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 http://www.nwchem-sw.org/download.php?f=Nwchem-6.5.revision26243-src.2014-09-10.tar.gz -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 LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONVERSION=2.7
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"
export ARMCI_NETWORK=SOCKETS

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
./getmem.nwchem

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
export PYTHONLIBTYPE=so

586.Very Briefly: Gnuradio, RTL-SDR, GQRX and an R280T device on debian jessie

NOTE:
* I did this on debian jessie which at the time has gnuradio v 3.7.3-9+b1 and rtl-sdr v 0.5.3-3

* I'm having a lot of trouble getting gqrx working on debian wheezy even with backports. Whereas the backports versions of gnuradio, rtl-sdr and gqrx-sdr install just fine, when running gqrx I get the following error:

gqrx: symbol lookup error: /usr/lib/x86_64-linux-gnu/libQtNetwork.so.4: undefined symbol: _ZN16QIODevicePrivate13putCharHelperEc

* gqrx won't work on debian wheezy systems with 2 Gb of memory for some reason. I get the same error as is shown in this post: https://groups.google.com/forum/#!topic/gqrx/20F8RMWkNbU

---

The post:
I recently bought a DVB USB dongle based on RTL2832 and R280T: http://www.ebay.com.au/itm/221450623699?ssPageName=STRK:MEWNX:IT&_trksid=p3984.m1497.l2649. AU$11for a TV card which actually works flawlessly under linux really isn't bad!

As I already have a mythtv setup using leadtek DTV 1000S I was more interested in exploring the R820T dongle as a software defined radio (SDR).

 So, after glancing at  http://www.thepowerbase.com/2012/06/getting-started-with-rtl-sdr/2/ I did the following

sudo apt-get install rtl-sdr gnuradio gnuradio-dev libgnuradio-osmosdr0.1.1.4 git libboost-dev liblog4cpp5-dev libboost-system-dev libboost-program-options-dev checkinstall
mkdir ~/tmp
cd ~/tmp
git clone https://github.com/csete/gqrx.git gqrx.git
cd gqrx.git/
mkdir build
cd build
qmake ../
make
sudo checkinstall --install=no

0 -  Maintainer: [ root@niobium ]
1 -  Summary: [ gqrx ]
2 -  Name:    [ gqrx ]
3 -  Version: [ 20140726 ]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ amd64 ]
8 -  Source location: [ build ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ build ]
12 - Conflicts: [  ]
13 - Replaces: [  ]

sudo dpkg -i gqrx_20140726-1_amd64.deb

Starting gqrx and using it is easy:

gqrx

So far I haven't managed to get anything other than regular commercial radio signals (I've only explored the FM band).

579. TEMPerHum (0c45:7402 ) on debian linux wheezy

Yet another little usb device from PC sensors (I seem to have been giving them a fair amount of money recently ).

This is the device in question: http://pcsensor.com/index.php?_a=product&product_id=178 (note that I buy my devices via ebay where the prices are apparently always the campaign ones -- I paid AUD25 , not USD80)

It didn't come in a box so I have no scans or shots to show.

[See here for the regular TEMPer USB device (0c45:7401), and here for the TEMPer 1K4  (0c45:7403) USB thermocouple reader. Note that since the temper-usb code is in  a lot of flux you can't use the line numbers in those posts directly -- you'll have to read and understand the code before pasting it in. Luckily, it's quite simple -- even I managed to sort it out!]

I couldn't get temper-usb to work even when making (what I consider) the necessary edits, but instead got lots of errors (including " usb.USBError: could not detach kernel driver from interface 1: No data available"). So I finally gave up.

Instead, web searching led me to http://edorfaus.wordpress.com/2012/07/02/new-library-examples-and-features/ -- one of the replies by eg1l spelled out the solution -- I'll grant myself the liberty to repost it here, but please remember where it originally came from and link to the original article (exclusively or in addition).

mkdir ~/tmp
cd ~/tmp/
sudo apt-get install libudev-dev libusb-1.0.0-dev libfox-1.6-dev autoconf cmake

git clone git://github.com/signal11/hidapi.git
cd hidapi/
./bootstrap
./configure
cd libusb/
make
sudo make install

cd ../../

git clone git://github.com/edorfaus/TEMPered.git
cd TEMPered/
mkdir build
cd build/
cmake ..
make
cd utils/
sudo ./tempered 
cd ../
sudo make install

sudo ln -s /usr/local/lib/x86_64-linux-gnu/libtempered.so.0 /usr/local/lib/libtempered.so.0
sudo ln -s /usr/local/lib/x86_64-linux-gnu/libtempered-util.so.0 /usr/local/lib/libtempered-util.so.0
sudo ldconfig

sudo tempered

0006:000e:01 0: temperature 21.75 °C, relative humidity 49.1%, dew point 10.6 °C

Create an 80-temper.rules file in /etc/udev/rules.d:

SUBSYSTEMS=="usb", ATTRS{idVendor}=="0c45", ATTRS{idProduct}=="7401", GROUP="users", MODE="0666"
SUBSYSTEMS=="usb", ATTRS{idVendor}=="0c45", ATTRS{idProduct}=="7402", GROUP="users", MODE="0666"
SUBSYSTEMS=="usb", ATTRS{idVendor}=="0c45", ATTRS{idProduct}=="7403", GROUP="users", MODE="0666"

Then do

sudo usermod -a -G users $USER

And

sudo service udev restart

Unplug and re-plug your device, then open a new terminal and you're set (type group to make sure that users show up).

me@boron:~$ tempered
0006:000f:01 0: temperature 23.34 °C, relative humidity 46.8%, dew point 11.3 °C

569. Briefly: Dual monitor set-up on Debian Wheezy with Gnome and a single nvidia graphics card

This is very easy, but I might as well document it here anyway.

This morning another group threw out two functioning monitors and I grabbed both. While I haven't yet decided on what to do with the second one I decided to use one to make a dual monitor set-up for my work station.

My desktop has both onboard nvidia graphics and a separate pci-e nvidia (GT 430) graphics card. Using lspci only the external graphics card shows up, probably because the bios prioritises the external card and disables the onboard graphics.

The nvidia GT 430 card has three output ports: vga, hdmi and dvi. My main monitor (Dell P2411H, 1920x1080) has both vga and dvi, and my 'new' monitor (HP S1932, 1366x768) only has vga.

The first step was to physically connect both monitors to my computer. I originally thought I had to use one card per monitor, which would've necessitated me to reboot, change the bios and probably hand-craft an xorg.conf. I don't like rebooting, so I looked at the alternatives.

Apparently you can simply connect both monitors to the same card by using the different ports, so I hooked up the small screen to the vga port and the big one to the hdmi port.

