Niagara Quickstart: Difference between revisions

More detailed hardware characteristics of the Niagara supercomputer can be found [[Niagara|on this page]].

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If you do not have access yet (e.g. because you are new to SciNet and belonging to a group whose primary PI does not have an allocation as granted in the annual [https://www.computecanada.ca/research-portal/accessing-resources/resource-allocation-competitions Compute Canada RAC]), follow the old route of [https://ccdb.computecanada.ca/me/facilities requesting a SciNet Consortium Account on the CCDB site] to gain access to Niagara.  After clicking the "Apply" button, it usually takes only one or two business days for access to be granted.   

Please read this document carefully.  The [https://docs.scinet.utoronto.ca/index.php/FAQ FAQ] is also a useful resource.  If at any time you require assistance, or if something is unclear, please do not hesitate to [mailto:niagara@computecanada.ca contact us].

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NOTE: home is read-only on compute nodes.

=== Storage and quotas === <!--T:39-->

You should familiarize yourself with the [[Data_Management#Purpose_of_each_file_system | various file systems]], what purpose they serve, and how to properly use them.  This table summarizes the various file systems.  See the [[Data_Management | Data Management]] page for more details.

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If you need to move data to Niagara for analysis, or when you need to move data off of Niagara, use the following guidelines:

* If your data is less than 10GB, move the data using the login nodes.

* If your data is greater than 10GB, move the data using the datamover nodes nia-datamover1.scinet.utoronto.ca and nia-datamover2.scinet.utoronto.ca .

Details of how to use the datamover nodes can be found on the [[Data_Management#Moving_data | Data Management ]] page.

= Loading software modules = <!--T:48-->

You have two options for running code on Niagara: use existing software, or [[Niagara_Quickstart#Compiling_on_Niagara:_Example | compile your own]].  This section focuses on the former.

Other than essentials, all installed software is made available [[Using_modules | using module commands]]. These modules set environment variables (PATH, etc.), allowing multiple, conflicting versions of a given package to be available.  A detailed explanation of the module system can be [[Using_modules | found on the modules page]].

Common module subcommands are:

<li><code>module load &lt;module-name&gt;</code>: use particular software</li>

<li><code>module list</code>: list loaded modules</li>

Along with modifying common environment variables, such as PATH, and LD_LIBRARY_PATH, these modules also create a SCINET_MODULENAME_ROOT environment variable, which can be used to access commonly needed software directories, such as /include and /lib.

There are handy abbreviations for the module commands. <code>ml</code> is the same as <code>module list</code>, and <code>ml <module-name></code> is the same as <code>module load <module-name></code>.

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Solve these dependencies by using <code>module spider</code>.

* For most compiled software, one should use the Intel compilers (<tt>icc</tt> for C, <tt>icpc</tt> for C++, and <tt>ifort</tt> for Fortran). Loading an <tt>intel</tt> module makes these available.  

* The GNU compiler suite (<tt>gcc, g++, gfortran</tt>) is also available, if you load one of the <tt>gcc</tt> modules.

= Using Commercial Software = <!--T:67-->

May I use commercial software on Niagara?

Within these limits, jobs will still have to wait in the queue.  The waiting time depends on many factors such as the allocation amount, how much allocation was used in the recent past, the number of nodes and the walltime, and how many other jobs are waiting in the queue.

It is important to understand the file systems, so as to perform your file I/O (Input/Output) responsibly.  Refer to the [[Data_Management | Data Management]] page for details about the file systems.

* Your files can be seen on all Niagara login and compute nodes.

<source lang="bash">nia-login07:scratch$ sbatch mpi_job.sh</source>

<ul>

<li>First line indicates that this is a bash script.</li>