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

158. Setting up ecce with qsub at An Australian University computational cluster

EDIT: this works for G09 on that particular cluster. Come back in a week or two for a more general solution (end of May 2012/beginning of June 2012).

I don't feel comfortable revealing where I work. But imagine that you end up working at an Australian University in, say, Melbourne. I do recognise that I will be giving enough information here to make it possible to identify  who I am (and there are many reasons not to want to be identifiable -- partly because students can be mean and petty, and partly because I suffer from the delusion that IT rules apply to Other People, and not me -- and have described ways of doing things you're not supposed to be doing in this blog)

Anyway.

My old write-ups of ecce are pretty bad, if not outright inaccurate. Anyway, I presume that in spite of that you've managed to set up ECCE well enough to run stuff on nodes of your local cluster.

Now it's time for the next level -- on a remote site using SGE/qsub

So far I've only tried this out with G09 -- they are currently looking to set up nwchem on the university cluster. Not sure what the best approach to the "#$ -pe g03_smp2 2" switch is for nwchem.

--START HERE --

EVERYTHING I DESCRIBE IS DONE ON YOUR DESKTOP, NOT ON THE REMOTE SYSTEM. Sorry for shouting, but don't got a-messing with the remote computational cluster -- we only want to teach ecce how to submit jobs remotely. The remote cluster should be unaffected.

1. Creating the Machine
To set up a site with a queue manager, start
ecce -admin

Do something along the lines of what's shown in the figure above.

If you're not sure whether your qsub belongs to PBS or SGE, type qstat -help and look at the first line returned, e.g. SGE 6.2u2_1.

2. Configure the site
Now, edit your ecce-6.3/apps/siteconfig/CONFIG.msgln4  (local nodes go into ~/.ECCE  but remote SITES go in apps/siteconfig --  and that's what we're working with here).

   NWChem: /usr/local/bin/NWCHEM
   Gaussian-03: /usr/local/bin/G09
   perlPath: /usr/bin/perl
   qmgrPath: /usr/bin/qsub
 
   SGE {
   #$ -S /bin/csh
   #$ -cwd
   #$ -l h_rt=$wallTime
   #$ -l h_vmem=4G
   #$ -j y
   #$ -pe g03_smp2 2

   module load gaussian/g09
    }

A word of advice -- open the file in vim (save using :wq!) or do a chmod +w on it first since it will be set to read-only by default.

3. Queue limits
The same goes for the next file, which controls various job limits, ecce-6.3/apps/siteconfig/msgln4.Q:

# Queue details for msgln4
Queues:    squ8

squ8|minProcessors:       2
squ8|maxProcessors:       6
squ8|runLimit:       4320
squ8|memLimit:       4000
squ8|scratchLimit:       0

4. Connect
In the ecce launcher-mathingy click on Machine Browser, and Set Up Remote Access for the remote cluster. Basically, type in your user name and password.

Click on machine status to make sure that it's connecting

5.Test it out!
If all is well you should be good to go