scala - Spark out of memory when reducing by key -


i'm working on algorithm requires math operations on large matrix. basically, algorithm involves following steps:

inputs: 2 vectors u , v of size n

  1. for each vector, compute pairwise euclidean distance between elements in vector. return 2 matrix e_u , e_v

  2. for each entry in 2 matrices, apply function f. return 2 matrix m_u, m_v

  3. find eigen values , eigen vectors of m_u. return e_i, ev_i = 0,...,n-1

  4. compute outer product each eigen vector. return matrix o_i = e_i*transpose(e_i), = 0,...,n-1

  5. adjust each eigen value e_i = e_i + delta_i, delta_i = sum elements(elementwise product of o_i , m_v)/2*mu, mu parameter

  6. final return matrix = elementwise sum (e_i * o_i) on = 0,...,n-1

the issue i'm facing memory when n large (15000 or more), since matrices here dense matrices. current way implement may not best, , partially worked.

i used rowmatrix m_u , eigen decomposition using svd.

the resulting u factor of svd row matrix columns ev_i's, have manually transpose rows become ev_i. resulting e vector eigen values e_i.

since previous attempt of directly mapping each row ev_i o_i failed due out of memory, i'm doing 

r = u.map{     case(i,ev_i) => {       (i, ev_i.toarray.zipwithindex)     }   }//add index each element in vector   .flatmapvalues(x=>x)}   .join(u)//eigen vectors column appended   .map{case(eigenvecid, ((vecelement,elementid), eigenvec))=>(elementid, (eigenvecid, vecelement*eigenvec))}

to compute adjusted e_i's in step 5 above, m_v stored rdd of tuples (i, densevector). 

deltardd = r.join(m_v)   .map{     case(j,((i,row_j_of_o_i),row_j_of_m_v))=>     (i,row_j_of_o_i.t*densevector(row_j_of_m_v.toarray)/(2*mu))   }.reducebykey(_+_)

finally, compute a, again due memory issue, have first joining rows different rdds , reducing key. specifically, 

r_rearranged = r.map{case(j, (i, row_j_of_o_i))=>(i,(j,row_j_of_o_i))} termsfora = r_rearranged.join(deltardd) = termsfora.map{   case(i,(j,row_j_of_o_i), delta_i)) => (j, (delta_i + e(i))*row_j_of_o_i) } .reducebykey(_+_)

the above implementation worked step of termsfora, means if execute action on termsfora termsfora.take(1).foreach(println), succeeded. if execute action on a, a.count(), oom error occured on driver.

i tried tune sparks configuration increase driver memory parallelism level, failed.

use indexedrowmatrix instead of rowmatrix, in conversions , transpose. suppose indexedrowmatrix irm

svd = irm.computesvd(k, true) u = svd.u u =  u.tocoordinatematrix().transpose().toindexedrowmatrix()

you can convert irm blockmatrix multiplication distributed blockmatrix.


Comments

Post a Comment

Popular posts from this blog

angular - Ionic slides - dynamically add slides before and after -

hi i'm using ngfor create set of 3 slides while starting in middle i'm guaranteed able slide left or right on start. when slide right can simple listen reachedend , push slide array i'm looping. but have problem adding slide beginning. if same above , use e.g. array.unshift() or spread add item beginning, view think it's on position 0 , snaps view new slide. the code below work animates slide change index 1. slide = [0,1,2] //example loop slidechanged(event) { if(this.slides.isbeginning()){ this.slide = [this.slide[0]-1, ...this.slide]; this.slides.update(); this.slides.slideto(1) } } <ion-slides [initialslide]="1" (ionslidedidchange)="slidechanged($event)"> <ion-slide *ngfor="let item of slide"> <h1>slide {{item}}</h1> </ion-slide> </ion-slides> any appreciated! you can using ionslidenextend , ionslideprevend events slides . please
Read more

minify - Minimizing css files -

i want know how css files can minimized. currently, using external sites css minifier compress css files. however, after removing whitespaces, comments, etc, file sizes reduced 10-15%. how frameworks bootstrap manage make minimized versions kilobytes. as example, css is: body { background-color: #ff0; } the reduction goes 28 bytes 22 bytes other css files have lot more characters still smaller this. actually minifying code means it's remove thing code white space characters new line characters comments block delimiters it reduces amount of code has transferred on web , speed site load fastly.but unreadable format.
Read more

Add a dynamic header in angular 2 http provider -

i have http interceptor built via tutorial https://scotch.io/@kashyapmukkamala/using-http-interceptor-with-angular2 the problem need have dynamic header changes automatically once changes 'mode' in app. service able tell interceptor change header, or have interceptor pull header (which string)from service each request. able throwing away patch method, call http.patch('new header string') set header string. call in service controls 'mode' setting. wondering if there way interceptor pull recent value service each request or if can add method http provider via interceptor? i've tried call service in interceptor each request returns undefined. because creating new instance of service or copying value before service fired , loaded/changed data. i don't want pass header string every http provider call because defeats purpose of having interceptor, id able set once changes or have provider fetch service before makes request. tl;dr : need add autom
Read more