214. Compiling kernel 3.5 on Debian testing

I've posted how to compile quite a few different kernel versions already (3.4, 3.3, 3.2). With the exception of specific questions asked during the process, the are all compiled in the same way.

Compiling kernels is NOT scary on debian.

cd ~/tmp
wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.5.tar.bz2
tar xvf linux-3.5.tar.bz2
cd linux-3.5/
cat /boot/config-`uname -r`>.config
make oldconfig

Question time! See below.

make-kpkg clean
time fakeroot make-kpkg -j5 --initrd --revision=3.5.0 --append-to-version=-amd64 kernel_image kernel_headers

This takes a LONG TIME. Change 5 to number of cores+1. 35 minutes with -j5 on a six core desktop.

 mv ../*3.5.0*.deb .

sudo dpkg -i *.deb

And you're done.

Things to ponder in this version:
Tree-based hierarchical RCU leaf-level fanout value (RCU_FANOUT_LEAF) [16] (NEW
Cross Memory Support (CROSS_MEMORY_ATTACH) [Y/n/?] (NEW)
Enable frontswap to cache swap pages if tmem is present (FRONTSWAP) [N/y/?] (NEW)
Opportunistic sleep (PM_AUTOSLEEP) [N/y/?] (NEW)
User space wakeup sources interface (PM_WAKELOCKS) [N/y/?] (NEW)
"HMARK" target support (NETFILTER_XT_TARGET_HMARK) [N/m/?] (NEW)
Generic IEEE 802.15.4 Soft Networking Stack (mac802154) (MAC802154) [N/m/?] (NEW)
Controlled Delay AQM (CODEL) (NET_SCH_CODEL) [N/m/y/?] (NEW)
Fair Queue Controlled Delay AQM (FQ_CODEL) (NET_SCH_FQ_CODEL) [N/m/y/?] (NEW)
Bridge Loop Avoidance (BATMAN_ADV_BLA) [Y/n/?] (NEW)
NFC HCI implementation (NFC_HCI) [N/m/?] (NEW) 
BMP085 digital pressure sensor on I2C (BMP085_I2C) [N/m/?] (NEW)

BMP085 digital pressure sensor on SPI (BMP085_SPI) [N/m/y/?] (NEW)

TCM_QLA2XXX fabric module for Qlogic 2xxx series target mode HBAs (TCM_QLA2XXX) [N/m/?] (NEW) 

 FireWire SBP-2 fabric module (SBP_TARGET) [N/m/?] (NEW) 

PTP Hardware Clock (PHC) (IGB_PTP) [N/y/?] (NEW)

Intel(R) 10GbE PCI Express adapters HWMON support (IXGBE_HWMON) [Y/n/?] (NEW)

PTP Clock Support (IXGBE_PTP) [N/y/?] (NEW)

Data Center Bridging (DCB) Support (MLX4_EN_DCB) [Y/n/?] (NEW)

WIZnet devices (NET_VENDOR_WIZNET) [Y/n/?] (NEW)

WIZnet W5100 Ethernet support (WIZNET_W5100) [N/m/y/?] (NEW)

WIZnet W5300 Ethernet support (WIZNET_W5300) [N/m/y/?] (NEW)

TI Wireless LAN support (WL_TI) [N/y/?] (NEW)

Marvell WiFi-Ex Driver for USB8797 (MWIFIEX_USB) [N/m/?] (NEW) 

Matrix keymap support library (INPUT_MATRIXKMAP) [N/m/y/?] (NEW)

LM8333 keypad chip (KEYBOARD_LM8333) [N/m/?] (NEW) 

 Wacom Tablet support (I2C) (TOUCHSCREEN_WACOM_I2C) [N/m/?] (NEW)

Intel ICH GPIO (GPIO_ICH) [N/m/y/?] (NEW)

Texas Instruments INA219, INA226 (SENSORS_INA2XX) [N/m/?] (NEW)

Intel Atom E6xx Watchdog (IE6XX_WDT) [N/m/y/?] (NEW)

LM3533 Lighting Power chip (MFD_LM3533) [N/m/?] (NEW)

Freescale MC13783 and MC13892 SPI interface (MFD_MC13XXX_SPI) [N/m/y/?] (NEW)

Freescale MC13892 I2C interface (MFD_MC13XXX_I2C) [N/m/?] (NEW)

Intel ICH LPC (LPC_ICH) [M/y/?] (NEW)

 Afatech AF9035 DVB-T USB2.0 support (DVB_USB_AF9035) [N/m/?] (NEW) 

AST server chips (DRM_AST) [N/m/?] (NEW) 

Kernel modesetting driver for MGA G200 server engines (DRM_MGAG200) [N/m/?] (NEW)

Cirrus driver for QEMU emulated device (DRM_CIRRUS_QEMU) [N/m/?] (NEW) 

AUO-K190X EPD controller support (FB_AUO_K190X) [N/m/y/?] (NEW) 

Generic HID driver (HID_GENERIC) [M/n/?] (NEW) 

 Aureal (HID_AUREAL) [N/m/?] (NEW) 

BCMA usb host driver (USB_HCD_BCMA) [N/m/?] (NEW) 

SSB usb host driver (USB_HCD_SSB) [N/m/?] (NEW)

ChipIdea Highspeed Dual Role Controller (USB_CHIPIDEA) [N/m/?] (NEW) 

USB Quatech Serial Driver for USB 2 devices (USB_SERIAL_QT2) [N/m/?] (NEW)

NXP ISP1301 USB transceiver support (USB_ISP1301) [N/m/?] (NEW)

USB Gadget Target Fabric Module (USB_GADGET_TARGET) [N/m/?] (NEW) 

 LED Transient Trigger (LEDS_TRIGGER_TRANSIENT) [N/m/y/?] (NEW) 

 Emulex One Connect HCA support (INFINIBAND_OCRDMA) [N/m/?] (NEW) 

 Comedi default initial asynchronous buffer size in KiB (COMEDI_DEFAULT_BUF_SIZE_KB) [2048] (NEW) 