After that it was a simple matter of opening 'displays' in the gnome 3 systems settings, setting both monitors to 'on', and arranging them side by side correctly by dragging them with the mouse:

I also had a look at it in nvidia-settings:

The only issue that remained was guake -- it was showing up in the 'wrong' screen (i.e. the left-most, smaller one).  This post showed how to edit: http://haifzhan.blogspot.com.au/2013/10/guake-dual-monitor-setup.html

This is how to do it on the version currently in wheezy, 0.4.3:

sudo vim `which guake`

814     def get_final_window_rect(self):
 815         """Gets the final size of the main window of guake. The height
 816         is the window_height property, width is window_width and the
 817         horizontal alignment is given by window_alignment.
 818         """
 819         screen = self.window.get_screen()
 820         height = self.client.get_int(KEY('/general/window_height'))
 821         width = 100
 822         halignment = self.client.get_int(KEY('/general/window_halignment'))
 823 
 824         # get the rectangle just from the first/default monitor in the
 825         # future we might create a field to select which monitor you
 826         # wanna use
 827 
 828         #monitor = 0 # use the left most monitor
 829         monitor = screen.get_n_monitors() - 1 # use the rightmost monitor
 830 
 831         monitor_rect = screen.get_monitor_geometry(monitor)
 832         window_rect = monitor_rect.copy()
 833         total_width = window_rect.width
 834         window_rect.height = window_rect.height * height / 100
 835         window_rect.width = window_rect.width * width / 100
 836 
 837         if width < monitor_rect.width:
 838             if halignment == ALIGN_CENTER:
 839                 window_rect.x = monitor_rect.x+(monitor_rect.width - window_rect.width) / 2
 840             elif halignment == ALIGN_LEFT:
 841                 window_rect.x = monitor_rect.x
 842             elif halignment == ALIGN_RIGHT:
 843                 window_rect.x = monitor_rect.x+monitor_rect.width-window_rect.width
 844         window_rect.y = monitor_rect.y
 845         return window_rect
 846 

Note that the edited version will be overwritten when you upgrade guake.

566. Briefly: Annoying warnings when plotting using gnuplot and octave on wheezy March 2014.

Note: I'm not going to give a proper fix for this, but rather a work-around -- and one which isn't very good at that.

When using gnuplot or plotting in octave on wheezy I keep getting the following warnings.

Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/64-arphic-uming.conf", line 8: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/64-arphic-uming.conf", line 21: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/64-arphic-uming.conf", line 34: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/64-arphic-uming.conf", line 47: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/65-droid-sans-fonts.conf", line 103: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/65-droid-sans-fonts.conf", line 138: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/90-fonts-baekmuk.conf", line 10: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/90-fonts-baekmuk.conf", line 23: Having multiple values in  isn't supported and may not work as expected

---

My 'solution' was a bit radical -- I had already set up a system with apt-pinning (http://verahill.blogspot.com.au/2014/03/562-pulling-in-glibc-214-from-testing.html) so I figured that pulling in the fonts from testing couldn't hurt, assuming there were no dependencies to worry about.

So I did:

sudo apt-get install -t testing fonts-arphic-uming

and this worked fine.

The old 41-arphic-uming.conf:

<?xml version="1.0"?>
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<fontconfig>

<!--
  Serif faces
 -->
        <alias>
                <family>AR PL ShanHeiSun Uni</family>
                <family>AR PL ShanHeiSun Uni MBE</family>
                <family>AR PL UMing CN</family>
                <family>AR PL UMing HK</family>
                <family>AR PL UMing TW</family>
                <family>AR PL UMing TW MBE</family>
                <default><family>serif</family></default>
        </alias>
<!--
  Monospace faces
 -->
        <alias>
                <family>AR PL ShanHeiSun Uni</family>
                <family>AR PL ShanHeiSun Uni MBE</family>
                <family>AR PL UMing CN</family>
                <family>AR PL UMing HK</family>
                <family>AR PL UMing TW</family>
                <family>AR PL UMing TW MBE</family>
                <default><family>monospace</family></default>
        </alias>
</fontconfig>

The new 41-arphic-uming.conf:

<?xml version="1.0"?>
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<fontconfig>

<!--
  Serif faces
 -->
        <alias>
                <family>AR PL ShanHeiSun Uni</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL ShanHeiSun Uni MBE</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL UMing CN</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL UMing HK</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL UMing TW</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL UMing TW MBE</family>
                <default><family>serif</family></default>
        </alias>
<!--
  Monospace faces
 -->
        <alias>
                <family>AR PL ShanHeiSun Uni</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL ShanHeiSun Uni MBE</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL UMing CN</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL UMing HK</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL UMing TW</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL UMing TW MBE</family>
                <default><family>monospace</family></default>
        </alias>
</fontconfig>

It just remained to pull in the rest of the offending fonts:

sudo apt-get install -t testing fonts-arphic-ukai fonts-droid fonts-baekmuk

497. Compiling Wine 1.7 in a chroot on debian

Here's a generic way of building Wine 1.7 which is the new testing branch. And yes, it's the instructions for 1.5.28-1.6 recycled, with a few small amendments.

See here for information about 3D acceleration using libGL/U with Wine: http://verahill.blogspot.com.au/2013/05/429-briefly-wine-libglliubglu-blender.html

Getting started:
If you set up a e.g. chroot to build 1.6 you don't need to set up a new chroot to build 1.7. In that case, skip the set-up step below and instead re-enter your existing chroot like this:

sudo mount -o bind /proc wine32/proc
sudo cp /etc/resolv.conf wine32/etc/resolv.conf
sudo chroot wine32
su sandbox

cd ~/tmp

And skip to 'Building wine'.

Otherwise do this:
Setting up the Chroot

sudo apt-get install debootstrap
mkdir $HOME/tmp/architectures/wine32 -p
cd $HOME/tmp/architectures
sudo debootstrap --arch i386 wheezy $HOME/tmp/architectures/wine32 http://ftp.au.debian.org/debian/
sudo mount -o bind /proc wine32/proc
sudo cp /etc/resolv.conf wine32/etc/resolv.conf
sudo chroot wine32

You're now in the chroot:

apt-get update
apt-get install locales sudo vim
echo 'export LC_ALL="C"'>>/etc/bash.bashrc
echo 'export LANG="C"'>>/etc/bash.bashrc
echo '127.0.0.1 localhost beryllium' >> /etc/hosts
source /etc/bash.bashrc
adduser sandbox
usermod -g sudo sandbox
echo 'Defaults !tty_tickets' >> /etc/sudoers
su sandbox
cd ~/

Replace 'beryllium' with the name your host system (it's just to suppress error messages)

---

Building Wine
While still in the chroot, continue (the i386 is ok; don't worry about it -- you don't actually need it):

sudo apt-get install libx11-dev:i386 libfreetype6-dev:i386 libxcursor-dev:i386 libxi-dev:i386 libxxf86vm-dev:i386 libxrandr-dev:i386 libxinerama-dev:i386 libxcomposite-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libglu-dev:i386 libosmesa-dev:i386 libdbus-1-dev:i386 libgnutls-dev:i386 libncurses-dev:i386 libsane-dev:i386 libv4l-dev:i386 libgphoto2-2-dev:i386 liblcms2-dev:i386 libgstreamer-plugins-base0.10-dev:i386 libcapi20-dev:i386 libcups2-dev:i386 libfontconfig-dev:i386 libgsm1-dev:i386 libtiff-dev:i386 libpng-dev:i386 libjpeg-dev:i386 libmpg123-dev:i386 libopenal-dev:i386 libldap-dev:i386 libxrender-dev:i386 libxml2-dev:i386 libxslt-dev:i386 libhal-dev:i386 gettext:i386 prelink:i386 bzip2:i386 bison:i386 flex:i386 oss4-dev:i386 checkinstall:i386 ocl-icd-libopencl1:i386 opencl-headers:i386 libasound2-dev:i386 build-essential

mkdir ~/tmp
cd ~/tmp
wget http://prdownloads.sourceforge.net/wine/wine-1.7.0.tar.bz2

tar xvf wine-1.7.0.tar.bz2
cd wine-1.7.0/
./configure
time make -j3
sudo checkinstall --install=no

checkinstall 1.6.2, Copyright 2009 Felipe Eduardo Sanchez Diaz Duran
           This software is released under the GNU GPL.


