me sounds little bit odd. If you like ports why not use BSDs instead of trying to create BSD ports on the top of less stable Linux kernel and semi-functional GNU userland (OK I know I am bit bullshitting now but you get the point).
I hear that they are in big troubles. I hope they survive because the failure of any open source community is a sad day for everyone and makes all of us weaker. On a bright side I like Gentoo documentation.

I like Slackware very much but it doesn't have package management and that where the buck stops. Unfortunately it is just a hobbyist distro.


Cheers,
OKO
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Old 03-27-2009, 06:23 PM
BlackBox BlackBox is offline
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Default Re: Engineering applications in PC BSD
Originally Posted by AlexVader
Currently a Ubuntu user, I would like to test PC BSD for speed and performance when running apps like these...
By all means, test it!
But I would not currently trade a working Ubuntu installation for PC-BSD. The reason is that at least for me, PC-BSD still has too many quirks. In fact, I am half-convinced that the system is alive and semi-sentient and out to get us (me).
Just yesterday my 7.0.2 system decided on its own to not use GDM anymore, and switch to KDM. I fully expect it would have seen the errors of its ways eventually and quietly restored GDM, but I put a fresh installation of the 7.1 beta on the box. PC-BSD has pulled several such stunts on me ever since I began testing it (with 7.0 beta), so it doesn't even surprise me anymore. Things break by themselves and they fix themselves...

The 7.1 beta is pretty good, it feels faster than the previous release, but it still has a bit of a will of its own - this time, I cannot install the TrueType PBI or the GNOME PBI because they are supposedly corrupted. And having to use KDE 4.x is just... not my thing. Also, the system insists on having the display at 800 x 600 even though the graphics setup runs at a higher resolution and 1024 x 768 is set there.
Otherwise it's quite nice though.
But not noticeably faster than Ubuntu.
My issues with PC-BSD could be due to hardware (I'm using the OS on a computer that's even older than the one I have Ubuntu on). Or user error.
So your installation might work perfectly.
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Old 04-03-2009, 03:46 PM
AlexVader AlexVader is offline
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Default Re: Engineering applications in PC BSD
Hi BlackBox

I may even give it a try one of these days... does 7.1 Support Broadcom 4312 wireless, as well as the latest NVIDIA GPUs...?

Is it possible to install it in an external usb HDD without messing the MBR of the laptop's hdd drive..?

I know this can be done with other distros, but, as you may have noticed... I am totally new to BSD...

Thx

Alex
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Old 04-06-2009, 12:41 AM
tankist tankist is offline
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Default Re: Engineering applications in PC BSD
We do numerical simulations of financial models. A lot of floating point operations. For our tasks FreeBSD 7.x was faster than Ubuntu 8.x by 25 - 40%. Intel Core 2 Duo, 4GB RAM, 64 bit (of course). Ubuntu was faster than Fedora by 1 - 2%. During my tests X and other non-essential daemons were stopped.
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Old 04-06-2009, 01:10 PM
AlexVader AlexVader is offline
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Default Re: Engineering applications in PC BSD
Hi Tanklist

I Installed PC BSD 7.0.2 x 64 in an external USB HDD.

At first sight everything ran normal... the wireless an, intel 39... whatever, and the GPU 3200 Radeon ATI were recognised out of the box...

I did it in my older lappy : an Asus F3JR.

I must admit that the environment is pleasant, although I am more used to Gnome... ( BTW which one has the lower RAM footprint, KDE 4.x or the last GNOME...? )

Does the last version, PC BSD 7.1, has the drivers for Broadcom 4312 Wireless, and Nvidia GForce 9600 M...? These are the specs of my newest lappy...

On thing I noted, though, Linux Binaries wont run over PC BSD :-(

No Fluent, no Ansys, no Abaqus, no Adina, no Matlab

.... is there some sort of compatibility Layer to support this...? It is a POSIX system... there should be no problem with this ( am I wrong here....? )

Also, tried to compile GetDP from sources, and bash ( my default console ) reported that the compilers were missing... gcc, f77, g++, g77 is there some sort of "developer suite" in a PBI to support compiling most apps from source to PC BSD binaries...?

Are Mac OS binaries supposed to run over PC BSD...?

Thanks in advance for answering all these noobish questions... :-D

Best regards

Alex
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Old 04-06-2009, 07:54 PM
Oko Oko is offline
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Default Re: Engineering applications in PC BSD
Originally Posted by AlexVader
Hi Tanklist
I must admit that the environment is pleasant, although I am more used to Gnome... ( BTW which one has the lower RAM footprint, KDE 4.x or the last GNOME...? )
If the RAM footprint is of concern you would run neither GNOME nor KDE.



Originally Posted by AlexVader
Does the last version, PC BSD 7.1, has the drivers for Broadcom 4312 Wireless, and Nvidia GForce 9600 M...? These are the specs of my newest lappy...
Of course not. Broadcom is Win only company. OpenBSD has drivers for some Broadcom chipsets which are developed by reverse engineering despite fierce opposition from the company. I do not know about GForce. There are binary blob drivers for FreeBSD released by NVidia but I do not know what do they support. OpenGL doesn't have mature support for NVidia.



Originally Posted by AlexVader
On thing I noted, though, Linux Binaries wont run over PC BSD :-(
You are not right. About 90% of Linux binaries will run on FreeBSD. The only one which will
not run are the one which use Linux specific (not POSIX complaint) system calls.
The level of competency required to run Linux binaries (except the one which you can
find in ports) is system admin- developer.


Originally Posted by AlexVader
No Fluent, no Ansys, no Abaqus, no Adina, no Matlab
They are not certified to run on BSD. Why are you surprised? Actually, they will run but require high level of competency. As, I stated in my original message unless you have couple months to invest in becoming BSD proficient BSD is just going to make you much less
efficient.


Originally Posted by AlexVader
.... is there some sort of compatibility Layer to support this...? It is a POSIX system... there should be no problem with this ( am I wrong here....? )

No you are not wrong. You are naive to believe that application written for Linux are Posix complaint. Most of the time they are not. We call that illiterate programming to distinguish from literate programming invented by Donald Knuth.





Originally Posted by AlexVader
Also, tried to compile GetDP from sources, and bash ( my default console ) reported that the compilers were missing... gcc, f77, g++, g77 is there some sort of "developer suite" in a PBI to support compiling most apps from source to PC BSD binaries...?

Who reports. Autoconfig? BSDs do not use GNU config utility. If you want to use GNU config you have to use gconf. Which version of GCC? PCBSD should have at least two different versions of GCC. Chances that you compile GetDP on BSD without patching are zero next to none.

Originally Posted by AlexVader
Are Mac OS binaries supposed to run over PC BSD...?
Not even in dreams.
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