Comedi default maximum asynchronous buffer size in KiB (COMEDI_DEFAULT_BUF_MAXSIZE_KB) [20480] (NEW)

Amplicon PCI215 and PCI272 DIO board support (COMEDI_AMPLC_DIO200_PCI) [N/m/?] (NEW) 

 Amplicon PCI236 DIO board support (COMEDI_AMPLC_PC236_PCI) [N/m/?] (NEW)

Amplicon PCI263 relay board support (COMEDI_AMPLC_PC263_PCI) [N/m/?] (NEW) 

DAS-08 PCI support (COMEDI_DAS08_PCI) [N/m/?] (NEW)

Configurable Composite Gadget (STAGING) (USB_G_CCG) [N/m/?] (NEW)

 IndustryPack bus support (IPACK_BUS) [N/m/y/?] (NEW) 

GCT GDM72xx WiMAX support (WIMAX_GDM72XX) [N/m/y/?] (NEW)

External Connector Class (extcon) support (EXTCON) [N/m/y/?] (NEW) 

Memory Controller drivers (MEMORY) [N/y] (NEW)

 Log panic/oops to a RAM buffer (PSTORE_RAM) [N/m/y/?] (NEW) 

NFS client support for NFS version 2 (NFS_V2) [Y/n/?] (NEW) 

Codepage macroman (NLS_MAC_ROMAN) [N/m/y/?] (NEW)

Codepage macceltic (NLS_MAC_CELTIC) [N/m/y/?] (NEW)

Codepage maccenteuro (NLS_MAC_CENTEURO) [N/m/y/?] (NEW)

Codepage maccroatian (NLS_MAC_CROATIAN) [N/m/y/?] (NEW) 

Codepage maccyrillic (NLS_MAC_CYRILLIC) [N/m/y/?] (NEW) 

Codepage macgaelic (NLS_MAC_GAELIC) [N/m/y/?] (NEW)

Codepage macgreek (NLS_MAC_GREEK) [N/m/y/?] (NEW)

Codepage maciceland (NLS_MAC_ICELAND) [N/m/y/?] (NEW) 

Codepage macinuit (NLS_MAC_INUIT) [N/m/y/?] (NEW) 

Codepage macromanian (NLS_MAC_ROMANIAN) [N/m/y/?] (NEW) 

Codepage macturkish (NLS_MAC_TURKISH) [N/m/y/?] (NEW)

Generate readable assembler code (READABLE_ASM) [N/y/?] (NEW)

Enable uprobes-based dynamic events (UPROBE_EVENT) [N/y/?] (NEW)

JEDEC DDR data (DDR) [N/y/?] (NEW) 

---

Links to this page:
http://srmulcahy.github.com/2012/12/24/debian-x230.html
http://stackoverflow.com/questions/13533307/installing-headers-for-3-5-kernel-in-debian-wheezy

209. Quantum Espresso on Debian

Quantum Espresso seems to be a fairly capable software package for ab initio QM and MD calculations. In their own words:
"Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.It is based on density-functional theory, plane waves, and pseudopotentials."

Reading between the lines it seems to be particularly geared towards solid state simulations, but given that I haven't used it much (I'm just an interested observer), you may take that statement with a grain of salt.

Anyway. Here's how to get it up and running.
Don't ask me how to USE these pieces of software though. For that, read the documentation at the Quantum Espresso website or look in /opt/QE/Doc

---

The download page can be found here: http://qe-forge.org/frs/?group_id=10. You won't need all the packages, since the espresso-5.0.tar.gz bundles most of them.

1. Housekeeping:
sudo mkdir /opt/QE
sudo chown $USER /opt/QE
mkdir ~/tmp/QE -p
cd ~/tmp/QE

2. Downloading:
wget http://qe-forge.org/frs/download.php/211/espresso-5.0.tar.gz
wget http://qe-forge.org/frs/download.php/214/PWgui-5.0.tgz
wget http://qe-forge.org/frs/download.php/204/xspectra-5.0.tar.gz

3. Extraction:
tar xvf espresso-5.0.tar.gz
tar xvf PWgui-5.0.tgz
tar xvf xspectra-5.0.tar.gz

4. Compilation:
cd espresso-5.0/

Edit environment_variables and set them to e.g.

PREFIX=/opt/QE
TMP_DIR=/scratch
PARA_PREFIX=" mpirun -n 3"

Don't know if any of those params are ever read though.

The following parameters will depend on your system. I tried compiling with openblas without luck. who knows? It might be due to mixing debian fftw3 and my own openblas.

Instead, install libblas-dev, libfftw3-dev, libopenmpi-dev etc.

./configure --prefix=/opt/QE/bin --exec-prefix=/opt/QE/bin/ FC=mpif90 BLAS_LIBS=-lblas LIBS="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread" CPPFLAGS="-I/usr/lib/openmpi/include"
cd PW/
make

cd ../
make all -j5 
echo 'export PATH=$PATH:/opt/QE/bin' >>~/.bashrc
echo 'export PSEUDO_DIR=/opt/QE/pseudo' >>~/.bashrc
(replace 5 with  the number of cores you compile with +1)

cp * -R /opt/QE/
source ~/.bashrc

For some reason I had to move everything by hand. Oh well.

[It should be enough to set the env var PSEUDO_DIR to point at /opt/QE/pseudo, but it didn't work for me. Instead I symmlinked the entire /opt/QE to ~/espresso. Desperate? Sure...
ln -s /opt/QE/ /home/me/espresso]

5. Testing PW
Some examples are found in /opt/QE/PW/examples
cd /opt/QE/PW/examples/example01
./run_examples

/opt/QE/PW/examples/example01 : starting
This example shows how to use pw.x to calculate the total energy and
the band structure of four simple systems: Si, Al, Cu, Ni.
  executables directory: /opt/QE/bin
  pseudo directory:      /opt/QE/pseudo
  temporary directory:   /scratch
  checking that needed directories and files exist... done
  running pw.x as: mpirun -n 3 /opt/QE/bin/pw.x
  cleaning /scratch... done
  running the scf calculation for Si... done
  running the band-structure calculation for Si... done
  cleaning /scratch... done
  ..
  cleaning /scratch... done
  running the scf calculation for Ni... done
  running the band-structure calculation for Ni... done

Or you can try

cd /opt/QE/PW/tests/
./check-pw.x.j
A number of tests will now be executed.  Most will pass.
IF YOU DON'T HAVE A vdw_kernel_table file one of the tests will fail.

