Showing posts with label jessie. Show all posts
Showing posts with label jessie. Show all posts

06 February 2016

629. Google drive with rclone on debian jessie

My free dropbox account has 6Gb storage, whereas my google drive has 15Gb. Dropbox pro is way too expensive, so here's what you can do to get your google drive to work ok-ish with linux.

To set up rclone, do:
cd ~/Downloads
cd rclone-v1.27-linux-amd64
sudo cp rclone /usr/bin/
rclone config
No remotes found - make a new one n) New remote q) Quit config n/q> n name> google_drive What type of source is it? Choose a number from below 1) amazon cloud drive 2) b2 3) drive 4) dropbox 5) google cloud storage 6) swift 7) hubic 8) local 9) onedrive 10) s3 11) yandex type> 3 Google Application Client Id - leave blank normally. client_id> Google Application Client Secret - leave blank normally. client_secret> Remote config Use auto config? * Say Y if not sure * Say N if you are working on a remote or headless machine or Y didn't work y) Yes n) No y/n> y If your browser doesn't open automatically go to the following link: Log in and authorize rclone for access Waiting for code... Got code -------------------- [google_drive] client_id = client_secret = token = {"access_token":"y**5","token_type":"Bearer","refresh_token":"1/o**T","expiry":"2016-02-06T18:41:22.167889627+11:00"} -------------------- y) Yes this is OK e) Edit this remote d) Delete this remote y/e/d> y Current remotes: Name Type ==== ==== google_drive drive e) Edit existing remote n) New remote d) Delete remote q) Quit config e/n/d/q> q

Syncing is a bit of an issue as you can't sync based on last changed file. So, my solution is that each device has it's own folder that it syncs up to, and each device syncs down all other folders. For my two devices, nb and be, I have thus set it up like this:

Create new dirs and sync:
mkdir ~/gdrive/nbdrive -p
mkdir ~/gdrive/bedrive

On Nb the crontab looks like this:
*/2 *    * * * rclone sync /home/me/gdrive/nbdrive google_drive:/nbdrive
*/10 *   * * * rclone sync google_drive:/bedrive /home/me/gdrive/bedrive

and on Be it looks like this:
*/10 *    * * * rclone sync google_drive:/nbdrive /home/me/gdrive/nbdrive 
*/2 *   * * * rclone sync /home/me/gdrive/bedrive google_drive:/bedrive 

If I do work on a file on Be I then copy it to bedrive, and edit it. To edit it late on Nb I copy it from bedrive to nbdrive and edit it. Of course I could always sync manually and avoid this, but the above is a solution for people who might not feel comfortable working on the command line or if you want everything automated.

19 January 2016

627. Very briefly: Turn off screen blanking in GNOME/debian jessie

The only thing that worked for turning off screen-blanking when using youtube or vlc was an ugly little hack:
I installed xdotool and ran crontab -e and added:
*/2 * * * * DISPLAY=:0 XAUTHORITY=/home/andy/.Xauthority xdotool key Ctrl

Original post
In spite of not having any screen saver activate and in spite of setting "Blank Screen" to "Never' under Power options, my screen kept on blanking out after 1-3 minutes of watching TV using mythtv. I tried a lot of things, including using xset, but the only thing that worked in the end was editing my /etc/X11/xorg.conf (I use an nvidia driver) and adding the bits in red:
Section "ServerLayout"
    Identifier     " Configured"
    Screen      0  "Screen0" 0 0
    Screen      1  "Screen1" RightOf "Screen0"
    Screen      2  "Screen2" RightOf "Screen1"
    InputDevice    "Mouse0" "CorePointer"
    InputDevice    "Keyboard0" "CoreKeyboard"
    Option "BlankTime" "0"
    Option "StandbyTime" "0"
    Option "SuspendTime" "0"
    Option "OffTime" "0"
    Option "DPMS" "0"
Now the screen never blanks when watching TV using mythtv. On the other hand, it still blanks when watching DVDs in VLC...

15 October 2015

624. Gaussian fails with "traps: l502.exe[12449] general protection ip:d75df7 sp:7f7de40dcce0 error:0 in l502.exe[400000+dc8000]" on i7-5820K

* The systems is rock solid with nwchem and ADF.  Only G09 crashes
* Gaussian has now released G09E, and the release notes say: "A Sandybridge/Haswell binary distribution is also available". Remains to be found out if this new version solves the issue. I can't check, as I don't have access to that version.

