161. Compiling Me-TV 1.4 on debian testing/wheezy

Quite some time ago me-tv crapped out on me (it's working again as of 9 Jan 2013). While good things came out of it (set up vlc with dvb -- and the image quality is much better for some reason) me-tv does the whole EPG thing really well -- and VLC doesn't really.

[Edit: note that me-tv isn't actively developed anymore: https://answers.launchpad.net/me-tv/+question/216266.]

This 'guide' will put your metv in your home directory and won't interfere with the debian package version. --prefix is your friend, always.

me-tv 1.3.7-2 

Anyway, here's how to compile me-tv v 1.4.0.9

Start here
sudo apt-get install gnome-common libglibmm-2.4-dev libxml++2.6-dev libgtkmm-2.4-dev libgconfmm-2.6-dev libunique-dev libvlc-dev libgstreamer0.10-dev libgstreamer-plugins-base0.10-dev libsqlite3-dev libdbus-glib-1-dev

You'll probably need more than what I've shown above -- intltool, automake etc. But those packages were the ones that were missing on my particular system. As always, if a package is missing, do
aptitude search package|grep dev
and chances are that you find what you're looking for

Continuing...
mkdir ~/tmp
cd ~/tmp
wget https://launchpad.net/me-tv/1.4/1.4.0/+download/me-tv-1.4.0.9.tar.gz
tar xvf me-tv-1.4.0.9.tar.gz
cd me-tv-1.4.0.9/
./autogen.sh --prefix=/home/${USER}/.metv-1.4.0.9

Configure summary:
        Source code location .......: .
        Compiler ...................: gcc
        Compiler flags .............:  -O0 -g
        Enable compile warnings ....: minimum
        Enable more warnings .......: yes
        Extra Compiler Warnings ....: -g -O2 -Wall -Wno-unused  -Wextra -Wcast-align -Wcast-qual -Wcomment -Wformat -Wimplicit -Wmissing-braces -Wpacked -Wparentheses -Wpointer-arith -Wreturn-type -Wsequence-point -Wstrict-aliasing -Wstrict-aliasing=2 -Wswitch-default -Wundef
        Debug support ..............: yes
        Installing into prefix .....: /home/me/.metv-1.4.0.9
Type make to build Me TV 1.4.0.9

Now type `make' to compile Me TV

Who am I to argue with that?
make
make install 

Add ~/.metv-1.4.0.9/bin/ to your PATH
echo 'export PATH=$PATH:/home/${USER}/.metv-1.4.0.9/bin'>>~/.bashrc

(important that you use ' and not " )

Done.

---

Toubleshooting:

If you get

2012-05-22 17:55:00: Me TV Server 1.4.0.9 started
2012-05-22 17:55:00: An unhandled exception was generated
2012-05-22 17:55:00: Error: The Me TV database version does not match the Me TV server version.

then you may shed a tear and
rm /home/${USER}/.local/share/me-tv/me-tv.db

160. Compiling kernel 3.4 on debian

The steps are the usual ones. At this point compiling your kernel is perhaps more of a hobby than a necessity to most people, unless you happen to have some fancy piece of hardware that's about to become supported.

It's not difficult, so there's no reason not to give it a spin.

UPDATE 9/7: Works fine with 3.4.4 as well (as it should). Compile time with -j7 on AMD X6 1055 is

real 33m27.472s
user 84m7.295s
sys 15m58.668s

which is underwhelming.


-- Start Here --
sudo apt-get install kernel-package fakeroot build-essential

mkdir ~/tmp
cd ~/tmp
wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.4.tar.bz2
tar xvf linux-3.4.tar.bz2
cd linux-3.4/
cat /boot/config-`uname -r`>.config
make oldconfig

If your current kernel is 3.3.5 the questions that await are given at the bottom of this post with links to descriptions of the different options. As usual, if in doubt, just hit enter.

make-kpkg clean

Building takes ages (depending on number of cores committed), so don't launch it at 4 pm on a Friday if you need to shut down your computer before going home... As usual, use the -jX switch for parallel builds, where X is the number of cores+1 (i.e. 4 cores => -j5)

The following command goes on a single line
time fakeroot make-kpkg -j5 --initrd --revision=3.4.0 --append-to-version=-amd64 kernel_image kernel_headers

Once the build is done, move the .deb files out of the way and to your linux-3.4 directory for safe-keeping
 mv ../*3.4.0*.deb .
sudo dpkg -i *.deb

Done.

