Misc. Linux

There's an enormous back-log of posts to add, so don't forget to use google too.

Misc.
509. Very briefly: Send remote commands via the dropbox folder
508. Very, very briefly: why apt-get purge exists (anecdote)
507. (re)assembling a Dell C521 -- pictures
505. Testing KDE on Debian (if you're a gnome user) -- getting set up
504. Swap file and hibernation on debian
502. Spell checking in WPS office on linux -- changing language by replacing the default files
501. Briefly: Adding a new node to SGE
500. Changing language in Debian (GNOME 3, terminal) to e.g. fr_CH
499. Briefly: Drawing NMR sequences using metapost and Mark White's pulse.mp
498. Briefly: Drawing NMR pulse sequences using APSEQ and Mathematica
496. Briefly: New email -- adding to PGP/GPG key and changing email account order in Thunderbird
494. Very briefly: issue with thunderbird, failed connections and repeatedly being asked for the password
493. Very, Very Briefly: libreoffice 4 on wheezy -- wheezy-backports
492. Briefly: fixing no sound when playing youtube videos in chrome, iceweasel/firefox
490. WACOM CTH-470 -- Bamboo Pen and Touch on Debian
489. Briefly: dvb-fe-tda10048-1.0.fw on debian
488. Screencasting on debian wheezy
486. MS data, part IV: Making a stacked spectrum plot using gnuplot
485. Arch linux - kernel 3.10 issues? Won't boot/no network.
484. Putting Tomato (USB) on Cisco/Linksys E2500-AU 300M
483. MS data, part III: generating a matrix by combining several spectra, and plotting it in gnuplot
481. A little bit of samba on the command line
480. MS data, part II. Plotting and comparing with predicted isotopic enveloped
478. Briefly: proftpd on debian
477. OpenChrom - Dempster
476. Rehash: using a browser proxy via tunnel, through a router and with reverse ssh
474. MS data, part I: Exporting data as csv from wsearch32, and generating MS assignments using Matt Monroe's molecular weight calculator
473. Programming a Metrohm Titrino -- not a how-to, just a ramble
471. Debian Jessie -- gnome-shell bug
470. Very briefly: compiling nwchem 6.3 with ifort and mkl
469. Intel compiler on Debian
467. wget and tor issue
466. morph xyz -- python script to morph .xyz files
465. The Intel MKL (Math Kernel Library) on Linux (Debian) -- for free
464. bytes2words -- python script
463. Very Briefly: Installing ia32-libs
462. Olex2 (1.1) on Debian
461. Briefly: setting up SHELX on linux (crystallography)
460. Briefly: Crystallography software: CCSD Mercury
458. Briefly: Converting GRAMS ASP ascii data to two-column ascii data
457. Very Briefly: Microsoft has a Tor exit node?
453. Very Briefly: internet crud: feedreader
441. Links to two good articles on windows, piracy and linux.
438. Very briefly: Freeing up RAM (sort of)
437. system-config-firewall on debian
436. Miramath on debian
435. Briefly: Frippery extensions for Gnome 3.8
428. system-config-kickstart on debian
426 Multibooting Windows XP, Vista and Debian
425. Briefly: Megapov
420. Setting up a FreeBSD virtual machine
419. Talking to Myself in Public: DKMS, your own kernel and Virtualbox
415. Briefly: making a polyhedral figure in gdis
414. Frequency vs cores? Crude benchmarking on AMD FX 8150
413. Povray 3.7-rc7 on debian wheezy
412. system-config-samba on debian
408. Briefly: Tor on Debian -- the quick option
407. Building less (458) as a temporary solution on Debian Jessie
406. Briefly: Missing package in debian wheezy -- forgot apt-pinning settings
405. First breakage in Debian Jessie? less vs man-db
404. Briefly: Debian Jessie now out (sort of, and in places)
402. Very briefly: what I forgot about gnome 3...a short rant
401. AMD FX 8150:issues building kernel -- random failures.
400. XpressConnect on Debian, Arch: step by step
399. Looking at speeding up (re)boot on debian wheezy.
394. Eduroam using wicd and network-manager
393. Solved: XpressConnect on Ubuntu vs Debian. Extra focus on Swinburne university (AU/Melbourne)
384. Another (vaguely) TeX-related headache
383. WPS for Linux on Debain Wheezy -- Kingsoft Office for Linux
379. [Solved] Debian Wheezy -- Thinkpad SL410: reboot instead of shutdown when on battery
378. Briefly: Windows/Dialogues that are too large for a laptop screen
377.  Wine 1.5.27 and Office 2003: Equation editor now supported!
375. Bisecting the kernel -- looking for the commit behind the kworker/i915 issue.
374. Briefly: Evolution Mail on Debian Testing/Wheezy seems to have been improved
368. Slow mouse and keyboard triggered by kworker running custom 3.8.0 kernel on debian wheezy on laptop SL410
366. nspluginwrapper on debian testing/wheezy
363. Generating an image in PyMol
362. Sun Grid Engine: Limit number of running jobs for a user
360. Screenshots from a desktop based Scientific Linux installation
357. Annoying desktop experience -- zoneminder, nouveau, nvidia and other things
349. SGE: removed node while jobs were queued
345. Replacing gEdit with Kate
343. 'track changes' in LaTeX: collaborative writing
341. Upgrading/installing BankID on 64 bit linux
338. Annotating PDFs in linux -- revisited. Still no obvious solution
332. Gnuplot: bug(?) in current debian testing package
329. ECCE, xterm and X forwarding: fixing broken "tail -f on output" in ECCE/'untrusted X11 forwarding' error
328. Liberate your router: dd-wrt on Netgear WGT624 v4
327. Installing Octave, Gnuplot on OSX 10.8.2 via macports
324. Setting up a private git server
322. Libreoffice and zotero for reference management
317. Compiling samba 4.0.0 on Debian Testing/Wheezy
316. Briefly: Automated chroot/sandbox creation
313. Which Office for linux users? Libreoffice, Openoffice, Lotus Symphony, Google Docs, Microsoft Live/Skydrive, Wine/Office2003 and Office2003 in Virtualbox
312. Tau + OpenMPI profiling on Debian Testing/Wheezy
311. Compiling MPE for MPI profiling
310. Remote mounting using sshfs
307. Burning audio CDs from the command line in debian testing/wheezy
306. Insync with Google Drive and Google Docs on Debian Testing/Wheezy
154. Vim -- weird pasting behaviour
107. Fun with gnu screen -- setting up a screenrc
25. Linux The Basics: Google talk using Gajim or mcabber
23. Configuring Mutt for two IMAP accounts

