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

341. Upgrading/installing BankID on 64 bit linux

Note: the post below is aimed at installing BankID on Debian (should be ok for ubuntu/mint too). For Arch Linux, see here (item 16)

There are a few ways to get around the rotten behaviour of bankid. This is one of them:

NOTE: to install nspluginwrapper you need to enable the stable/squeeze repos by e.g. adding

deb http://ftp.au.debian.org/debian/ squeeze main contrib non-free

to your /etc/apt/sources.list.

That's normally reasonably safe since apt by default pulls in the newest package and I haven't had any issues. Just be careful though.

You can also install nspluginwrapper by compiling it as shown here: http://verahill.blogspot.com.au/2013/03/366-nspluginwrapper-on-debian.html


Note that there's a FOSS alternative in Fribid (http://verahill.blogspot.se/2012/02/debian-testing-wheezy-64-fribid-as.html) which seems to be working perfectly -- and if you can use it, use it. The main limitation is that in practice you'll have to collect your certificate/ID with it, since newer versions of BankID saves the ID in an incompatible format. Like many foreigners, I don't have the opportunity to visit Sweden for the sole sake of picking up a new ID, so I'm stuck with BankID. But you may not be.

0. Things to install:

sudo apt-get install iceweasel nspluginwrapper ia32-libs

1. Download BankID and uninstall any previous installations

cd ~/Downloads
mkdir bankid
cd bankid
wget https://install.bankid.com/Download?defaultFileId=Linux -O bankid.tar.gz
tar xvf bankid.tar.gz
cd BISP-4.19.1.11663/
sudo sh install.4.19.1.11663.sh u

2. If you're upgrading, make sure to remove any previous libplugins.so

sudo updatedb && locate libplugins.so

/home/me/Downloads/bankid/BISP-4.19.1.11663/libplugins.so
/usr/lib/mozilla/plugins/libplugins.so
/usr/lib/mozilla/plugins/npwrapper.libplugins.so
/usr/lib/nspluginwrapper/plugins/npwrapper.libplugins.so

sudo nspluginwrapper -r /usr/lib/mozilla/plugins/npwrapper.libplugins.so
sudo rm /usr/lib/mozilla/plugins/libplugins.so
sudo rm /usr/lib/nspluginwrapper/plugins/npwrapper.libplugins.so

3. Install the new version

sudo sh install.4.19.1.11663.sh i

Installing BankID Security Application
ln: failed to create symbolic link `/usr/lib/firefox-addons/plugins': No such file or directory
WARNING: Failed installing plugin for Firefox 3. Manually add symlink to libplugins.so in your Firefox 3 plugin directory if this browser is to be used.
Installation complete.
sudo nspluginwrapper --install /usr/local/lib/personal/libplugins.so

4. Test your installation
Don't bother with test.bankid.com since the idiots won't let you test anything that identifies itself as 64 bit (more about that later). Instead

• go to http://www.skatteverket.se
• click on personbevis
• log in. This should work

5. Testing against test.bankid.com
Everything is in working order but for some idiotic reason bankid.com won't even allow you to test you fancy new 64 bit installation -- and it all boils down the useragent string in iceweasel/firefox identifying itself as running on a 64 bit system (paradoxically, a real 32 bit browser running in a chroot won't work either since the kernel is 64 bit -- in schroot you can use personality=linux32 to get around it, but good luck dealing with the massive memory leaks).

Anyway,

• open your iceweasel browser
• type in about:config in the address bar
• promise that you'll be careful
• right-click on the page, select New, String
• In the first box, type general.useragent.override
• In the second box paste Mozilla/5.0 (X11; Linux i686; rv:10.0.12) Gecko/20100101 Firefox/10.0.12 Iceweasel/10.0.12

You can now go to https://test.bankid.com. I find this a bit humiliating though, and you can use bankid everywhere but bankid.com without having to set the useragent to identify your system as being i686.

---

If you're having issues, the first thing to check is about:plugins in firefox:

340. Issues when compiling Nwchem 6.1.1 -- missing *.fh in src/include

The problem:
If you modify the nwchem sources, build, do a make realclean and then pack them up to export your patched sources to other nodes you might find that compiling doesn't work that well, yielding errors such as (I'll list them all to help google):

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/stdio.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/nwc_const.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1
nwchem.F:3:0: fatal error: errquit.fh: No such file or directory
compilation terminated.
stubs.F:15:0: fatal error: errquit.fh: No such file or directory

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/errquit.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(bas_input.o)'.  Stop.

and

/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util.fh:1:0: fatal error: printlevels.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(bas_input.o)] Error 1
make[1]: *** Waiting for unfinished jobs....

and

basisP.F: In function 'nbf_from_ucont':
basisP.F:427:0: warning: '__result_nbf_from_ucont' may be used uninitialized in this function [-Wmaybe-uninitialized]
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/msgids.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(geom.o)'.  Stop.

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)'.  Stop.

and

In file included from pstat_alloc.F:12:0:
/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh:11:0: fatal error: bitops_decls.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)] Error 1

and

In file included from pstat_alloc.F:12:0:
/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh:12:0: fatal error: bitops_funcs.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)] Error 1

and

make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/itri.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(sym_sh_pair.o)'.  Stop.
make[2]: *** Waiting for unfinished jobs....

and

make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bgj.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwints.a(exactd_mem.o)'.  Stop.

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/numerical_constants.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/librimp2.a(rimp2_v_e2.o)'.  Stop.

and

make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util_sgroup.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libdntmc.a(gibbs.o)'.  Stop.

and

nwchem.F:11:0: fatal error: bgj_common.fh: No such file or directory

---

Solution:
This has been mentioned before on the nwchem forum, but not in explicit enough detail.
The solution is to copy a series of files from src/util and to remove make realclean from your build instructions (or at least do the copying after the make realclean step).

Copy these files

cp src/util/stdio.fh src/include/
cp src/util/nwc_const.fh src/include/
cp src/util/errquit.fh src/include/
cp src/util/util.fh src/include/
cp src/util/printlevels.fh src/include/
cp src/util/msgids.fh src/include/
cp src/util/bitops.fh src/include/
cp src/util/bitops_decls.fh src/include/
cp src/util/bitops_funcs.fh src/include/
cp src/util/itri.fh src/include/
cp src/util/bgj.fh src/include/
cp src/util/numerical_constants.fh src/include/
cp src/util/util_sgroup.fh src/include/
cp src/util/bgj_common.fh src/include/

Then build, using e.g.

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"
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran 1>make.log 2>make.err
export FC=gfortran
cd ../contrib
./getmem.nwchem