I need an advice on how optimizing my implementation of the Needleman-Wunsch algorithm in CUDA.
I want to optimize my code to fill the dynamic programming matrix in CUDA. Due to the data dependence between matrix elements (each next element depends on the other ones - left to it, up to it, and left-up to it), I'm filling [anti-diagonal matrix elements] (http://imgur.com/gallery/gapnyno/new) in parallel as follows:
__global__ void alignment_kernel(int *T, char *A, char *B, int t_M, int t_N, int d) {
int row = BLOCK_SIZE_Y * blockIdx.y + threadIdx.y;
int col = BLOCK_SIZE_X * blockIdx.x + threadIdx.x;
// Check if we are inside the table boundaries.
if (!(row < t_M && col < t_N)) {
return;
}
// Check if current thread is on the current diagonal
if (row + col != d) {
return;
}
int v1;
int v2;
int v3;
int v4;
v1 = v2 = v3 = v4 = INT_MIN;
if (row > 0 && col > 0) {
v1 = T[t_N * (row - 1) + (col - 1)] + score_matrix_read(A[row - 1], B[col - 1]);
}
if (row > 0 && col >= 0) {
v2 = T[t_N * (row - 1) + col] + gap;
}
if (row >= 0 && col > 0) {
v3 = T[t_N * row + (col - 1)] + gap;
}
if (row == 0 && col == 0) {
v4 = 0;
}
// Synchronize (ensure all the data is available)
__syncthreads();
T[t_N * row + col] = mmax(v1, v2, v3, v4);
}
Nevertheless, one obvious problem of my code is that I do multiple kernel calls (code bellow). Until now, I don't know how to use threads to process the anti-diagonal synchronously without doing that. I think this is a major problem to reach a better performance.
How can I process the anti-diagonal in parallel and, maybe, using shared memory to increase the speedup?
// Invoke kernel.
for (int d = 0; d < t_M + t_N - 1; d++) {
alignment_kernel<<< gridDim, blockDim >>>(d_T, d_A, d_B, t_M, t_N, d);
//CHECK_FOR_CUDA_ERROR();
}
Beyond this problem, is there any way to do the back trace step of the needleman-wunsch algorithm in parallel?
Hi community (first post here), is there any video or resource where they explain these algorithms, the papers are rough and I would like to understand them very well
http://ds9a.nl/nwunsch/ has a live demo of this important algorithm. Enter some strings and see how they align, and why!
Can anyone compile a list, search index, etc that can archive the names / companies of sus articles like the WSJ article yesterday?
Company, outlet (msm, twitter, Reddit, etc), sus or not. Maybe voted on by community?
I know it might seem like just about all msm, however, it might help root out connections?
Titel sagt es eigentlich. Sehr oft kriegt man es mit, dass Leute (meine Eltern) die Klimaanlage im Auto am Anfang der Fahrt kurz aufs Maximum schalten. Weil das ja schneller ginge.
Ich denke mir, ne, die macht im gleichen Speed heiß bis zum Erreichen der Solltemperatur. Egal ob das 22°C oder 29°C ist.
Hat hier wer Ahnung?
Today is my last vacancynday of the Christmas holidays, and since nothing was supposed to happen, I was calmy relaxing in my bath since 9 am.
But 5 mn ago, i hear ringing at my door. So since I was bathing for 3 hours I just just accepted it as a fate of destiny, but I went to answer the door wrapped in a towel, just slightly opening it to understand who was that that ringed at my home.
Turns out it was a delivery guy with a package delivered unexpectedly early. I thank him, put my signature, then when going back he told me :
"du hat gute Wunsch hier"
And I am not sure on how to interpret it. Is it the same as "best wishes for the new year", or does it mean something like "you've got life easy hier, lucky guy".
I just want to know if I should be have regret or not for not leaving my bath by myself earlier and show myself on a presentable manner.
Also, question inside a question, I always leave a tip for lieferando delivery guys, but I realised I never did it for amazon/dhl/... Delivery guys. What is the étiquette here ? Do Germans tip every delivery guys? Oder?
[ Removed by reddit on account of violating the content policy. ]
Tastes To Our By Everything We Guests’ Provide.Grown-Up Exceptional An Being In Experience A Cut-Above That Dining Satisfies Do
Diverse Denny’S And Our Suppliers Our Beneficial Pricing. Business Mission Establish Sh
Denkt Mal zurück an den Moment, wo ihr als Kind den ersten Brief ans Christkind geschrieben habt.
Welcher Wunsch wäre es jetzt?
(Ein Wunsch s'Christkindl muss die Überstunden vom Vorjahr noch abbauen)