Encryption and security
459. Briefly: Proxies, browsing and paranoia
451. Seahorse plugins on gnome 3.4 -- PGP encrypting/decrypting in nautilus
450. Tor and Chrome on Debian
398. Securing your Dropbox
391. encfs on debian testing
385. OTPW -- connecting from an insecure computer using one-time passwords
381. Encrypting chat, voice, video-- revisited
373. Cracking Windows passwords if you are a Linux user
371. Hashcat on debian
367. Some post-install steps on Debian Wheezy/Testing
346. Tripwire -- keeping an eye on important files
128. Encrypting your email, chat and VOIP in linux (Debian Wheezy)
120. Using truecrypt with dropbox

Installing linux
367. Some post-install steps on Debian Wheezy/Testing
361. Installing Debian on a USB stick (from a running Debian system)
359. Installing Scientific Linux (CentOS, RHEL) via a chroot in a running debian installation
358. Gentoo in a virtual machine

Firefox
365. Compile firefox 19 on Debian Testing/Wheezy
348. Using the firefox binary on debian testing/wheezy
315. Briefly: Compile firefox 18 on debian testing/wheezy

Thunderbird
326. Compiling Thunderbird 17.0.2 on Debian Testing
254. Compiling Thunderbird 16 on Debian Wheezy
187. Thunderbird 13.0 from source on debian wheezy
129. Thunderbird 12.01 on debian
109. Building Thunderbird 11 on Debian testing
71. Building Thunderbird 10.0.2 on debian testing

Arch
440. Briefly: Upgrading Arch -- consolidation of /sbin, /bin and /usr/sbin
400. XpressConnect on Debian, Arch: step by step
372. Leadtek DTV1000S on Arch linux
355. Compiling kernel 3.8.2 on Arch linux -- exploration
354. Some Arch linux post-installation steps/observations
335. Compiling sinfo in Arch linux
334. Compiling nwchem with openmpi and python on Arch linux
333. Arch linux with Gnome in virtualbox
331. A full linux install on a USB stick: Arch and LXDE on a thumbdrive
330. Installing Arch linux: installing from existing linux onto an external USB HDD

Red hat/CentOS/Scientific Linux
364. Setting up a new user on a ROCKS cluster
339. Compiling ncdu on ROCKS 5.4.3/Centos 5.6
314. Briefly: Installing talkd on ROCKS 5.4.3

60 comments:

  1. Hello:

    I have looked at many of the posts here and feel that I have a kindred spirit that can maybe help me with Linux.

    I like using Debian Wheezy.

    But I am using the aptsoid distribution (http://www.aptosid.com/) . It's fine, but I want to really use bare metal Debian and add packages on top of that. I would like to free myself from using someone else's distribution.

    I also use smxi for maintenance and sgfxi for installing nvidia drivers (http://smxi.org/). The aptosid developers don't like this because it's not pure Debian.

    Do you think there is a way that I could move away from this a ready-made distribution to something as you are doing? I know Linux but not as well as you.

    Do you have a fail-proof receipe for installation?

    How do I install drivers within the basic Debian structure.

    And applications. I know how to do that, but sometimes one needs very basic packages to ensure a proper boot.

    If this is too off-topic or requires too overwhelming amount of effort to respond, I certainly understand.

    Thanks for your attention to this.

    Kind regards,

    Angelo

    ReplyDelete
  2. Angelo, I'll respond.

    If you don't mind I might turn it into a blog post since it'll allow me a bit more space and formatting (and it might help other people with similar concerns). The bottom line is that there are no simple, straightforward answers.

    First of all, debian is quite user friendly -- if you can run aptosid, you won't have any issues with debian. It has a graphical installer, there's a lot of support online, and as long as you stick to stable/wheezy you shouldn't run into any situations that makes life too troublesome. Testing is normally ok too, but there's occasionally the odd issue which can cause anything from a mild headache to thoroughly a broken system.

    Empirically, I'd say that installing debian using the provided CD1 is fool-proof, but e.g. forums.debian.net have plenty of examples to the contrary.

    If you are more adventurous you can install a new debian system from your running aptosid -- and I'd recommend this if you're thinking about upgrading your harddrive anyway. You can do this via debootstrap and a chroot, and while I've had a 100% successrate with it, others haven't been as lucky. The real advantage of this is that you can make your installation as sparse as you like. The downside to that is obviously that you need to have a good clue as to what you are doing.

    Drivers are typically already included in the kernel, but when they aren't, there's no single way of getting new drivers. Sometimes it's just a matter of compiling your own kernel (which is easy), and sometimes it's a matter of downloading sources from the manufacturer's website, which can range from simple to impossible (I have problems building anything from realtek, while other people have no such issues). In this sense it would be no different from what you are already used to with aptosid.

    smxi/sgfxi are not officially supported by debian, but I know that several people from forums.debian.net have been contributing to it (whether it's just bug fixes and/or feature suggestions, I don't know) and no-one there is going to have any issues with someone using smxi. Since you'll never explicitly speak with a debian developer, the quality of the user forums is what you should look at.

    Let me know more about the hardware you are looking to install this on, as well as intended use (personal laptop, professional desktop, computational node)

    ReplyDelete
    Replies
    1. Hello:

      Thank you so much for your discussion of debian installation.

      In addition, I apologize for taking so long to reply again.

      I am so happy you asked about hardware.

      I need a new linux laptop with a 64-bit version of debian installed. But money is an issue.

      I like the laptops at http://www.emperorlinux.com/, perhaps the Toucan model with 12 GBytes of memory. But, gosh, they seem on the expensive side. I need a good graphics adapter too.

      Can you suggest a workaround to these models, i.e. how one can obtain the most for the least money?

      Again, thanks so much for your help.

      Kind regards,

      Angelo

      Delete
    2. I've never bought a laptop with linux preinstalled, and I don't know which companies are better.

      Otherwise linlap.com has information about linux compatibility. It's hardly complete, but it's not too bad.

      There's a more philosophical aspect to take into account though:
      1. given the premium on high performance laptops vs similarly spec:ed desktops (especially if you don't mind spending an hour building your own), I've given up on performance laptops
      2. a high performance laptop for a 'good' price is unlikely to last long (own experience -- if overheating doesn't kill it, bad build quality leads to broken hinges and -- true story -- the odd screw coming loose and short-circuiting the graphics card and ending up welded to it). After going through three laptops in 8 years I ended up buying a low-performance Lenovo thinkpad SL410. We're pushing five years together and it's as good as ever.

      zareason.com is another well-known source of laptops with linux pre-installed, but they aren't cheap either.

      http://linuxpreloaded.com/ has a more extensive list of vendors.

      Delete
    3. Hello:

      Thank you for the information.

      I really apologize for confusing you.

      If I bought a laptop, it's the hardware I am after. I would wipe out any pre-installed operating system and install some flavor of Debian. It seems all vendors come with some type of operating system pre-installed.

      I am very open to building my own laptop, but need direction for this. Indeed, I started to really look into this, but gave up.

      How do you test applications on the low-performance laptop? Are you using a 64-bit version of Debian on the laptop?

      I have more to say, but maybe you could respond to this.

