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POFilling sparse matrix in Eigen is very slow
 

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  1. POFilling sparse matrix in Eigen is very slow
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    <p>I have this code which calls a c++ method in java in a for loop:</p> <pre><code>JNIEXPORT void JNICALL Java_com_jp_algi_CoreC_MMload(JNIEnv *env3, jobject clazz3, jdoubleArray inputv, jintArray inputi, jint poc, jint pozic) { jdouble* fltv2 ; jint* fltind2; jsize sizedat = env3-&gt;GetArrayLength(inputi); fltv2 = new jdouble[sizedat]; fltind2 = new jint[sizedat]; jint i; jint jm; env3-&gt;GetIntArrayRegion(inputi,0,sizedat,fltind2); env3-&gt;GetDoubleArrayRegion(inputv,0,sizedat,fltv2); // default is column major matA.reserve(VectorXi::Constant(1,sizedat)); for ( jm = 0; jm &lt; sizedat; jm++) { //matA.insert(fltind2[jm],pozic) = fltv2[jm]; // alternative: mat.coeffRef(i,j) += v_ij; matA.insert(fltind2[jm],pozic)= fltv2[jm]; //matA.insertBack(fltind2[jm],pozic)= fltv2[jm]; //matA.ins //matA.insertBackUncompressed(); //matA.coeffRef(fltind2[jm],pozic) += fltv2[jm]; // optional } matA.makeCompressed(); //k++; //blbe zayklenji!!! env3-&gt;SetIntArrayRegion(inputi,0,sizedat,fltind2); env3-&gt;SetDoubleArrayRegion(inputv,0,sizedat,fltv2); delete[] fltv2; delete[] fltind2; } </code></pre> <p>Where inputv are values of columns of matA.; and inputi are indexes of these values.</p> <p>I read in the docs for eigen that the insert function is the fastest, and it's ok when the number of non-zero coefficients are about 5000. But when I have 25000 it takes 5 sec per column!</p> <p>I tried insrtback, but the values are the same? What exactly does this command do? Is there some way to improve this code?</p> <p>Once advantage (maybe): the values and indexes in every column are sorted by the values from highest to lowest...</p>
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    1. USjam
    1. USDaniela Agelova
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      1. POFilling sparse matrix in Eigen is very slow
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    1. CODo you call this function with increasing pozic values, or with a random pattern? Also if the value are sorted "from highest to lowest", then reverse your loop such that the insert command boils down to simple push-back. The reserve command is not correct.
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      1. POFilling sparse matrix in Eigen is very slow
      1. USggael
    2. CO1. yes with increasing; the pozic is from 0 to sizeof columns of matA.; the next you mean that reserve com. take from this method to initialize metho.-of matA.????or whats the coorect way ow write reserve command??
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      1. POFilling sparse matrix in Eigen is very slow
      1. USDaniela Agelova
    3. COthen the fastest is to call reserve(sizedat); matA.startVec(pozic); for(...) mat.insertBack(fltind2[jm],pozic) = ...; making sure that fltind2[jm] are in increasing order.
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      1. POFilling sparse matrix in Eigen is very slow
      1. USggael
 

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