6. Installing PWgui
Assuming you downloaded and extracted the PWgui-5.0.tgz file in step 2 above.
sudo apt-get install itk3 iwidgets4
cd ~/tmp/QE/
mv PWgui-5.0 /opt/QE/
cd /opt/QE/bin
ln -s /opt/QE/PWgui-5.0/pwgui /opt/QE/bin/pwgui

Start by typing
pwgui

settings

You can try e.g. opening /opt/QE/PW/examples/example01/results/al.scf.cg.in if you ran the test in step 5 above. Then run it.

7. Installing Xspectra
This assumes you downloaded and extracted as shown in steps 2-3 above.
cd ~/tmp/QE/
mv XSpectra/ espresso-5.0/
cd espresso-5.0/XSpectra/
make
cd ..
mv XSpectra/ /opt/QE/
cd /opt/QE/bin
ln -s /opt/QE/XSpectra/src/xspectra.x xspectra.x

---

Notes: in an ideal world the --prefix during configure should suffice in telling a program where to install. No luck for me here though. Also, I had to start the compile in the PW directory and only by using make without any switches, or there would be complaints about a missing libpw.a

187. Thunderbird 13.0 from source on debian wheezy

First look here for dependencies:
http://verahill.blogspot.com.au/2012/05/thunderbird-1201-on-debian.html

In terms of building it's almost exactly the same as for the 12-series: the only difference is that you have to build outside the source tree.

cd ~/tmp
rm comm-release -rf
wget ftp://ftp.mozilla.org/pub/mozilla.org/thunderbird/releases/13.0/source/thunderbird-13.0.source.tar.bz2
tar xvf thunderbird-13.0.source.tar.bz2
mkdir thunderbird13
cd thunderbird13
../comm-release/./configure --disable-necko-wifi

The next step takes a while (30-60 minutes)
make 

sudo make install

Done.

What's new: http://www.ghacks.net/2012/06/06/whats-new-in-thunderbird-13/

---

Errors
No rule to make target ../../../xpcom/idl-parser/xpidllex.py
Solution:

Build outside the source tree as shown above.

179. Building ECCE on Debian Testing/Wheezy

UPDATE: Build went fine. Upgrade went fine. But the organizer doesn't show my jobs properly i.e. the files are there but they aren't recognised as jobs. I haven't had a solid look at this yet, and it might just be because I need to restart more services than just the http server. It's been a long day...

UPDATE 2: An update on a different computer went without a hitch, with all the old job files being imported properly.

UPDATE 3: I started ECCE and let the data manger chew on it for four hours. No luck on the troublesome computer. The only difference is the java -- openjdk 7 worked fine, oracle jre/jdk didn't. Dunno if this is the reason, but currently in the process of installing the binaries to see whether that works better. Updates will come...

UPDATE 4: Installing the prebuilt ECCE binaries did the trick. In summary: as far as I know you MUST use openjdk 7. SUN/Oracle Java does not appear to work. It's exhibited in a lack of ability to recognise old jobs as being...jobs rather than just folders and files.


POST BEGINS HERE:
I'm trying to document everything I'm doing these days, no matter how simple or (at least in retrospect) obvious it is.

Here's how to build the 4th of June 2012 version of ecce v6.3.

You need to be registered with EMSL/PNNL to download ecce. There are plans to open-source the software properly (i.e. no need to register) sometime this coming northern summer. But for now you need to be an academic group leader to have access.

(I originally posted a somewhat different post where I recommended making some changes to the build scripts re ECCE_HOME. Eventually I saw the light and realised the error of my ways)

Download ecce-v6.3.src.tar.bz2, and put it in a suitable folder, e.g. ~/tmp

cd ~/tmp

tar -xvf ecce-v6.3-src.tar.bz2
cd ecce-v6.3/
export ECCE_HOME=`pwd`

cd build/

./build_ecce

The first time you run ./build_ecce you'll be asked a series of questions relating to installed packages. If it's all good, answer
Do you want to skip these checks for future build_ecce invocations (y/n)? y
If anything came up, then read the message carefully and install the missing package.

NOTE: on one box I noticed different version of java and javac being found, as I had both openjdk 6 and 7 installed. I couldn't set javac to 6 but I could do
sudo update-alternatives --config java
and set it to openjdk 7.

[From my small, statistically unsound sample set Oracle/SUN java will NOT work.]

Then do ./build_ecce again. And again. And again. In all, I think you do it six or seven times - each time a new package is built.
I always get a

lib: No such file or directory.

at the end of the httpd build. Not sure why, but everything seems to be ok in spite of that.
Anyway, you know that you're done running ./build_ecce when you get

ECCE built and distribution created in /home/verahill/tmp/ecce-v6.3

At this point, you are ready to install
DO NOT USE ./install_ecce

GO UP ONE LEVEL AND DO
./install_ecce.v6.3.csh

But that's a different story. install_ecce will give you weird error messages about missing tar files. install_ecce.v6.3.csh on the other hand will work fine.