Update 18 Oct 2015:
TL;DR version: G09D (EM64T and AMD64) crash within the first 30 min to 4 hours. An NWChem job has so far run 6 days without crashing and is still going strong.

Original post:
This isn't much of a post yet. I'm mostly posting this so that people searching online will see that they aren't alone.

I just built a new node:
AU$559 Intel BX80648I75820K 6 Core i7-5820K 3.3Ghz 15MB LGA-2011-V3 (No Heatsink)
AU$407 Gigabyte X99-SLI Intel X99 S2011-3 8xDDR4/4xPCI-E/Intel GBLan/ATX Motherboard
AU$50 DeepCool FrostWin v2.0 CPU cooler
AU$155x2 Patriot 16G Kit (8Gx2) DDR4 2133 Desktop RAM
AU$185 Antec HCG-900 High Current Gamer Gaming PSU
AU$39 Gigabyte N210SL-1GI 1GB GT210 PCI-E VGA Card
AU$68 Seagate 3.5" Barracuda 1TB ST1000DM003 SATA3 7200RPM 64MB HDD (carbon)
AU$76 Antec GX500B-W Dominator Window USB3.0 Gaming Case without PSU

I've got an installation of up-to-date Jessie on it, with the following kernel: Debian 3.16.7-ckt11-1+deb8u5 (2015-10-09) x86_64 GNU/Linux.

When running G09D rev. 01 EM64T I keep getting random errors along these lines (these are collected over a couple of days and between restarts):
[100433.566789] traps: l703.exe[11236] general protection ip:df18ca sp:7fc96f595268 error:0 in l703.exe[400000+a46000] [ 2587.899019] traps: l703.exe[3727] general protection ip:9c9757 sp:7fa6fc436ce0 error:0 in l703.exe[400000+a46000] [26439.755347] traps: l502.exe[3235] general protection ip:ab8a55 sp:7ffe29504c10 error:0 in l502.exe[400000+dc8000] [43030.457126] traps: l502.exe[427] general protection ip:11565a7 sp:7f2ec1fff268 error:0 in l502.exe[400000+dc8000] [ 2587.899019] traps: l703.exe[3727] general protection ip:9c9757 sp:7fa6fc436ce0 error:0 in l703.exe[400000+a46000] [37460.207608] traps: l703.exe[14649] general protection ip:a38ae0 sp:7f1a813cf8c0 error:0 in l703.exe[400000+a46000] [ 8865.403861] traps: l502.exe[12449] general protection ip:d75df7 sp:7f7de40dcce0 error:0 in l502.exe[400000+dc8000]

Sometimes the crashes happen after 30 minutes, sometimes after 3 hours. Most happen within four hours. I seem to remember that one ran up to 12 hours, but nothing's gone beyond that. Some short (1h 30 min) calculations have managed to run to completion.

I've checked each RAM stick with memtest+ -- they are fine -- and they are distributed as recommended in the motherboard manual.

The temperature is running below 40 degrees Celsius.

The harddrive is fine according to SMART.

I log everything every two minutes, and so can go back and look at what happened right before the crash, but there's nothing odd.

My current best three hypotheses are:

* There's an issue with G09D EM64T and the new generation of LGA2011-v3 i7 intel cpus specifically

* There's an issue with any version of G09D and the new generation of LGA2011-v3 i7 intel cpus

* There's an issue with my system which is independent of G09D.

To test, I'll be:
* Do runs with G09D rev. 01 AMD64
                         Done -- this also crashed.

* Do runs with NWChem 6.5 (ifort, mkl)
                         Running -- 6 days so far without a crash!

* Update the BIOS (long shot)

* Remove CPU and check for bent pins (long, arduous shot)

I'll be posting updates...

15 September 2014

593. nwchem 6.5 on debian jessie and wheezy

A new version of nwchem is out now, and this time we're seeing a new solvation model: SMD! Given how long it took to get COSMO right, the involvement of Truhlar in implementing SMD is a very good thing.

