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Originally acknowledging a distinct adroitness affiliate in a distinct department, the Bowdoin HPC ambiance now supports dozens of adroitness and acceptance beyond a array of disciplines, including biology, chemistry, computer science, agenda and computational studies, anatomy studies, economics, geology, history, sociology, math, and physics, as able-bodied as abounding alone apprentice and adroitness assay projects.
A advanced array of software bales and programming languages are accessible aural the Linux HPC environment, both bartering and Open Source, including but not apprenticed to ADF, Beast, C, C , CUDA, Fortran, Gamess, Gaussian, Grass, IDL, Java, Mathematica, Matlab, Mopac, NBO, NWChem, Perl, Python, R (along with RStudio), Ruby, Sage, SPSS, Stata-MP, SuperMongo, Topspin, and hundreds more.
There are two altered methods for appliance the Linux HPC resources; interactively, and via a accumulation scheduler that manages the HPC Grid.
Interactive Accretion is the way that best bodies use a computer. This is about sitting at a distinct computer, active programs, and interacting with those programs either through a GUI (Graphical User Interface) or command band interface. Checking e-mail, browsing the web, and basic a certificate are examples of alternate computing. You would use alternate accretion if you were active any software that displayed graphics, or appropriate chiral alternation with the affairs while it is running, such as inputting added data, accounting added information, or beat on an icon. Alternate accretion is best acclimated back you are able to achieve your goals during the time that you will be sitting at the computer, and can abdicate the affairs back you leave (ie, you are not abrogation the computer active your job back you airing abroad from it).
The Bowdoin Accretion Filigree is a accumulation of Linux servers which arise as one big, multiprocessor, compute server that can run abounding computationally accelerated jobs concurrently. The Filigree supports a advanced ambit of jobs from simple carapace scripts to abundant computational jobs and alongside processes. Jobs demography several canicule on a archetypal desktop apparatus adeptness accomplishment aural hours appliance the Filigree environment, appropriately absolution up the desktop computer for added tasks while the Filigree assets action the job on committed computational nodes. Bodies collaborate with the Bowdoin Accretion Filigree via the Son of Filigree Engine (SGE), which is a software ambiance that coordinates the assets of assorted computers. SGE accepts jobs, puts them in a cat-and-mouse chain until they can be run, sends them to a computational node, manages them during the run, and notifies the being back they are finished.
Typically if a job takes added than a few hours to run on a desktop machine, or the desktop apparatus needs to be accessible for added tasks, you should accede active the job on the Grid.
Computational nodes aural the Filigree ambit from 16 CPU core, 128 Gb RAM systems, to 56 CPU core, 256 Gb RAM systems. The Filigree additionally offers GPU computational nodes utilizing NVidia GPU cards.
“My collaborator, Tim Divoll from Indiana State University, and I use the HPC to conduct bioinformatic analyses of aerial throughput DNA sequencing data. The DNA sequences are a metabarcoding abstraction to accept the diet of a Neotropical bat species, the frog-eating bat Trachops cirrhosus. T. cirrhosus has been able-bodied advised in bondage for its behavior of hunting frogs by eavesdropping on their calls, but their diet in the agrarian is abundantly unknown. We calm begrimed samples from added than 100 T. cirrhosus individuals over assorted years and beyond dry and wet seasons in Panama. We again sequenced two gene regions, 16S and CO1 (using 454 sequencing and illumina sequencing respectively), from casualty charcoal in the begrimed samples. We are appliance the HPC to array and accredit anatomy to the millions of sequences that aftereffect from these next-generation sequencing approaches. Our ambition is to be able to assiduously call the diet of this bat for the aboriginal time, as able-bodied as appraise how diet varies amid adults and juveniles, beyond abduction sites, and beyond seasons. Compassionate a species’ diet is a aboriginal footfall in bigger compassionate its ecology, and abeyant approaches to conservation.” — Patricia Jones, Biology
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“Several of my contempo projects abode how accessible abetment like abundance affect the continued run outcomes of children. For example, one activity focuses on the role of accessible abetment in dabbling the access of assertive diseases or altitude like diabetes, asthma, and aerial claret pressure. This requires longitudinal abstracts area we can chase bodies from adolescence to adulthood. The activity uses the Panel Abstraction of Assets Dynamics (PSID), an anniversary sample that follows households to today alpha in 1968. Several thousand families accomplish a lot of abstracts back followed for 40 years with all-encompassing advice on demographics, income, labor, health, etc. The abstraction estimates alteration models of age at adverse bloom access appliance computationally accelerated abeyant capricious methods that acquiesce collective clay of ancestors assets and accessible assistance. The HPC ambiance allows me to appraisal models that use up to canicule of CPU time, and run added than one at a time . This would artlessly not be achievable on a desktop computer.” –John Fitzgerald, Economics
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“I am appliance a abysmal neural arrangement to abstraction a botheration in abstract mathematics: what is the minimum cardinal of scalar multiplications all-important to accumulate two matrices. This is a abiding botheration that has never been analyzed appliance apparatus learning. Based on some antecedent abstracts appliance Bowdoin’s GPUs, it looks the accepted accepted apprenticed on the cardinal of multiplications can be improved, conceivably substantially.” –Thomas Pietraho, Mathematics
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“I am a biologist belief Gulf of Maine abyssal organisms’ acknowledgment to alteration amnion and the basal abiogenetic mechanisms of adaptation. In adjustment to do my work, I use the Bowdoin HPC Filigree to adjust and assay ample datasets of DNA and RNA sequences. In addition, I accouter the accretion adeptness of the HPC Filigree to articulation basal abiogenetic aberration with ancestry that amount to the bacilli in the wild, e.g. how able-bodied a mollusk can abide to body its carapace in acerb water.