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

155. Gromacs with external fftw3 and blas on debian testing

This is based on http://verahill.blogspot.com.au/2012/03/building-gromacs-with-fftw3-and-openmpi.html

Make sure your build environment is set up:
sudo apt-get install build-essential gfortran libopenmpi-dev

---

fftw
sudo mkdir /opt/fftw/
sudo chown ${USER} /opt/fftw
mkdir ~/tmp
cd ~/tmp
wget ftp://ftp.fftw.org/pub/fftw/fftw-3.3.2.tar.gz
tar xvf fftw-3.3.2.tar.gz
cd fftw-3.3.2/

./configure --enable-float --enable-mpi --enable-threads --with-pic --prefix=/opt/fftw/fftw-3.3.2/single

make && make install

make clean

./configure --disable-float --enable-mpi --enable-threads --with-pic --prefix=/opt/fftw/fftw-3.3.2/double

make && make install

---

openblas
sudo mkdir /opt/openblas
sudo chown ${USER} /opt/openblas
cd ~/tmp
wget http://nodeload.github.com/xianyi/OpenBLAS/tarball/v0.1.1
tar xvf v0.1.1
cd xianyi-OpenBLAS-e6e87a2/
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
cp lib*.*  /opt/openblas/lib

add

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

to your ~/.bashrc

[for later use with nwchem and ecce, add /opt/openblas/lib to /etc/ld.so.conf and do sudo ldconfig]

---

gromacs


sudo mkdir /opt/gromacs
sudo chown ${USER} /opt/gromacs
cd ~/tmp
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz

tar xvf gromacs-4.5.5.tar.gz

cd gromacs-4.5.5/

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

single
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/single/lib -L/opt/openblas/lib -lopenblas"
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/single/include -I/opt/openblas/include"

./configure --disable-mpi --enable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_sp --prefix=/opt/gromacs/gromacs-4.5.5
make -j3
make install

double
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/double/lib -L/opt/openblas/lib -lopenblas" 
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/double/include -I/opt/openblas/include"

./configure --disable-mpi --disable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_dp --prefix=/opt/gromacs/gromacs-4.5.5
make -j3
make install

single + mpi
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/single/lib -L/opt/openblas/lib -lopenblas"
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/single/include -I/opt/openblas/include"

./configure --enable-mpi --enable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_spmpi --prefix=/opt/gromacs/gromacs-4.5.5
make -j3
make install


double + mpi
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/double/lib -L/opt/openblas/lib -lopenblas"
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/double/include -I/opt/openblas/include"

./configure --enable-mpi --disable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_dpmpi --prefix=/opt/gromacs/gromacs-4.5.5
make -j3
make install

Make sure to put this in your ~/.bashrc

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/openblas/lib
export PATH=$PATH:/opt/gromacs/gromacs-4.5.5/bin

 You now have four versions of each binary -- with and without mpi, with single and with double precision.

---

133. Compiling Openbabel 2.3.1 and CMake on ROCKS/centos

Open Babel is a convenient tool for converting between chemistry-related file formats. Sadly, it's not included in ROCKS 5.4.3 from what I can see and I could only install a severely outdated rpm package which doesn't support gaussian 09 and nwchem well.

The easiest way to compile openbabel is by using cmake.

Cmake:
wget http://www.cmake.org/files/v2.8/cmake-2.8.8.tar.gz
tar -xvf cmake-2.8.8.tar.gz
cd cmake-2.8.8.8/
./configure --prefix=/home/me/.cmake
make
make install

Add the following to your ~/.bashrc and source it:
export PATH=$PATH:/home/me/.cmake/bin

Note: this works in Scientific Linux (Boron) 5.4 as well

Openbabel
wget http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.1/openbabel-2.3.1.tar.gz?r=http%3A%2F%2Fopenbabel.org%2Fwiki%2FGet_Open_Babel&ts=1336048328&use_mirror=aarnet
tar -xvf openbabel-2.3.1.tar.gz
cd openbabel-2.3.1/
cmake -DCMAKE_INSTALL_PREFIX:PATH=/home/me/.babel
make
make install

Add the following to your ~/.bashrc and source it:
export PATH=$PATH:/home/me/.babel/bin

Note: this works in Scientific Linux (Boron) 5.4 as well

Do
babel -L formats 
to get a list of formats.

114. Nwchem 6.0 with openmpi support on debian testing

I still haven't managed to compile a working versin of Nwchem 6.1 on Debian 64 bit regardless of whether I'm using mpich or openmpi. The number of posts relating to compiling nwchem is steadily growing, but I'd rather have post which are almost, but not quite, identical if it makes it's unambiguous for the average user how to build and use nwchem.

Anyway, since I'm using openmpi on my rocks cluster(s), I figure I might as well start using openmpi on debian too. In addition, the only way you can get nwchem 6.0 to work with mpich2 on debian seems to be by using the old v1.2 package which causes problems of its own (see apt-pinning).

Note: See here for information about python support: http://verahill.blogspot.com.au/2012/04/adding-python-support-to-nwchem-under.html

Long story short -- nwchem with openmpi:
mkdir ~/tmp
sudo apt-get install openmpi-bin libopenmpi-dev
wget http://www.nwchem-sw.org/images/Nwchem-6.0.tar.gz
tar -xvf Nwchem-6.0.tar.gz
cd nwchem-6.0/

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=/home/me/tmp/nwchem-6.0
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/usr/lib/openmpi/lib
export MPI_INCLUDE=/usr/lib/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

This will take a good 20-30 minutes.


Your binary will be in nwchem-6.0/bin/LINUX64/

Finally, see whether openmpi is already in your LD_LIBRARY_PATH

echo $LD_LIBRARY_PATH

/lib/openmm:/usr/lib/nvidia-cuda-toolkit:/usr/lib/nvidia

If not, edit ~/.bashrc and add
export LD_LIBRARY_PATH=/usr/lib/openmpi/lib:$LD_LIBRARY_PATH
export PATH=$PATH:/home/me/tmp/nwchem-6.0/bin/LINUX64

112. Kernel 3.3.x on debian testing

Compiling a kernel on debian is easy. Kernel 3.3 came out today, and here's how to build it for debian testing:
sudo apt-get install kernel-package fakeroot
wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.3.tar.bz2
tar -xvf linux-3.3.tar.bz2 
cd linux-3.3/

cat /boot/config-`uname -r`>.config
make oldconfig

EDIT: 3.3.1 is here: http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.3.1.tar.bz2 -- the build instructions are the same
EDIT 2: This has been tried with 3.3.4 as well. All is fine.
EDIT 3: And it's fine with 3.3.5

You'll also be asked about the new inclusions in the kernel. You can pick the default if you don't know - Yes means to compile into the kernel, m mean to provide as a module and no means don't support. Some drivers are better provided as modules -- see e.g. http://justlinux.com/forum/archive/index.php/t-127876.html
"Some things obviously have to be compiled into the kernel - file system support for your / filesys, stuff like that. Most everything else can be modules, if you desire." and "f you hot-swap different usb peripherals then I would recommend compiling those drivers as modules". Same goes for network drivers.