Either way, in order to be able to compile nwchem 6.5 on wheezy you'll need to do a few things:
sudo apt-get install build-essential libopenmpi-dev openmpi-bin
wget -O Nwchem-6.5.revision26243-src.2014-09-10.tar.gz
tar xvf Nwchem-6.5.revision26243-src.2014-09-10.tar.gz 
cd Nwchem-6.5.revision26243-src.2014-09-10/

Create a patch file, e.g. 6.5.patch with the following content (most of the patches are for compatibility with gabedit, but a few of them are needed in order to compile nwchem on debian):
diff -rupN src.original/config/makefile.h src/config/makefile.h --- src.original/config/makefile.h 2014-09-15 12:28:58.153787833 +1000 +++ src/config/makefile.h 2014-09-15 12:30:58.745787161 +1000 @@ -2208,7 +2208,7 @@ endif ifeq ($(BUILDING_PYTHON),python) # EXTRA_LIBS += -ltk -ltcl -L/usr/X11R6/lib -lX11 -ldl - EXTRA_LIBS += -lnwcutil -lpthread -lutil -ldl -lz + EXTRA_LIBS += -lnwcutil -lpthread -lutil -ldl -lz -lssl LDOPTIONS = -Wl,--export-dynamic endif ifeq ($(NWCHEM_TARGET),CATAMOUNT) diff -rupN src.original/ddscf/movecs_pr_anal.F src/ddscf/movecs_pr_anal.F --- src.original/ddscf/movecs_pr_anal.F 2014-09-15 12:28:58.229787833 +1000 +++ src/ddscf/movecs_pr_anal.F 2014-09-15 12:32:33.801786632 +1000 @@ -195,7 +195,7 @@ c 22 format(1x,2(' Bfn. Coefficient Atom+Function ',5x)) write(LuOut,23) 23 format(1x,2(' ----- ------------ ---------------',5x)) - do klo = 0, min(n-1,9), 2 + do klo = 0, min(n-1,199), 2 khi = min(klo+1,n-1) write(LuOut,2) ( $ int_mb(k_list+k)+1, diff -rupN src.original/ddscf/rohf.F src/ddscf/rohf.F --- src.original/ddscf/rohf.F 2014-09-15 12:28:58.229787833 +1000 +++ src/ddscf/rohf.F 2014-09-15 12:33:12.897786414 +1000 @@ -153,7 +153,7 @@ c ilo = 1 ihi = nmo endif - call movecs_print_anal(basis, ilo, ihi, 0.15d0, g_movecs, + call movecs_print_anal(basis, ilo, ihi, 0.01d0, g_movecs, $ 'ROHF Final Molecular Orbital Analysis', $ .true., dbl_mb(k_eval), oadapt, int_mb(k_irs), $ .true., dbl_mb(k_occ)) diff -rupN src.original/ddscf/scf_vec_guess.F src/ddscf/scf_vec_guess.F --- src.original/ddscf/scf_vec_guess.F 2014-09-15 12:28:58.229787833 +1000 +++ src/ddscf/scf_vec_guess.F 2014-09-15 12:34:41.533785920 +1000 @@ -511,19 +511,19 @@ c nprint = min(nclosed+nopen+30,nmo) if (scftype.eq.'RHF' .or. scftype.eq.'ROHF') then call movecs_print_anal(basis, 1, - & nprint, 0.15d0, g_movecs, + & nprint, 0.01d0, g_movecs, & 'ROHF Initial Molecular Orbital Analysis', & .true., dbl_mb(k_eval), oadapt, int_mb(k_irs), & .true., dbl_mb(k_occ)) else nprint = min(nalpha+20,nmo) call movecs_print_anal(basis, max(1,nbeta-20), - & nprint, 0.15d0, g_movecs, + & nprint, 0.01d0, g_movecs, & 'UHF Initial Alpha Molecular Orbital Analysis', & .true., dbl_mb(k_eval), oadapt, int_mb(k_irs), & .true., dbl_mb(k_occ)) call movecs_print_anal(basis, max(1,nbeta-20), - & nprint, 0.15d0, g_movecs(2), + & nprint, 0.01d0, g_movecs(2), & 'UHF Initial Beta Molecular Orbital Analysis', & .true., dbl_mb(k_eval+nbf), oadapt, int_mb(k_irs+nmo), & .true., dbl_mb(k_occ+nbf)) diff -rupN src.original/ddscf/uhf.F src/ddscf/uhf.F --- src.original/ddscf/uhf.F 2014-09-15 12:28:58.229787833 +1000 +++ src/ddscf/uhf.F 2014-09-15 12:35:25.225785676 +1000 @@ -144,11 +144,11 @@ C enddo ihi = max(ihi-1,1) 9611 continue - call movecs_print_anal(basis, ilo, ihi, 0.15d0, g_movecs, + call movecs_print_anal(basis, ilo, ihi, 0.01d0, g_movecs, $ 'UHF