The package documentation directory ./doc-pak does not exist. 
Should I create a default set of package docs?  [y]: 

Preparing package documentation...OK

Please write a description for the package.
End your description with an empty line or EOF.
>> wine 1.7.0
>> 

*****************************************
**** Debian package creation selected ***
*****************************************

This package will be built according to these values: 

0 -  Maintainer: [ root@beryllium ]
1 -  Summary: [ wine 1.7.0]
2 -  Name:    [ wine ]
3 -  Version: [ 1.7.0]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ i386 ]
8 -  Source location: [ wine-1.7.0 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ wine ]
12 - Conflicts: [  ]
13 - Replaces: [  ]

Checkinstall takes a little while (In particular this step: 'Copying files to the temporary directory...').

**********************************************************************

 Done. The new package has been saved to

 /home/sandbox/tmp/wine-1.7.0/wine_1.7.0-1_i386.deb
 You can install it in your system anytime using:

      dpkg -i wine_1.7.0-1_i386.deb

**********************************************************************

---

Installing Wine

Exit the chroot

sandbox@beryllium:~/tmp/wine-1.7.0$ exit
exit
root@beryllium:/# exit
exit
me@beryllium:~/tmp/architectures$ 

On your host system
 Enable multiarch* and install ia32-libs, since you've built a proper 32 bit binary:

sudo dpkg --add-architecture i386
sudo apt-get update
sudo apt-get install ia32-libs libgstreamer-plugins-base0.10-0

*At some point I think ia32-libs may be replaced by proper multiarch packages, but maybe not. So we're kind of doing both here.

 Copy the .deb package and install it

sudo cp wine32/home/sandbox/tmp/wine-1.7.0/wine_1.7.0-1_i386.deb .
sudo chown $USER wine_1.7.0-1_i386.deb
sudo dpkg -i wine_1.7.0-1_i386.deb

---

424. NWChem 6.3 on Debian Wheezy

Update 23 May 2013: The execution times are pretty much the same as for 6.1.1 with a new patch. I've updated the instructions below to incorporate this new patch (http://www.nwchem-sw.org/images/Iswtch.patch.gz)

Update 21 May 2013: The execution times can be improved considerably by setting

ARMCI_NETWORK=SOCKETS

They are still ca 30% longer than 6.1.1 though due to slower SCF convergence. See http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id834/Nwchem_6.3_running_2-5_times_slo....html

Update 20 May 2013: I did a bit of basic benchmarking. NWChem 6.3 is incredibly slow (ca 190s vs 40s for the 8 core, 3.6 GHz benchmark in http://verahill.blogspot.com.au/2013/05/414-frequency-vs-cores-crude.html). It's parallellising properly from what I can see (i.e. it is not running 8 serial jobs). I've repeated the calc with an unpatched version of nwchem 6.3, and it is just as slow.
 I'll post updates here if I figure this one out.

Original post:
NWChem 6.3 is just out. Here's how to build it for CPU computations.

To build on CentOS 5.6, see http://verahill.blogspot.com.au/2013/05/421-nwchem-63-on-rocks-543centos-56.html

---

Math library:
Use either openblas (for intel or AMD) or ACML (for AMD).

• To set up Openblas, see here:
 http://verahill.blogspot.com.au/2013/05/423-openblas-on-debian-wheezy.html

• To set up ACML, see here:
 http://verahill.blogspot.com.au/2013/05/422-set-up-acml-on-linux.html

---

My GabEdit/Python NWChem patch
This is NOT the patch alluded to in the 23 May update and is optional. It enables python support, and makes the output more verbose so that gabedit can be used as an alternative to ECCE. Hence, it is required if, but only if, you want to enable python and to be able to use GabEdit to open output files.

First create a patch file, e.g. diff.patch.

diff -rupN src.original/config/makefile.h src/config/makefile.h
--- src.original/config/makefile.h 2013-04-15 12:41:45.016853322 +1000
+++ src/config/makefile.h 2013-04-15 12:38:44.933319544 +1000
@@ -2039,7 +2039,7 @@ endif
 
      ifeq ($(BUILDING_PYTHON),python)
 #   EXTRA_LIBS += -ltk -ltcl -L/usr/X11R6/lib -lX11 -ldl
-     EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl
+     EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl -lssl -lz
   LDOPTIONS = -Wl,--export-dynamic 
      endif
 ifeq ($(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 2013-04-15 12:41:45.036852381 +1000
+++ src/ddscf/movecs_pr_anal.F 2013-04-15 12:23:28.100409225 +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 2013-04-15 12:41:45.036852381 +1000
+++ src/ddscf/rohf.F 2013-04-15 12:23:28.100409225 +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 2013-04-15 12:41:45.036852381 +1000
+++ src/ddscf/scf_vec_guess.F 2013-04-15 12:23:28.100409225 +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 2013-04-15 12:41:45.036852381 +1000
+++ src/ddscf/uhf.F 2013-04-15 12:23:28.096409414 +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 2013-04-15 12:41:45.000854073 +1000
+++ src/mcscf/mcscf.F 2013-04-15 12:23:23.748613695 +1000
@@ -719,7 +719,7 @@ 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 2013-04-15 12:41:45.604825677 +1000
+++ src/nwdft/scf_dft/dft_mxspin_ovlp.F 2013-04-15 12:23:28.228403211 +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 2013-04-15 12:41:45.608825490 +1000
+++ src/nwdft/scf_dft/dft_scf.F 2013-04-15 12:23:28.228403211 +1000
@@ -1774,7 +1774,7 @@ c
             else
                blob='DFT Final Beta Molecular Orbital Analysis' 
             endif
-            call movecs_print_anal(ao_bas_han, ilo, ihi, 0.15d0, 
+            call movecs_print_anal(ao_bas_han, ilo, ihi, 0.01d0, 
      &           g_movecs(ispin), 
      &           blob, 
      &           .true., dbl_mb(k_eval(ispin)), oadapt, 
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 2013-04-15 12:41:45.612825303 +1000
+++ src/nwdft/scf_dft_cg/dft_cg_solve.F 2013-04-15 12:23:28.220403588 +1000
@@ -183,7 +183,7 @@ 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),

