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What is installed on the clusters

To see the list of installed software (modules), load the compiler and the MPI implementation you intend to use and do

module spider

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On our systems, we have compiled and installed software modules either with Intel Compiler and Intel MPI or GCC and MVAPICH2 and those are the only supported compiler/MPI combinations.

Getting the examples

Once you have logged in to the machine, we suggest you download the examples with the command:

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git clone https://c4science.ch/diffusion/SCEXAMPLES/scitas-examples.git

Here is a list of our examples:

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Advanced
	- FakeJobArray
	- JobArray
	- JobArray2
	- OccupyOneNode


Basic
	- hello.run
	- MPI
	- one_GPU.run
	- Pi_integral
	- Pi_mc


Modules
	- Abaqus
	- adf
 	- Ansys
	- Comsol
	- cp2k
	- cpmd
	- fluent
	- gaussian
	- GPU_amber
 	- GPU_gromacs
	- maple
	- Mathematica
	- Matlab
	- molpro
	- oommf
	- ParaView
	- R
	- spark
	- tensorflow
	- vasp

Running the examples
Enter the directory scitas-examples and choose the example to run by navigating the folders. We have three categories of examples: Basic (examples to get you started), Advanced (including hybrid jobs and job arrays) and Modules (specific examples of installed software).
To run an example, e.g. HPL-mpi of the Advanced category, do:
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sbatch --partition=debug hpl.run
or, if you do not wish to run on the debug partition,
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sbatch hpl.run

Running interactive jobs

An interactive job allows you to connect directly to a compute node and type commands that run on the compute node. Simply type the command Sinteract from the login node to start an interactive session with 1 core and 4GB of memory for 30 minutes.

You can use the parameters to Sinteract (for help type: interact -h) to request more resources or more time.

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usage: Sinteract [-c cores] [-n tasks] [-t time] [-m memory] [-p partition] [-a account] [-q qos] [-g resource] [-r reservation]

options:
 -c cores cores per task (default: 1)
 -n tasks number of tasks (default: 1)
 -t time as hh:mm:ss (default: 00:30:00)
 -m memory as #[K|M|G] (default: 4G)
 -p partition (default: parallel)
 -a account (default: phpc2017)
 -q qos as [normal|gpu|gpu_free|mic|...] (default: )
 -g resource as [gpu|mic][:count] (default is empty)
 -r reservation reservation name (default is empty

e.g. to run an mpi job with 16 processes for one hour using 32 GB of memory on a debug node:

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Sinteract -n 16 -t 01:00:00 -m 32G -p debug

Warning
On the Izar cluster, the -g option is required necessary to request the desired number of GPUs. For example: Sinteract -g gpu:1

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