Final Alpha Molecular Orbital Analysis', $ .true., dbl_mb(k_eval), oadapt, int_mb(k_irs), $ .true., dbl_mb(k_occ)) - call movecs_print_anal(basis, ilo, ihi, 0.15d0, g_movecs(2), + call movecs_print_anal(basis, ilo, ihi, 0.01d0, g_movecs(2), $ 'UHF Final Beta Molecular Orbital Analysis', $ .true., dbl_mb(k_eval+nbf), oadapt, int_mb(k_irs+nmo), $ .true., dbl_mb(k_occ+nbf)) diff -rupN src.original/mcscf/mcscf.F src/mcscf/mcscf.F --- src.original/mcscf/mcscf.F 2014-09-15 12:28:58.441787832 +1000 +++ src/mcscf/mcscf.F 2014-09-15 12:35:55.233785509 +1000 @@ -723,7 +723,7 @@ c if (util_print('final vectors analysis', print_default)) $ call movecs_print_anal(basis, $ max(1,nclosed-10), min(nbf,nclosed+nact+10), - $ 0.15d0, g_movecs, 'Analysis of MCSCF natural orbitals', + $ 0.01d0, g_movecs, 'Analysis of MCSCF natural orbitals', $ .true., dbl_mb(k_evals), .true., int_mb(k_sym), $ .true., dbl_mb(k_occ)) c diff -rupN src.original/nwdft/scf_dft/dft_mxspin_ovlp.F src/nwdft/scf_dft/dft_mxspin_ovlp.F --- src.original/nwdft/scf_dft/dft_mxspin_ovlp.F 2014-09-15 12:28:58.457787831 +1000 +++ src/nwdft/scf_dft/dft_mxspin_ovlp.F 2014-09-15 12:37:23.401785018 +1000 @@ -184,14 +184,14 @@ c call ga_sync() c call movecs_print_anal(basis,int_mb(k_non),int_mb(k_non) - & ,0.15d0,g_alpha,'Alpha Orbitals without Beta Partners', + & ,0.01d0,g_alpha,'Alpha Orbitals without Beta Partners', & .false., 0.0 ,.false., 0 , .false., 0 ) c if (nct.GE.2) then do i = 2,nct ind = int_mb(k_non+i-1) call movecs_print_anal(basis,ind,ind - & ,0.15d0,g_alpha,' ', + & ,0.01d0,g_alpha,' ', & .false., 0.0 ,.false., 0 , .false., 0 ) enddo endif @@ -350,7 +350,7 @@ c endif c endif c 9990 format(/,18x,'THERE ARE',i3,1x,'UN-PARTNERED ALPHA ORBITALS') c - call movecs_print_anal(basis, 1, nalp, 0.15d0, g_ualpha, + call movecs_print_anal(basis, 1, nalp, 0.01d0, g_ualpha, & 'Alpha Orb. w/o Beta Partners (after maxim. alpha/beta overlap)', & .false., 0.0 ,.false., 0 , .false., 0 ) c diff -rupN src.original/nwdft/scf_dft/dft_scf.F src/nwdft/scf_dft/dft_scf.F --- src.original/nwdft/scf_dft/dft_scf.F 2014-09-15 12:28:58.457787831 +1000 +++ src/nwdft/scf_dft/dft_scf.F 2014-09-15 12:38:29.713784648 +1000 @@ -2097,7 +2097,7 @@ c endif c ... jochen: replaced 0.15 at the end of the line with 'tanalyze' c which can be read from input -c call movecs_print_anal(ao_bas_han, ilo, ihi, 0.15d0, +c call movecs_print_anal(ao_bas_han, ilo, ihi, 0.01d0, call movecs_print_anal(ao_bas_han, ilo, ihi, tanalyze, & g_movecs(ispin), & blob, diff -rupN src.original/nwdft/scf_dft_cg/dft_cg_solve.F src/nwdft/scf_dft_cg/dft_cg_solve.F --- src.original/nwdft/scf_dft_cg/dft_cg_solve.F 2014-09-15 12:28:58.445787832 +1000 +++ src/nwdft/scf_dft_cg/dft_cg_solve.F 2014-09-15 12:39:25.497784337 +1000 @@ -193,7 +193,7 @@ c blob = 'DFT Final Beta Molecular Orbital Analysis' endif call movecs_fix_phase(g_movecs(ispin)) - call movecs_print_anal(basis, ilo, ihi, 0.15d0, + call movecs_print_anal(basis, ilo, ihi, 0.01d0, & g_movecs(ispin),blob, & .true., dbl_mb(k_eval+(ispin-1)*nbf), & oadapt, int_mb(k_irs+(ispin-1)*nbf), @@ -216,7 +216,7 @@ c endif call movecs_fix_phase(g_movecs) blob = 'DFT Final Molecular Orbital Analysis' - call movecs_print_anal(basis, ilo, ihi, 0.15d0, + call movecs_print_anal(basis, ilo, ihi, 0.01d0, & g_movecs,blob, & .true., dbl_mb(k_eval), & oadapt, int_mb(k_irs),

