Start with standard workstation install of GinGin 64.
add gv to packages

BLAS and LAPACK from acml:
  http://www.developwithamd.com/acml
  install in /usr/local/acml
  cd /usr/local/acml
  ln -s Doc/acml.info ../info
  cd /usr/local/lib64; ln -s -v ../acml/gnu64/* .
  cd /usr/local/lib; ln -s -v ../acml/gnu32/* .
  rpm -e octave lapack blas

ATLAS library for BLAS:
  http://sourceforge.net/project/showfiles.php?group_id=23725
  install in /usr/local/atlas
  cd /usr/local/lib64; ln -s -v ../atlas/lib/lib* .
  ln -s -v include/*.h ../include
  do-lab /sbin/ldconfig -v  # update linker everywhere
  #Contrary to the documentation, mpirun looks in /usr/local/share 
  ln -s -f /usr/local/mpich/util/machines/machines.LINUX /usr/local/share


build mpich-1.2.5:
 ./configure --disable-short-longs --with-comm=shared --with-device=ch_p4 --prefix=/usr/local --libdir=/usr/local/lib64 -opt="-O2 -m64" >& configure.log
  make >& make.log
gcc-3.3 bug stops compile of mpich:
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=11183
There is a bug in shared memory that causes semaphores
to pile up.  If this happens: do-lab semaphore

Set up all three ethernets as static in /etc/sysconfig/network-scripts
For some reason, eth1 and eth2 are switched...

Set up Mathematica fonts:  
  add lines to /etc/X11/fs/config

        /usr/local/mathematica/SystemFiles/Fonts/Type1,
        /usr/local/mathematica/SystemFiles/Fonts/X,
        /usr/lib/openoffice/share/fonts/truetype

  copy -a mathematica /usr/local/mathematica from barak
  service xfs restart

see support.wolfram.com/mathematica/systems/unix/interface/fonterrors.html

Get 32 bit glibc libraries from barak and add them to jael.
This allows a working compile of gcc-3.3:

  rpm -q --list glibc glibc-devel | grep "/lib/" > junk
  tar cvf 32_bit_libs.tar -T junk --absolute-names

  tar xf 32_bit_libs.tar --keep-old-files
  ../gcc-3.3/configure --enable-languages=c,c++,f77,java,objc
  make -j 2 bootstrap >& make_bootstrap.log &

Install java:
  Download install script from www.blackdown.org,
     j2re-1.4.2-rc1-linux-amd64.bin
  Install in /usr/local by running script
  ln -s /usr/local/j2re1.4.2/plugin/amd64/mozilla/libjavaplugin_oji.so /usr/lib64/mozilla/plugins

build kernel-2.4.21:

Network device support
  Ethernet (100 Mbit)
    Y 3COM 3C590 etc. support
  Ethernet (1000 Mbit)
    Y Broadcom Tigon 3 support
  Wireless LAN
    N Wireless LAN (otherwise, a module compile error)
  WAN 
    N WAN (otherwise, module compile error)
Networking options
  N  IP: multicasting (cruft)
  N  IP: advanced router (cruft)
  Y  IP: kernel level autoconfiguration
  Y  IP: DHCP support
File systems
  Network file systems
    Y NFS file system suppor
    Y Root file system
Turned off sound support (due to a module compile error)
Turned off support, IrDA, Firewire, and Bluetooth (cruft)

  make -j 4 dep
  make -j 4 bzImage; make -j 4 modules

Install for use on diskless nodes.  This kernel
will not work on the server since it has NFS root file system.

  cp arch/x86_64/boot/bzImage /tftpboot/vmlinuz
  make modules_install INSTALL_MOD_PATH=/export/abimelech
  cp System.map /export/abimelech/System.map-2.4.21
  cd /export/abimelech; ln -s System.map-2.4.21 System.map

Copy files over to diskless nodes

  cp -a /dev/ /export/abimelech
  cp -a /etc /export/abimelech
  cp -a /var /export/abimelech
  cp -a /bin /export/abimelech
  cp -a /sbin /export/abimelech
  cp -a /root /export/abimelech
  cp -a /mnt /export/abimelech
  cp -a /lib /export/abimelech
  cp -a /lib64 /export/abimelech
  mkdir /export/abimelech/usr
  mkdir /usr45
  mkdir /export/abimelech/usr/bin
  mkdir /export/abimelech/home
  mkdir /export/abimelech/tmp
  #
  # else XFree86 doesn't start
  # crashes with obscure error 
  # "  Fatal server error : could not open default font Fixed ."
  #
  chomod a+w /export/abimelech/tmp 
  mkdir /export/abimelech/proc
  # no extra network cards
  rm -f /export/abimelech/etc/sysconfig/network-scripts/ifcfg-eth2
  rm -f /export/abimelech/etc/raidtab #no raid
  echo "ServerName jael" >> /export/abimelech/etc/cups/client.conf

turn off ipforwarding in /export/abimelech/etc/sysctl.conf
modify /export/abimelech/modules.conf to remove network card
remove extra kernel versions from /export/abimelech/lib/modules

