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Old 10-06-2012, 11:50 AM   #1
Jeherr
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Linux for newbie wanting to do computational chemistry


So I have a very very VERY basic knowledge of Linux, but for all intents and purposes, I have no knowledge other than it's a command line system unless you have a friendly GUI, and a few other things such as virtual ram. Let's say I got my toes in the water in high school once or twice, but the water was too cold. That was about 5-6 years ago. But I would put my computer skills above average. I've been fixing my own computer since I was a kid, as my dad owned a PC repair business so I have been on computers since my fingers could reach the keyboard and mouse (my dad stopped me from printing 42 copies of a page that was just solid purple about 5 pages in once)

So I want to learn the command line and Linux in general. I am a chemistry undergrad major and I want to do computational chemistry. I've talked to the Linux IT person for the chemistry department and it seems most of the computational systems run Red Hat. So I am going to start with a computational Prof. this winter after the semester but want to get some basic Linux knowledge now so I can hit the ground running. I really have no idea where to start.

I want to set up a dual boot on my laptop with Linux and Windows. Windows will be for most everything I do, Linux just as a source for me to get started in being able to use it. I'd like to get some computational chemistry software on there as well to begin working with that sort of thing. I believe I have to compile the software? I don't have the time to experiment like I used to otherwise I would just play with it until I figured it out with a little help here and there from the internet and my computer science buddy.

So where do I start? It seems there are several versions of Red Hat with different features and geared for different applications. I know Linux is almost completely customizable so what would be best for me? I will likely need help getting the dual boot set up so maybe pointing me to a guide for newbies on installing the dual boot would be good. Also I really don't know how much to partition out of my hard-drive space. I think from what I've read there will be several partitions, one for windows, one for root, one for /home, and I think there was another. Is one of these like a shared hard-drive partition for files to be accessed by Windows and Linux? If it helps, I have an Acer Aspire 7745 this will be going on. Thanks for any help.
 
Old 10-06-2012, 12:12 PM   #2
amani
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You can use Debian or *buntu as well. RHEL will not provide binaries for many packages. For derivatives like scientific linux, I am not aware of a specific repository for chemistry.
Take a look at Bio linux too.

See the LQ wiki for install
 
Old 10-07-2012, 07:20 PM   #3
chrism01
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It sounds like you'd want to get as close as possible that whatever your Uni uses (RedHat ie RHEL).
However, actual RHEL itself requires a paid subscription, so I'd ask your IT guy for a bit more detail.
The usual options are Centos (free rebuild of RedHat) and Scientific Linux (also a free rebuild, but with extras related to Physics/Chem etc.)
https://en.wikipedia.org/wiki/Centos
https://en.wikipedia.org/wiki/Scientific_Linux
 
Old 10-08-2012, 12:22 AM   #4
Jeherr
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Thanks for the suggestions/guidance. I just discovered Scientific Linux about 5 minutes before reading your reply chrism, so I am actually downloading a live dvd for SL while I type this. I feel like I should probably get some more experience with Linux before I go and partition out my hard drive for a dual boot, which I'm sure can be a long process for someone who has never done a Linux install before and possibly a pain to get working properly. So I am going to work with the live dvd for now and then go from there.
 
Old 10-09-2012, 07:20 PM   #5
flshope
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I have been doing computational fluid dynamics (CFD) under Ubuntu, presently at 12.04 LTS. I don't have experience doing administrative support with Red Hat, but under Ubuntu it is relatively easy: just just check for software updates every few days or weeks. Whenever you command, Ubuntu will download and install any updates. New software installation is easy if there is a .deb package available. In that case, the Software Center will know how to install it.

The software I run is Fortran and I compile it with gfortran, which Ubuntu supports. One chemistry code I use is NASA CEA (chemical equilibrium and analysis), but that's probably not the sort of software you mean when you say "computational chemistry".

If your code is C, Ubuntu includes gcc.
 
Old 10-10-2012, 11:18 AM   #6
DavidMcCann
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Firstly, Scientific Linux is not Linux for scientists, but Linux by scientists: the people at CERN just couldn't think of a better name. The software is just what you'd get from Red Hat.

There's certainly a lot of stuff available:
http://sourceforge.net/directory/sci...ently-updated/
Taking the first program, Avogadro, and looking here
http://pkgs.org/
shows that it's available from Debian, Fedora, Mandriva, Mageia, OpenSUSE, and Ubuntu. Mandriva is dying and Mageia is new and hasn't got its act together yot, but the others are OK.
Sometimes, you just have to get things from the developer; Debian has a reputation of having everything, but I see that doesn't include DWSIM.
 