Apply it with
patch -p0 < 6.5.patch

Then build using something along the lines of
export NWCHEM_TOP=`pwd`
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_MODULES="all python"
export PYTHONHOME=/usr
export BLASOPT="-L/opt/openblas/lib -lopenblas"

export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib/openmpi/lib
export MPI_INCLUDE=/usr/lib/openmpi/include
export LIBRARY_PATH="$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/openblas/lib"

export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"

cd $NWCHEM_TOP/src

make clean
make nwchem_config
make FC=gfortran 1> make.log 2>make.err

cd $NWCHEM_TOP/contrib
export FC=gfortran

See other posts for using different math libs: openblas, intel mkl, AMD acml

If you're building for Jessie, set the following flags before building:
export PYTHONCONFIGDIR=config-x86_64-linux-gnu

28 July 2014

587. Very Briefly: Getting pictures off of a corrupted Compact Flash card using testdisk

Nothing terribly complicated here. My CFII card (above, at /dev/sdb1)  is about a decade old and occasionally becomes corrupted. To recover the photos I use photorec which is part of testdisk:

sudo apt-get install testdisk
sudo photorec

Select the correct device, in this case /dev/sdb


Pick the correct file system, typically FAT16 or 32
Also select a place to store the recovered photos. Then recover:

And you're done.

02 July 2013

471. Debian Jessie -- gnome-shell bug

Update 3/7/2013:
there are now *gnome-bluetooth packages (3.8.1-2) in the jessie repos now. While I haven't looked closer at them, I presume that they fix this issue.

(on a different note: dist-upgrade currently removes gnome...)

Original post:
I've used debian testing since early 2011, and I've only had a few minor issues during that time.

However, sometimes things happen that reminds you that the Testing release is not meant for mission critical work (and makes me happy that I only use Jessie on my laptop, which I mainly use at home).


Last night I did upgrade and dist-upgrade, which installed the following packages according to /var/log/apt/history:
Start-Date: 2013-07-01  22:03:17
Commandline: apt-get dist-upgrade
Install: p11-kit:amd64 (0.18.3-2, automatic), libgnome-bluetooth11:amd64 (3.8.1-1, automatic), libgcr-base-3-1:amd64 (3.8.2-3, automatic), libtasn1-6:amd64 (3.3-1, automatic), libgcr-ui-3-1:amd64 (3.8.2-3, automatic)
Upgrade: libnm-gtk0:amd64 (,, libgcr-3-1:amd64 (3.4.1-3, 3.8.2-3), gir1.2-gcr-3:amd64 (3.4.1-3, 3.8.2-3), network-manager-gnome:amd64 (,, gnome-keyring:amd64 (3.4.1-5, 3.8.2-2), gcr:amd64 (3.4.1-3, 3.8.2-3), gnome-bluetooth:amd64 (3.4.2-1, 3.8.1-1), gir1.2-gnomebluetooth-1.0:amd64 (3.4.2-1, 3.8.1-1), gir1.2-gck-1:amd64 (3.4.1-3, 3.8.2-3)
End-Date: 2013-07-01  22:03:29

Now what happens when I log in to gnome via gdm3 I get an empty desktop with no menus, no hot-spots or anything else indicating that things worked out. Alt+F2 doesn't work either, and conky doesn't start.

The only thing that does work is
* my keyboard shortcuts (I've mapped ctrl+shift+Down arrow to chromium)
* guake (which starts with gnome)

ps aux|grep gnome-shell
returns nothing, which might be a clue.