The image weighs in at about 33 Mb and the headers at 7.6 Mb
And compile time with 4 out of 6 cores?  Well, not too bad:

real    34m51.027s
user    73m35.644s
sys     15m9.169s

---

Questions:
Boottime Graphics Resource Table support (ACPI_BGRT) [N/m/y/?] (NEW)
      Default ASPM policy
      > 1. BIOS default (PCIEASPM_DEFAULT) (NEW)
        2. Powersave (PCIEASPM_POWERSAVE) (NEW)
        3. Performance (PCIEASPM_PERFORMANCE) (NEW)
      choice[1-3]: 1
Enable PCI resource re-allocation detection (PCI_REALLOC_ENABLE_AUTO) [N/y/?] (NEW)
x32 ABI for 64-bit mode (EXPERIMENTAL) (X86_X32) [N/y/?] (NEW) See also cateee
Connection tracking timeout (NF_CONNTRACK_TIMEOUT) [N/y/?] (NEW)
Connection tracking timeout tuning via Netlink (NF_CT_NETLINK_TIMEOUT) [N/m/?] (NEW)
LOG target support (NETFILTER_XT_TARGET_LOG) [N/m/?] (NEW) M
Plug network traffic until release (PLUG) (NET_SCH_PLUG) [N/m/y/?] (NEW)
PEAK PCAN-PC Card (CAN_PEAK_PCMCIA) [N/m/?] (NEW)
 PEAK PCAN-ExpressCard Cards (CAN_PEAK_PCIEC) [Y/n/?] (NEW)
PEAK PCAN-USB/USB Pro interfaces (CAN_PEAK_USB) [N/m/?] (NEW)
 Support for DiskOnChip G4 (EXPERIMENTAL) (MTD_NAND_DOCG4) [N/m/?] (NEW)
Universal Flash Storage host controller driver (SCSI_UFSHCD) [N/m/?] (NEW)
virtio-scsi support (EXPERIMENTAL) (SCSI_VIRTIO) [N/m/?] (NEW)
 Verity target support (EXPERIMENTAL) (DM_VERITY) [N/m/?] (NEW)
Solarflare SFC9000-family hwmon support (SFC_MCDI_MON) [Y/n/?] (NEW)
Solarflare SFC9000-family SR-IOV support (SFC_SRIOV) [Y/n/?] (NEW)
 Drivers for the AMD PHYs (AMD_PHY) [N/m/?] (NEW)

QMI WWAN driver for Qualcomm MSM based 3G and LTE modems (USB_NET_QMI_WWAN) [N/m/?] (NEW)

support MFP (802.11w) even if uCode doesn't advertise (IWLWIFI_EXPERIMENTAL_MFP) [N/y/?] (NEW)

Additional debugging output (RTLWIFI_DEBUG) [Y/n] (NEW)

TI OMAP4 keypad support (KEYBOARD_OMAP4) [N/m/y/?] (NEW)

Synaptics USB device support (MOUSE_SYNAPTICS_USB) [N/m/y/?] (NEW)

Cypress TTSP touchscreen (TOUCHSCREEN_CYTTSP_CORE) [N/m/y/?] (NEW) 

Ilitek ILI210X based touchscreen (TOUCHSCREEN_ILI210X) [N/m/?] (NEW)

Xen Hypervisor Multiple Consoles support (HVC_XEN_FRONTEND) [Y/n/?] (NEW)

HSI support (HSI) [N/m/y/?] (NEW)

Intel PCH EG20T as PTP clock (PTP_1588_CLOCK_PCH) [N/m/?] (NEW) 

Dallas 2781 battery monitor chip (W1_SLAVE_DS2781) [N/m/?] (NEW) 

 2781 battery driver (BATTERY_DS2781) [N/m/?] (NEW)

Summit Microelectronics SMB347 Battery Charger (CHARGER_SMB347) [N/m/?] (NEW) 

Microchip MCP3021 (SENSORS_MCP3021) [N/m/?] (NEW) 

TPS65217 Power Management / White LED chips (MFD_TPS65217) [N/m/?] (NEW)

