274. Kernel 3.7-rc3

There's a specific driver (Silicom devices) included in the new kernel (3.7) that interests a friend. I do not suggest people in general run an -rc kernel, so I'm not going to put any effort into making this post user-friendly.

Having said that, in general you should be fine. In general.

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

mkdir ~/tmp
cd ~/tmp
wget http://www.kernel.org/pub/linux/kernel/v3.0/testing/linux-3.7-rc3.tar.bz2
tar xvf linux-3.7-rc3.tar.bz2 
cd linux-3.7-rc3/
cat /boot/config-`uname -r`>.config
make oldconfig

At this stage you'll be asked questions about all the shiny new things that are found in the kernel. See bottom of the post for a list of the questions.

If you regret the answer to a question you can change your mind later by doing

make menuconfig

Once you're done answering questions, compile!

make-kpkg clean
time fakeroot make-kpkg -j3 --initrd --revision=3.7.0 --append-to-version=-rc3 kernel_image kernel_headers

It takes 43 minutes on my old AMD X3.



To install the kernel:

mv ../linux-*-3.7.0-rc3*.deb .
sudo dpkg -i *.deb

And you're done!

---

New stuff (compared to kernel 3.6.3):

* CPU/Task time and stats accounting
*
Cputime accounting
> 1. Simple tick based cputime accounting (TICK_CPU_ACCOUNTING) (NEW)
  2. Fine granularity task level IRQ time accounting (IRQ_TIME_ACCOUNTING)
choice[1-2]: 1

Consider userspace as in RCU extended quiescent state (RCU_USER_QS) [N/y/?] (NEW) 
Module signature verification (MODULE_SIG) [N/y/?] (NEW)  
Legacy cpb sysfs knob support for AMD CPUs (X86_ACPI_CPUFREQ_CPB) [Y/n/?] (NEW) 
Packet: sockets monitoring interface (PACKET_DIAG) [N/m/y/?] (NEW)
IPv6: GRE tunnel (IPV6_GRE) [N/m/y/?] (NEW) 
IPv4 NAT (NF_NAT_IPV4) [N/m/?] (NEW) 
IPv6 NAT (NF_NAT_IPV6) [N/m/?] (NEW) 
OMAP OCP2SCP DRIVER (OMAP_OCP2SCP) [N/m/y/?] (NEW) 
Maximum expected bad eraseblock count per 1024 eraseblocks (MTD_UBI_BEB_LIMIT) [20] (NEW)
UBI Fastmap (Experimental feature) (MTD_UBI_FASTMAP) [N/y/?] (NEW)
Calxeda Highbank SATA support (SATA_HIGHBANK) [N/m/?] (NEW) 
Virtual eXtensible Local Area Network (VXLAN) (VXLAN) [N/m/y/?] (NEW) Y
PCH PTP clock support (PCH_PTP) [N/y/?] (NEW)
Solarflare SFC9000-family PTP support (SFC_PTP) [Y/n/?] (NEW)
Drivers for Atheros AT803X PHYs (AT803X_PHY) [N/m/?] (NEW)
MAX310X support (SERIAL_MAX310X) [N/y/?] (NEW)
SCCNXP serial port support (SERIAL_SCCNXP) [N/m/y/?] (NEW)
TPM HW Random Number Generator support (HW_RANDOM_TPM) [M/n/?] (NEW) 
TPM Interface Specification 1.2 Interface (I2C - Infineon) (TCG_TIS_I2C_INFINEON) [N/m/?] (NEW) 
NXP SC18IS602/602B/603 I2C to SPI bridge (SPI_SC18IS602) [N/m/?] (NEW)
OMAP HDQ driver (HDQ_MASTER_OMAP) [N/m/?] (NEW)
Analog Devices ADT7410 (SENSORS_ADT7410) [N/m/?] (NEW)
Maxim MAX197 and compatibles (SENSORS_MAX197) [N/m/y/?] (NEW)
generic cpu cooling support (CPU_THERMAL) [N/y/?] (NEW) Y
Fairchild FAN53555 Regulator (REGULATOR_FAN53555) [N/m/?] (NEW)
Media USB Adapters (MEDIA_USB_SUPPORT) [N/y/?] (NEW)
Media PCI Adapters (MEDIA_PCI_SUPPORT) [N/y/?] (NEW) 
Media test drivers (V4L_TEST_DRIVERS) [N/y] (NEW) 
ISA and parallel port devices (MEDIA_PARPORT_SUPPORT) [N/y/?] (NEW) 
Autoselect tuners and i2c modules to build (MEDIA_SUBDRV_AUTOSELECT) [Y/n/?] (NEW) 
Maximum debug level (NOUVEAU_DEBUG) [5] (NEW)
Default debug level (NOUVEAU_DEBUG_DEFAULT) [3] (NEW)
Backlight Driver for LM3630 (BACKLIGHT_LM3630) [N/m/?] (NEW)
Backlight Driver for LM3639 (BACKLIGHT_LM3639) [N/m/?] (NEW)
Sony PS3 BD Remote Control (HID_PS3REMOTE) [N/m/?] (NEW)
HID Sensors framework support (HID_SENSOR_HUB) [N/m/?] (NEW)
ZTE USB serial driver (USB_SERIAL_ZTE) [N/m/?] (NEW)
Functions for loading firmware on EZUSB chips (USB_EZUSB_FX2) [M/y/?] (NEW) 
OMAP USB2 PHY Driver (OMAP_USB2) [N/m/y/?] (NEW)
LED support for LM3642 Chip (LEDS_LM3642) [N/m/?] (NEW)
LED support for LM355x Chips, LM3554 and LM3556 (LEDS_LM355x) [N/m/?] (NEW)
LED CPU Trigger (LEDS_TRIGGER_CPU) [N/y/?] (NEW)
Dallas DS2404 (RTC_DRV_DS2404) [N/m/y/?] (NEW) 
Silicom devices (NET_VENDOR_SILICOM) [Y/n/?] (NEW) Y
Silicom BypassCTL library support (SBYPASS) [N/m/?] (NEW)m
Silicom BypassCTL net support (BPCTL) [N/m/?] (NEW) m
Cambridge Electronic Design 1401 USB support (CED1401) [N/m/?] (NEW)
Digi Realport driver (DGRP) [N/m/y/?] (NEW)
STE-Modem remoteproc support (STE_MODEM_RPROC) [N/m/y/?] (NEW)
SMB2 network file system support (EXPERIMENTAL) (CIFS_SMB2) [N/y/?] (NEW)
Red-Black tree test (RBTREE_TEST) [N/m/?] (NEW)
Interval tree test (INTERVAL_TREE_TEST) [N/m/?] (NEW)
CAST5 (CAST-128) cipher algorithm (x86_64/AVX) (CRYPTO_CAST5_AVX_X86_64) [N/m/y/?] (NEW)
CAST6 (CAST-256) cipher algorithm (x86_64/AVX) (CRYPTO_CAST6_AVX_X86_64) [N/m/y/?] (NEW)
Asymmetric (public-key cryptographic) key type (ASYMMETRIC_KEY_TYPE) [N/m/y/?] (NEW)