---

Compile NWChem
This examples uses the ACML libs. See e.g. this post for openblas settings.

sudo apt-get install build-essential gfortran python2.7-dev libopenmpi-dev openmpi-bin
sudo mkdir /opt/nwchem
sudo chown $USER:$USER /opt/nwchem
cd /opt/nwchem/
wget http://www.nwchem-sw.org/download.php?f=Nwchem-6.3-src.2013-05-17.tar.gz
mv download.php\?f\=Nwchem-6.3-src.2013-05-17.tar.gz Nwchem-6.3-src.2013-05-17.tar.gz
tar xvf Nwchem-6.3-src.2013-05-17.tar.gz
cd nwchem-6.3-src.2013-05-17/
patch -p0 < diff.patch

patching file src/config/makefile.h
patching file src/ddscf/movecs_pr_anal.F
patching file src/ddscf/rohf.F
patching file src/ddscf/scf_vec_guess.F
patching file src/ddscf/uhf.F
patching file src/mcscf/mcscf.F
patching file src/nwdft/scf_dft/dft_mxspin_ovlp.F
patching file src/nwdft/scf_dft/dft_scf.F
patching file src/nwdft/scf_dft_cg/dft_cg_solve.F

cd src/
wget http://www.nwchem-sw.org/images/Iswtch.patch.gz
gzip -d Iswtch.patch
patch -p0 < Iswtch.patch
cd ../
export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export BLASOPT="-L/opt/acml/acml5.3.1/gfortran64_int64/lib -lacml"

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/acml/acml5.3.1/gfortran64_int64/lib"
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"

export ARMCI_NETWORK=SOCKETS

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
./getmem.nwchem

---

Settings
Create /opt/nwchem/default.nwchemrc

nwchem_basis_library /opt/nwchem/nwchem-6.3-src.2013-05-17/src/basis/libraries/
ffield amber
amber_1 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_s/
amber_2 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_x/
amber_3 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_q/
amber_4 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_u/
amber_5 /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/custom/
spce /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/solvents/spce.rst
charmm_s /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/charmm_s/
charmm_x /opt/nwchem/nwchem-6.3-src.2013-05-17/src/data/charmm_x/

Symmlink to this file in each user's home:

ln -s /opt/nwchem/default.nwchemrc ~/.nwchemrc

423. Openblas on Debian Wheezy

Update 23 May 2013: the url for the openblas tarball has been updated and a tab has been removed from the lapack url.

Note that the links to the openblas file tends to die after a while, so you might have to download it manually.

Original post:
I need more modular posts. I've covered how to build openblas several times before, but I need a simple post I can use as a reference. So here it is:

openblas

sudo mkdir /opt/openblas
sudo chown ${USER} /opt/openblas
cd ~/tmp
wget http://github.com/xianyi/OpenBLAS/tarball/v0.2.6

tar xvf v0.2.6
cd xianyi-OpenBLAS-87b4d0c

wget http://www.netlib.org/lapack/lapack-3.4.1.tgz
make all BINARY=64 CC=/usr/bin/gcc FC=/usr/bin/gfortran USE_THREAD=0 INTERFACE64=1 1> make.log 2>make.err
make PREFIX=/opt/openblas install

nm: '/lib/libpthread.so*': No such file
make -j 2 -f Makefile.install install
make[1]: Entering directory `/home/me/tmp/xianyi-OpenBLAS-87b4d0c'
Generating openblas_config.h in /opt/openblas/include
Generating f77blas.h in /opt/openblas/include
Generating cblas.h in /opt/openblas/include
Copying LAPACKE header files to /opt/openblas/lib
Copy the static library to /opt/openblas/lib
cp: cannot stat `libopenblas_opteronp-r0.2.6.a': No such file or directory
make[1]: *** [install] Error 1
make[1]: Leaving directory `/home/me/tmp/xianyi-OpenBLAS-87b4d0c'
make: *** [install] Error 2

Don't worry about the errors -- as long as you have libopenblas_PROCESSOR_rX.X.X.so, you're fine.

cp lib*.* /opt/openblas/lib

add

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openblas/lib

to your ~/.bashrc, and/or add

/opt/openblas/lib

to your /etc/ld.so.conf

399. Looking at speeding up (re)boot on debian wheezy.

I'd be interested in getting my beowulf cluster nodes to boot a little bit faster -- (re)boots of the nodes very are infrequent, but the front node doubles as my work desktop and is normally rebooted at least once per month (kernel upgrades etc.) -- rebooting the front node makes me nervous, however, and the faster it boots, the better it is.

I should probably build a low-powered front node specifically for my cluster though...but that takes money, and money takes time.

Anyway, boot. In spite of the impetus for this post I'm testing this on my laptop which has wheezy, gnome 3.4 and an SSD -- it's not that representative of the target system and I'll have to repeat this on a normal desktop with a spinning hdd at a later stage.

I'm more or less following http://wiki.debian.org/BootProcessSpeedup. Note that insserv seems to be set up and enabled by default in Wheezy.

---

Timing it -- Setting up bootchart2
I first tried to define boot times arbitrarily as the time from me hitting enter in GRUB, to the visual appearance of the log-in prompt in GDM3, but it was too imprecise (up to +- 2) relative to the time a boot took (ca 9-10s).

I ended up installing bootchart and bootchart-view instead.

sudo apt-get install bootchart2

Then edit /etc/default/grub as shown here:

GRUB_CMDLINE_LINUX_DEFAULT="quiet initcall_debug printk.time=y init=/sbin/bootchartd"

and run

sudo update-grub

After a boot, run

pybootchartgui
eog bootchart.png

You'll get something like this:

Look at the top, right above the first chart -- it says 'time: 6.61s'. I'll use that as the metric.

Most of the time bootchart2 worked fine, but for the odd boot the /var/log/bootchart.tgz wasn't accepted by pybootchartgui.

---

Normal boot, pre-optimisation: 
'Cold' reboots: 6.61, 5.77 seconds
Warm* reboots: 6.46, 5.79, 5.97 seconds

*using shutdown -r now

The variability is very high -- there's almost a second between the fastest and slowest boots. Keep that in mind when looking at the numbers later on.

---

Using readahead-fedora to pre-load files

sudo apt-get install readahead-fedora

After install, readhead-early, -late and stop were enabled in rcconf.

The first boot took over 7 seconds, but later boots were typically around 6 seconds or faster. Note that readahead is solving an issue which isn't really present when using high bandwidth SSDs, and may even slow things down under conditions where you use an SSD or a spinning disk with a high rpm (e.g. >7200 rpm)

First run

'normal' run

Not exactly an improvement. Looking at /etc/readahead.d/custom.early shows that the wrong kernel files are loaded -- I'm using a custom kernel (3.8.5-ck1) but the stock kernel files are loaded (3.2.0-4). I edited custom.early to point towards my current kernel, and then did a warm reboot.

