Initial Setup: Difference between revisions

Latest revision as of 23:56, 14 February 2021

In High-Performance computing (HPC) there are several compiler and message passing interface systems for users to choose. Selecting a combination of compiler and message passing interface systems for a particular computational job is an involved process that depends upon the intricacies of the calculation and the specifications of the HPC system. This initial setup tutorial will guide the user in setting up a new account to use the most common combination of compiler and message passing interface system: GNU Compiler Collection, and Open MPI.

Startup Scripts

When logging into the cluster, the bash shell starts, and a series of dot files are executed. To setup aliases, functions, or to run specific commands every time a new shell starts, the .bashrc dot file, located in the home directory ( ${HOME}/.bashrc, or, equivalently, ~/.bashrc ), is used.

The .bashrc File

This file will be used in subsequent sections of this article to setup an environment suitable for computational calculations on the cluster. To see the contents of your .bashrc file, use the following command:

user $cat ${HOME}/.bashrc

Your file should look similar to this:

FILE ${HOME}/.bashrc

# .bashrc

# Test for an interactive shell.  There is no need to set anything              
# past this point for scp and rcp, and it's important to refrain from           
# outputting anything in those cases.                                           
if [[ $- != *i* ]] ; then                                                       
        # Shell is non-interactive.  Be done now!                               
        return                                                                  
fi                                                                              

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

# User specific aliases and functions

If you'd like to make changes to your .bashrc file, use the nano editor:

user $nano -w ${HOME}/.bashrc

To save any change you make, use Ctrl+O, then hit Enter to accept the file name. Use Ctrl+X to exit nano.

Important
To avoid problems copying files to and from the cluster, make sure that the test for an interactive shell is included at the top of the ${HOME}/.bashrc file.

Installed Programs and Software

Most of the scripts and programs are activated by use of the module command. As there are many modules installed on Magnolia, it is recommended to use the keyword option to module to search for a specific module. For example, to show a list of all programming languages installed as a module, use

user $module keyword programming

perl/5.30.0          : programming language perl
cuda-toolkit/10.1.243: cuda toolkit programming cuda-toolkit
cuda-toolkit/8.0.61  : cuda toolkit programming cuda-toolkit
gcc/6.4.0            : programming language c++ cpp fortran gcc
gcc/7.3.0            : programming language c++ cpp fortran gcc
gcc/8.3.0            : programming language c++ cpp fortran gcc
gcc/9.2.0            : programming language c++ cpp fortran gcc
go/1.11.1            : programming language go
go/1.13.4            : programming language go
go/1.9.3             : programming language go
intel/2017.4.196     : programming language c++ fortran intel
nasm/2.13.02         : programming language assembler assembly nasm
python/2.7.14        : programming language python
python/3.5.4         : programming language python
python/3.6.2         : programming language python
python/3.8.6         : programming language python

and to show a list of all MPI modules, use

user $module keyword mpi

impi                 : intel MPI impi
mpich/gcc            : MPI mpich
mpich/intel          : MPI mpich
openmpi-1.6/gcc      : MPI openmpi
openmpi-1.6/intel    : MPI openmpi
openmpi-1.8/gcc      : MPI openmpi
openmpi-1.8/intel    : MPI openmpi
openmpi-2.0/gcc      : MPI openmpi
openmpi-2.0/intel    : MPI openmpi

The first column of output is the name of the individual modules. Therefore, to load the newest version of Open MPI with the GNU Compiler Collection (GCC) use

user $module load openmpi-2.0/gcc

and to show all loaded modules:

user $module list

Currently Loaded Modulefiles:
  1) openmpi-2.0/gcc

This module loads Open MPI 2.0, and the GNU Compiler Collection environment; to check this, use the --version option with gcc and mpirun:

user $gcc --version

gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-11)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

user $mpirun --version

mpirun (Open MPI) 2.0.1

Report bugs to http://www.open-mpi.org/community/help/

Note
The settings so far affect only the currently running shell and will be lost when logging back in at a later date. To make changes persistent across logins, see the next section.

Make Changes Persistent and Global

Before a job can be successfully submitted to the cluster it is required to have the same settings on all nodes of the cluster, two common methods to accomplish this are:

Persistent settings across logins
Custom job submission scripts

Custom job submission scripts are useful if you plan to use a variety of programs and/or software packages, while persistent settings across logins are used when only one program or software package will be used.

Persistent setting across logins are explained below, while custom job submission scripts can be found by using the update examples command.

To make the compiler and message passing system settings persistent across logins and all nodes we need to edit the .bashrc file in the home directory. The directions below will be for using the nano editor, but you are free to use whichever text editor you are most comfortable with.

Use the following to start editing the file:

user $nano -w ${HOME}/.bashrc

If this is your first time editing the .bashrc file, it should look just like the one shown in the .bashrc section.

We need to add the module command we used earlier to the bottom of this file. It should look like this:

FILE ${HOME}/.bashrc(after editing)

# .bashrc

# Test for an interactive shell.  There is no need to set anything              
# past this point for scp and rcp, and it's important to refrain from           
# outputting anything in those cases.                                           
if [[ $- != *i* ]] ; then                                                       
        # Shell is non-interactive.  Be done now!                               
        return                                                                  
fi                                                                              

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

# User specific aliases and functions
module load openmpi-2.0/gcc

To save the changes, use Ctrl+O, then hit Enter to accept the file name. Use Ctrl+X to exit nano.

Now every time you login, the GNU compiler and Open MPI compiled with the GNU compiler will be the default.

Next Step / Examples

To get a set of examples showing how to run jobs on the cluster, go to the update examples wiki page.