You can also look up the different options here: http://cateee.net/lkddb/web-lkddb/.
Seems like there's a lot of network and touch/screen drivers. And the fabled android drivers are available now:

Make audit loginuid immutable (AUDIT_LOGINUID_IMMUTABLE) [N/y/?] (NEW) Yes
Memory Resource Controller Kernel Memory accounting (EXPERIMENTAL) (CGROUP_MEM_RES_CTLR_KMEM) [N/y/?] (NEW) No
EFI stub support (EFI_STUB) [N/y/?] (NEW) No
UNIX: socket monitoring interface (UNIX_DIAG) [N/m/y/?] (NEW) m
UDP: socket monitoring interface (INET_UDP_DIAG) [N/m/?] (NEW)  m
Netfilter NFACCT over NFNETLINK interface (NETFILTER_NETLINK_ACCT) [N/m/y/?] (NEW) m
Supply CT list in procfs (OBSOLETE) (NF_CONNTRACK_PROCFS) [Y/n/?] (NEW) Yes
"nfacct" match support (NETFILTER_XT_MATCH_NFACCT) [N/m/?] (NEW) No
IPVS source hashing table size (the Nth power of 2) (IP_VS_SH_TAB_BITS) [8] (NEW)
"rpfilter" reverse path filter match support (IP_NF_MATCH_RPFILTER) [N/m/?] (NEW) No
"rpfilter" reverse path filter match support (IP6_NF_MATCH_RPFILTER) [N/m/?] (NEW) No
Open vSwitch (OPENVSWITCH) [N/m/y/?] (NEW) No
Network priority cgroup (NETPRIO_CGROUP) [N/m/y/?] (NEW) m
ISA Bus based legacy SJA1000 driver (CAN_SJA1000_ISA) [N/m/?] (NEW) No
Bosch CC770 and Intel AN82527 devices (CAN_CC770) [N/m] (NEW) No
NFC LLCP support (EXPERIMENTAL) (NFC_LLCP) [N/y/?] (NEW) No
Block Device Driver for Micron PCIe SSDs (BLK_DEV_PCIESSD_MTIP32XX) [N/m/?] (NEW) No
NVM Express block device (BLK_DEV_NVME) [N/m/y/?] (NEW) No
Ethernet team driver support (EXPERIMENTAL) (NET_TEAM) [N/m/y/?] (NEW) Yes
Calxeda 1G/10G XGMAC Ethernet driver (NET_CALXEDA_XGMAC) [N/m/y/?] (NEW) No
Micrel KS8995MA 5-ports 10/100 managed Ethernet switch (MICREL_KS8995MA) [N/m/y] (NEW) No
Atheros ath9k bluetooth coexistence support (ATH9K_BTCOEX_SUPPORT) [Y/n/?] (NEW) Yes
Hardware support that overlaps with the brcmsmac driver (B43_BCMA_EXTRA) [Y/n] (NEW) Yes
Broadcom IEEE802.11n PCIe SoftMAC WLAN driver (BRCMSMAC) [N/m/?] (NEW) No
iwlwifi experimental P2P support (IWLWIFI_P2P) [N/y/?] (NEW) No
Enable full debugging output in iwlegacy (iwl 3945/4965) drivers (IWLEGACY_DEBUG) [N/y/?] (NEW)  No
TCA8418 Keypad Support (KEYBOARD_TCA8418) [N/m/?] (NEW) No
AUO in-cell touchscreen using Pixcir ICs (TOUCHSCREEN_AUO_PIXCIR) [N/m/?] (NEW) No
EETI eGalax multi-touch panel support (TOUCHSCREEN_EGALAX) [N/m/?] (NEW) No
PIXCIR I2C touchscreens (TOUCHSCREEN_PIXCIR) [N/m/?] (NEW) No
Sharp GP2AP002A00F I2C Proximity/Opto sensor driver (INPUT_GP2A) [N/m/?] (NEW) No
Polled GPIO tilt switch (INPUT_GPIO_TILT_POLLED) [N/m/y/?] (NEW) No
SBS Compliant gas gauge (BATTERY_SBS) [N/m/?] (NEW) No
National Semiconductor LP8727 charger driver (CHARGER_LP8727) [N/m/?] (NEW) No
Battery charger manager for multiple chargers (CHARGER_MANAGER) [N/y/?] (NEW)  No?
VIA Watchdog Timer (VIA_WDT) [N/m/y/?] (NEW) No
Support STMicroelectronics STMPE (MFD_STMPE) [N/y/?] (NEW) No
Support Dialog Semiconductor DA9052/53 PMIC variants with SPI (MFD_DA9052_SPI) [N/y/?] (NEW) No
Enable IR raw decoder for the Sanyo protocol (IR_SANYO_DECODER) [M/n/?] (NEW) No
JL2005B/C/D USB V4L2 driver (USB_GSPCA_JL2005BCD) [N/m/?] (NEW) m
V4L PCI(e) devices (V4L_PCI_DRIVERS) [Y/n/?] (NEW) Yes
V4L ISA and parallel port devices (V4L_ISA_PARPORT_DRIVERS) [N/y/?] (NEW) No
V4L platform devices (V4L_PLATFORM_DRIVERS) [N/y/?] (NEW)  No
Intel GMA5/600 KMS Framebuffer (DRM_GMA500) [N/m/?] (NEW) No
Roccat Isku keyboard support (HID_ROCCAT_ISKU) [N/m/?] (NEW) No
Microsoft Hyper-V mouse driver (HID_HYPERV_MOUSE) [N/m/?] (NEW) No
EHCI support for Marvell on-chip controller (USB_EHCI_MV) [N/y/?] (NEW) No
Inventra Highspeed Dual Role Controller (TI, ADI, ...) (USB_MUSB_HDRC) [N/m/?] (NEW) No
Marvell USB2.0 Device Controller (USB_MV_UDC) [N/m/?] (NEW) No
LED Support for TCA6507 I2C chip (LEDS_TCA6507) [N/m/?] (NEW) No
LED support for the Bachmann OT200 (LEDS_OT200) [N/m/y/?] (NEW) No
InfiniBand SCSI RDMA Protocol target support (INFINIBAND_SRPT) [N/m/?] (NEW) No
Support for rtllib wireless devices (RTLLIB) [N/m/?] (NEW)
Android Drivers (ANDROID) [N/y/?] (NEW) No
Fujitsu Tablet Extras (FUJITSU_TABLET) [N/m/y/?] (NEW) No
Fujitsu-Siemens Amilo rfkill support (AMILO_RFKILL) [N/m/?] (NEW) No
AMD IOMMU Version 2 driver (EXPERIMENTAL) (AMD_IOMMU_V2) [N/m/y/?] (NEW) No
Btrfs with integrity check tool compiled in (DANGEROUS) (BTRFS_FS_CHECK_INTEGRITY) [N/y/?] (NEW) No
NFS server manual fault injection (NFSD_FAULT_INJECTION) [N/y/?] (NEW) No
Kernel memory leak detector (DEBUG_KMEMLEAK) [N/y/?] (NEW) No
NMI Selftest (DEBUG_NMI_SELFTEST) [N/y/?] (NEW) No
Serpent cipher algorithm (x86_64/SSE2) (CRYPTO_SERPENT_SSE2_X86_64) [N/m/y/?] (NEW) 
No