      Kind regards,

      Angelo

      Delete
    4. I run a 64 bit version of Debian (been following testing since wheezy) on my SL410. While the specs may not look very impressive (2 cores, 4 gb ram) it's good enough for anything I've thrown at it. Admittedly, when I was building Gnome in Gentoo in a virtual machine things were a bit slow, but I used to do a lot of my compilation work on that laptop.

      In terms of computational power it's good enough to check input files and running small jobs and it doesn't overheat -- which is why I'm suggesting spending the money on a 'good quality' laptop rather than paying for performance.

      I have to admit that I've got enough computers (six desktops, one micro-server, three laptops) that if I need more computational grunt I'm almost always able to submit it to a proper (and properly cooled) workstation.

      As for building, I meant building a desktop. While you can build laptops it's not worth it other than as a learning experience.

      I have to admit that I've never used any of the new-fangled UEFI laptops, and I don't know whether that's causing real issues these days. However, if you go with a Thinkpad you should /presumably/ be safe since this is what corporations -- including tech-savvy linux-based startups -- tend to use. And they are good quality.

      Delete
  3. Hello:

    I forgot to say in my last post that I am a computational chemist and use all the common computational codes (i.e. both electronic structure and molecular dynamics).

    Regards,

    Angelo

    ReplyDelete
  4. Hello Lindqvist:

    I hope you remember me. A while ago, we discussed which machine Ilaptop I might get. See your latest post to me on that topic.

    Well, I purchased a Lenovo Y510p laptop that has Windows 8 installed. I am not a Windows fan, but I don't want to destroy it. Anyway, I didn't understand at the time, the part of your post about "new-fangled UEFI" laptops. And now, that is just what I have run up against. I wanted a dual-boot machine, and it seems that many of the Linux distributions are not offering me a solution. The distribution I like, Aptosid, really hasn't been helpful along these lines, although there is information there that I cannot completely understand.

    So, I writing to you to see if you have come up to speed on this issue, since we last blogged, and maybe you can offer some advice. The Lenovo Y510p is a nice machine.

    Thanks for your help.

    Kind regards,

    Angelo

    ReplyDelete
    Replies
    1. Hi Angelo,
      looking at https://forums.lenovo.com/t5/Linux-Discussion/Lenovo-y510p-and-Linux/td-p/1170629 you aren't the only one who's struggling.

      You don't explain what your main issues are -- are you having problems booting, or can't you install the OS at all? Or is it graphics?

      From what I can see your first move should be to switch from UEFI to legacy mode (i.e. to BIOS):
      "Only way I could boot was to resort to Legacy mode. Good news is that Lenovo (at least on this model) doesn't restrict you only to UEFI. Even though I don't use Windows, I decided to keep the windows partition, and it still does boot using Legacy mode."

      For your graphics you need to use Bumblebee: https://wiki.debian.org/Bumblebee

      There's no shortage of post on forums.debian.net by users struggling to sort out optimus/bumblebee, but at least the debian page makes it look easy.

      Finally, it might help to use the unofficial CD with firmware/non-free if you're willing to use debian: http://cdimage.debian.org/cdimage/unofficial/non-free/cd-including-firmware/7.4.0-live+nonfree/amd64/iso-hybrid/debian-live-7.4-amd64-standard+nonfree.iso

      Download the iso, become root and do (if your usb is at /dev/sdc)
      cat myiso > /dev/sdc

      Make sure not to unmount if there's any doubt as to whether the system is still writing to it. The writing will continue for a while after the command exits, which is a bit unfortunate -- you can monitor it with e.g. iotop

      Presumably aptosid should work as well.

      Delete
    2. Hello:

      Thanks so much for your help.

      Can I please impose upon you? You indicated above, correctly, that I didn't tell you the problem. Would you be willing to look at

      1. http://www.aptosid.com/
      2. click on Forum on the left
      3. click on Installation
      4. The third entry for Rossi tells the story so far.

      I used the aptosid iso, and it boots fine, in the manner you suggest above, on the Lenovo with NO network. I tried everything they suggest, but have no network.

      In addition, the support team seems to not understand I want a dual boot.

      There is information on making a dual boot, but I am not sure it is what I should or could do, if I had a network connection:

      http://manual.aptosid.com/en/hd-install-en.htm

      I really appreciate your help with this.

      Warm regards,

      Angelo

      Delete
    3. Angelo, I had a look at the thread at http://www.aptosid.com/index.php?name=PNphpBB2&file=viewtopic&t=2746 and if I understand it correctly your chief objective is to upgrade your kernel from 3.9 to 3.13.

      I also get the impression that you are not entirely sure what to do with any downloaded .deb files, is that correct?

      In the thread it's suggested you simply download the .deb files directly and install them. The most direct way to do that would be to do the following on your already installed system:
      cd ~/Downloads
      wget http://aptosid.com/debian/pool/main/l/linux-aptosid/linux-image-3.13-3.slh.1-aptosid-amd64_3.13-12_amd64.deb
      wget http://aptosid.com/debian/pool/main/l/linux-aptosid/linux-headers-3.13-3.slh.1-aptosid-amd64_3.13-12_amd64.deb
      sudo dpkg -i linux-image-3.13-3.slh.1-aptosid-amd64_3.13-12_amd64.deb
      sudo dpkg -i linux-headers-3.13-3.slh.1-aptosid-amd64_3.13-12_amd64.deb

      Typically you would not have to manually load any kernel modules -- udev should take care of that for you.

      Let me know if this answers your question.

      Delete
    4. I just realised that I made a cardinal mistake: you don't have network, so obviously using wget isn't going to help. On the other hand, if you can download the .deb files under windows you should be able to access the windows partition from your linux partition, copy over the .deb files and then install using dpkg as shown above.

      Delete
    5. Finally, note that I have no experience of aptosid, only of debian. On debian my recommendation would have been to install wheezy and try with the latest kernel version from backports OR using Jessie (i.e. testing). If the kernel version still wasn't new enough I'd then recommend compiling your own kernel and making sure that you compile support for your network cards.

      Compiling, and customising, your own kernel is generally surprisingly easy. However, in your case the key would be to install all the packages needed for the compiler to work -- and to do that somehow without having an internet connection, which may or may not be trivial.

      Delete
  5. Hello:

    Thanks so much for looking into my situation.

    I will try to answer your questions.

    I want to have a dual boot on my Lenovo Y510p laptop and I don't fully understand the UEFI implications I sort of think what you said to me in a previous post is that I can possibly have a dual boot if I switch to legacy mode (i.e. to BIOS). Actually, I did that before I started posting to you.

    I down loaded the available iso distribution which is a live distribution and burned it onto a DVD. Then I booted the live distro on the DVD (By-the way, the DVD won't boot in UEFI mode.). This is one way to check if the current aptosid distribution finds all the requisite hardware. As you saw, the live DVD boot was not able to find the any type of internet connection. There was a glimmer of hope for the wireless but that proved fruitless.