  TI TPS62360 Power Regulator (REGULATOR_TPS62360) [N/m/?] (NEW) 

  GPIO IR remote control (IR_GPIO_CIR) [N/m/?] (NEW) 

 Keene FM Transmitter USB support (USB_KEENE) [N/m/?] (NEW)

AzureWave 6007 and clones DVB-T/C USB2.0 support (DVB_USB_AZ6007) [N/m/?] (NEW) 

Realtek RTL28xxU DVB USB support (DVB_USB_RTL28XXU) [N/m/?] (NEW)

Allow to specify an EDID data set instead of probing for it (DRM_LOAD_EDID_FIRMWARE) [N/y/?] (NEW)

  DisplayLink (DRM_UDL) [N/m/?] (NEW)

Intel740 support (EXPERIMENTAL) (FB_I740) [N/m/y/?] (NEW) 

Exynos Video driver support (EXYNOS_VIDEO) [N/y/?] (NEW)

Backlight driver for TI LP855X (BACKLIGHT_LP855X) [N/m/?] (NEW)

Saitek non-fully HID-compliant devices (HID_SAITEK) [N/m/?] (NEW)

TiVo Slide Bluetooth remote control support (HID_TIVO) [N/m/?] (NEW)

 Generic OHCI driver for a platform device (USB_OHCI_HCD_PLATFORM) [N/y/?] (NEW) 

Generic EHCI driver for a platform device (USB_EHCI_HCD_PLATFORM) [N/y/?] (NEW)

USB Fintek F81232 Single Port Serial Driver (USB_SERIAL_F81232) [N/m/?] (NEW) 

USB Metrologic Instruments USB-POS Barcode Scanner Driver (USB_SERIAL_METRO) [N/m/?] (NEW)

 LED support for PCA9633 I2C chip (LEDS_PCA9633) [N/m/?] (NEW)

Xen ACPI processor (XEN_ACPI_PROCESSOR) [M/n/?] (NEW) 

Memory allocator for compressed pages (ZSMALLOC) [M/y/?] (NEW) 

 Intel Management Engine Interface (Intel MEI) (INTEL_MEI) [N/m/y/?] (NEW) 

USB over WiFi Host Controller (USB_WPAN_HCD) [N/m/?] (NEW) 

Apple Gmux Driver (APPLE_GMUX) [N/m/y/?] (NEW) 

QNX6 file system support (read only) (QNX6FS_FS) [N/m/y/?] (NEW) 

 NFSv4.1 Implementation ID Domain (NFS_V4_1_IMPLEMENTATION_ID_DOMAIN) [kernel.org] (NEW) 

RPC: Enable dprintk debugging (SUNRPC_DEBUG) [N/y/?] (NEW) 

Print additional diagnostics on RCU CPU stall (RCU_CPU_STALL_INFO) [N/y/?] (NEW)

Yama support (SECURITY_YAMA) [N/y/?] (NEW)

Camellia cipher algorithm (x86_64) (CRYPTO_CAMELLIA_X86_64) [N/m/y/?] (NEW)

CRC32 perform self test on init (CRC32_SELFTEST) [N/y/?] (NEW) 

 CRC32 implementation

  > 1. Slice by 8 bytes (CRC32_SLICEBY8) (NEW)

    2. Slice by 4 bytes (CRC32_SLICEBY4) (NEW)

    3. Sarwate's Algorithm (one byte at a time) (CRC32_SARWATE) (NEW)

    4. Classic Algorithm (one bit at a time) (CRC32_BIT) (NEW)

  choice[1-4?]: 

---

Links to this post:
http://askubuntu.com/questions/147725/ubuntu-12-04-fail-to-upgrade-to-kernel-3-4
http://www.deltageek.fr/installer-un-nouveau-noyau-linux/
http://thinkpad-forum.de/threads/141365-Linux-Probleme-mit-neuen-Modellen-(W-L-X-Tx30)/page2
http://crunchbang.org/forums/viewtopic.php?id=24814

159. PES scanning of methanol bonds, angles, torsion using nwchem, nwgeom and python

NOTE: there's something dodgy with the potential/bond length plots -- they optimal bond lengths are way too long. I'll leave this post up here anyway, but be WARNED.

This is more of an overview of an idea of how to do it together with some explicit examples. This is more of a sketch than a step-by-step account.

