[Genabel-commits] r1861 - in pkg/OmicABELnoMM: examples src
L.C. Karssen
lennart at karssen.org
Tue Oct 28 12:40:17 CET 2014
Hi Alvaro,
On 28-10-14 11:20, noreply at r-forge.r-project.org wrote:
> Author: afrank
> Date: 2014-10-28 11:20:35 +0100 (Tue, 28 Oct 2014)
> New Revision: 1861
>
> Modified:
> pkg/OmicABELnoMM/examples/exclude_individuals.txt
> pkg/OmicABELnoMM/src/AIOwrapper.cpp
> pkg/OmicABELnoMM/src/Utility.cpp
> pkg/OmicABELnoMM/src/Utility.h
> Log:
> More code cleanup around unused fakefile feature.
Great work! I love removal of unused code :-). The cleaner the code
base, the easier maintenance will be.
Thanks!
Lennart.
>
> Modified: pkg/OmicABELnoMM/examples/exclude_individuals.txt
> ===================================================================
> --- pkg/OmicABELnoMM/examples/exclude_individuals.txt 2014-10-28 09:59:23 UTC (rev 1860)
> +++ pkg/OmicABELnoMM/examples/exclude_individuals.txt 2014-10-28 10:20:35 UTC (rev 1861)
> @@ -2,4 +2,4 @@
> 5
> 7
> 9 11
> -10
> \ No newline at end of file
> +13
> \ No newline at end of file
>
> Modified: pkg/OmicABELnoMM/src/AIOwrapper.cpp
> ===================================================================
> --- pkg/OmicABELnoMM/src/AIOwrapper.cpp 2014-10-28 09:59:23 UTC (rev 1860)
> +++ pkg/OmicABELnoMM/src/AIOwrapper.cpp 2014-10-28 10:20:35 UTC (rev 1861)
> @@ -200,7 +200,7 @@
> }
> else
> {
> - //other params come from outside
> + //no longer used
> }
>
> params.mb = min(params.m,params.mb);
> @@ -791,7 +791,7 @@
> {
> //cout << "async_io\n" << flush;
> type_fileh* Fhandler = (type_fileh *)ptr;
> - int size_buff,tmp_y_blockSize,tmp_ar_blockSize;
> + int tmp_y_blockSize,tmp_ar_blockSize;
>
> struct timespec timeToWait;
> FILE* fp_Y;
> @@ -967,7 +967,6 @@
> tmp_y_blockSize = Fhandler->y_to_readSize;
>
> Fhandler->y_to_readSize -= tmp_y_blockSize;
> - size_buff = Fhandler->n * tmp_y_blockSize;
>
>
>
> @@ -983,14 +982,7 @@
>
> if(Fhandler->fakefiles)
> {
> - fseek ( fp_Y , 0 , SEEK_SET );
> - size_t result = fread (tobeFilled->buff,sizeof(type_precision),size_buff,fp_Y);
> - result++;
> - int old_seed = Fhandler->seed;
> - srand (old_seed);
> - re_random_vec(tobeFilled->buff, size_buff );
> - re_random_vec_nan(tobeFilled->buff, size_buff );
> - Fhandler->seed += 75;
> + //no longer used
> }
> else
> {
> @@ -1052,7 +1044,6 @@
> #endif
>
> Fhandler->Ar_to_readSize -= tmp_ar_blockSize;
> - size_buff = Fhandler->n * tmp_ar_blockSize*Fhandler->r;
>
> pthread_mutex_lock(&(Fhandler->m_buff_upd));
> type_buffElement* tobeFilled = Fhandler->ar_empty_buffers.front();
> @@ -1066,12 +1057,7 @@
>
> if(Fhandler->fakefiles)
> {
> -// fp_Ar.seekg ( 0 , ios::beg );
> -// fp_Ar.read ((char*)tobeFilled->buff,sizeof(type_precision)*size_buff);
> -//
> -// re_random_vec(tobeFilled->buff , Fhandler->n * tmp_ar_blockSize*Fhandler->r );
> -// re_random_vec_nan(tobeFilled->buff , Fhandler->n * tmp_ar_blockSize*Fhandler->r );
> -
> + //no longer used
> }
> else
> {
> @@ -1292,11 +1278,7 @@
> Fhandler->write_full_buffers.pop();
>
>
> - if(Fhandler->fakefiles)
> - {
>
> - }
> -
> if(!Fhandler->fakefiles && !tobeWritten->empty())
> {
>
> @@ -2001,62 +1983,39 @@
> void AIOwrapper::load_AL(type_precision** AL)
> {
>
> - if(Fhandler->fakefiles)
> - {
> - FILE *fp;
> - fp = fopen("tempAL.bin", "rb");
> - if(fp == 0)
> - {
> - cout << "Error Reading File tempAL.bin" << endl;
> - exit(1);
> - }
>
> - size_t result = fread (Fhandler->AL,sizeof(type_precision),Fhandler->l*Fhandler->n,fp);
> - result++;
> - fclose(fp);
> - srand(22);
> - re_random_vec(Fhandler->AL,Fhandler->n*Fhandler->l);
> - re_random_vec_nan(Fhandler->AL,Fhandler->n*Fhandler->l);
> - (*AL) = Fhandler->AL;
> - }
> - else
> + FILE *fp;
> + fp = fopen((Fhandler->fnameAL+".fvd").c_str(), "rb");
> + if(fp == 0)
> {
> - FILE *fp;
> - fp = fopen((Fhandler->fnameAL+".fvd").c_str(), "rb");
> - if(fp == 0)