---

Speeding up reboots -Kexec

sudo apt-get install kexec-tools

Shutdown your computer once, then boot up. After that first time you can do warm reboots (sudo shutdown -r now) without going through the BIOS and grub stages. The only -- visible -- downside is that your screen will go crazy for a few seconds as the running kernel is being overwritten by the new kernel (I presume). Doesn't look pretty, but reboot is fast.

I couldn't get bootchart to time the hot reboots, but they look 'fast'.

---

I'll be repeating this on a system with a spinning disk at a later stage.

391. encfs on debian testing

Truecrypt is nice and all, but the way it's managed is a bit un-linux like. It IS open source though, but because it isn't completely clear who the maintainers are, and while the source code is probably safe to use, most people use pre-built binaries -- just because it's open source doesn't mean that the binaries are built from that source. I'm happy with truecrypt, but if we're going to be paranoid, we might as well go all the way. Also, it would be nice with an encryption tool which can be installed from the repos, and as a binary built by a trusted party (i.e. the debian maintainers).

Note that truecrypt wins hands down on features -- as always, pick the tool that does the job.

encfs is a well-established encryption tool for linux systems and is available in most distro repos -- it does encryption of files, and while it lacks many of the options of truecrypt, it is useful for encrypting directory structures.

Installation

sudo apt-get install encfs

Yes, that's it. If you're having issues, make sure that fuse is installed, and that you belong to the group fuse (too add, do sudo usermod -a -G fuse $USER . To check do cat /etc/group|grep fuse)

---

Set-up
Set-up is equally easy.

 encfs ~/.secret ~/encrypted

The directory "/home/me/encrypted" does not exist. Should it be created? (y,n) Y
Creating new encrypted volume.
Please choose from one of the following options:
 enter "x" for expert configuration mode,
 enter "p" for pre-configured paranoia mode,
 anything else, or an empty line will select standard mode.
?> 

Standard configuration selected.

Configuration finished. The filesystem to be created has
the following properties:
Filesystem cipher: "ssl/aes", version 3:0:2
Filename encoding: "nameio/block", version 3:0:1
Key Size: 192 bits
Block Size: 1024 bytes
Each file contains 8 byte header with unique IV data.
Filenames encoded using IV chaining mode.
File holes passed through to ciphertext.

Now you will need to enter a password for your filesystem.
You will need to remember this password, as there is absolutely
no recovery mechanism. However, the password can be changed
later using encfsctl.

New Encfs Password: 
Verify Encfs Password: 

At the end of this your encryption folder will be mounted.

---

How it works:
A (to me) nice way of illustrating how it works is the following:

ls ~/encrypted/ -lah

total 24K
drwxr-xr-x   2 me me 4.0K Apr 18 14:29 .
drwxr-xr-x 212 me me  20K Apr 18 14:29 ..

ls ~/.secret/ -lah

total 32K
drwxr-xr-x   2 me me 4.0K Apr 18 14:29 .
drwxr-xr-x 212 me me  20K Apr 18 14:29 ..
-rw-r--r--   1 me me 1.1K Apr 18 14:29 .encfs6.xml
-rw-r--r--   1 me me  411 Nov 14  2011 .passwd.gpg
touch ~/encrypted/test
ls ~/encrypted/ -lah

total 24K
drwxr-xr-x   2 me me 4.0K Apr 18 14:32 .
drwxr-xr-x 212 me me  20K Apr 18 14:29 ..
-rw-r--r--   1 me me    0 Apr 18 14:32 test

ls ~/.secret/ -lah

total 32K
drwxr-xr-x   2 me me 4.0K Apr 18 14:32 .
drwxr-xr-x 212 me me  20K Apr 18 14:29 ..
-rw-r--r--   1 me me 1.1K Apr 18 14:29 .encfs6.xml
-rw-r--r--   1 me me    0 Apr 18 14:32 IfSGAzSkFsuN2A,SpPmnKSYu
-rw-r--r--   1 me me  411 Nov 14  2011 .passwd.gpg

df -h

encfs                                                   734G  525G  172G  76% /home/me/encrypted

In other words, anything that is put into ~/encrypted ends up as an encrypted file in ~/.secret. It's a little bit different from truecrypt, which uses a filesystem container -- this is more similar to encrypting each file with gpg/pgp, just with a good way of managing it from a filesystem pov.

Also, this means that you don't have to dedicate a certain amount of space to the encrypted file system as you would have to with truecrypt.

Anyway, unmount ~/encrypted and no-one will have access to the decrypted forms of the files.

sudo umount ~/encrypted

To mount it again, just do

encfs ~/.secret ~/encrypted

You can change the name of the directory you want to mount it in.

It is also possible to mount automatically on boot, but this would defeat most purposes of encrypting in the first place.

365. Compile firefox 19 on Debian Testing/Wheezy

There are issues with the official firefox binary since it's a 32 bit build and Wheezy isn't handling multiarch properly yet (plenty of conflicts between 32 and 64 bit packages)

So here's how to build a proper 64 bit firefox 19 on debian testing:

sudo apt-get install bzip2 build-essential python zip unzip pkg-config libgtk2.0-dev gconf2 libdbus-1-dev libdbus-glib-1-dev yasm libasound2-dev libcurl4-gnutls-dev libxt-dev mesa-common-dev
mkdir ~/tmp/firefox -p
cd ~/tmp/firefox
wget ftp://ftp.mozilla.org/pub/firefox/releases/19.0.2/source/firefox-19.0.2.source.tar.bz2
rm mozilla-release -rf
tar xvf firefox-19.0.2.source.tar.bz2
mkdir buildfirefox19/
cd buildfirefox19/
../mozilla-release/./configure --prefix=$HOME/.firefox19
make
make install
echo "alias firefox19='$HOME/.firefox19/bin/firefox'" >> $HOME/.bashrc
source $HOME/.bashrc

Start by running firefox19 from the terminal.

363. Generating an image in PyMol

For some reason I needed to quickly generate a publication quality figure of a protein.

Deep View (SWiss PDB viewer) isn't available for linux anymore, and the old versions rely on 32 bit libs (which is increasingly a headache on debian). Rasmol is a classic, but I haven't used it properly since 1997 -- and all attempts at exporting png, jpg etc. failed on my debian wheezy box.

Jmol is awesome, and while I managed to make some pretty convincing figures I never quite got to where I wanted.

So I tried pymol

Pymol, like rasmol and jmol, has a visual interface which can be controlled via an integrated terminal. The learning curve is steep, but it's quick and easy to make figures once you've got the basics.