Continuing,
make-kpkg clean
fakeroot make-kpkg -j7 --initrd --revision=3.3.0 --append-to-version=amd64 kernel_image kernel_headers  

The build takes a LONG time. Once it's done:

mv ../linux*3.3.0*.deb .
sudo dpkg -i *.deb

Done.

Linux tantalum 3.3.0-amd64 #1 SMP Tue Mar 20 06:29:46 EST 2012 x86_64 GNU/Linux

---

110. Compiling, installing Gnuplot 4.6 on Debian

A new version of gnuplot doesn't happen very often, and this one has an interesting added feature in terms of support for using braces in algorithms.
http://www.gnuplot.info/announce.4.6.0

Building gnuplot 4.6 is similar to building 4.4.4 and is pretty straightforward:

sudo apt-get install libgd2-xpm-dev checkinstall

wget http://sourceforge.net/projects/gnuplot/files/latest/download?source=files
mv download\?source\=files gnuplot-4.6.tar.gz
tar -xvf gnuplot-4.6.tar.gz
cd gnuplot-4.6.0/

./configure --with-linux-vga
make
checkinstall -install=no
 sudo rm /usr/local/share/info/dir -rf
sudo dpkg -i gnuplot_4.6.0-1_amd64.deb

You may get an error if trying to install on a system with a home-compiled version of octave (see below).

The problem with handling small numbers is not present in this version (http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-bug-in-debian.html).

---

Error:

Selecting previously unselected package gnuplot.
(Reading database ... 258722 files and directories currently installed.)
Unpacking gnuplot (from gnuplot_4.6.0-1_amd64.deb) ...
dpkg: error processing gnuplot_4.6.0-1_amd64.deb (--install):
 trying to overwrite '/usr/local/share/info/dir', which is also in package octave 3.6.1-1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Errors were encountered while processing:
 gnuplot_4.6.0-1_amd64.deb

Solution:

 sudo dpkg --force-overwrite -i gnuplot_4.6.0-1_amd64.deb

109. Building Thunderbird 11 on Debian testing

The build is fairly straightforward and pretty much identical to building 10.0.2 (earlybird): http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-building.html

As always, uninstall existing versions before installing a new one.

--start here --
First install the dependencies:
sudo apt-get install libdbus-glib-1-dev gir1.2-notify-0.7 libnotify-dev yasm checkinstall libzip-dev zip 


Download the sources  and untar:
mkdir ~/tmp
cd ~/tmp

wget ftp://ftp.mozilla.org/pub/mozilla.org/thunderbird/releases/11.0/source/thunderbird-11.0.source.tar.bz2
tar -xvf thunder-bird-11.0.source.tar.bz2
cd comm-release/

Start the build
./configure --disable-necko-wifi
make -j3

3 is the number of cores +1. If you have a quadcore CPU substitute 3 with 5. The build takes a while so you will probably want to do a parallel build.

Finally, to install
sudo make install

checkinstall is segfaulting for me.

---

Error:

/home/me/tmp/comm-release/mozilla/js/src/config/nsinstall -R -m 644 ../mozilla-config.h ../../../config/nsStaticComponents.h  ../../../dist/include
make[5]: /home/me/tmp/comm-release/mozilla/js/src/config/nsinstall: Command not found
make[5]: *** [export] Error 127
make[5]: Leaving directory `/home/me/tmp/comm-release/mozilla/js/src/config'
make[4]: *** [export] Error 2
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory `/home/me/tmp/comm-release/mozilla/js/src'
make[3]: *** [export_tier_js] Error 2
make[3]: Leaving directory `/home/me/tmp/comm-release/mozilla'
make[2]: *** [tier_js] Error 2
make[2]: Leaving directory `/home/me/tmp/comm-release/mozilla'
make[1]: *** [default] Error 2
make[1]: Leaving directory `/home/me/tmp/comm-release/mozilla'

Solution:

I got this error because I accidentally untared the new sources into an existing directory with an older version of thunderbird. The solution was to delete the directory and untar the sources again.

105. Nwchem 6.1 with openmpi on ROCKS 5.4.3/CentOS 5.6

EDIT 18 May 2012: 
Compiling nwchem 6.1 with internal libs on debian: http://verahill.blogspot.com.au/2012/05/compiling-nwchem-61-with-internal-libs.html
Compiling nwchem 6.1 with openblas on debian: http://verahill.blogspot.com.au/2012/05/building-nwchem-61-on-debian.html


I can build and use nwchem on ROCKS 5.4.3 -- see instructions below.