As for Intel devices the pre-existing settings were:

Intel devices (NET_VENDOR_INTEL) [Y/n/?] y
      Intel(R) PRO/100+ support (E100) [M/n/y/?] m
      Intel(R) PRO/1000 Gigabit Ethernet support (E1000) [M/n/y/?] m
      Intel(R) PRO/1000 PCI-Express Gigabit Ethernet support (E1000E) [M/n/y/?] m
      Intel(R) 82575/82576 PCI-Express Gigabit Ethernet support (IGB) [M/n/y/?] m
        Direct Cache Access (DCA) Support (IGB_DCA) [Y/n/?] y
        PTP Hardware Clock (PHC) (IGB_PTP) [N/y/?] n
      Intel(R) 82576 Virtual Function Ethernet support (IGBVF) [M/n/y/?] m
      Intel(R) PRO/10GbE support (IXGB) [M/n/y/?] m
      Intel(R) 10GbE PCI Express adapters support (IXGBE) [M/n/y/?] m
        Intel(R) 10GbE PCI Express adapters HWMON support (IXGBE_HWMON) [Y/n/?] y
        Direct Cache Access (DCA) Support (IXGBE_DCA) [Y/n/?] y
        Data Center Bridging (DCB) Support (IXGBE_DCB) [Y/n/?] y
        PTP Clock Support (IXGBE_PTP) [N/y/?] n
      Intel(R) 82599 Virtual Function Ethernet support (IXGBEVF) [M/n/y/?] m
      Intel (82586/82593/82596) devices (NET_VENDOR_I825XX) [Y/n/?] y
        Zenith Z-Note support (EXPERIMENTAL) (ZNET) [N/m/y/?] n

