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This question gets a little complicated so please bear with me.

So we have a new custom designed desktop which we will be mostly a dedicated machine for scientific computations in FORTRAN and MATLAB. The IT initially installed Windows 7 on it and gave it to us. Our preferred OS is Ubuntu. The second choice is Fedora but we won't go there unless we absolutely have to and if someone here can give us good arguments that Fedora makes things mentioned below easier than Ubuntu.

If we were to just reformat the entire drive and install Ubuntu, things are easy but my adviser makes a good case that we should keep Windows too in addition to ubuntu.

  1. First question, are there any good replacements for microsoft office in a linux environment? I know about open office of course and have even used it but if I receive a complicated .doc form or something and open it in open office, boxes/tables/text/spaces/margins are messed up and misaligned. Same happens in power point. In addition, if I prepare documents in open office (document or a presentation) it is messed up when opened in microsoft office. So what is the "best" replacement for office for linux? If this question has no good answer, then we have to keep windows.
    Keeping windows, I was just going to repartition the hard drive, give windows a tiny bit of space and have ubuntu on the rest. But then there is the problem of sharing files between the two. So then I thought about having a tiny partition for windows, a decent chunk for ubuntu, and the largest one for documents.

  2. What is a good file system for my documents partition which will be stable in the long run and both windows and ubuntu can read and write to easily? Note some files will be quite large like giant text files containing the output from a long simulation. Should I use NTFS or ext3 or what? Windows can't use ext3, right? But how good is ubuntu with NTFS? There won't be any read/write/checksum errors/issues? And what about FAT32? Any better alternatives I don't know about?

  3. Any recommendations for a good free partitioning/formatting utility? I won't be able to format the entire drive. Windows is already on it and we want to keep it without removing it and reinstalling it. So I'll just shrink windows partition, repartition the rest into two more, then format the other two appropriately. There is only one physical drive involved in all this.

  4. Now is the complicated part, given two partitions on the same physical hard drive, one with windows and one with ubuntu, is there any way for me to have some sort of a virtual machine which can mount another physical partition on the same physical HD? For example, if I am logged onto ubuntu and I have some figures I need to add into and modify a powerpoint, I want to be able to start a VM in ubuntu, mount my (physical) windows partition and use powerpoint. Is there anything for ubuntu that can do this like VMWare or something? Preferably free? What about the other way if I want to use ubuntu quickly while logged into windows?

  5. Given question 3, will there be any licensing issues when mounting windows on a VM from a physical partition? We only have a single license and I imagine the MAC address will change when mounting windows to a virtual drive so will windows ask us to put in the license info again or something?

I know too many questions but they are all related. Just trying to plan carefully to build this machine in the least complicated way that can do everything we need and make sure it lasts a long time. I put this all here together so that the bigger picture can be seen by all and perhaps a better suggestion/strategy will be offered.

FYI, I am a fairly advanced computer user, as you can tell, not afraid to partition/reformat drives but I am rather inexperienced with linux so don't be afraid to go into detail if necessary.

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Sounds like a superuser post. –  Karthik T Jan 9 '13 at 9:25
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4 Answers

up vote 1 down vote accepted
  1. LibreOffice or OpenOffice. While the LibreOffice is fork of the OO, it is by far more actively developed (and the default in most Linux distributions).

  2. NTFS is probably the only reasonable option, see also File system compatible with all OSes?.

  3. gdisk or parted

  4. This is doable, but you might want to set up a special device that would present the VM with something that is writable only in selected regions. There are several virtualisation solutions: KVM, VirtualBox, XEN, VMWare. KVM is able to use anything as VM image (i.e. even a partition or the whole disk - like /dev/sda), I'm not sure about the other ones.

    However, since the VM uses it as a harddrive image, you can't use a single partition with an already installed system right away, because the VM's BIOS won't recognize it - it would try to interpret the data as a whole harddrive and hence it would expect the first sector to be the MBR. That is why you have to give it either the whole disk (e.g. /dev/sda) or create a DM device. Such a device would have to either at least prepend a standalone MBR to the partition or create a mapping of the whole disk, that would only allow writing to the partitions used from the virtualised system - that way you would make sure, that the OS running inside the VM won't damage data, that do belong to the host. If you trust the virtualised system enough to have it running from the same harddrive normally, it's probably ok to let it do so in VM as well.