EDIT: the gfortran version is GNU Fortran (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50)
On debian, which yields a segfaulting binary, the version is GNU Fortran (Debian 4.6.3-1) 4.6.3

I'm still having no luck building binaries which don't segfault on execution on debian though. The openmpi versions are the same for both ROCKS and debain: 1.4.3.

--START HERE --

ROCKS 5.4.3/CentOS
The build is essentially the same as for nwchem-6.0 (http://verahill.blogspot.com.au/2012/03/building-nwchem-60-on-rocks-543centos.html) - the single difference is that you need to define USE_MPIF4 or you get errors

To build:

wget http://www.nwchem-sw.org/images/Nwchem-6.1-2012-Feb-10.tar.gz

tar -xvf Nwchem-6.1-2012-Feb-10.tar.gz

cd nwchem-6.1/

export LARGE_FILES=TRUE

export TCGRSH=/usr/bin/ssh

export NWCHEM_TOP=/export/home/me/tmp/nwchem-6.1

export NWCHEM_TARGET=LINUX64

export NWCHEM_MODULES=all

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

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

cd $NWCHEM_TOP/src

make clean

make  nwchem_config

make  FC=gfortran

Building takes a little while.

---

Running:
Make sure that you make the reference to your openmpi libs permanent and make life easier by putting the following in your ~/.bashrc or /etc/profile:

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

export NWCHEM_EXECUTABLE=/export/home/me/tmp/nwchem-6.1/bin/LINUX64/nwchem
export NWCHEM_BASIS_LIBRARY=/export/home/me/tmp/nwchem-6.1/src/basis/libraries/
PATH=$PATH:/export/home/me/nwchem-6.1/bin/LINUX64

To run on multiple procs do

mpirun -n 3 nwchem input.nw

where 3 is the number of cores

100. Compile strace on ROCK 5.4.3

Maybe I've set things up wrong, but I can't find any strace package in the yum repos on my ROCKS 5.4.3 installation.

The compilation is very easy, but I'll show it here for those who feel nervous about compiling their own programmes:

mkdir ~/tmp
cd ~/tmp

The wget takes a while to figure out where to download from -- be patient:
wget http://sourceforge.net/projects/strace/files/latest/download?source=files
unxz strace-4.6.tar.xz
tar -xvf strace-4.6.tar
cd strace-4.6/
./configure
make
sudo make install

---

How to use:
While I've spent a couple of years with Debian I'm a CentOS newbie, and I keep being confused about the location of the libs -- for my compiles I need to put libs in /usr/lib, but to execute I seem to need to put symlinks in /usr/lib64. strace can help you track where a program is looking for its libs

e.g. to see what the program sinfo is up to
 strace -o sinfo.log sinfo

Here is a snippet from sinfo.log:

open("/lib64/libc.so.6", O_RDONLY)      = 3
open("/usr/local/lib/sinfo/librt.so.1", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/opt/openmpi/lib/librt.so.1", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/lib64/librt.so.1", O_RDONLY)     = 3
open("/usr/local/lib/sinfo/libdl.so.2", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/opt/openmpi/lib/libdl.so.2", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/lib64/libdl.so.2", O_RDONLY)     = 3

You can see that it e.g. looks for libdl.so.2 first in /usr/local/lib/sinfo, then in /opt/openmpi/lib/ and finally finds it in /lib64

93. Building and installing samba from source

Here's how to compile and get started with SAMBA, which may come in handy if you need to set up a mixed environment.

---

Compiling

sudo apt-get install build-essential


wget http://ftp.samba.org/pub/samba/samba-latest.tar.gz
tar -xvf samba-latest.tar.gz 
cd samba-3.6.3/
cd source3
./configure
make
sudo checkinstall

You may want to look through the checkinstall settings:

*****************************************
**** Debian package creation selected ***
*****************************************
This package will be built according to these values:
0 -  Maintainer: [ root@barebone ]
1 -  Summary: [ samba 3.6.3 ]
2 -  Name:    [ samba ]
3 -  Version: [ 3.6.3 ]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ amd64 ]
8 -  Source location: [ source3 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ source3 ]
12 - Conflicts: [  ]
13 - Replaces: [  ]
Enter a number to change any of them or press ENTER to continue:

Once the package is installed you need to put symlinks in your /usr/lib to the installed samba libs:
sudo ln -s /usr/local/samba/lib/libtalloc.so.2 /usr/lib/libtalloc.so.2
 sudo ln -s /usr/local/samba/lib/libtdb.so.1 /usr/lib/libtdb.so.1



Finally, create smb.conf in /etc/samba/ and make samba find it using a symlink
sudo mkdir /etc/samba
sudo touch /etc/samba/smb.conf
sudo ln -s /etc/samba/smb.conf /usr/local/samba/lib/smb.conf

Done. Sort of. You need to configure samba using smb.conf...a minimal configuration file can be found at the end of the post.

---

Errors:

checking for gcc... no
checking for cc... no
checking for cl.exe... no
configure: error: in `/home/verahill/tmp/samba-3.6.3/source3':
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details.

Solution:
sudo apt-get install build-essential

---

error:

-bash: smbclient: command not found

solution:
 put /usr/local/samba/bin in PATH
export $PATH=PATH:/usr/local/samba/bin

---

error:

/usr/local/samba/bin/smbclient: error while loading shared libraries: libtalloc.so.2: cannot open shared object file: No such file or directory

solution:
sudo ln -s /usr/local/samba/lib/libtalloc.so.2 /usr/lib/libtalloc.so.2

---

error:

/usr/local/samba/bin/smbclient: error while loading shared libraries: libtdb.so.1: cannot open shared object file: No such file or directory

solution:
 sudo ln -s /usr/local/samba/lib/libtdb.so.1 /usr/lib/libtdb.so.1

---

Error:

/usr/local/samba/bin/smbclient: error while loading shared libraries: libwbclient.so.0: cannot open shared object file: No such file or directory

Solution:
 sudo ln -s /usr/local/samba/lib/libwbclient.so.0 /usr/lib/libwbclient.so.0

