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README_macprolinux
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Installing linux and simulation on a mac pro:
See notes at bottom for mac pro 2009
(we do this because linux runs faster than OS X, and to keep things
homogeneous).
Resize the hard drive partition: Use bootcamp assistant for this
(pre-installed on the mac).
Then use "diskutil disableJournal disk0s1" or something like that to
disable journaling so that linux can write to it. ("diskutil list" will
show what is available)
install refit (google it).
This will then allow dual booting.
Put legacyfirst in the config file after installation (NOT the disk
image file - which is read only).
Then, may need to poweroff rather than reboot.
Download the ubuntu TEXT installer, 64 bit, desktop edition.
Boot into this. Don't worry if it takes a while.
When partitioning disks, select just 1 large ext3 partition.
Don't bother with swap - will create that later as a swapfile.
After install, reboot, and select the new install at refit.
If you get a "no bootable device" message, see the ubuntu
forums... but basically, you want to select the disk partition tool
from the refit menu. Then after this, select linux again to boot.
This may freeze at the refit penguin screen - in which case, power off
the machine, power back on, and try again. This worked for me...
Add http_proxy="http://wwwcache.dur.ac.uk:8080" to /etc/bash.bashrc
cpufreq-selector -c N -g performance where N is 0 to 7.
/etc/event.d/control-alt-delete
/etc/cron.hourly/autopoweroff
Create /etc/apt/apt.conf and insert:
Acquire::http::Proxy "http://wwwcache.dur.ac.uk:8080";
Run setup.sh, setup[2-6].sh (latest versions on gig44) - remember to
read them first, and see what files need copying. setup3.sh needs
doing by hand.
Customisations:
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install emacs
#swapsudo apt-get install python-mode
sudo apt-get install build-essential
sudo apt-get install gfortran
sudo apt-get install g77
sudo apt-get install python-dev
sudo apt-get install swig
sudo apt-get install manpages-dev
sudo apt-get install nfs-kernel-server
sudo apt-get install python-processing
Enable swap:
dd if=/dev/zero of=/swapfile bs=1024 count=33554432
mkswap /swapfile
swapon /swapfile
Add to /etc/fstab:
/swapfile swap swap defaults 0 0
python-Scientific
python-mpi
python-scipy
ubuntu boot without GUI (save some memory):
create /etc/inittab with:
id:2:initdefault:
and then changes services for run level 2...
ie delete entries in /etc/rc2.d/
Install mkl:
download it, and then when you get the email, use the licence file
(not just the serial number) given here.
Optional - install openmpi. I don't think this is actually
needed... it was when I was using mkl scalapack, but am not anymore...
Then do all the standard aosim installations. When doing numpy/scipy,
you may wish to use the mkl blas for these...
to do this, in numpy/, copy site.cfg.example to site.cfg, and edit it,
the fftw lines and the mkl lines. Then do a setup.py build and
install.
Note, mkl 10.3.0.020 doesn't work, but 10.0.1.014 does work - so use
this one.
Also, put the library path (/opt/intel/mkl/10.0.1.014/lib/em64t in
/etc/ld.so.conf and run ldconfig. This ensures that mpirun works -
otherwise some of the jobs can't find the correct directory for mkl...
When building scipy with mkl, it failed because it wasn't given the
directory for mkl includes. So, I just softlinked
ln -s /opt/intel/mkl/10.0.1.014/include/* build/src.linux-x86_64-2.5/
and it then seemed to work.
Actually, don't seem to need to do this anymore...
For NIS/automount, follow:
https://help.ubuntu.com/community/SettingUpNISHowTo
https://help.ubuntu.com/community/SettingUpNFSHowTo#Mounts
The nis domain is giggroup
The nis server is 192.168.3.18.
If you have trouble with /etc/init.d/nis restart, try editing
etc/yp.conf
Also, edit /etc/cron.daily/apt search for http_proxy and insert your
proxy manually - the default stuff doesn't seem to work. If testing,
can use
sudo run-parts -v /etc/cron.daily
When doing this, comment out the random_sleep part of apt (2 places)
otherwise the test will block for some minutes...
MacPro 2009 with Ubuntu 9.04:
Have to use the standard desktop installer (not alternative
installer). The network doesn't work, so get hold of a usb-ethernet
adaptor (Deli has one), and use this to do the following:
sudo apt-get build-dep linux
sudo apt-get install fakeroot build-essential makedumpfile
mkdir kernel
cd kernel
sudo apt-get build-dep linux-image-$(uname -r)
apt-get source linux-image-$(uname -r)
Then modify linux-2.6.*/drivers/net/e1000e/ files with the following
patch:
From: Bruce Allan <[email protected]>
Add device ID for a new variant of the 82574 adapter.
Signed-off-by: Bruce Allan <[email protected]>
Acked-by: John Ronciak <[email protected]>
Signed-off-by: Jeff Kirsher <[email protected]>
---
drivers/net/e1000e/hw.h | 1 +
drivers/net/e1000e/netdev.c | 1 +
2 files changed, 2 insertions(+), 0 deletions(-)
diff --git a/drivers/net/e1000e/hw.h b/drivers/net/e1000e/hw.h
index 11a2f20..d8b8229 100644
--- a/drivers/net/e1000e/hw.h
+++ b/drivers/net/e1000e/hw.h
@@ -339,6 +339,7 @@ enum e1e_registers {
#define E1000_DEV_ID_82573E_IAMT 0x108C
#define E1000_DEV_ID_82573L 0x109A
#define E1000_DEV_ID_82574L 0x10D3
+#define E1000_DEV_ID_82574LA 0x10F6
#define E1000_DEV_ID_82583V 0x150C
#define E1000_DEV_ID_80003ES2LAN_COPPER_DPT 0x1096
diff --git a/drivers/net/e1000e/netdev.c b/drivers/net/e1000e/netdev.c
index f388a01..15424ba 100644
--- a/drivers/net/e1000e/netdev.c
+++ b/drivers/net/e1000e/netdev.c
@@ -5130,6 +5130,7 @@ static struct pci_device_id e1000_pci_tbl[] = {
{ PCI_VDEVICE(INTEL, E1000_DEV_ID_82573L), board_82573 },
{ PCI_VDEVICE(INTEL, E1000_DEV_ID_82574L), board_82574 },
+ { PCI_VDEVICE(INTEL, E1000_DEV_ID_82574LA), board_82574 },
{ PCI_VDEVICE(INTEL, E1000_DEV_ID_82583V), board_82583 },
{ PCI_VDEVICE(INTEL, E1000_DEV_ID_80003ES2LAN_COPPER_DPT),
Probably you can just insert these 2 lines by hand... (the 2 lines
starting with +) - this is what I did.