---

Install pymol from the repos in debian:
sudo apt-get install pymol

(on Archlinux you can get it via AUR  -- you'll need to install python-pmw first)

Download 1SU4.pdb from here http://www.rcsb.org/pdb/explore.do?structureId=1su4

In the directory where your pdb file is, do

pymol 1SU4.pdb

select helices, chain A

Click on the A(ction) by (helices), select preset/publication.

 select calcium, (res 995-996)
 show spheres, calcium

 Note that 'helices' and 'calcium' are just handles or aliases that I made up.

 alter calcium, vdw=5
 show spheres, calcium

 color purple calcium
 bg_color white

 set antialias=1
 set sphere_mode=5

where sphere_mode 5 means shading.

 ray 1000,1000

 save 1SU4.png

And here's the final figure:

342. Compiling Kernel 3.8 on Debian Testing/Wheezy

NOTE: It seems like series 3.8 has issues with intel (i915) graphics -- it occasionally generates kworker threads that causes unresponsiveness as seen by slow mouse and keyboard response when e.g. plugging or unplugging mains power. No issues on e.g. nvidia though.
http://verahill.blogspot.com.au/2013/03/368-slow-mouse-and-keyboard-triggered.html
http://forums.gentoo.org/viewtopic-p-7278760.html
https://bbs.archlinux.org/viewtopic.php?pid=1248190

Post:

Kernel 3.8 is out now. Not much to say -- the compilation works well using the standard method. The compressed kernel is about 81 Mb to download.

The approach below shows how to compile the kernel on Debian. If you're interested in a more generic approach, see this post: http://verahill.blogspot.com.au/2013/02/344-compile-kernel-38-without-using-kpkg.html

NOTE: kernel 3.8 -- in contrast to the 3.7 series -- now compiles fine on AMD FX 8150.

NOTE: kernel 3.8 plays well with nvidia dkms

Here we go:

sudo apt-get install kernel-package fakeroot build-essential ncurses-dev
mkdir ~/tmp
cd ~/tmp
wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.8.tar.bz2
tar xvf linux-3.8.tar.bz2
cd linux-3.8/
cat /boot/config-`uname -r`>.config
make oldconfig

You will be asked a lot of questions -- how many depends on what version you upgrade from. If in doubt, pick the default answer (i.e. hit enter). If really in doubt, use google.

Then continue:

make-kpkg clean

Do

make menuconfig

if you want to make any specific changes to the kernel (e.g. add support for certain devices)

Then continue:

time fakeroot make-kpkg -j4 --initrd kernel_image kernel_headers

As usual 4 is the number of threads you wish to launch -- make it equal to the number of cores that you have for optimum performance during compilation (more about that here).

The build takes around 20 minutes on a four-core intel i5-2400 with -j4, and 14 minutes on an fx-8150 with -j8 (96 minutes with -j1).

Install:

sudo dpkg -i ../linux-image-3.8.0_3.8.0-10.00.Custom_amd64.deb ../linux-headers-3.8.0_3.8.0-10.00.Custom_amd64.deb

---

New stuff/Questions:

Offload RCU callback processing from boot-selected CPUs (RCU_NOCB_CPU) [N/y/?] (NEW) *
Memory placement aware NUMA scheduler (NUMA_BALANCING) [N/y/?] (NEW) *
Enable to assign a node which has only movable memory (MOVABLE_NODE) [N/y/?] (NEW)
Allow for memory hot-add (MEMORY_HOTPLUG) [Y/n] y
Allow for balloon memory compaction/migration (BALLOON_COMPACTION) [Y/n/?] (NEW)
Set default setting of cpu0_hotpluggable (BOOTPARAM_HOTPLUG_CPU0) [N/y/?] (NEW
Debug CPU0 hotplug (DEBUG_HOTPLUG_CPU0) [N/y/?] (NEW)
ACPI tables can be passed via uncompressed cpio in initrd (ACPI_INITRD_TABLE_OVERRIDE) [N/y/?] (NEW)
Support multiple cpuidle drivers (CPU_IDLE_MULTIPLE_DRIVERS) [N/y/?] (NEW)
"NOTRACK" target support (DEPRECATED) (NETFILTER_XT_TARGET_NOTRACK) [N/m] (NEW

Default SCTP cookie HMAC encoding
  > 1. Enable optional MD5 hmac cookie generation (SCTP_DEFAULT_COOKIE_HMAC_MD5) (NEW)
    2. Enable optional SHA1 hmac cookie generation (SCTP_DEFAULT_COOKIE_HMAC_SHA1) (NEW)
    3. Use no hmac alg in SCTP cookie generation (SCTP_DEFAULT_COOKIE_HMAC_NONE) (NEW)
  choice[1-3?]:   Enable optional MD5 hmac cookie generation (SCTP_COOKIE_HMAC_MD5) [Y/?] (NEW) y

Enable optional SHA1 hmac cookie generation (SCTP_COOKIE_HMAC_SHA1) [N/y/?] (NEW) *
Enable optional MD5 hmac cookie generation (SCTP_COOKIE_HMAC_MD5) [Y/?] (NEW) y
Distributed ARP Table (BATMAN_ADV_DAT) [N/y/?] (NEW)
Kvaser CAN/USB interface (CAN_KVASER_USB) [N/m/?] (NEW)
LSI MPT Fusion SAS 3.0 Device Driver (SCSI_MPT3SAS) [N/m/?] (NEW)
Chelsio Communications FCoE support (SCSI_CHELSIO_FCOE) [N/m/?] (NEW) *
Marvell 88E6060 ethernet switch chip support (NET_DSA_MV88E6060) [N/m/y/?] (NEW)
Marvell 88E6085/6095/6095F/6131 ethernet switch chip support (NET_DSA_MV88E6131) [N/m/y/?] (NEW)
Marvell 88E6123/6161/6165 ethernet switch chip support (NET_DSA_MV88E6123_61_65) [N/m/y/?] (NEW) *
Cadence devices (NET_CADENCE) [Y/n/?] (NEW)
AT91RM9200 Ethernet support (ARM_AT91_ETHER) [N/m/y/?] (NEW)
Cadence MACB/GEM support (MACB) [N/m/y/?] (NEW)
Broadcom devices (NET_VENDOR_BROADCOM) [Y/?] y
Marvell MDIO interface support (MVMDIO) [N/m/y/?] (NEW)
CDC MBIM support (USB_NET_CDC_MBIM) [N/m/?] (NEW)
Atheros Wireless Cards (ATH_CARDS) [N/m/?] (NEW)
Atheros AR5523 wireless driver support (AR5523) [N/m/?] (NEW)
Wilocity 60g WiFi card wil6210 support (WIL6210) [N/m/?] (NEW) *
Realtek RTL8723AE PCIe Wireless Network Adapter (RTL8723AE) [N/m/?] (NEW)
ARC UART driver support (SERIAL_ARC) [N/m/y/?] (NEW) *
CBUS I2C driver (I2C_CBUS_GPIO) [N/m/?] (NEW)
TS-5500 DIO blocks and compatibles (GPIO_TS5500) [N/m/y/?] (NEW) 
TI BQ2415x battery charger driver (CHARGER_BQ2415X) [N/m/?] (NEW)
Board level reset or power off (POWER_RESET) [N/y/?] (NEW) *

 Default Thermal governor
  > 1. step_wise (THERMAL_DEFAULT_GOV_STEP_WISE) (NEW)
    2. fair_share (THERMAL_DEFAULT_GOV_FAIR_SHARE) (NEW)
    3. user_space (THERMAL_DEFAULT_GOV_USER_SPACE) (NEW)
  choice[1-3?]:   Fair-share thermal governor (FAIR_SHARE) [N/y/?] (NEW)