During the Fall, my Bowdoin Abyssal Science Division acceptance apprentice to use the bioinformatic pipelines on the HPC Filigree to investigate citizenry genomic patterns in a built-in Gulf of Maine intertidal snail species. These snails display concrete differences amid populations in cloistral shorelines against wave-exposed shorelines; the BMSS acceptance activated abutting bearing sequencing techniques and the HPC to anticipate the abiogenetic architectonics basal these concrete differences.
This Spring 2017 semester, I am teaching The Omics Revolution: Computational Genomics and Big Abstracts in the Field of Biology, area acceptance apprentice to use the HPC Filigree to assay a array of all-embracing datasets accepted in the ‘Omics’ fields. The Omics Revolution acceptance will accept a catechism and absolute omic-scale dataset of interest, assay that abstracts to assay their hypothesis, and address a accurate cardboard summarizing their findin
gs.” –Sarah Kingston, Biology
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“I accept congenital Amsterdam Density Functional (ADF) calculations into my assay efforts with acceptance back 2001. ADF calculations acquiesce them to bigger accept the bonding and photochemical backdrop of molecules absolute metals such as platinum, gold, iridium, ruthenium, and osmium. Alpha about 2005, I added a computational allure activity as allotment of Allure 3400, an Advanced Inorganic Allure course. The activity requires acceptance to accomplish ADF calculations on a atom of their choosing, and to address a address anecdotic and interpreting the after-effects of the calculations. This activity complements the added genitalia of the advance and, amid added things, provides acceptance absorbed in alum assignment in allure with admired computational allure experience. Back 2008, the Bowdoin HPC Filigree has accustomed us to run abundant beyond jobs, and assorted jobs at the aforementioned time, which is a abundant advance over active on desktop computers, and additionally frees up the desktop computer for added tasks.” –Jeff Nagle, Chemistry
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“The HPC Filigree has been a abundant adeptness for teaching and accomplishing assay with computational argument analysis. I was able to be up and active quickly; the action is not intimidating. Acceptance in my Aboriginal Year Academy “How to Apprehend 1,000,000 Books” use programs accounting in R to abstract accent acceptance patterns in over 1.2 billion abstracts credibility calm from Google Books. My altered assay projects use abate abstracts sets: 1 actor tweets, about 46,000 account articles, and about 1,000 books. Having the HPC allows me to run my analyses after attached up the computer that I use for teaching and circadian activities and my apprentice assay administration can do the same, which helps with collaboration. Sometimes this agency reconfiguring a cast with billions of elements, added times it agency creating bags of abate abstracts for comparison. Commutual these jobs, and commutual them in a reasonable time frame, artlessly wouldn’t be accessible after the HPC.” –Crystal Hall, Agenda and Computational Studies
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“My acceptance and I use the Bowdoin Accretion Filigree to accomplish after relativity simulations of atramentous holes. Einstein’s approach of gravity, accepted relativity, is encoded in Einstein’s equations, a complicated set of fractional cogwheel equations. The equations can be apparent absolutely alone for appropriate cases. In general, we accept to await on some approximation address in adjustment to abstraction the behavior and interactions of atramentous holes, as able-bodied as the gravitational radiation that they emit. A accurate able address are after simulations. In contempo years we accept acclimated such ’numerical relativity’ simulations to study, for example, binaries of two orbiting atramentous holes, as able-bodied as alleged ‘critical phenomena’ in the accumulation of atramentous holes. These simulations crave cogent computational assets and can be performed alone in high-performance accretion environments. It is acutely advantageous to accept such assets actuality at Bowdoin.” –Thomas Baumgarte, Physics
“I am utilizing the HPC for my assay on cricket’s neuronal bendability in acknowledgment to injury. In Dr. Horch’s wet lab, we extracted RNA from the terminal ganglion of developed macho crickets and are now architecture a transcriptome from the sequences. Appropriately far, we accept acclimated the HPC Filigree to run programs such as bowtie, Fastqc, trim galore! to body our transcriptome. To analyze ambition candidates complex in neuronal bendability such as advice molecules aperture and semaphorin, we will use the Trinity affairs apartment on the HPC filigree and conduct cogwheel analysis. The HPC’s aerial accretion accommodation accomplish it accessible for me to abide jobs that do not use bounded assets on my computer, nor booty years to accomplishment accustomed the aerial aggregate files I am alive with. It would be absurd for me to complete my activity in a absolute or able address after the HPC Grid.” –Meera Prasad, Assay and Religious Studies bifold major
“I am an economics and mathematics above and the HPC has been a abundant adeptness for my assay with Prof. Nelson in the economics administration and for my absolute abstraction with Prof. Pietraho in the mathematics department.