    I don't have an existing version of the kernel and want an upgrade. The interactive iso contains the 3.9 kernel. The current aptosid DVD boots fine, but the only kernel aptosid offers on an interactive iso is 3.9 and not new enough to have ethernet/wireless drivers for the Lenovo Y510p.

    Thus, if the aptosid 3.9 iso had found all the hardware and provided a working internet connection, then

    a) I would have used gparted to partition the 1 TByte drive
    b) Followed the instructions carefully on the interactive 3.9 iso to install debian to the hard drive, I didn't get that far.
    c)After a successful installation, I would follow that up with apt-get update; apt-get dist upgrade.

    "I also get the impression that you are not entirely sure what to do with any downloaded .deb files, is that correct?"

    I am familiar with installing .deb files (dpkg -i xxx.deb), but I got the sense that the aptosid people wanted me to use the entire drive for the debian installation. I kept asking how to have a dual boot, and they kept discussing the .deb kernel.

    So there are two basic flaws in my understanding:

    1, I don't fully understand if I can eventually have a dual boot given the UEFI situation. If you read the aptosid part of the instructions, http://manual.aptosid.com/en/hd-install-en.htm, it's very confusing to me.

    I understand what UEFI is, but not enough to make sure I won't trash the whole machine. Also, there is also discussion about GTP disks, whirling about, and I am not sure about this as well.

    2, Is there a way to get a dual boot without the aptosid distribution but is the cutting edge version of debian?

    Again, thanks for your patience about all my troubles.

    Warm regards,

    Angelo

    ReplyDelete
    Replies
    1. Angelo,
      the usual disclaimers apply: since I don't have the system in front of me I can only speculate, and while I think I know what I'd doing, there's always the Dunning-Kruger effect to take into account.

      First the Boot/Dual boot issue:

      OK, so you can boot from the DVD when using legacy mode. Does windows too boot in legacy mode? If yes, then you should not have any issues dual-booting.

      If you need to use UEFI, aptosid/debian should still be ok, but you need to make sure Secure Boot is turned off. Again, before installing linux, make sure windows boots with secure boot turned off.

      You should be able to boot from a DVD on a computer with UEFI, but with Secure Boot turned off. If you can't, it's probably just a simple matter of a setting in the UEFI 'bios'.

      If you absolutely need to use UEFI with Secure Boot you will need to add the cryptographic keys of your distribution/use a shim (e.g. the Linux Foundation one) with an approved key. I don't have any practical experience of doing that, so I can't give you an explanation of how that would work.

      So, assuming you've found a combination of setting that will allow you to boot the CD as well as Windows, you should be good to set up a dual boot system.

      Btw, the reason why no-one is offering you help on setting up a dual boot system is probably because the issues that arise are really issues caused by and to the windows installation. Partly that means that the linux folks don't really feel it's any of their problem ('MS caused it'), and secondly it may well be -- as in my case -- that it was such a long time ago that they had a dual boot system that they only have practical experience of setting up with Windows XP. I'm sure Windows 8 is different, and I have never touched, booted or even seen a windows 8 system (except on tv), so I'd feel uncomfortable suggesting how to set up a dual boot system with it, just in case the person I help ends up with an unusable system. So don't be too harsh with them

      Delete
    2. So the main issue with UEFI isn't really UEFI at all, but Secure Boot. Most modern linux systems work perfectly well with UEFI (I have a desktop with UEFI and Wheezy), so look at the setting to allow for booting from a DVD -- something SecureBoot will probably prevent you from doing.

      Either way, you won't be making changes to the MBR/GPT until the very last step of the installation -- and if the linux installer doesn't detect windows, then don't let it make changes to your harddrive MBR. On the other hand, you can always install GRUB to a USB stick/floppy for the time being and boot that way.

      Either way, the next issue is the network. I think the advice you're getting -- and what I would suggest -- is to install linux first. Yes, you won't have network while you're installing, and maybe that will prevent you from pulling in a few packages during installation, but all that can be remedied later.

      So install linux, accept the fact that you have no network during the installation and install whatever you can. Then boot up windows, download the deb files in windows.

      Then boot linux, copy the .deb files from the windows partition (note: you'll need ntfs-3g installed in linux to read NTFS partitions) to the linux partition, and install them using dpkg.

      Reboot and use the new kernel, with the new fancy network connection and all.

      I THINK that should work.

      Delete
    3. Your second question: As usual I'll try to reply in a way that will help future readers, so I'm probably pointing out a lot of things that you know already.

      The short answer is yes, you should be able to dual boot without any issues.

      Try this CD and see if the network is working: http://cdimage.debian.org/cdimage/unofficial/non-free/cd-including-firmware/weekly-builds/amd64/iso-cd/firmware-testing-amd64-netinst.iso

      The choice is really about what version of debian to pick, since you write 'cutting-edge'.

      There are three versions of Debian, depending on how much the packages are in flux: Stable (Wheezy), Testing (Jessie) and Unstable (Sid). You can probably install sid directly but I'd recommend against it -- presumably the aptosid folks do some quality testing of the sid packages before letting packages through from debian. So although you may be used to sid via aptosid, aptosid may well be significantly more stable than the 'true' sid. Also, since aptosid is a distribution, but sid isn't, the debian folks have no interest in making sid usable if it breaks. That's not what it's there for.

      So no sid then. Testing is a better bet -- it's got new packages (typically it only takes a week or two for packages to go from sid to testing), but it is less likely to suffer from catastrophical breakages. Note: 'less likely' doesn't mean 'unlikely'. Also, you may well have packages break which will affect the usability. As with Sid, the debian folks don't explicitly care whether Testing is actually usable -- that's not it's purpose. It's purpose is to break repeatedly, get fixed with new packages from sid, break again, until it slowly gets more and more robust.

      Stable is the actual debian release -- stable doesn't mean stable as in 'unbreakable', but means that the packages aren't in flux (except for security updates). Yes, it may look out of date to the untrained eye, but if you enable backports (http://backports.debian.org/) you can choose what new (and perhaps less tried and tested) packages you want to use in conjunction with your stable system.

      Currently, the kernel version in backports is 3.12, 3.2.54 in wheezy, 3.12.9 in testing, 3.12.9 in sid.

      According to https://wiki.debian.org/alx, the version in wheezy-backports (i.e. 3.12.9) should be sufficient. 3.13 isn't required.

      There are a number of debian CDs with firmware on that you can try. If you're interested in debian testing, try http://cdimage.debian.org/cdimage/unofficial/non-free/cd-including-firmware/weekly-builds/amd64/iso-cd/firmware-testing-amd64-netinst.iso

      Delete
    4. Hello:

      OK. Thanks for all this helpful info.

      Here is what I did:

      1) I burned a CD of firmware-testing-amd64-netinst.iso
      It booted fine, and it seemed as if it were going to going to make an internet connection via ethernet.
      But, I stopped, I turned back. Please don't think less of me. It seemed that it was going to install, but I wasn't sure what it was going to do. I didn't find out about the internet connection because of stopping the install.