  5. You can choose whatever MAC pleases you for the VM. It should not collide with the one used by the hardware though, since that might cause problems with DHCP (in case it were using MAC - IP mapping). MAC collisions might also have an adverse effect on network performance in some cases, since MAC may be used in packet delivery decisions in some cases. Also note, that you usually can change the MAC of your hardware as well.

That said, you might also want to consider abandoning the stand-alone Windows completely and only run them inside a VM. That would lift some restrictions, most importantly the filesystem one: you would be able to store the data on Linux partition with whatever filesystem you choose and export one or more directories with samba which would be mountable from windows as a network drive.

Another option would be running the windows applications under WINE and getting rid of Windows completely.

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Can KVM, VirtualBox, XEN, VMWare mount a physical partition virtually? If yes, any particular recommendation for VM? Also, I can choose the MAC for the VM? And why shouldn't it collide with the hardware MAC because the problem is the different MACs. If they are different, then I may have to enter license info every time the MAC changes. So if I can keep the same MAC, windows wouldn't go crazy on me thinking I am using a pirated copy. –  Fixed Point Jan 9 '13 at 23:48
    
@FixedPoint yes, you can choose MAC (see updated answer), I wouldn't expect windows to bother you because of that - you can even change the MAC in Windows (depending on whethwer the driver supports it). As for choosing the VM - I'm a happy user of KVM, can't tell you much about the others. :) IMHO it pulls the least additional stuff into your system - you just need a kernel module (which is already in kernel since a couple of years), and a version of QEMU that knows how to use it (anything reasonably recent - like 1.0.0 and newer - should do IIRC). –  peterph Jan 10 '13 at 9:03
    
All good answers but you get the green check for mentioning WINE. It is a great idea but wish it was a bit easier to use. I used PlayOnLinux to get/setup WINE and then installed Microsoft Office. Thanks! –  Fixed Point Jan 18 '13 at 8:49
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Microsoft Office should run fairly well in WINE on linux with no need for a separate Windows or VM. That being said, if you do have to go the Windows route anyways, I have had bad luck writing to NTFS in linux - it seems to work for a while, and then corruption all over the place. If I'm lucky, Windows can recover it, but I had one hard drive that needed a complete reformat to work properly again. Since then, I mount NTFS as read only on linux, and use exFAT to share between the too, having no problems with corruption and still being able to use large file sizes.

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Office alternatives- Open office or Libre office (open office fork)

#1 - NTFS works just fine minus the unix permissions. Issues- My main issue is that I cant seem to set executable permission to files on NTFS. I expect there are other issues with unable to own files, modifiable by all users of the system, etc. However this might be irrelevant if we are considering a document partition for a single user system.

#2 - gparted works great for partitioning and formatting.

#3 - This is being tackled at Booting the already installed Windows from the VirtualBox installed in Ubuntu . Ubuntu from windows I am not sure about.

#4 - Should be OK since it is using your own Windows installation, but I cant be sure.

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What would be the issues with unix permissions? Would they cause any accessing/reading/writing/modifying problems? –  Fixed Point Jan 9 '13 at 23:31
    
@FixedPoint NTFS doesnt support unix partitions, so it has all the issues that would come with that, issues should be limited to none when dealing with document files however. You can check my edit. –  Karthik T Jan 10 '13 at 1:55
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I have a similar situation since were I'm working at, we have some windows specific apps. Answering your question about Microsoft Office, and this is my opinion, there is no such good alternative for Linux when dealing with the docs with more advanced functions on it. I suffer the same situation when dealing with documents, getting then unformatted, fonts not being recognize. Besides if you open the file in Microsoft Office, alter it in OpenOffice / LibreOffice, you will notice that even the size of the file changes considerably.

In my case and what I found it was best the best option was to install a a virtual machine with Linux (mostly because it requires less resources to my type of work) and have a shared folder between the Windows 7 system (physical) and the Linux installation (Virtual).

I choose to not convert my physical installation into a VM and also I did not choose to make the W7 bootable from physical and virtual due to windows getting messy and weird with the extra drivers and stuff, basically I took the safe path to avoid wasting time trying to fix something.

I recommended, leave your windows partition and install a virtual machine. Share a folder or folders into your linux box and you are good to go. You don't need to worry about choosing the right filesystem to be mounted from both sides.

Though this worked for me, for you might be different of course !

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More than 99% of the time I will be working in Ubuntu so need to boot into linux, work, and then quickly use windows when needed. –  Fixed Point Jan 9 '13 at 23:35
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