Then:
chmod a+x debian/scripts/misc/*
debian/scripts/misc/oldconfig amd64
CONCURRENCY_LEVEL=8 AUTOBUILD=1 NOEXTRAS=1 skipabi=true fakeroot debian/rules binary-generic
sudo dpkg -i linux-image-2.6.28-13*.deb
sudo apt-get install linux-headers-2.6.28-13
sudo dpkg -i linux-headers-2.6.28-13*.deb
Then reboot, and network should work (after standard configuration if
not using DHCP)
A script can be used to install simulation libraries, (not this may
not work on the 2009 mac pro particularly the stuff turning off X).:
#files needed:
#setupswap: contains
#/swapfile swap swap defaults 0 0
#setupbash: contains
export PYTHONPATH=/home/ali/cvsstuff/aosim:/home/ali/py
export PYTHONSTARTUP=/home/ali/.init.py
export PATH=$PATH:/home/ali/cvsstuff/aosim/gui/bin
#setup etcbashrc
export EDITOR="emacs -nw"
export CVSROOT=":pserver:$USER@localhost:/cfai_sw"
alias cvstunnel="ssh -f -L 2401:localhost:2401 -l cvsd -N aipc42"
alias cvslogin="cvs login"
dd if=/dev/zero of=/swapfile bs=1024 count=33554432
mkswap /swapfile
swapon /swapfile
cat setupswap >> /etc/fstab
apt-get --yes update
apt-get --yes upgrade
apt-get --yes install build-essential
apt-get --yes install gfortran
apt-get --yes install g77#doesnt install???
apt-get --yes install python-dev
apt-get --yes install swig
apt-get --yes install manpages-dev
apt-get --yes install emacs
apt-get --yes install python-scipy
#apt-get --yes install python-imaging
apt-get --yes install python-matplotlib
apt-get --yes install gsl-bin
apt-get --yes install libgsl0-dev
apt-get --yes install openssh-server
Then, by hand:
mkdir /downloads
cd /downloads
scp ali@aicp52:l_mkl*.tgz .
scp ali@aipc52:NCOM* .
tar -zxvf l_mkl_p_10.0.1.014.tgz
cd l_mkl*
./install.sh
Use option 2, then specify the path to /downloads/NCOM*...
Then:
#needs setupetcbashrc, setupbash, and the various install files (eg
pygist, mpich2, scientificPython, fftw3 fftw2)
apt-get --yes install cvs
cat setupetcbashrc >> /etc/bash.bashrc
cat setupbash >> /home/ali/.bashrc
echo /opt/intel/mkl/10.0.1.014/lib/em64t >> /etc/ld.so.conf
ldconfig
cd /downloads
tar -zxvf pygist-1.5.28.tar.gz
cd pygist-1.5.28
apt-get --yes install xorg-dev
python setup.py config
python setup.py build
python setup.py install
cd ..
tar -zxvf mpich2-1.0.8.tar.gz
cd mpich*
./configure
make
make install
cd ..
tar -zxvf ScientificPython*
cd ScientificPython*
python setup.py build
python setup.py install
cd Src/MPI
python compile.py
cp mpipython /usr/local/bin/
cd ../..
cd ..
apt-get --yes install python-tk
apt-get --yes install libpng-dev
apt-get --yes install python-gtk2-dev
tar -zxvf fftw-3*
cd fftw-3*
make clean
./configure --enable-shared
make install
make clean
./configure --enable-shared --enable-threads
make install
make clean
./configure --enable-shared --enable-threads --enable-float
make install
make clean
./configure --enable-shared --enable-float
make install
make clean
cd ..
tar -zxvf fftw-2.1.5.tar.gz
cd fftw-2.1.5
make clean
./configure --enable-shared
make install
make clean
./configure --enable-shared --enable-float --enable-type-prefix
make install
cd ..
tar -zxvf numpy*
cd numpy*
cp site.cfg.example site.cfg
echo "[fftw]" >> site.cfg
echo "libraries = fftw3" >> site.cfg
echo "[mkl]" >> site.cfg
echo "library_dirs = /opt/intel/mkl/10.0.1.014/lib/em64t" >> site.cfg
echo "lapack_libs = mkl_lapack" >> site.cfg
echo "mkl_libs = mkl, guide" >> site.cfg
python setup.py build
python setup.py install
cd ..
tar -zxvf scipy*
cd scipy*
python setup.py build
python setup.py install
cd ..
sudo apt-get install nfs-kernel-server nfs-common
echo "id:2:initdefault" > /etc/inittab
rm /etc/rc2.d/S30gdm
echo "umask 0011" >> /etc/bash.bashrc
Other things: Also see README.
on fedora: yum install atlas-devel
on ubuntu libatlas-dev libatlas-base-dev