      If I kept going would I have been able to test the network connection and THEN reverse my steps?

      I wasn't ready for an install. I hadn't shrunk the filesystem and subsequently add partitions for a debian install.

      2. I then tried a debian live CD. That gave me no internet connection.

      3. I booted a CD with gparted on it, shrunk the 1 TByte filesystem to about 200 MBytes, leaving ~780 MBytes for debian but did not create new partitions with the released space.

      I shutdown and rebooted the system immediately in order to allow windows to perform a check of the hard drive. The Windows 8 system booted nicely. But, when I rebooted after shrinking the filesystem, I did not see any checking by the Windows system. Rebooting with the Linux/gparted iso, showed that the redefined, shrunken filesystem was still there.

      How far can I proceed with the firmware-testing-amd64-netinst.iso without installing and being able to back out of any steps I have performed?

      Regards,

      Angelo

      Delete
    5. Angelo, there are two major mile stones in terms of irreversible changes:
      The first one is the partititioning -- once you agree to write changes to disk you will have made your first recorded changes to the hard drive. This should not affect the windows installation though.
      The second one is the installation of grub, which is the very last step. This is the riskiest step of them all, but as long as the windows partition is reported to have been found, you should be alright.

      I think the network configuration will before any of these stages. Note that of course you won't be able to use wireless during the installation since the installer only handles WEP, so hook up an ethernet cable.

      If you're really worried about the order of steps you can try it out in a virtual machine first. It will answer most of the questions that you may have. There are screenshots of the installation process here, http://verahill.blogspot.com.au/2012/03/installing-debian-in-virtualbox-in.html, but they don't show the exact moment the network is tested.

      Delete
    6. Dear Lindqvist:

      Excellent!!! I'll give this a try. I looked at the screen shots, and I like them already, as they say in New York.

      After the installation, I'll need to worry about the nvidia drivers, etc. ... But, first things first,

      Also, I like the idea of installing Debian directly. If I can do this, then I won't be so dependent on ready-made distributions.

      Warm regards,

      Angelo

      Delete
  6. Hello:

    I tried three times to install debian off the cd firmware-testing-amd64-netinst.iso, and each time it failed. The connection is made, and it installs lots of stuff. I used the option "Recommended for Beginners" because everything is installed from /. It gets to the point "Select and Install Software", downloads 1283 files, configures the, installs them, and I am left on the page "Select and Install Software". Nothing happens after that. Do you have any idea what might be happening?

    Kind regards,

    Angelo

    ReplyDelete
    Replies
    1. I'll try it with a virtual machine to see what's happening -- I've never seen any 'recommended for beginner' options as far as I can remember, but maybe that's something I've simply glossed over before.

      Delete
    2. Angelo, it's a current bug: https://lists.debian.org/debian-cd/2014/02/msg00015.html

      To confirm it, I tried to install using the netinstall iso in a virtualbox and it keeps hanging during the installation of software after the software selection part. Unfortunately these unofficial weekly/daily installation isos aren't QA tested.

      This doesn't make us Debianites look good.

      I know this image works: http://ftp.acc.umu.se/mirror/cdimage/unofficial/non-free/cd-including-firmware/7.4.0-live+nonfree/amd64/iso-hybrid/debian-live-7.4-amd64-gnome-desktop+nonfree.iso

      However, the kernel there is likely too old for everything to work out of the box. You can give that one last shot and if that doesn't work, wait for the netinst image to be fixed or install any distro of your choice without network, then download the kernel .debs that you need via your windows partition.

      Delete
    3. Dear Lindqvist:

      I will wait. If this bug is fixed, then there is real potential to have a nice Debian system.

      One other note. I wasn't totally correct when I said that I used only the "beginners" option for the install. I tried one of the other options for the install as well, including putting /home on a separate filesystem.

      The point is that after each failure, I would boot with apotsid distribution which has no network, bring up gparted and cleaned up the filesystem. One time I deleted all the partitions formed by the debian install. Each time, I tested if Windows 8 would boot (which it did) and then tried another debian install. If one is careful, there seems to be some flexibility in partitioning the hard drive,

      Thanks again for all your help.

      Can I ask one more question. When I eventually get on working debian install with a fairly recent kernel, how would I go about installing the appropriate nvidia drivers? I looked at documentation, but I am not sure.

      Warm regards

      Angelo

      Delete
    4. Angelo,
      while life with debian testing /can/ be 'exciting' at times, if you're conservative about upgrading, and make sure to install apt-listbugs, you will be fine.

      As for nvidia, your situation is a bit more complex than what I have experience of. For a simple system with a simple nvidia graphics card you can easily install the nvidia drivers using smxi (http://smxi.org/), which is a shell script that will know what packages to install, as well as being able to install the drivers straight from the nvidia site.

      Your situation /may/ be more complex since you have an optimus hybrid graphics card which is supported by the bumblebee project (http://bumblebee-project.org/). From what I've read I think you can use the regular nvidia driver and things will work, but you won't necessarily get the increased battery life associated with switching between the nvidia and the intel graphics. For that you'll probably need the bumblebee stuff.

      Bumblebee /may/ only work with certain kernel versions.

      NOTE: key whenever installing an nvidia driver is to blacklist nouveau or you may end up with a black screen with a blinking cursor.

      Either way. there are plenty of posts (of varying quality) on forums.debian.net about optimus/bumblebee, e.g.
      http://forums.debian.net/viewtopic.php?f=7&t=105677
      http://forums.debian.net/viewtopic.php?f=7&t=86111&hilit=bumblebee&start=15

      Delete
    5. I also don't know whether there'll be an update to https://lists.debian.org/debian-cd/2014/02/msg00015.html -- you might just have to try the next version of the netinst iso on a virtual machine to see whether the issue has been resolved. You can select the minimum amount of packages when testing. Alt+F1 will show whether you're getting the 'pkgsel finished' message

      Delete
    6. I tried the updated iso (24th of February) -- it's even worse as it freezes during 'Scanning of the CD-ROM' as part of the 'Configuring APT' step.

      Delete
    7. Dear Lindqvist:

      Thanks for all the important hints.

      Yup, I also tried the updated iso (24th of February) and got the same problem.

      I'll keep trying.

      Kind regards,

      Angelo

      Delete
    8. Hello Lindqvist:

      Is there a downside from trying to install

      http://cdimage.debian.org/cdimage/unofficial/non-free/cd-including-firmware/weekly-builds/amd64/iso-cd/firmware-7.4.0-amd64-netinst.iso

      This iso image is right there along with the defunct image

      http://cdimage.debian.org/cdimage/unofficial/non-free/cd-including-firmware/weekly-builds/amd64/iso-cd/firmware-testing-amd64-netinst.iso

      I know one is testing and the other stable, but what are the disadvantages of the stable version, assuming it would install ok?

      Regards,

      Angelo

      Delete
    9. There's no downside, other than the kernel being at 3.2 i.e. it might be too old for your needs.

