FASTA

FASTA is a software package for aligning nucleotide or amino acid sequences. Its primary use is to search databases for sequences that are similar to a given candidate sequence.

Computational considerations

Work locally

Many of the features in FASTA require access to database flatfiles, and standard practice when running a compute cluster is to copy all necessary files to a node local directory before any work is done with them. This behaviour is highly encouraged on most resources, since multiple simultaneous accesses to the same large files on a shared disk is likely to cause problems for all computations currently running on the resource, and not only for the owner of the badly behaving jobs.

Do not run out of memory

If possible, you should ensure that you have enough RAM to hold the database as well as the results and still have some headroom. This ensures that FASTA will not need to read data from disk unnecessarily, which otherwise would cause significant slowdown. This can be done for example by:

• Choose a system with enough RAM
  Multiprocessor systems generally have more memory than single processor systems, and the database will also require proportionally less memory, since only one copy is needed in the OS file cache regardless of the number of processors using it.
• Partition the search space
  For huge databases or very restricted amounts available memory it may be required to split the database into manageable chunks and process them as separate jobs.

Availability

Resource	Centre	Description
Triolith	NSC	Capability cluster with 338 TFLOPS peak and 1:2 Infiniband fat-tree

License

License: Free.

Experts

No experts have currently registered expertise on this specific subject. List of registered field experts:

		Field	AE FTE	General activities
Anders Hast (UPPMAX)	UPPMAX	Visualisation, Digital Humanities	30	Software and usability for projects in digital humanities
Anders Sjölander (UPPMAX)	UPPMAX	Bioinformatics	100	Bioinformatics support and training, job efficiency monitoring, project management
Anders Sjöström (LUNARC)	LUNARC	GPU computing MATLAB General programming Technical acoustics	50	Helps users with MATLAB, General programming, Image processing, Usage of clusters
Birgitte Brydsö (HPC2N)	HPC2N	Parallel programming HPC		Training, general support
Björn Claremar (UPPMAX)	UPPMAX	Meteorology, Geoscience	100	Support for geosciences, Matlab
Björn Viklund (UPPMAX)	UPPMAX	Bioinformatics Containers	100	Bioinformatics, containers, software installs at UPPMAX
Chandan Basu (NSC)	NSC	Computational science	100	EU projects IS-ENES and PRACE. Working on climate and weather codes
Diana Iusan (UPPMAX)	UPPMAX	Computational materials science Performance tuning	50	Compilation, performance optimization, and best practice usage of electronic structure codes.
Frank Bramkamp (NSC)	NSC	Computational fluid dynamics	100	Installation and support of computational fluid dynamics software.
Hamish Struthers (NSC)	NSC	Climate research	80	Users support focused on weather and climate codes.
Henric Zazzi (PDC)	PDC	Bioinformatics	100	Bioinformatics Application support
Jens Larsson (NSC)	NSC	Swestore
Jerry Eriksson (HPC2N)	HPC2N	Parallel programming HPC		HPC, Parallel programming
Joachim Hein (LUNARC)	LUNARC	Parallel programming Performance optimisation	85	HPC training Parallel programming support Performance optimisation
Johan Hellsvik	PDC	Materialvetenskap	30	materials theory, modeling of organic magnetic materials,
Johan Raber (NSC)	NSC	Computational chemistry	50
Jonas Lindemann (LUNARC)	LUNARC	Grid computing Desktop environments	20	Coordinating SNIC Emerging Technologies Developer of ARC Job Submission Tool Grid user documentation Leading the development of ARC Storage UI Lunarc Box Lunarc HPC Desktop
Krishnaveni Chitrapu (NSC)	NSC	Software development
Lars Eklund (UPPMAX)	UPPMAX	Chemistry Data management FAIR Sensitive data	100	Chemistry codes, databases at UPPMAX, sensitive data, PUBA agreements
Lars Viklund (HPC2N)	HPC2N	General programming HPC		HPC, General programming, installation of software, support, containers
Lilit Axner (PDC)	PDC	Computational fluid dynamics	50
Marcus Lundberg (UPPMAX)	UPPMAX	Computational science Parallel programming Performance tuning Sensitive data	100	I help users with productivity, program performance, and parallelisation. I also work with allocations and with sensitive data questions
Martin Dahlö (UPPMAX)	UPPMAX	Bioinformatics	10	Bioinformatic support
Matias Piqueras (UPPMAX)	UPPMAX	Humanities, Social sciences	70	Support for humanities and social sciences, machine learning
Mikael Djurfeldt (PDC)	PDC	Neuroinformatics	100
Mirko Myllykoski (HPC2N)	HPC2N	Parallel programming GPU computing		Parallel programming, HPC, GPU programming, advanced support
Pavlin Mitev (UPPMAX)	UPPMAX	Computational materials science	100
Pedro Ojeda-May (HPC2N)	HPC2N	Molecular dynamics Machine learning Quantum Chemistry		Training, HPC, Quantum Chemistry, Molecular dynamics, R, advanced support
Peter Kjellström (NSC)	NSC	Computational science	100	All types of HPC Support.
Peter Münger (NSC)	NSC	Computational science	60	Installation and support of MATLAB, Comsol, and Julia.
Rickard Armiento (NSC)	NSC	Computational materials science	40	Maintainer of the scientific software environment at NSC.
Szilard Pall	PDC	Molecular dynamics	55	Algorithms & methods for accelerating molecular dynamics, Parallelization and acceleration of molecular dynamics on modern high performance computing architectures, High performance computing, manycore and heterogeneous architectures, GPU computing
Thomas Svedberg (C3SE)	C3SE	Solid mechanics
Torben Rasmussen (NSC)	NSC	Computational chemistry	100	Installation and support of computational chemistry software.
Wei Zhang (NSC)	NSC	Computational science Parallel programming Performance optimisation		code optimization, parallelization.
Weine Olovsson (NSC)	NSC	Computational materials science	90	Application support, installation and help
Åke Sandgren (HPC2N)	HPC2N	Computational science	50	SGUSI

Links

• Official site