---

error:
/usr/local/samba/bin/smbclient: Can't load /usr/local/samba/lib/smb.conf - run testparm to debug it
solution:
because I know where debian normally puts the smb.conf --
sudo mkdir /etc/samba
sudo touch /etc/samba/smb.conf
sudo ln -s /etc/samba/smb.conf /usr/local/samba/lib/smb.conf

---

Configuration:
Following https://www.samba.org/samba/docs/man/Samba-HOWTO-Collection/install.html#id2551954

Minimal /etc/samba/smb.conf:

[global]
workgroup = WKG
netbios name = MYNAME
[share1]
path = /tmp

Also, open up the relevant ports in your firewall:
Iptables
sudo iptables -A INPUT -p udp -m udp --dport 137 -j ACCEPT
sudo iptables -A INPUT -p udp -m udp --dport 138 -j ACCEPT
sudo iptables -A INPUT -p tcp --dport 139 -j ACCEPT
sudo iptables -A INPUT -p tcp --dport 445 -j ACCEPT

86. Building sinfo 0.0.45 on Debian Testing

I use sinfo to keep an eye on my cluster:
http://www.ant.uni-bremen.de/whomes/rinas/sinfo/#down

The debian repo version is 0.0.42-1
The latest version is sinfo 0.0.45

Here's the changelog since 0.0.42

sinfo 0.0.45- Tue, 13 Mar 2012 07:07:27 +0100corrected README compile hint for FreeBSDadded configure flag --disable-IPv6 to disable IPv6 supportsinfo 0.0.44 - Tue, 13 Dec 2011 18:32:33 +0100added reconnect for TCP connectionsadded LIBADD to make it --as-needed linkable tnx to T.Hardersinfo 0.0.43 - Thu, 01 Sep 2011 09:00:13 +0200fixed printing bug (integer underflow) when using sinfo -L or -W tnx to J.Erkkilae

There's little reason for compiling it yourself, but there's really no reason not to try either. I like debian and I like using apt-get to manage my system. Learning to be a bit more independent won't hurt though.
So here we go:

--START HERE --
wget http://www.ant.uni-bremen.de/whomes/rinas/sinfo/download/sinfo-0.0.45.tar.gz

tar -xvf sinfo-0.0.45.tar.gz 

cd sinfo-0.0.45/

sudo apt-get install libboost-dev libasio-dev libboost-signals-dev

./configure
(If your interface configuration has disabled IPv6 you must use ../configure --disable-IPv6 or sinfod will silently exit)
make 
sudo checkinstall


Done.

Start the sinfo daemon by
sudo sinfod --quiet --bcastaddress=192.168.1.255


Use
sinfo
to monitor

If you had sinfo installed before, autoremove it, then edit the left-behind /etc/init.d/sinfo script and change

/usr/sbin/sinfod

 to

 /usr/sbin/local/sinfod

Otherwise see http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-building_23.html for an example of writing your own init.d script.


To see all the cluster nodes running sinfo, just start
sinfo

If you don't see anything, then you've most likely not opened up your firewall -- you need to be able to listen to bcast.

---

Build errors:

---

Error:

In file included from message.cc:2:0:

message.h:5:34: fatal error: boost/shared_array.hpp: No such file or directory

compilation terminated.

make[2]: *** [message.lo] Error 1

make[2]: Leaving directory `/home/me/tmp/sinfo-0.0.45/libmessage'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/home/me/tmp/sinfo-0.0.45/libmessage'

make: *** [all-recursive] Error 1

Solution:

sudo apt-get install libboost-dev

---

Error:
In file included from udpmessagereceiver.cc:2:0:
udpmessagereceiver.h:4:20: fatal error: asio.hpp: No such file or directory
compilation terminated.
make[1]: *** [udpmessagereceiver.lo] Error 1
make[1]: Leaving directory `/home/me/tmp/sinfo-0.0.45/libmessageio'
make: *** [all-recursive] Error 1

Solution:
sudo apt-get install libasio-dev

which provides

/usr/include/asio.hpp
which is different from the asio.hpp included in libboost

---

Error:

/usr/bin/ld: cannot find -lboost_signals-mt

collect2: ld returned 1 exit status

make[2]: *** [sinfod] Error 1

make[2]: Leaving directory `/home/me/tmp/sinfo-0.0.45/sinfod'

make[1]: *** [all] Error 2

make[1]: Leaving directory `/home/me/tmp/sinfo-0.0.45/sinfod'

make: *** [all-recursive] Error 1

Solution:

sudo apt-get install libboost-signals-dev

---

Links to this post:
http://ant.uni-bremen.de/whomes/rinas/sinfo/

3. Compiling nwchem on Ubuntu 10.10 64 bit

** See post on 15/12/2011 for information about Debian 64 bit. It builds fine on Squeeze but not Wheezy. This seems to have to do with the version of mpich2.**

Figuring out how to compile nwchem with mpich support took a little while, but this seems to have worked:

First mpich2 and gfortran need to be installed (since it was not installed on a virgin system there may have been other required packages already installed)
sudo apt-get install mpich2 gfortran

I created a file called myconfig.sh in the nwchem directory, with the following content:

setenv LARGE_FILES TRUE
setenv TCGRSH /usr/local/bin/ssh
setenv NWCHEM_TOP /work/nwchem
setenv NWCHEM_TARGET LINUX64
setenv NWCHEM_MODULES all
setenv USE_MPI y
setenv USE_MPIF y
setenv MPI_LOC /usr
setenv MPI_LIB $MPI_LOC/lib
setenv MPI_INCLUDE $MPI_LOC/include/mpich2
setenv LIBMPI "-lfmpich -lmpich"
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran >& make.log

do a csh myconfig.sh and you should be good to go.

I then added the following to the end of my ~/.bashrc and sourced it:

PATH=$PATH://work/nwchem/bin/LINUX64
export NWCHEM_EXECUTABLE=/work/nwchem/bin/LINUX64/nwchem

Jobs can then be submitted (assuming that mpd is up) by
mpdrun -n 2 nwchem nameofjob.nw