      I'd go straight for http://cdimage.debian.org/cdimage/unofficial/non-free/cd-including-firmware/7.4.0-live+nonfree/amd64/iso-hybrid/debian-live-7.4-amd64-gnome-desktop+nonfree.iso if you can spare the bandwidth -- it's the live version and will tell you immediately whether it'll work with your setup. Also, it's not a weekly build so it should have been tested to make sure that it's stable.

      Delete
    10. Dear Lindqvist:

      debian-live-7.4-amd64-gnome-desktop+nonfree.iso is not the answer. No ethernet. Now, I am like enterprise is Star Wars, my tractor beam is focussed on debian. And I gonna get a successful install soon .... I just know it.

      Regards,

      Angelo

      Delete
    11. There's one other thing you can try in the mean time --regular testing, which you can download via https://www.debian.org/CD/http-ftp/

      It will help if all you need is the right kernel version -- it won't give you the non-free firmware during the installation. The likely effect is going to be that your wireless card won't work until you've installed the non-free firmware, but that your ethernet card should work during the installation.

      No guarantees though...and I don't know if the official testing isos have the same issue as the non-official ones.

      Delete
  7. Dear Lindqvist:

    How are you? I am confused.

    If you go to the web site

    http://cdimage.debian.org/cdimage/unofficial/non-free/cd-including-firmware/weekly-builds/amd64/iso-cd/

    and look at the weekly builds, it gives the following date:

    firmware-testing-amd64-netinst.iso 2014-03-10 07:12 236M

    so it APPEARS to be updated from the one I tried weeks ago.

    But, when I downloaded/burned it to dvd/tried to install, then I get
    the same hanging error as before. It seems as if it hasn't been updated at all.

    What am I missing?

    Regards,

    Angelo

    ReplyDelete
    Replies
    1. I honestly don't know why they haven't managed to sort it out.

      I'll see if I can come up with a reasonable solution.

      Note that you don't have to burn the iso to a cd or dvd -- you can write it to a usb stick instead (called hybrid iso).

      as root (not sudo in this case) do
      cat myiso.iso > /dev/sdc

      assuming that /dev/sdc is your usb stick.

      Delete
    2. Assuming that the official debian testing iso works, use that and sideload the firmware.

      The process is described on
      https://www.debian.org/releases/stable/i386/ch06s04.html.en
      but I haven't test it. I might get around to trying it out in a virtual machine towards the end of the coming week.

      We've identified what you need:
      1) a newer kernel than what is found in debian stable, but which is found in testing
      2) non-free firmware

      It shouldn't be impossible to combine the two...

      Finally, a 'safe' but more difficult method is to install via a chroot -- http://verahill.blogspot.com.au/2013/03/361-installing-debian-on-usb-stick-from.html

      People seem to have mixed experiences with that method, but it should/must work. It'd require access to a system with a working installation of linux (preferrable debian/debian-based). Either way, I wouldn't recommend it just yet.

      Delete
  8. Dear Lindqvist:

    OK. I tried your latest suggestion I tried the regular testing distribution, I downloaded via https://www.debian.org/CD/http-ftp/
    The ethernet worked and it installed everything. At the last step, i.e.
    the installation of grub, where it is searching for other partitions, presumably the windows partition, the installation just stops. It hangs.

    I guess I can't keep bothering you with this. I will have to begin giving feedback to the debian people.

    Thanks so much for all your help.

    Kind regards,

    Angelo

    ReplyDelete
    Replies
    1. It's unfortunate that it didn't work in the end -- I really don't know why it's proving so tricky. Normally installing debian is a breeze. I wish you the best of luck with sorting this out

      Delete
  9. Dear Lindqvist:

    I want to report to you a successful installation. You were right, it's quite painless and quite easy.

    Here are some observations, and maybe you will be able to comment to help me.

    1) ISO
    The iso that worked was debian-testing-amd64-DVD-1.iso
    The dual boot is "working" but not the way I wanted. It seems grub found all of the existing operating systems and put them in, but the mbr got overr written, and Windows 8 won't boot from the grub selection screen. If I press f12 on booting, I get the Windows manager, and Windows 8 will boot that way.

    I guess one could try the System Rescue CD 4.1.0 (http://www.sysresccd.org/SystemRescueCd_Homepage) and try to write just the mbr again. I don't know, though

    2) Firmware
    I downloaded and installed the newest firmware with the anticipation that it would solve the wireless problem. It didn't.

    But, if one issues the following command

    rossi@debian:~$ dmesg | grep -i wireless
    [ 4.712053] Intel(R) Wireless WiFi driver for Linux, in-tree:
    [ 4.962369] iwlwifi 0000:09:00.0: Detected Intel(R) Centrino(R) Wireless-N 2230 BGN, REV=0xC8

    Then one can see what type of driver is needed. I went to this site
    http://wireless.kernel.org/en/users/Drivers/iwlwifi , downloaded the correct driver, followed the simple instructions for installation, and it seems to be working.

    3) Package Updates

    When I perform the command apt-get update, I obtain the following at the end of the update

    Fetched 472 kB in 5s (87.5 kB/s)
    W: Failed to fetch http://ftp.us.debian.org/debian/dists/jessie/InRelease Unable to find expected entry 'main/binary-i86/Packages' in Release file (Wrong sources.list entry or malformed file)

    W: Failed to fetch http://security.debian.org/dists/jessie/updates/InRelease Unable to find expected entry 'main/binary-i86/Packages' in Release file (Wrong sources.list entry or malformed file)


    HELP!

    4) Graphics
    Gosh this is so disappointing. I cannot get my important visualization programs going.

    rossi@debian:~$ vmd

    Info) Multithreading available, 8 CPUs detected.
    Info) Free system memory: 7087MB (91%)
    Warning) Detected a mismatch between CUDA runtime and GPU driver
    Warning) Check to make sure that GPU drivers are up to date.
    Info) No CUDA accelerator devices available.
    Warning) Detected X11 'Composite' extension: if incorrect display occurs
    Warning) try disabling this optional X server feature.
    Xlib: extension "GLX" missing on display ":0.0".
    ERROR) The X server does not support the OpenGL GLX extension. Exiting ...
    Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
    Info) Unable to create OpenGL window.

    rossi@debian:~$ pymol
    Xlib: extension "GLX" missing on display ":0.0".
    freeglut (pymol): OpenGL GLX extension not supported by display ':0.0'
    PyMOL: abrupt program termination.

    rossi@debian:~$ glxinfo
    name of display: :0.0

    Xlib: extension "GLX" missing on display ":0.0".
    Error: couldn't find RGB GLX visual or fbconfig

    8X - one for each processor?

