Gabriel Altay's Fortran 90 Linux Software Installation Notes

Intel Fortran Compiler

• Find a link to the free non-comercial download here. (I installed version 10.1, you might find a different version by following the link)
• You will be asked for an email address and be given a seriel number. Afterwards you can choose the appropriate tar file for your system. A set of confusing letters and numbers label the different files. Use the excerpt below to find the correct file for your computer. (For me it was IA-32 so I'll make that assumption in the rest of this document)
  
  

  *IA-32*
  IA-32 Architecture refers to systems based on 32-bit processors generally compatible with the Intel Pentium(R) II processor, (for example, Intel(R) Pentium(R) 4 processor or Intel(R) Xeon(R) processor), or processors from other manufacturers supporting the same instruction set, running a 32-bit operating system ("Linux x86").
  
  *Intel(R) 64 *
  Intel(R) 64 Architecture refers to systems based on IA-32 architecture processors which have 64-bit architectural extensions, (for example, Intel(R) Core(TM)2 processor family), running a 64-bit operating system ("Linux x86_64"). If the system is running a 32-bit version of the Linux operating system, then IA-32 architecture applies instead. Systems based on AMD* processors running a "Linux x86_64" operating system are also supported by Intel compilers for Intel(R) 64 architecture applications.
  
  *IA-64*
  Refers to systems based on the Intel(R) Itanium(R) processor running a 64-bit operating system.

  
  
  
• Move the tar file to a directory where you have write access. I usually put these kind of things in ~/usr (~/ is shorthand for your home directory).
  Untar the file,

  tar xvfz l_fc_p_10.1.015_ia32.tar.gz

  
  This will create the directory l_fc_p_10.1.015_ia32 . Move into this directory and run the install script.
  

  cd l_fc_p_10.1.015_ia32
sudo ./install.sh

  
  If you dont have root access, you can omit the sudo command. The install shell will ask you if want to do a root user install and you just select no. This just means it will install the files into your home directory instead of the default ( /opt/intel ). Follow the on screen prompts until it asks you for your serial number. This should be in an email that was sent to the address you gave them. It also appears on the download page after you give them your email. Follow the rest of the on screen prompts and you should be good to go.
  
  

MPICH2

• Find a link to the download page here . The latest release (when I wrote this) was MPICH2 1.0.7. Download the tar file mpich2-1.0.7.tar.gz .
  
  
• Move the tar file to a directory where you have write access. I usually put these kinds of things in a directory called usr in my home directory.
  Now untar the file ( tar xvfz mpich2-1.0.7.tar.gz ).
  
  
• This will create the source directory mpich2-1.0.7 Before we start, we are going to create two other directories which will be useful. (These instructions are taken from the install guide). So we can put everything (intel compiler, mpich2, and fftw) in the same place, we will create a build and an install directory in /opt . Note that you will probably need root access to do this. If you dont have root access, just make these directories somewhere in your home directory.
  

  mkdir /opt/mpich2-1.0.7-build
mkdir /opt/mpich2-1.0.7-install
  

  These directories should be present on each machine that you will be sending jobs to. This will happen automatically if you are using a shared file system. If not, you will have to create the directories on each machine.
  
  
• Move to the build directory and execute the configure script in the source directory, using -prefix to tell it where to install the files. We will also want to set the environment variables F77 and F90 to ifort. (Note <username> means your username with no angular brackets.)

  cd /opt/mpich2-1.0.7-build
export F77=ifort
export F90=ifort
/home/<username>/usr/mpich2-1.0.7/configure -prefix=/opt/mpich2-1.0.7-install 2>&1 | tee configure.log

  The configure script ran for a couple minutes on my machine. If it is successful ( if the last line is configuration completed. ) you can build and install the libraries.

  make 2>&1 | tee make.log
make install 2>&1 | tee install.log

  When these steps are complete all of the MPICH2 executables should be in /opt/mpich2-1.0.7-install/bin and you should add this directory to your path. The two makes took on the order of fifteen minutes to run on my machine. You can check that the executables are in your path by using the following commands,
  

  which mpd
which mpicc
which mpif90
which mpiexec
which mpirun

• Last thing you have to do before running tests is to create a file called .mpd.conf in your home directory. Add the line secretword=<your_secret_word> to this file where <your_secret_word> is a string you make up. Execute the command chmod 600 .mpd.conf to make this file only visible to you.


• Sanity checks,

  mpd &
mpdtrace
mpdallexit

  Which should return your local host name.

  mpd &
mpiexec -n 1 /bin/hostname
mpdallexit

  Which should also return your local host name, perharps in a slightly different format. Now we are going to bring up a ring of mpd daemons. Create a file named mpd.hosts , and add one entry per machine that you want to run jobs on. The number of processors on each machine should be indicated using :nproc . For example, if I have four machines on my cluster with names node1 - node4 and they each have a quad core processor, my mpd.hosts file would have the following lines,

  nodel:4
node2:4
node3:4
node4:4

  Now we can bring up the ring of mpd daemons. Continuing with the example above, the command would be,

  mpdboot -n 5 -f mpd.hosts

  This brings up five daemons. One for the machine where the command is run, and one for each of the machines in the hosts file. You can run jobs using mpiexec . Some usefull flags,

  -1 (thats the number one) will override the default behaviour of trying to place the first process locally.
  -l (thats the letter el) will preface each line of output with the process that produced it.
  -machinefile < file_name > will run processes on the machines listed in < file_name > in the order that they appear in that file.

  I've found that it is important to put all the optional flags before the -n < nprocs > flag when using mpiexec . Thats it, now you're good to go. Don't forget to take down the mpd daemons when your done with mpdallexit .