Looking at the debian forums the closest post seems to be (although erroneously labelled -- gdm3 DOES start):

That in turn led to this bug report:

My gnome-shell version is 3.4.2-8,

I don't understand how gnome-bluetooth causes this, especially given that I've disabled bluetooth in rcconf, but whatever it takes...

I tried applying the patch but it failed:
mkdir ~/tmp
cd ~/tmp
wget ";filename=GnomeBluetooth.patch;att=1;bug=712861" -O blue.patch
sed -i 's_js/ui/status/bluetooth.js_/usr/share/gnome-shell/js/ui/status/bluetooth.js_g' blue.patch
sudo patch -p0 < blue.patch

Instead, I ended up making the changes to /usr/share/gnome-shell/js/ui/status/bluetooth.js by hand (remember that you can always use the ttys using ctrl+Fx):
  6 const Gio =;
  7 const GnomeBluetoothApplet =;
  8 const GnomeBluetooth =;
  9 const Gtk =;

and then delete the Applet part in GnomeBluetoothApplet so that it reads
 38         this._killswitch.connect('toggled', Lang.bind(this, function() {
 39             let current_state = this._applet.killswitch_state;
 40             if (current_state != GnomeBluetooth.KillswitchState.HARD_BLOCKED &&
 41                 current_state != GnomeBluetooth.KillswitchState.NO_ADAPTER) {
 42                 this._applet.killswitch_state = this._killswitch.state ?
 43                     GnomeBluetooth.KillswitchState.UNBLOCKED:
 44                     GnomeBluetooth.KillswitchState.SOFT_BLOCKED;
 45             } else
 46                 this._killswitch.setToggleState(false);

Then do it again:
 96     _updateKillswitch: function() {
 97         let current_state = this._applet.killswitch_state;
 98         let on = current_state == GnomeBluetooth.KillswitchState.UNBLOCKED;
 99         let has_adapter = current_state != GnomeBluetooth.KillswitchState.NO_ADAPTER;
100         let can_toggle = current_state != GnomeBluetooth.KillswitchState.NO_ADAPTER &&
101                          current_state != GnomeBluetooth.KillswitchState.HARD_BLOCKED;

At this point I rebooted and everything was back to normal (you can try simply doing 'sudo service gdm3 restart' instead of rebooting).
Anyway, done.

01 June 2013

436. Miramath on debian

For no particular reason (well, because of this: here's a very brief how-to to get miramath up and running. There may well be more packages required and which I had pre-installed. The pre-built miramath binaries don't work on debian jessie, but since this is python...well..Anyway:

First compile and install PyQwt-Polar. It takes quite a while. Note that there's a conflict between PyQwt-Polar and python-qwt5-qt4 which may potentially be serious. A side-effect of this is that you can't build a proper package, since dpkg would detect this conflict (hence the make install). What this means is that PyQwt-Polar will over-write files installed by the python-qwt5-qt4 files i.e. A potentially Bad Thing.  Consider setting it up in a chroot.

There's another reason why I wouldn't recommend miramath for serious work at the moment -- it is in pre-alpha and the degree to which is it maintained isn't entirely clear to me. For scientific work, use octave and maxima, which are well-maintained and have been around for ages.

The flip-side of this is obviously that there's no harm in checking out a new and interesting piece of software, and presumably no-one is preventing you from contributing. Anyway. The main reason for checking this out was the debian forum post referenced above.

I did this on Debian Jessie, but it should work on Wheezy as well.

sudo apt-get install python-sip-dev python-qt4-dev python-scipy python-qt4-gl python-sympy python-ply python-qwt5-qt4 python-qwt3d-qt4 python-guiqwt python-dev libqwt-dev libqwt5-qt4
mkdir ~/tmp/
cd ~/tmp
tar xvf PyQwt-Polar-5.2.0.tar.bz2
cd PyQwt-Polar-5.2/
cd configure/
python -Q ../qwt-5.2
sudo make install

Then continue:
cd ~/miramath
sed -i 's/sympy.abs/sympy.Abs/g'
chmod +x

05 May 2013

404. Briefly: Debian Jessie now out (sort of, and in places)

update 6/5/13: The first upgrades and dist-upgrades are now in jessie. Nothing particularly exciting, beyond a new lsb_release package. As far as I can tell the gnome desktop background hasn't been touched either, but if memory serves me right the themes for the new stable is decided around the time of the freeze of testing, so there're another 2-3 years to go.

update: jessie is now at too

Original post now has a copy of jessie, even though still doesn't.