For my economics assay I use the HPC to administer a apparatus acquirements amalgamation to appraisal the likelihood and to call the factors that affect fishing spots in the Gulf of Maine. The dataset contains 21 bio-psychical and socio-economic variables for about 2.6 actor coordinates in the Gulf of Maine. The processing adeptness of the HPC allows for accessible administration of this dataset to apprentice how these variables collaborate together, which can again be acclimated to allocate the agnate accident of fishing spots.
On the added hand, for my absolute abstraction in mathematics I am appliance a abysmal neural arrangement to allocate images. The cold is to use a pre-trained neural arrangement that has been accomplished on a ample dataset and assorted categories and again to retrain it on my abate dataset. Such re-training allows us to analyze how analyze how accurateness of allocation is affected.
Both my projects could not accept been implemented on my PC. The HPC has been a abundant facilitator for exploring the assay questions I accept and for demystifying the apple of computing.” –Parikshit Sharma, Economics and Mathematics Major
“I am a Neuroscience above and Mathematics accessory appliance the HPC for the bioinformatics aspects of my assay on the compensatory advance responses to abrasion in crickets. In lab, I calm the prothoracic ganglion from 21 macho developed crickets for RNA abstraction and sequencing. During the summer of 2016, appliance the Trinity affairs apartment on the HPC Grid, I accumulated a de novo transcriptome of RNAseq apprehend abstracts and began cogwheel announcement assay appliance EdgeR. I accept additionally acclimated bowtie, FastQC, the BLAST suite, and Tophat on the HPC for added assay of my dataset. After an an antecedent assuming of the advice cue peptidome in my transcriptome, I will aim to analyze atypical applicant genes for captivation in the compensatory bendability in acknowledgment to abrasion appliance cogwheel announcement analysis. The aerial accretion adeptness of the Filigree and adeptness to abide jobs that don’t crave bounded assets on my computer accept been badly benign to my project.” –Harris Fisher, Neuroscience Major
Spring 2003 – Creation of specialized Physics array (16 CPU cores total) acknowledging one computational appliance for Thomas Baumgarte
Spring 2008 – Hiring of Dj Merrill to abutment HPC / Assay Computing
Fall 2008 – Creation of accepted purpose HPC Filigree to abutment campus-wide research. Dan O’Leary, Chemistry, was the aboriginal adroitness to use the new resource
Fall 2009 – HPC acceptance expands to the classroom teaching environment, acknowledging both assay and bookish use. Chemistry, Computer Science, Math, Physics, Geology, Economics, and Assay are actively appliance the HPC environment
Spring 2010 – Code ported from the old Physics array to the new HPC Grid
Summer 2010 – Specialized Physics array retired
Summer 2010 – Dhiraj Murthy, Sociology, starts appliance the HPC ambiance for allegory Twitter content
Summer 2011 – GPU compute capabilities added to HPC Grid
Fall 2012 – Agenda and Computational Studies Above created
Summer 2013 – Gluster aerial acceleration abstracts accumulator band-aid added to HPC environment
Summer 2014 – Campus amount server ambiance upgraded. “Best of” these systems re-purposed as HPC compute nodes, breaking the 500 CPU amount barrier
Summer 2014 – Sarah Kingston, Biology, starts accomplishing bioinformatics assay appliance the HPC environment
Summer 2015 – Upgraded HPC amount networking appliance Cisco’s 10 Gb ultra-low cessation Nexus 3548 switches, alms speeds commensurable to Infiniband networking
Summer 2016 – Sarah Kingston teaches academy on appliance the Bowdoin Accretion Filigree to run bioinformatics analysis
Fall 2016 – Institutional Research, Analytics & Consulting Division starts appliance the HPC ambiance for abstracts set analysis, apery the aboriginal business (non-Academic) usage
Winter 2017 – In accession to the accustomed assay efforts, bristles classes, an Honors Thesis, and assorted absolute studies are appliance the HPC ambiance this term.
Fall 2018 – Accepted status: 1192 CPU cores, 9 GPU compute nodes, 15 Bartering applications, hundreds of Open Source applications
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