Step_wise thermal governor (STEP_WISE) [Y/?] (NEW) y
User_space thermal governor (USER_SPACE) [N/y/?] (NEW)
SSB GPIO driver (SSB_DRIVER_GPIO) [N/y/?] (NEW) *
BCMA GPIO driver (BCMA_DRIVER_GPIO) [N/y/?] (NEW)
Support for Realtek PCI-E card reader (MFD_RTSX_PCI) [N/m/y/?] (NEW)
TI ADC / Touch Screen chip support (MFD_TI_AM335X_TSCADC) [N/m/y/?] (NEW)
Support for Nano River Technologies Viperboard (MFD_VIPERBOARD) [N/m/?] (NEW)
Support for Retu multi-function device (MFD_RETU) [N/m/?] (NEW) *
Maxim MAX8973 voltage regulator  (REGULATOR_MAX8973) [N/m/?] (NEW)
TI TPS51632 Power Regulator (REGULATOR_TPS51632) [N/m/?] (NEW)
Siano SMS1xxx based MDTV receiver (SMS_USB_DRV) [N/m/?] (NEW)
Siano SMS1xxx based MDTV via SDIO interface (SMS_SDIO_DRV) [N/m/?] (NEW)   *
Stanton Control System 1 MIDI (SND_SCS1X) [N/m/?] (NEW) *
ION iCade arcade controller (HID_ICADE) [N/m/?] (NEW)
HID over I2C transport layer (I2C_HID) [N/m/?] (NEW) *
Renesas R-Car USB phy support (USB_RCAR_PHY) [N/m/?] (NEW)   *
SDHCI support for ACPI enumerated SDHCI controllers (MMC_SDHCI_ACPI) [N/m/?] (NEW)
NXP PCF8523 (RTC_DRV_PCF8523) [N/m/?] (NEW)
Philips PCF8563/Epson RTC8564 (RTC_DRV_PCF8563) [M/n/?] m
Userspace platform driver with generic irq and dynamic memory (UIO_DMEM_GENIRQ) [N/m/?] (NEW)
Microsoft Hyper-V Balloon driver (HYPERV_BALLOON) [N/m/?] (NEW) *
SystemBase PCI Multiport UART (SB105X) [N/m/y/?] (NEW)
TTY over Firewire (FIREWIRE_SERIAL) [N/m/?] (NEW) *
F2FS filesystem support (EXPERIMENTAL) (F2FS_FS) [N/m/y/?] (NEW) *
Enable CIFS debugging routines (CIFS_DEBUG) [Y/n/?] (NEW)
Simplified Mandatory Access Control Kernel Support (SECURITY_SMACK) [N/y/?] (NEW)
Camellia cipher algorithm (x86_64/AES-NI/AVX) (CRYPTO_CAMELLIA_AESNI_AVX_X86_64) [N/m/y/?] (NEW)

---

Links to this post:
http://forum.notebookreview.com/lenovo/575569-linux-x220-41.html
http://www.reddit.com/r/CrunchBang/comments/196zx5/whats_the_best_way_to_install_a_new_kernel_in/
http://www.lubuntu.ru/forum/viewtopic.php?t=1125
http://forums.linuxmint.com/viewtopic.php?f=143&p=711457
https://www.linux.org.ru/forum/linux-install/9128362
http://stackoverflow.com/questions/16573913/compile-new-kernel-on-debian-wheezy
http://crunchbang.org/forums/viewtopic.php?id=26825
http://mygoodluck.org/debian-obnovil-yadro-do-38

328. Liberate your router: dd-wrt on Netgear WGT624 v4

UPDATE 1 Feb 2013: I haven't had any explicit problems with my router since flashing it. Everything is apparently working well and my network connection is reliable and fine (if only subjectively a bit slower than before --  running a speed test shows that it's as fast as ever so not sure what's happening). HOWEVER, I've suddenly started having issues with ECCE and submitting jobs via a frontendMachine -- I kept getting "cannot 'cd' to run directory" errors, but the ECCE log contains no errors messages at all. This wouldn't happen for very small NWChem input files, and it would happen ca 80% of the time. Normally I wouldn't suspect this was a router issue, but changing back to my (unflashed) AR430W resolved the issues immediately. Somehow I suspect this is a router version of this http://verahill.blogspot.com.au/2012/09/briefly-packet-corrupt-during-ssh.html, but then I should see error messages in the ECCE log...

Other than that I'm really happy with dd-wrt (no sarcasm intended -- I've had no other issues and I love the power dd-wrt gives me over my hardware).

Finally, there's the old adage about correlation vs causuality. We'll see if the errors start popping up again while using my AR430W.

Original post:

I've been using Tomato with my WRT54G for a couple of years now, and I'm incredibly happy with it. Since I have a couple of old routers (airlink 1010 ar430w and netgear wgt624 v4) with stock firmware lying around I figured it was time to turn them into something useful. So here's how to flash the netgear router. If it stands up to sustained use I'll be writing an AR430W guide later.

dd-wrt

Lengthy preamble
The stock firmware basically does nothing for me -- it's clunky, slow, and there's no terminal access. In particular, I want busybox/ssh, Tomato does all that for me, but it doesn't support a particularly wide range of routers (I reckon that Tomato is the reason why Linksys WRT54GL still costs $90 in Australia, in spite of being old as sin -- those who doubt the value of opening up their hardware may want to consider the RoI on that one)

In addition to Tomato, there's also DD-WRT (supported devices) and OpenWRT (supported devices). DD-WRT support a huge number of routers, but it appears to be a whole lot more complicated to install than Tomato. Maybe this varies according to the router as well.

For instructions you're referred via the database to the dd-wrt forum thread about your router. The problem with this is that you'll be facing 30-odd pages with instructions, problems, dead-ends etc. Some threads end with a step-by-step summary on how to install dd-wrt, but not all do.

Anyway, here's my best attempt at writing a simple and complete step-by-step guide to replacing the stock firmware on Netgear WGT24 v4 with DD-WRT on Debian Testing/Wheezy. I'm basically just following this blog post: http://lauriaus.no-ip.org/blog/?p=90 , but hopefully I've added enough detail to make it possible for just about anyone to follow this guide.

Please consult http://www.dd-wrt.com/site/support/router-database to see what files you need. NOTE: the files below only apply to v4 of Netgear WGT624. Installing them on any other router may brick it.