@@ Line 6: / Line 6: @@
 == Startup Scripts ==
-When logging into the cluster, the [//wikipedia.org/wiki/Bash_(Unix_shell) bash] shell starts, and a series of [//wikipedia.org/wiki/Hidden_file_and_hidden_directory#Unix_and_Unix-like_environments dot files] are executed. To setup aliases, functions, or to run specific commands every time a new shell starts, the {{C|.bashrc}} dot file, located in the [//www.wikipedia.org/wiki/Home_directory home directory] ( {{Path|${HOME}/.bashrc}}, or, equivalently, {{Path|~/.bashrc}} ), is used.
+When [[Connect to Magnolia|logging into the cluster]], the [//wikipedia.org/wiki/Bash_(Unix_shell) bash] shell starts, and a series of [//wikipedia.org/wiki/Hidden_file_and_hidden_directory#Unix_and_Unix-like_environments dot files] are executed. To setup aliases, functions, or to run specific commands every time a new shell starts, the {{C|.bashrc}} dot file, located in the [//www.wikipedia.org/wiki/Home_directory home directory] ( {{Path|${HOME}/.bashrc}}, or, equivalently, {{Path|~/.bashrc}} ), is used.
 === The {{C|.bashrc}} File===
@@ Line 41: / Line 41: @@
 {{Important|To avoid problems copying files to and from the cluster, make sure that the test for an interactive shell is included at the top of the {{Path|${HOME}/.bashrc}} file. }}
+== Installed Programs and Software ==
-== Set Defaults ==
+Most of the scripts and programs are activated by use of the {{C|module}} command. As there are many modules installed on Magnolia, it is recommended to use the ''keyword'' option to {{C|module}} to search for a specific module. For example, to show a list of all programming languages installed as a module, use
-Most of the scripts and programs are activated by use of the {{C|module}} command. As there are many modules installed on Magnolia, it is recommended to use the ''keyword'' option to {{C|module}} to search for a specific module. For example, to show a list of all MPI modules, use
+{{Cmd|module keyword programming|output=<pre>
+perl/5.30.0          : programming language perl
+cuda-toolkit/10.1.243: cuda toolkit programming cuda-toolkit
+cuda-toolkit/8.0.61  : cuda toolkit programming cuda-toolkit
+gcc/6.4.0            : programming language c++ cpp fortran gcc
+gcc/7.3.0            : programming language c++ cpp fortran gcc
+gcc/8.3.0            : programming language c++ cpp fortran gcc
+gcc/9.2.0            : programming language c++ cpp fortran gcc
+go/1.11.1            : programming language go
+go/1.13.4            : programming language go
+go/1.9.3             : programming language go
+intel/2017.4.196     : programming language c++ fortran intel
+nasm/2.13.02         : programming language assembler assembly nasm
+python/2.7.14        : programming language python
+python/3.5.4         : programming language python
+python/3.6.2         : programming language python
+python/3.8.6         : programming language python
+</pre>}}
+and to show a list of all MPI modules, use
 {{Cmd|module keyword mpi|output=<pre>
@@ Line 88: / Line 108: @@
 == Make Changes Persistent and Global ==
-Before a job can be successfully submitted to the cluster it is required to have:
+Before a job can be successfully submitted to the cluster it is required to have the same settings on all nodes of the cluster, two common methods to accomplish this are:
 * Persistent settings across logins
-* Same settings on all nodes of cluster
+* Custom job submission scripts
+Custom job submission scripts are useful if you plan to use a variety of programs and/or software packages, while persistent settings across logins are used when only one program or software package will be used.
+Persistent setting across logins are explained below, while custom job submission scripts can be found by using the [[Update Examples|update examples]] command.
-To make the compiler and message passing system settings persistent across logins and all nodes we need to edit the {{C|.bashrc}} file in the [//www.wikipedia.org/wiki/Home_directory home directory]. The directions below will be for using the {{C|nano}} editor, but you are free to use whatever text editor you are most comfortable with.
+To make the compiler and message passing system settings persistent across logins and all nodes we need to edit the {{C|.bashrc}} file in the [//www.wikipedia.org/wiki/Home_directory home directory]. The directions below will be for using the {{C|nano}} editor, but you are free to use whichever text editor you are most comfortable with.
 Use the following to start editing the file:
@@ Line 99: / Line 124: @@
 If this is your first time editing the {{C|.bashrc}} file, it should look just like the one shown in the [[#The .bashrc File|.bashrc section]].
-We need to add the two commands we typed earlier ([[#GNU Compiler Collection|here]] and [[#Open MPI|here]]) to the bottom of this file. It should look like this:
+We need to add the {{C|module}} command we used earlier to the bottom of this file. It should look like this:
 {{FileBox|title=(after editing)|filename=${HOME}/.bashrc|1=
@@ Line 118: / Line 143: @@
 # User specific aliases and functions
-source /home/bgo/shared/bin/selector-compiler -g -q
+module load openmpi-2.0/gcc
-source /home/bgo/shared/bin/selector-mpi -i gnu-openmpi -q
 }}
-You'll notice that the two commands are slightly different than what we used before; they both have a {{C|-q}} added. The {{C|-q}} tells the commands to be 'quiet' and not show any output. You can omit the {{C|-q}} from each command if you'd like to be reminded of what compiler and message passing system is set during each login.
 To save the changes, use {{Key|Ctrl}}+{{Key|O}}, then hit {{Key|Enter}} to accept the file name. Use {{Key|Ctrl}}+{{Key|X}} to exit {{C|nano}}.
 Now every time you login, the GNU compiler and Open MPI compiled with the GNU compiler will be the default.
+== Next Step / Examples ==
+To get a set of examples showing how to run jobs on the cluster, go to the [[Update Examples|update examples]] wiki page.
 [[Category:Tutorials]]