This means that you can switch to the new testing (jessie) by editing your /etc/apt/sources.list:
deb jessie main contrib non-free deb jessie main non-fre

At this point jessie is simply a copy of the 'old' testing, wheezy, so if you've got an up-to-date wheezy there are currently no updates involved in switching to jessie.

If I've understood things right sid was frozen at the same time as wheezy, so that it will take a little while before changes will occur in jessie since they first need to be introduced to sid, and then filter through.

Note that once updates start flowing into jessie the odd breakage might occur, so make sure to install apt-listbugs to get warnings about known bugs.

Upgrading from Squeeze to Wheezy
Upgrading from the old stable to the new stable is simple enough.

First make sure that Squeeze is up to date
sudo apt-get update && sudo apt-get upgrade && sudo apt-get dist-upgrade

Edit /etc/apt/sources.list and replace all instances of squeeze with wheezy. Then update, and download all updates before upgrading (-d).
sudo apt-get update && sudo apt-get dist-upgrade -d
sudo apt-get upgrade && sudo apt-get dist-upgrade

If you get an error about default-jre you can uninstall openjdk-6-jre and then run dist-upgrade again. It should work.

31 July 2012

217. Recently...

Recently I've been busy preparing lectures (phew!), which means I've been kinder to my computer than is normal. Still, I managed to get myself into a few situations. The need to 'get stuff done' overrode the importance of documentation, but here's the low-down in case someone finds themselves in a similar situation:

1. Upgrades keep on getting stuck when restarting nfs/nfsd (nfs-common, nfs-kernel-server).
Normally I don't have any problems with nfs -- it's a tried and tested technology -- but one of my cluster nodes was giving me grief.

The key was to comment out everything in /etc/exports and commenting out nfs mounted partitions in /etc/fstab, then adding nfs and nfsd to /etc/modprobe.d/blacklist.conf (not sure this actually did anything), rebooting, throwing in

sudo rmmod nfs nfsd 

to be on the safe side, then doing

sudo dpkg --configure -a

to get dpkg/apt back in working order. After that I could uncomment everything in /etc/exports and /etc/fstab, and whitelist my drivers again.

Problem solved.

2. Nvidia is still a headache.
Since I was given a rare opportunity to reboot my front node I did a bit of work on it. Mainly, I wanted to allow gdm to start again, and figured I'd return to my nvidia driver managment to dkms-y goodness.

So I fired up smxi, selected 'debian-nvidia' and...everything was messed up. Long story short: I got it working with gdm3 by picking 'current driver' in smxi (always blacklist nouveau if you want to use/install nvidia drivers), making sure that there was no 'vga' (e.g.  vga=0x0318 ) in GRUB_CMDLINE_LINUX in /etc/default/grub and rebooting liberally.

I later got the debian-nvidia (dkms) version working by 1) not using frambuffer and 2) manually removing all nvidia legacy drivers that smxi pulled in. Well, that's working as in no error messages and the desktop looking fine.

3. GNOME 3 not diplaying all letters
e.g. 'guake' was rendered as 'g ak '. This happened on a low-powered system. A 'fix' was to go to advanced settings (gnome-tweak-tool), select font and change scaling from 1.0 to 1.2 and above.

It's not much of a 'fix', so I ended up nuking GNOME from that system and replacing it with KDE to have a reason to get more familiar with it. In the interest of balance I nuked all other DEs from another box and put LXDE on it. To paraphrase the Dos Equis commercial: I don't always use a DE, but when I do, I want to learn something new.

I've used KDE and GNOME on and off over the past 12 years, but you get rusty -- and both KDE and GNOME have changed enough from v 3.x and 2.x, respectively, that they aren't the same environment anymore. I still get an initial feeling of joy when I sit down by an NMR console and discover a red hat system with a 3.x desktop. Which is quickly followed by being annoyed over not having root access, but whatever. As for the usual gnome 2 vs gnome 3 arguments -- I like gnome3 in general. I just hate the idea of settings being hidden or disabled, and functionality being reduced. Enough so that I'm still looking for a potential replacement.

So far :
KDE -- I like it. It's overdoing the desktop effects a bit (out of the box) but, since it's KDE, it's easy to turn things on and off. I'm still a GNOME man, and KDE doesn't have the warm fuzzy feeling of home yet, but I can see how I could get used to it. I just need to get over my outdated idea that KDE is for windows users (I've never used a Mac so I guess I'm a reformed windows -- actually DOS -- user more than anything else).