Today's molecule is Methanol.

0. ecce and nwgeom/python
You need to set PYTHONPATH to /opt/nwchem/nwchem-6.1/contrib/python in order for nwchem to find the nwgeom module. That's easy enough on a local system since ~/.bashrc is read -- but it won't read ~/.bashrc on remote systems. For this you need to edit your CONFIG.<machine> files (in ~/.ECCE on your main node)  -- add

setup {
     setenv PYTHONPATH /opt/nwchem/nwchem-6.1/contrib/python
}

and/or

NWChemEnvironment {
          PYTHONPATH /opt/nwchem/nwchem-6.1/contrib/python
}      

1. Draw the molecule,
Draw the Carbon, then the oxygen, then the protons on the carbon, then the protons on the oxygen. Basically, draw the backbone first, then add protons by hand.  Turn it into a residue-based system (under 'build') and optimise the structure using e.g. RHF/6-31G* (this was written with MM/FF parametrisation in mind -- for simple scanning, just do whatever you want )

2. Calculate the partial charges (rhf/6-31g*).  Can skip this
You can e.g. constrain the methyl groups, or force all the methyl protons to be equal. It's a bit of a soft science, really. After the calc has finished, assign charges. I can't claim to understand which method is better (RESP, CRESP, CRESP2 etc.).

 (this was written with MM/FF parametrisation in mind -- for simple scanning, skip this step)

Here's CRESP2 (some variability...):
C -0.721
O -0.368
H 0.240
H 0.240
H 0.240
H 0.368

Also, assign (atom) Types (CT, OH, HC, HC, HC, HO) -- this is done by hand. Pick atom table, select residue view (or something similar), and fill in the Type column.

Then click on Tools, check Residue table, click on the menu-looking icon in the residue view, and select write fragment. Make sure you put the fragment file in a place where ecce and nwchem will find it (e.g. amber_u). For some reason I can't get ecce to actually change the name of my residues, so edit the fragment file by hand and change all instance of UNK to the same name as the fragment file, e.g. TST if you called it TST.frg.


3. Write down the bonds, angles and dihedral angles.
Bonds
H-C 1.087
C-O 1.400
O-H 0.946

Angles
H-O-C 109.467
O-C-H 112.039
H-C-H 108.682

Torsion
H-C-O-H -61.229

When you scan the parameters using python you want to be able to
1) see if the lowest energy conf make sense and
2) not deviate too much from the ideal angle/bond/torsion.

Things get weird if you do.

4. Try to determine bond strength
This is best done outside of ecce, and you really should have compiled nwchem with python-support to make this easier.

Copy the input file you used for the ESP calc. Call it bonds.nw. Remove anything about esp and all task directives, then add:

<pre> python from nwgeom import * geom = ''' geometry adjust zcoord   bond 1 2 %f cccc constant end end ''' results=scan_input(geom,[1.0],[5.0],60,'dft',task_energy) for i in range(0,len(results)): print results[i][0][0],results[i][1] end task python </pre>

Technically I think the bond strengths only really need two data points unless you want to fit the Lennard-Jones equation to them, but it certainly looks neater getting the full behaviour.

Then run using
mpirun -n 2 nwchem bonds.nw | tee bond12.nw

You can also do it in ecce -- but the plotting will have to be done by hand (I open the out file with vim, select the energy/atom-distance columns, :w angle.dat and then plot with gnuplot)

Do the same for atom pair 1-6 and 2-3. Make sure to pull the atoms far enough apart that the energy tails out (the 1-6 pair in the figure needs to be separated more)

5. Angles
As you'll discover, it's not just a matter of throwing in random numbers and scanning -- if you don't collect enough points, or if your first point is far away from the optimal angle, the data will look very odd.
python from nwgeom import * geom = ''' geometry adjust zcoord angle 2 1 3 %f cccc constant end end ''' results=scan_input(geom,[40],[130],90,'scf',task_energy) for i in range(0,len(results)): print results[i][0][0],results[i][1] end task python

6. Torsion
python from nwgeom import * geom = ''' geometry adjust zcoord torsion 6 2 1 3 %f cccc constant end end ''' results=scan_input(geom,[-180],[180],200,'scf',task_energy) for i in range(0,len(results)): print results[i][0][0],results[i][1] end task python