    Following your helpful information previously, here is what is installed:

    rossi@debian:~$ dpkg -l | grep -i nvidia
    ii bbswitch-dkms 0.8-1 amd64 Interface for toggling the power on NVIDIA Optimus video cards
    ii bumblebee 3.2.1-5 amd64 NVIDIA Optimus support for Linux
    ii bumblebee-dbg 3.2.1-5 amd64 NVIDIA Optimus support - debugging symbols
    ii libnvtt-bin 2.0.8-1+dfsg-4+b1 amd64 NVIDIA Texture Tools (Binaries)
    ii libnvtt2:amd64 2.0.8-1+dfsg-4+b1 amd64 NVIDIA Texture Tools
    ii primus 0~20131127-2 amd64 client-side GPU offloading for NVIDIA Optimus
    rossi@debian:~$

    I am not sure what to do next. HELP!

    Best regards,

    Angelo



    ReplyDelete
    Replies
    1. Issue number 3 -- you have a typo in "http://ftp.us.debian.org/debian/dists/jessie/InRelease Unable to find expected entry 'main/binary-i86/Packages" -- i86 should be i386. However, the architecture wouldn't be given in /etc/apt/sources.list, so did you do "sudo dpkg --add-architecture i386" and mistype it? Either way, you can do --remove-architecture i86 and see if it helps.

      Delete
    2. Issue number 4 -- graphics.

      Searching I found that you're not the only person who have observed similar issues:
      https://github.com/Bumblebee-Project/Bumblebee/issues/41

      Note that "The package clearly states that you need to install the drivers separately." and that it lists nvidia-bumblebee as needing to be installed to support the nvidia card. Presumably the intel card will be supported via i915, but have a look at the page above since there are several people all having somewhat different issues.

      In addition to that, I've never used an optimus system, so I can't offer much help. On a regular nvidia box I'd make sure that the glx packages were installed, e.g. libgl1-nvidia-glx. Maybe you can install the same ones, or there's a package for optimus/bumblebee. Or try mesa: libgl1-mesa-glx. I have no idea if there will be conflicts.

      Note that in the worst case you have a couple of options -- for your system to work as intended (i.e. switchable graphics) you need bumblebee. An alternative is to not use your nvidia card at all, and simply use the intel graphics (i915 module and libgl1-mesa-glx). A last alternative is to always use the nvidia card, in which case your battery life will be less than stellar (nvidia module and libgl1-nvidia-glx).

      Delete
    3. issue 2 -- wifi. Am I reading it correctly in that you installed the firmware-iwlwifi package, but that it didn't work?

      Delete
    4. Issue 1 -- grub -- sounds similar to http://ubuntuforums.org/showthread.php?t=2082751 and http://www.linuxquestions.org/questions/linux-laptop-and-netbook-25/grub-won%27t-load-windows-dual-booting-windows-8-and-linux-mint-4175479820/ ? Presumably System Rescue CD does the same thing though.

      There's also a debian thread at http://forums.debian.net/viewtopic.php?f=17&t=107955 suggesting solutions for both bios legacy mode and uefi.

      Delete
    5. Dear Lindqvist:

      Thanks so much for your help.

      Issue 3. Fixed per your help. Duhhh.

      Issue 4. Fixed per your help. I installed bumblebee-nvidia, and vmd and pymol work. HoooraaaaY. pymol gives a segmentation fault, but I see that is related to something else, maybe.

      Issue 2. I think this is correct, but I did everything so quickly, that I am not absolutely sure. I am using wireless now, and it's fast.

      Issue 1. During the grub process, it asked me if I wanted to install the mbr somewhere else. Next time, I will do this. Meanwhile, thanks for the link above. I will try it soon, but not right away.

      Issue 5. OK I adding an iissue. Sound. I don't have any. This time I tried to do my own homework and looked at many, many, many debian threads. The problem is out there, and I tried a lot of "remedies" to no avail.

      Lindqvist, thanks to your help, I think I am weened off aptosid and not dependent on any other operating system. I really appreciate all your help (and, of course patience.)

      Kind regards,

      Angelo

      Delete
  10. Dear Lindqvist:

    I got the sound card working.

    The only problem that remains is a segmentation fault when a pdb file is loaded into pymol. This is a persistent problem out there on debian. I recompiled it from source thinking that I would like to the libraries that are on my system, but the same thing happens ... a segmentation fault. I wanted to run the gdb debugger on the executable, but pymol doesn't have a binary, but points to a python link. The following shows up in dmesg when I try to load a molecule into pymol:

    [ 1079.275939] python2.7[3943]: segfault at 7fff3db85830 ip 00007ff499d2c202 sp 00007fff3d982330 error 6 in swrast_dri.so[7ff499a3f000+55c000]

    I just wonder if python needs to load the i386 version of the shared library swrast_dri,so

    Regards,

    Angelo

    ReplyDelete
    Replies
    1. Dear Angelo, I'll have a look at pymol on my testing laptop later. Is it a publicly available pdb which you could give me the link to?

      I've tried and there's at least no general issue with opening pdb files in the wheezy version of pymol.

      Delete
    2. I forgot to mention that pymol doesn't need the i386 version of the libraries, so the error lies elsewhere.

      1) post the GL output from when you start pymol e.g.
      GL_VENDOR: NVIDIA Corporation
      GL_RENDERER: GeForce GT 430/PCIe/SSE2
      GL_VERSION: 4.2.0 NVIDIA 304.88

      2) try starting pymol with catchsegv e.g.
      catchsegv pymol

      Note that the output will probably mean as little to me as it will to you.

      swrast_dri.so is part of libgl1-mesa-dri which would indicate that you're either using the intel kernel driver or nouveau.

      Delete
    3. I had a look at pymol on jessie just now and it looks like a mess -- it seems to be stuck in what I presume is stereoscopic mode with no way of exiting (there are two molecules side by side and the colours are...odd).

      Having said that, it does not crash on opening pdb files.

      Delete
  11. Dear Lindqvist:

    Thanks for your help again.

    Here is a link to pdb files:

    http://www.nyu.edu/pages/mathmol/library/hydrocarbons/

    I used the methane.pdb as an example in the catchseggv output to follow. I read your post several times, and it said for me to post it so here goes. Delete it, if it is over the top for post.

    Detected OpenGL version 2.0 or greater. Shaders available.
    Detected GLSL version 1.30.
    OpenGL graphics engine:
    GL_VENDOR: VMware, Inc.
    GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 256 bits)
    GL_VERSION: 2.1 Mesa 9.2.2
    Detected 8 CPU cores. Enabled multithreaded rendering.
    PyMOL: normal program termination.
    pure virtual method called
    terminate called without an active exception
    Aborted
    rossi@debian:~/Downloads$
    rossi@debian:~/Downloads$ catchsegv pymol methane.pdb
    PyMOL(TM) Molecular Graphics System, Version 1.7.0.0.
    Copyright (c) Schrodinger, LLC.
    All Rights Reserved.

    Created by Warren L. DeLano, Ph.D.

    PyMOL is user-supported open-source software. Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".

    Enter "help" for a list of commands.
    Enter "help " for information on a specific command.

    Hit ESC anytime to toggle between text and graphics.