KDE on one of my other systems seems to be messing up GNOME 3 though -- e.g. the mouse cursor theme gets transferred to gnome, and the pop-up notifications are those of kwin and not gnome-shell.  Not sure whether it's KDE causing it or whether I've messed a bit too much with my system.

LXDE -- it's functional and has long been my choice for virtual installations of linux for windows users. It's minimalistic in the sense that yes, it does provide a desktop, but no, it doesn't try to do anything beyond providing a set of menus and a bit of themeing. And that's a good thing. If you're going to impress a mate -- use gnome or kde. If you just need to get something done and launch a piece of software, lxde's your mate.

4. One of my systems lacked /etc/init.d/vboxdrv
Not all my collaborators use linux, so I keep a virtual copy of XP around for when I'm absolutely forced to use MS Word (OpenOffice sometimes changes the layout and it quickly becomes messy on collaborative documents). When taking a quick break to edit a manuscript in virtualbox I got the usual no driver present, 'run /etc/init.d/vboxdrv setup' message. Well, there was no /etc/init.d/vboxdrv in spite of dkms and vboxdrv-dkms being installed in addition to all the kernel headers. Turns out that the quickest way, assuming that locate vboxdrv doesn't come up empty (i.e. it's somewhere in the kernel tree) is just to mod it.
modprobe vboxdrv

To avoid it in the future, stick
somewhere in your /etc/modules

5. Mysteriously self-rotating gnuplot images in latex 
Came down to a stupid mistake. I was doing:

set term postscript enhanced colour
set output 'acid.eps'
set border 3
set xtics nomirror
set ytics nomirror

I forgot to add eps -- getting rusty I suppose.

set term postscript enhanced eps colour
set output 'acid.eps'
set border 3
set xtics nomirror
set ytics nomirror

Surprised it hasn't happened before during all these years of latex usage.

6. Setting default line printer
me@beryllium:$ lpq
lpq: Error - no default destination available.

me@beryllium:$ lpstat -a
AdobePDF accepting requests since Mon 06 Aug 2012 08:01:32 EST
AdobePDF7 accepting requests since Mon 06 Aug 2012 08:01:32 EST
AdobePDF8 accepting requests since Mon 06 Aug 2012 10:04:13 EST accepting requests since Mon 06 Aug 2012 08:01:32 EST
AdobePDF9 accepting requests since Mon 06 Aug 2012 08:01:32 EST
AdobePDF9@ accepting requests since Mon 06 Aug 2012 08:01:32 EST
biol08r159p1 accepting requests since Mon 06 Aug 2012 08:01:32 EST
Canon_iP4300 accepting requests since Mon 06 Aug 2012 08:01:32 EST
Canon_MP460 accepting requests since Mon 06 Aug 2012 10:09:36 EST
Colour_109a accepting requests since Mon 06 Aug 2012 08:01:32 EST
global-mfp accepting requests since Mon 28 May 2012 14:27:30 EST accepting requests since Mon 06 Aug 2012 08:01:32 EST
HP_LaserJet_Professional_P1102w accepting requests since Sat 04 Aug 2012 23:08:16 ESTHPColourLaserCP3505 accepting requests since Mon 06 Aug 2012 08:01:32 EST
HPLaserJetP3005 accepting requests since Mon 06 Aug 2012 08:01:32 EST

 me@beryllium:$ lpoptions -d HP_LaserJet_Professional_P1102w
auth-info-required=none copies=1 device-uri=hp:/usb/HP_LaserJet_Professional_P1102w?serial=000000000Q91K4WVSI1c finishings=3 job-hold-until=no-hold job-priority=50 job-sheets=none,none marker-change-time=0 number-up=1 printer-commands=AutoConfigure,Clean,PrintSelfTestPage printer-info='HPIJS -- drv:///hpijs.drv/hp-laserjet_professional_p1102w-hpijs.ppd' printer-is-accepting-jobs=true printer-is-shared=true printer-location printer-make-and-model='HP LaserJet Professional p1102w, hpcups 3.12.4, requires proprietary plugin' printer-state=5 printer-state-change-time=1344085696 printer-state-reasons=paused printer-type=8425484 printer-uri-supported=ipp://localhost:631/printers/HP_LaserJet_Professional_P1102w

7. The next Debian is codenamed Jessie!
I'm only 6 days late...apparently that's the cowgirl.