273. NWChem and COSMO: custom radii

There are two approaches described in the nwchem manual for using custom radii in COSMO calculations:

geometry
  H  0 0 0
  H  0 1 0
  O  1 0 0
end
cosmo
       radius 1.1
              1.1
              1.8
end

and

cosmo
end
set cosmo:map custom.par

where custom.par looks like this:

H 1.1
O 1.8

The downside to the first example is that it's a PITA to use -- you need to enter each vdw radius in the order you are listing the atoms in the geometry section. It means that for a 50 atom geometry you need to enter 50 values, even if all 50 atoms are the same element.

The downside with the second example is that you need to first create the run folder, put cosmo.par there and first then can you submit.

An easier approach is to create the custom.par on the fly using task shell:

task shell "echo -e 'H 1.1 \n O 1.8' > mycosmopars.par"
cosmo
end
set cosmo:map mycosmopars.par

272. Compiling NWChem 6.1.1.1 on ROCKS 5.4.3/CentOS 5.6

Nothing weird with this one and it's all but identical to the build on debian, but here's a step by step anyway to help those who are computational chemists, but not sysadmins.

---

Preparations:
First compile openblas according to http://verahill.blogspot.com.au/2012/05/building-nwchem-61-on-debian.html 

Next, create e.g. /share/apps/nwchem, like this

sudo mkdir /share/apps/nwchem
sudo chmod 755 /share/apps/nwchem

It will allows you to read, write and execute. It will allow group members and 'world' to read and execute, but not write.

If you've already built earlier versions of nwchem you want to skip the steps above.

---

NWChem:
You will need to go to http://www.nwchem-sw.org/index.php/Download and download version 6.1.1. Using the direct link (http://www.nwchem-sw.org/images/Nwchem-6.1.1-src.2012-06-27.tar.gz) with wget isn't working for me anymore.

Put your Nwchem-6.1.1-src.2012-06-27.tar.gz in /share/apps/nwchem and expand it.

tar xvf Nwchem-6.1.1-src.2012-06-27.tar.gz
cd nwchem-6.1.1-src/

Create buildconf.sh

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONHOME=/opt/rocks
export PYTHONVERSION=2.4
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/opt/openmpi
export MPI_INCLUDE=/opt/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/opt/openmpi/lib:/share/apps/openblas
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
export BLASOPT="-L/share/apps/openblas/lib -lopenblas -lopenblas_nehalem-r0.1.1 -lopenblas_nehalemp-r0.1.1"
cd $NWCHEM_TOP/src
export FC=gfortran
make clean
make  nwchem_config
make  FC=gfortran |tee make.log
cd ../contrib
./getmem.nwchem

Before running it, edit src/config/makefile.h and change line 1957:

1957      EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl -lz -lssl

You are now ready to build.

time sh buildconf.sh

It took about 15 minutes to build -- a clear improvement over 6.1 for me (30 min+)

Create a default.nwchemrc in your /share/apps/nwchem/nwchem-6.1.1-src/ folder

nwchem_basis_library /share/apps/nwchem/nwchem-6.1.1-src/src/basis/libraries/
ffield amber
amber_1 /share/apps/nwchem/nwchem-6.1.1-src/src/data/amber_s/
amber_2 /share/apps/nwchem/nwchem-6.1.1-src/src/data/amber_x/
amber_3 /share/apps/nwchem/nwchem-6.1.1-src/src/data/amber_q/
amber_4 /share/apps/nwchem/nwchem-6.1.1-src/src/data/amber_u/
amber_5 /share/apps/nwchem/nwchem-6.1.1-src/src/data/custom/
spce /share/apps/nwchem/nwchem-6.1.1-src/src/data/solvents/spce.rst
charmm_s /share/apps/nwchem/nwchem-6.1.1-src/src/data/charmm_s/
charmm_x /share/apps/nwchem/nwchem-6.1.1-src/src/data/charmm_x/

Then each user can do

ln -s /share/apps/nwchem/nwchem-6.1.1-src/default.nwchemrc ~/.nwchemrc

You might also want to add nwchem to path -- add

export PATH=$PATH:/share/apps/nwchem/nwchem-6.1.1-src
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi/lib:/share/apps/openblas

to your ~/.bashrc