Old 10-10-2012, 12:01 PM   #7
kooru
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Hi,

i did PhD in computational chemistry
More than a particolar distro, i suggest you to learn command line, bash scripting, awk/sed, because all this will be very useful.
 
Old 10-10-2012, 02:25 PM   #8
salasi
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Quote:
Originally Posted by Jeherr View Post
...I have no knowledge other than it's a command line system....
Not in any worthwhile sense.

If I was being very nit-picky, I would claim the Linux is a kernel and, as such, has neither a command line nor a GUI. But that's the technical and not the helpful answer: You are probably referring to a Linux Distro, which will have a GUI or choice of GUIs (usually), and can be used as a simple command line system, depending on what you choose to install and configure (and, even if your choice is GUI, there will be an 'emulated command line' that you can use, so choosing GUI doesn't prohibit you from using command line).

Quote:
Originally Posted by Jeherr View Post
So I want to learn the command line and Linux in general. I am a chemistry undergrad major and I want to do computational chemistry. I've talked to the Linux IT person for the chemistry department and it seems most of the computational systems run Red Hat.
With Red Hat itself, you pay for support; Centos and Scientific are virtually the same thing, but without the 'paying for' part. The 'zero cost' approach should allow you to learn - not that RH's support is any way bad, but your 'leg up' shouldn't need it, even if you want to pay for a supported workstation at your place of work (or not).

(Virtually = minus the Red Hat logos, and, in the case of Scientific, plus some extra repos which make extra office programs available, without compiling and pre-configure some common security stuff. Yes, office programs, for the focus of Scientific is to provide the admin staff with an easy to configure and secure way to accomplish their work and not anything 'Scientific' in particular. I guess the propeller heads at the accelerators are expected to sort out their own specific requirements...)

Quote:
Originally Posted by Jeherr View Post
I believe I have to compile the software?
In general, not even slightly. Most programs, for most people, are available from repos (repositories), and, unless it is impossible for one reason or another, you should always seek to use something from a repo rather than the last resort of self-compiling.

That said, for computational chemistry, you may be looking at some rather obscure programs, and that may push you into 'rolling your own'.

Quote:
Originally Posted by Jeherr View Post

I want to set up a dual boot on my laptop with Linux and Windows...

So where do I start? It seems there are several versions of Red Hat with different features and geared for different applications. I know Linux is almost completely customizable so what would be best for me? I will likely need help getting the dual boot set up so maybe pointing me to a guide for newbies on installing the dual boot would be good. Also I really don't know how much to partition out of my hard-drive space. I think from what I've read there will be several partitions, one for windows, one for root, one for /home, and I think there was another. Is one of these like a shared hard-drive partition for files to be accessed by Windows and Linux? If it helps, I have an Acer Aspire 7745 this will be going on. Thanks for any help.
Start by getting some (say 1 - 5 ) Live CDs. Have a play around. What do you like, what do you dislike? In particular, is there any GUI that you prefer? Any that you couldn't stand?

That info will come in handy later.

Partitions? Swap and one other (/) will work fine. Add a /home partition and it will reduce the effort when it comes to upgrade/re-install/new install time, but that should be it. Well, plus whatever windows needs, if you must, which you probably will at first.

The guide for dual boot:
  • backup
  • sort out windows, giving it the space it requires, leaving some room available for Linux
  • use whatever partitioner comes with your distro to turn this spare space into partitions for Linux (warning: prior to this be sure that you know which partition(s) are which - the easiest thing to go wrong is to get confused here); if your choice of distro doesn't do a good job here (which it probably will, these days), there are independent choices that you could use
  • install; the distro should sort out the dual boot for you, including whatever boot manager app they use
 
Old 10-10-2012, 03:02 PM   #9
JaseP
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Be careful partitioning, as some machines ship with hybrid GPT/MBR partitioning. You want a copy of the gParted Live and the PartedMagic Live CDs lying around, in case you need them. A friend with a commercial partitioning program disk (for resizing Windows partitions, if the partitions are too much for the two tools I mentioned) wouldn't be a bad mistake, either.

Keep in mind that some PC manufacturers do things like hide partitions in overlapping space, etc. They hide recovery partitions, and those light, Linux based, quick start systems in those spaces... And generally make it a pain to install Linux along side of Windows as a result.

Depending in what you currently have on your machine and what you want run in Windows,... It might actually be easier to back up your data, completely wipe Windows, install Scientific Linux 6.3 and KVM virtualization, and put a Windows install on a Virtual Machine. But to do that, you'd need a processor that's got hardware virtualization support (you do,... all three versions of that Acer system, i3, i5 & i7,... have processors that support at least VTx), and a stand alone Windows install disk or USB. But that's a matter of choice.
 
  


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