---

On your linux computer:

Get the files:

sudo apt-get install atftpd tftp putty
cd /tmp
mkdir ftpdboot
cd ftpdboot/
wget http://www.dd-wrt.com/dd-wrtv2/downloads/others/redboot_collection/images_default/redboot_ap61_16M_4M_admtek.rom
wget http://www.dd-wrt.com/routerdb/de/download/Netgear/WGT624/v4/linux.bin/3614 -O linux.bin
wget http://www.dd-wrt.com/routerdb/de/download/Netgear/WGT624/v4/wgt624v4-firmware.bin/3613 -O wgt624v4-firmware.bin

Edit /etc/default/atftpd:

USE_INETD=false #true
OPTIONS="--tftpd-timeout 300 --retry-timeout 5 --mcast-port 1758 --mcast-addr 239.239.239.0-255 --mcast-ttl 1 --maxthread 100 --verbose=5 /tmp/ftpdboot"

Edit /etc/inetd.conf

32 tftp        dgram   udp4    wait    nobody /usr/sbin/tcpd /usr/sbin/in.tftpd --tftpd-timeout 300 --retry-timeout 5 --mcast-port 1758 --mcast-addr      239.239.239.0-255 --mcast-ttl 1 --maxthread 100 --verbose=5 /tmp/ftpdboot

and do

sudo /etc/init.d/openbsd-inetd reload

for good luck. If you don't have openbsd-inetd you may have xinetd or inetutils-inetd installed instead (I think openbsd-inetd is default on debian). Edit the command as necessary.

Edit your /etc/network/interfaces file:

auto eth0
iface eth0 inet static
address 192.168.1.155
gateway 192.168.1.1
netmask 255.255.255.0

and run

sudo service networking restart

Make sure that your card came up ok (do e.g. ip addr)

2: eth0: broadcast mtu 1500 qdisc pfifo_fast state UP qlen 1000 link/ether 00:26:9e:27:9b:20 brd ff:ff:ff:ff:ff:ff inet 192.168.1.155/24 brd 192.168.1.255 scope global eth0

Continue.

Prepare two terminals, side by side (or start a screen session with two tabs open). In one, type

echo "^C"> end.txt
putty telnet 192.168.1.1:9000 -m end.txt

But don't hit enter after the second command.

In the other terminal, type

ping 192.168.1.1

but don't hit enter.

Connect the ethernet port on your computer to one of the ethernet LAN ports (not WAN/Internet) on your router.

You are next going to unplug the power from the router, and hit enter after the ping command. Immediately when you get ping replies:

64 bytes from 192.168.1.1: icmp_req=4 ttl=64 time=0.371 ms

you hit enter after the putty command in the other window. If nothing good happens, then redo (i.e. unplug the router, hit enter after the ping command etc. Don't start the ping until you're re-plugged the router).

Ready? GO!

ping 192.168.1.1

64 bytes from 192.168.1.1: icmp_req=1 ttl=64 time=0.371 ms

putty telnet 192.168.1.1:9000 -m end.txt

And you should get

Before you continue make sure that you've opened up your firewall e.g. if you're not connected to the internet you can go crazy like this:

sudo iptables -P INPUT ACCEPT
sudo iptables -P OUTPUT ACCEPT
sudo iptables -P FORWARD ACCEPT

And don't forget to restore your firewall once you're done.
Time to get dangerous.

RedBoot> fis init

About to initialize [format] FLASH image system - continue (y/n)? Y
*** Initialize FLASH Image System
... Erase from 0xbffe0000-0xbfff0000: .
... Program from 0x80ff0000-0x81000000 at 0xbffe0000: .
RedBoot> ip_address -h 192.168.1.155
IP: 192.168.1.1/255.255.255.0, Gateway: 192.168.1.254
Default server: 192.168.1.155

RedBoot> load -r -b %{FREEMEMLO} redboot_ap61_16M_4M_admtek.rom

Using default protocol (TFTP)
TFTP timed out 1/15
Can't load 'redboot_ap61_16M_4M_admtek.rom': operation timed out

Try again:
RedBoot> load -r -b %{FREEMEMLO} redboot_ap61_16M_4M_admtek.rom

Using default protocol (TFTP)
Raw file loaded 0x80040c00-0x8005007f, assumed entry at 0x80040c00


RedBoot> fis create -l 0x30000 -e 0xbfc00000 RedBoot                                                                                         
                                        fis create -l 0x30000 -e 0xbfc00000 RedBoot
An image named 'RedBoot' exists - continue (y/n)? y
... Erase from 0xbfc00000-0xbfc30000: ...
... Program from 0x80040c00-0x80050080 at 0xbfc00000: .
... Erase from 0xbffe0000-0xbfff0000: .
... Program from 0x80ff0000-0x81000000 at 0xbffe0000: .

RedBoot> reset

You'll see a couple of flashing lights on the router as the only indication that something just happened. Kill your current putty connection and start a new one.

=~=~=~=~=~=~=~=~=~=~=~= PuTTY log 2013.01.28 20:29:38 =~=~=~=~=~=~=~
^C

RedBoot> fis init

About to initialize [format] FLASH image system - continue (y/n)? y
*** Initialize FLASH Image System
... Erase from 0xbffe0000-0xbfff0000: .
... Program from 0x80ff0000-0x81000000 at 0xbffe0000: .

RedBoot> ip_address -h 192.168.1.155

IP: 192.168.1.1, Default server: 192.168.1.155

RedBoot> load -r -b 0x80041000 linux.bin

Using default protocol (TFTP)
Raw file loaded 0x80041000-0x803ecfff, assumed entry at 0x80041000

RedBoot> fis create linux

Be patient -- this step takes a long time: 19 minutes in my case (some routers take an hour). Write down the time when it starts and WAIT at least 20 minutes.

... Erase from 0xbfc10000-0xbffbc000: ...........................................................
... Program from 0x80041000-0x803ed000 at 0xbfc10000: ...........................................................
... Erase from 0xbffe0000-0xbfff0000: .
... Program from 0x80ff0000-0x81000000 at 0xbffe0000: .

RedBoot> fconfig

Run script at boot: true
Boot script: 
.. fis load -l kernel
.. go
Enter script, terminate with empty line

>> fis load -l linux
>> exec
>> 
Boot script timeout (1000ms resolution): 12  
Use BOOTP for network configuration: false
bootp_my_gateway_ip: 192.168.1.254
Local IP address: 192.168.1.1
bootp_my_ip_mask: 255.255.255.0
Default server IP address: 192.168.1.55
Console baud rate: 9600
GDB connection port: 9000
Force console for special debug messages: false
net_debug: false
Update RedBoot non-volatile configuration - continue (y/n)? y
... Erase from 0xbffe0000-0xbfff0000: .
... Program from 0x80ff0000-0x81000000 at 0xbffe0000: .
RedBoot> reset

Done!

You can now navigate to 192.168.1.1 in your router, but unplug, replug the router for good luck.

Success!

I created a user called admin and set a password i.e. there's no pw or username you need to know a priori.

click on services

check sshd

Don't trust important infrastructure with passwords. Use keys.

And finally

ssh root@192.168.1.1

and hopefully you're in.

---

First impressions:
The busybox ('linux') version is a bit too sparse for my liking -- no netstat command...but it's still obviously a major step up from the stock firmware. dd-wrt is different from tomato -- if you're used to one you're not necessarily going to feel comfortable with the other. Luckily, dd-wrt is widely used and there are plenty of resource online. In addition, there's a demo ( http://www.dd-wrt.com/demo/ ) so you can try it out before installing it.

How to set up 'static' dhcp (i.e. make sure that some computers always have the same IP address while still running a dhcp server) wasn't completely obvious either, but this post helped: http://www.dd-wrt.com/wiki/index.php/Static_DHCP