Last update: 04/09/09

A lot of these notes are geared toward 64-bit arch.  Make sure you point `wget`
to the proper files for your architecture.


*** MPICH2 ***

    1. mkdir /home/cmalone/install/mpich2/mpich2-1.0.7

    2. mkdir /usr/local/mpich2

    3. export CC="gcc"
       export F90="gfortran"
       export CXX="g++"
       export F77="gfortran"

    4. mkdir /home/cmalone/install/mpich2/mpich-build

    5. in /home/cmalone/install/mpich2/mpich-build

       ../mpich2-1.0.7/configure -prefix=/usr/local/mpich2/ --without-mpe --with-device=ch3:ssm --enable-f90 --enable-cxx >& configure.out

    6. gmake

    7. (as root) gmake install

    8. add 
 
       export PATH=/usr/local/mpich2/bin:$PATH
       export GFORTRAN_UNBUFFERED_ALL=1
 
       to .bashrc

    9. create .mpd.conf with secretword=?

       and readable and writeable only by you

   10. test mpd:

       mpd &
       mpiexec -n 1 /bin/hostname
       mpdallexit

   11. setup root:

       make /etc/mpd.conf with secret work
       chmod 600 /etc/mpd.conf

   12. in /etc/rc.local

       /usr/local/mpich2/bin/mpd --ncpus=2 >&	/usr/local/mpich2/bin/mpd.out &

   13. in .bashrc

       export MPD_USE_ROOT_MPD=1


*** HDF5 for use with FLASH2.5 ***   

    Note: The version of HDF5 stored in the Fedora repositories is version
          1.8.x which has new API mappings which are incompatible with the 
	  FLASH2.5 calls to HDF5 functions.  
	  http://hdf.ncsa.uiuc.edu/HDF5/release/obtain5.html provides 
	  several binaries for various architectures and compilers.  As of this
	  writing, there was no 64-bit binary available which used the gnu
	  compilers.  Therefore, we build from source.

    1. mkdir ~/install/hdf5

    2. mkdir /usr/local/hdf5

    3. obtain latest source from 
       http://hdf.ncsa.uiuc.edu/HDF5/release/obtain5.html and unpack in 
       ~/install/hdf5

       wget "ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.1.tar.gz"

    4. export CC="gcc"
       export FC="gfortran"

    5. in ~/install/hdf5/hdf5-1.8.1 (as root)

       ./configure --prefix=/usr/local/hdf5 --enable-fortran --with-default-api-version=v16 >& config.out

    6. make (as root)

    7. make install (as root)

    8. add

       export LD_LIBRARY_PATH=/usr/local/hdf5/lib:$LD_LIBRARY_PATH

       to .bashrc
       

*** IDL 7.0 ***

    1. mkdir ~/install/idl

    2. mv idl70linux.x86.tar.gz ~/install/idl
       cd ~/install/idl
       tar xzf idl70linux.x86.tar.gz

    3. move the license to the proper location
       Note: we had to regenerate the license for the new (7.0) version of IDL

       cp ~/license.dat ./license

    4. after untarring and moving license.dat, run (as root)
 
       ./install

    5. agree to the terms and conditions

    6. choose installation option 1; this creates the appropriate symbolink 
       links in /usr/local/itt/

    7. add 
   
       /usr/local/itt/idl70/bin/lmgrd -c /usr/local/itt/license/license.dat > /usr/local/itt/idl70/bin/logfile

       to /etc/rc.d/rc.local

    8. add
    
       IDL_DIR=/usr/local/itt/idl70
       export IDL_PATH=$IDL_PATH:~/FLASH2.5/tools/fidlr2:$IDL_DIR/lib:$IDL_DIR
       
       to .bashrc


*** VisIt ***
    NOTE: The pre-built binaries available from 
          https://wwci.llnl.gov/codes/visit seem to be working for the 64-bit
	  architecture.  If the following does not work on your machine you 
	  might want to build from source using the build_visit script 
	  available from the above website.

    1. mkdir ~/install/visit

    2. in ~/install/visit

       wget "https://wci.llnl.gov/codes/visit/1.10.0/visit1_10_0.linux-x86_64.tar.gz"

    3. after untarring, add

       export PATH=$PATH:~/install/visit/visit/bin

       to .bashrc

*** Setting Up New Disk ***
    We bought a new 750 GB disk and plugged it into SATA0 on the motherboard.
    With no other disk plugged in, the OS knew to boot from this HDD.  We 
    plugged the old 300 GB disk into SATA2 and made sure the BIOS knew to boot
    from SATA0.  Once booted into Fedora, we opened up a terminal and setup an
    ext3 filesystem on the old 300 GB drive:

    1. remove the old partitions and create a new one
    
       /sbin/fdisk /dev/sdb

         (p) to print out the information to make sure we have the correct HDD

         (d) is used to delete the already existent partitions on the old drive

	 (n) to create new partition
	   (p) as a primary partition of number (1) and default starting
           location for first cylinder

	 (w) to write it out to the partition table

    2. setup filesystem with large blocksize (4096)

       /sbin/mkfs.ext3 -b 4096 /dev/sdb1

    3. mkdir /backup

    4. change /etc/fstab to automagically mount /dev/sdb1 to /backup at boot

       [cmalone@xrb ~]$ more /etc/fstab
       /dev/VolGroup00/LogVol00 /                       ext3    defaults        1 1
       UUID=9b5e0481-a455-47eb-b477-0bd8407a8ae9 /boot  ext3    defaults        1 2
       tmpfs                   /dev/shm                tmpfs   defaults        0 0
       devpts                  /dev/pts                devpts  gid=5,mode=620  0 0
       sysfs                   /sys                    sysfs   defaults        0 0
       proc                    /proc                   proc    defaults        0 0
       /dev/VolGroup00/LogVol01 swap                    swap    defaults        0 0
       /dev/sdb1               /backup                 ext3   defaults         1 3