To test the file system, try /usr/sbin/chroot /exports/abimelech.
Also ldd will tell if a given binary has the libraries needed.
The script /etc/rc.d/rc.sysinit is based on on /bin/bash.  
However, /bin/bash needs two /user/bin files to run:

  cp -a /usr/bin/id /export/abimelech/usr/bin
  cp -a /usr/bin/dircolors /export/abimelech/usr/bin

untar the modified files from barak:

  cd /; tar xf /export/barak_export.tar
  
Since many initscripts need /usr files, add to the end of 
/export/abimelech/rc.d/rc.sysinit.
Portmapper is not started, so we need -o nolock.
We need /usr mounted before we can start portmap.

  action $"Mounting /usr via nfs:  " mount -o nolock /usr

Modify /etc/rc.d/init.d/halt:

  # Try them all, one last time.
  #BvdS:  this will unmount / and we have trouble
  #umount -a -f

Modify /etc/rc.d/init.d/netfs (don't include /usr in list):

93c93
< 		remaining=`LC_ALL=C awk '!/^#/ && $3 ~ /^nfs/ && $2 != "/" {print $2}' /proc/mounts`
---
> 		remaining=`LC_ALL=C awk '!/^#/ && $3 ~ /^nfs/ && $2 != "/" && $2 != "/usr" {print $2}' /proc/mounts`
97c97
< 				action $"Unmounting NFS filesystems (retry): " umount -f -l -a -t nfs
---
> 				action $"Unmounting NFS filesystems (retry): " umount $remaining
99c99
< 				action $"Unmounting NFS filesystems: " umount -f -l -a -t nfs
---
> 				action $"Unmounting NFS filesystems: " umount $remaining
102c102
< 			remaining=`LC_ALL=C awk '!/^#/ && $3 ~ /^nfs/ && $2 != "/" {print $2}' /proc/mounts`
---
> 			remaining=`LC_ALL=C awk '!/^#/ && $3 ~ /^nfs/ && $2 != "/" && $2 != "/usr" {print $2}' /proc/mounts`

/export/abimelech/etc/rc.d/init.d/network:

198,205c198
< 	for i in $interfaces ; do
< 		eval $(fgrep "DEVICE=" ifcfg-$i)
< 		if [ -z "$DEVICE" ] ; then DEVICE="$i"; fi
< 
< 		if ! check_device_down $i; then
< 		   action $"Shutting down interface $i: " ./ifdown $i boot
< 		fi
< 	done
---
> 	echo "Shut down of interfaces disabled"

on abimelech, turn off nfs,tftp,dhcpd using /sbin/chkconfig ... off
and /sbin/service ... stop

on jepthah:
  echo "bvds@bvds" > /root/.forward

to get network stuff to work:
  
  etc/sysconfig/network contains only "NETWORKING=yes"
  make etc/hosts.equiv file
  chmod go-r etc/hosts.equiv
  modify etc/xinetd.d/rsh and rlogin to turn off disable
  /sbin/service xinetd restart
  add rsh and rlogin to etc/securetty (allows root rsh)
  add .rhosts  file to /root (allows root rsh)

to make more nodes:
  new entry in /etc/dhcpd.conf
  new entry in /etc/hosts
  copy /exports/directory
  edit etc/fstab for the node


------------------------------------------------------------

make local lab user:

make initial account on one machine:
/usr/sbin/useradd -d /lhome -s /bin/tcsh -m luser
rm -r -f /etc/skel
cp -a -f /lhome /etc/skel
copy /etc/skel to all other machines
do-lab /usr/sbin/useradd -d /lhome -s /bin/tcsh -m luser
#
# there must be a better way of doing this
# for instance, the user could be sent over NIS
do-lab passwd luser

------------------------------------------------------------

          Sept. 2003 linux kernel 2.4.22 install 
          with lm_sensors 2.8.0 patch

 cd linux-2.4.22
 cp ../linux-2.4.20-9.2/configs/kernel-2.4.20-x86_64-smp.config .config
 patch -p 1 < /home/bvds/scratch/lm_sensors/linux-2.4.22-i2c-2.8.0.patch
 cp -a /usr/src/linux-2.4.22 /usr/src/linux-2.4.22-diskless

on standard:
Network device support
  Wireless LAN
    N Wireless LAN (otherwise, a module compile error)
  WAN 
    N WAN (otherwise, module compile error)
Character devices
  I2C support
    M I2C support
    M I2C PCF 8584 interfaces
        M elector ISA card  (no idea if I need this)
    M I2C device interface
    M I2C /proc interface (definitely need this)
Turned off sound support (due to a module compile error)
Turned off IrDA, Firewire, and Bluetooth (cruft)

on diskless nodes:

Network device support
  Ethernet (100 Mbit)
    Y 3COM 3C590 etc. support
  Ethernet (1000 Mbit)
    Y Broadcom Tigon 3 support
  Wireless LAN
    N Wireless LAN (otherwise, a module compile error)
  WAN 
    N WAN (otherwise, module compile error)
Networking options
  N  IP: multicasting (cruft)
  N  IP: advanced router (cruft)
  Y  IP: kernel level autoconfiguration
  Y  IP: DHCP support
SCSI support
  M  SCSI support
  M  SCSI disk support
Character devices
  I2C support
    M I2C support
    M I2C PCF 8584 interfaces
        M elector ISA card  (no idea if I need this)
    M I2C device interface
    M I2C /proc interface (definitely need this)
File systems
  Network file systems
    Y NFS file system support
    Y Root file system
USB support
  M USB mass storage support (for memory sticks)
Turned off sound support (due to a module compile error)
Turned off IrDA, Firewire, and Bluetooth (cruft)

Install on jael is standard:  need to modify grub
  cp System.map /boot/System.map-2.4.22
  cp arch/x86_64/boot/bzImage /boot/vmlinuz-2.4.22
  # it automatically includes the raid1.o module
  cd /boot; /sbin/mkinitrd -v /boot/initrd-2.4.22.img 2.4.22

Add to /etc/modules.conf:
  # since we don't have a sound card:
  alias char-major-14 off 

Install for use on diskless nodes.  This kernel
will not work on the server since it has NFS root file system.
  cp arch/x86_64/boot/bzImage /tftpboot/vmlinuz-2.4.22
modify tftpboot configure files
  make modules_install INSTALL_MOD_PATH=/export/barak
  cp System.map /export/barak/System.map-2.4.22
  cd /export/barak; ln -s System.map-2.4.22 System.map

------------------------------------------------------------------

   lm_sensors install on lab machines
   
If we do the kernel patches discussed above,
we don't have to do anything with i2c installation.

Modifications to lm_sensors Makefile for use on jael:
  KERNELVERSION := 2.4.22
  LINUX := /usr/src/linux-2.4.22-diskless
  I2C_HEADERS := $(LINUX_HEADERS)
  PREFIX := /usr/local
  MODPREF := /export/barak/lib/modules/2.4.2
  ETCDIR := /export/barak/etc
  LIBDIR := $(PREFIX)/lib64
  CFLAGS := -m64
lm_sensors Makefile has some lines missing the tabs
  make all; make install

after installing, on barak run:
  depmod -a
  /sbin/modprobe i2c-proc
  lspci -v  # see what is there (use 8111 )
typo on first line of http://www2.lm-sensors.nu/~lm78/cvs/lm_sensors2/doc/busses/i2c-amd8111
  /sbin/modprobe i2c-amd8111
  /sbin/ldconfig
  prog/mkdev/mkdev.sh
  prog/detect/sensors-detect
  
on barak, add to /etc/modules.conf:
  # I2C module options
  alias char-major-89 i2c-dev
on barak, add to /etc/rc.d/rc.local:
  # I2C adapter drivers
  /sbin/modprobe i2c-isa
  # I2C chip drivers
  /sbin/modprobe w83781d
  # sleep 2 # optional
  /usr/local/bin/sensors -s # recommended

copy from barak to other machines:
  etc/sensors.conf
  etc/modules.conf
  etc/rc.d/rc.local
  lib/modules/2.4.22  (and subdirectories)

----------------------------------------------------------------------------

Nov. 11 update:
(also made separate update to kernel on gideon to support sound card)

rpm -U esound-devel-0.2.28-5.1.x86_64.rpm esound-0.2.28-5.1.x86_64.rpm

rpm -U XFree86-4.3.0-16.EL.x86_64.rpm  XFree86-libs-4.3.0-16.EL.x86_64.rpm XFree86-xfs-4.3.0-16.EL.x86_64.rpm  XFree86-twm-4.3.0-16.EL.x86_64.rpm XFree86-devel-4.3.0-16.EL.x86_64.rpm XFree86-libs-data-4.3.0-16.EL.x86_64.rpm

March 2, 2004 update:  usb-storage only on gideon in kernal
/exports/vmlinuz-2.4.22-sound

------------------------------------------------------------------------------