    Detected OpenGL version 2.0 or greater. Shaders available.
    Detected GLSL version 1.30.
    OpenGL graphics engine:
    GL_VENDOR: VMware, Inc.
    GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 256 bits)
    GL_VERSION: 2.1 Mesa 9.2.2
    Detected 8 CPU cores. Enabled multithreaded rendering.
    CmdLoad: "methane.pdb" loaded as "methane".
    Segmentation fault
    *** Segmentation fault
    Register dump:

    RAX: 000000000318bfa8 RBX: 000000000000ffff RCX: 0000000000000000
    RDX: 00007fc795d14640 RSI: 00000000ffffffff RDI: 00007fff7e3f8180
    RBP: 00007fff7e1f81a0 R8 : 0000000000000000 R9 : 0000000000000000
    R10: 000000000285ed00 R11: 0000000002862bf0 R12: 0000000003095310
    R13: 00007fc78fe470fc R14: 00007fff7e1f80b4 R15: 0000000000000000
    RSP: 00007fff7e1f8030


    ReplyDelete
    Replies
    1. The pdb works fine in wheezy with pymol.

      This bothers me:
      GL_VENDOR: VMware, Inc.
      GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 256 bits)

      Why does it say VMware and Gaillium? I would have expected something along the lines of
      GL_VENDOR: Intel Open Source Technology Center
      GL_RENDERER: Mesa DRI Mobile Intel GM45 Express Chipset

      It doesn't necessarily mean that it's wrong, but it's not what I would have expected.

      Not sure if this post (https://bbs.archlinux.org/viewtopic.php?id=175164) is relevant, but the solution was to
      usermod -a -G video $USER

      This post looks very relevant: http://forums.gentoo.org/viewtopic-p-7427364.html

      Delete
    2. I installed debian testing in a virtual machine (virtualbox) to see if it would produce the same garbled graphics as I was seeing on my laptop. Instead I reproduced your observations -- in the virtual machine debian jessie uses Gallium and segfaults on opening any file.

      I don't have a solution at the moment.

      Delete
    3. Dear Lindqvist:

      Thank you so much for be responsive to my problems.

      Regards,

      Angelo

      Delete
    4. Angelo,
      After looking into this a little bit more I think we've managed to condense the issue to the following:
      1. pymol under jessie has issues using the intel driver -- see http://verahill.blogspot.com.au/2014/03/568-pymol-troubles-in-jessie-no.html
      2. pymol under jessie has issues using the generic software acceleration driver i.e. gallium
      3. Your system should be using the intel drivers, but for some reason isn't.

      There's little that can currently be done about issues 1 and 2, but issue 3 should be fixed.

      To see what glx driver is loaded install inxi and run
      inxi -G

      This thread talks about intel vs gallium drivers: http://forums.linuxmint.com/viewtopic.php?f=42&t=117294

      Seems like manually configuring xorg.conf is the most direct solution to force intel drivers to be loaded: http://forums.linuxmint.com/viewtopic.php?f=42&t=117294#p652291

      If it's more complicated with bumblebee I'm not sure.

      Delete
  12. Dear Lindqvist:

    It turns out one cannot use xorg.conf. If one does, then on reboot, the system will hang.

    I think the file to modify is /etc/bumblebee/xorg.conf.nvidia (https://bbs.archlinux.org/viewtopic.php?id=134551), although I am not sure. This is what is in the /etc/bumblebee directoryz:

    Wed Mar 26 20:25:08 [rossi@debian bumblebee]$ls
    bumblebee.conf xorg.conf.d/ xorg.conf.nouveau xorg.conf.nvidia

    I tried putting in the information from the web page you quoted, and if you do this is what you get

    Wed Mar 26 20:21:25 [rossi@debian bumblebee]$inxi -G
    Graphics: Card-1: Intel 4th Gen Core Processor Integrated Graphics Controller
    Card-2: NVIDIA GK107M [GeForce GT 750M]
    X.Org: 1.15.0 drivers: fbdev,vesa,intel Resolution: 1920x1080@0.0hz
    GLX Renderer: Gallium 0.4 on llvmpipe (LLVM 3.3, 256 bits) GLX Version: 2.1 Mesa 9.2.2

    This is the same output whether or not one uses the default or uses the manual configuration from the web page you quoted.

    Regards,

    Angelo

    ReplyDelete
    Replies
    1. I don't have any other ideas at the moment -- it does sound like a bug in pymol/gallium is at the core of this.

      Btw, have you tried launching pymol with optirun and see whether that works?
      optirun pymol

      Delete
    2. Dear Lindqvist:

      Thanks for all you have done.

      For completeness:

      Thu Mar 27 12:45:46 [rossi@debian ~]$optirun pymol
      [ 382.247094] [ERROR]Cannot access secondary GPU - error: Could not load GPU driver

      Regards,

      Angelo

      Delete
  13. Dear Lindqvist:

    If you do the following:

    1. mkdir .pymolrc
    2.and the two lines
    set use_shaders, 0
    set sphere_mode, 0

    then pymol should work without causing a segmentation fault upon reading a pdb file.

    In my case the pymol screen flickers terribly upon rotation leaving the application almost unuseable. Searching on this problem doesn't provide a solution.

    Kind regards,

    Angelo

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  14. hey man like your laptop have architecture optimus bumbleed goes to take function alone that you need is to put in your terminal with the program that you will use "optirun" and you will see your gpu function :D

    ReplyDelete
  15. hey man like your laptop have architecture optimus bumbleed goes to take function alone that you need is to put in your terminal with the program that you will use "optirun" and you will see your gpu function :D

    ReplyDelete
  16. Dear Lindqvist:

    Another problem cropped up. I woneder if you can help.

    Mon Apr 14 08:34:34 [rossi@debian ~]$df -h
    Filesystem Size Used Avail Use% Mounted on
    /dev/sda10 316M 282M 14M 96% /
    udev 10M 0 10M 0% /dev
    tmpfs 774M 824K 773M 1% /run
    tmpfs 5.0M 0 5.0M 0% /run/lock
    tmpfs 4.7G 88K 4.7G 1% /run/shm
    /dev/sda15 748G 5.4G 704G 1% /home
    /dev/sda14 361M 2.1M 336M 1% /tmp
    /dev/sda11 8.2G 7.5G 260M 97% /usr
    /dev/sda12 2.7G 469M 2.1G 19% /var
    none 4.0K 0 4.0K 0% /sys/fs/cgroup

    As you can see / is filled, and I can't update the kernel.

    The problem is /, /usr, and /var are separate filesystems, and then comes swap and /home

    Is there a way to increase the space on /

    I apprecaite any help you can provide.

    As always grateful,

    Angelo

    ReplyDelete
    Replies
    1. You should be able to boot from a gparted cd and resize all of your partitions without too much issue: http://gparted.org/livecd.php
      I normally wouldn't suggest creating any partitions beyond / and /home, or you risk ending up in a situation with plenty of space in e.g. /var and nothing in /usr

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