> - {
> - cout << "Error Reading File " << Fhandler->fnameAL << endl;
> - exit(1);
> - }
> + cout << "Error Reading File " << Fhandler->fnameAL << endl;
> + exit(1);
> + }
>
> - list< pair<int,int> >* excl_List = Fhandler->excl_List;
> + list< pair<int,int> >* excl_List = Fhandler->excl_List;
>
> - int chunk_size_buff;
> - int buff_pos=0;
> - int file_pos;
> + int chunk_size_buff;
> + int buff_pos=0;
> + int file_pos;
>
> - for (int i=0; i < Fhandler->l; i++)
> + for (int i=0; i < Fhandler->l; i++)
> + {
> + for (list< pair<int,int> >::iterator it=excl_List->begin(); it != excl_List->end(); ++it)
> {
> - for (list< pair<int,int> >::iterator it=excl_List->begin(); it != excl_List->end(); ++it)
> - {
>
> - file_pos = i*Fhandler->fileN+ it->first;
> - fseek ( fp , file_pos*sizeof(type_precision) , SEEK_SET );
> - chunk_size_buff = it->second;
> + file_pos = i*Fhandler->fileN+ it->first;
> + fseek ( fp , file_pos*sizeof(type_precision) , SEEK_SET );
> + chunk_size_buff = it->second;
>
> - size_t result = fread (&(Fhandler->AL[buff_pos]),sizeof(type_precision),chunk_size_buff,fp); result++;
> - buff_pos += chunk_size_buff;
> - }
> + size_t result = fread (&(Fhandler->AL[buff_pos]),sizeof(type_precision),chunk_size_buff,fp); result++;
> + buff_pos += chunk_size_buff;
> }
> + }
>
> - //cout << Fhandler->n;
> + //cout << Fhandler->n;
>
> + fclose(fp);
>
> -// size_t result = fread (Fhandler->AL,sizeof(type_precision),Fhandler->l*Fhandler->n,fp);
> -//
> -// result++;
> - fclose(fp);
> - }
>
>
>
> @@ -2070,17 +2029,6 @@
>
> Fhandler->AL = new type_precision[columnsAL*n];
> Fhandler->l=columnsAL;
> - if(Fhandler->fakefiles)
> - {
> - FILE* fp_AL = fopen("tempAL.bin", "w+b");
> - if(fp_AL == 0)
> - {
> - cout << "Error creating temp File AL "<< endl;
> - exit(1);
> - }
> - fwrite(Fhandler->AL, sizeof(type_precision), n*columnsAL, fp_AL);
> - fclose(fp_AL);
> - }
> }
>
> void AIOwrapper::finalize_AL()
>
> Modified: pkg/OmicABELnoMM/src/Utility.cpp
> ===================================================================
> --- pkg/OmicABELnoMM/src/Utility.cpp 2014-10-28 09:59:23 UTC (rev 1860)
> +++ pkg/OmicABELnoMM/src/Utility.cpp 2014-10-28 10:20:35 UTC (rev 1861)
> @@ -28,28 +28,9 @@
> }
>
>
> -type_precision* random_vec(int size)
> -{
>
> - type_precision* vec =
> - (type_precision*)malloc(size * sizeof(type_precision));
>
> - if (vec == 0)
> - {
> - cout << "\nNot enough RAM! "
> - << (int)(size*sizeof(type_precision)/1024/1024) << "MB\n";
> - //system("pause");
> - exit(1);
> - }
>
> - for (int i = 0; i < size; i++)
> - {
> - vec[i] = (type_precision)rand() / (type_precision)RAND_MAX;
> - }
> - return vec;
> -}
> -
> -
> void re_random_vec(type_precision* vec, int size)
> {
> for (int i = 0; i < size; i++)
> @@ -59,25 +40,9 @@
> }
>
>
> -void re_random_vec_nan(type_precision* vec, int size)
> -{
> - //int i;
>
> -// for ( i = 0; i < size; i++)
> -// {
> -// if ((type_precision)rand() / (type_precision)RAND_MAX > 0.5)
> -// vec[i] = nanf("");
> -// }
> -}
>
>
> -//no allocation!
> -//inline void inlinecopy_vec(type_precision*old, type_precision* new_vec, int size)
> -//{
> -// memcpy( (type_precision*)new_vec, (type_precision*)old, size * sizeof(type_precision) );
> -//}
> -
> -
> type_precision* replicate_vec(type_precision* old, int size)
> {
> type_precision* vec =
> @@ -240,46 +205,6 @@
> }
> }
>
> -
> -void cpu_benchmark(int n, int samples, double &duration, double &GFLOPS)
> -{
> - type_precision* A = new type_precision[n * n];
> - type_precision* B = new type_precision[n * n];
> - type_precision* C = new type_precision[n * n];
> -
> - cputime_type start_tick, end_tick;
> - duration = 9999999999.0;
> - int b = 0;
> -
> - for (int i = 0; i < samples; i++)
> - {
> - re_random_vec(A, n*n);
> - re_random_vec(B, n*n);
> - re_random_vec(C, n*n);
> -
> - get_ticks(start_tick);
> - cblas_sgemm(CblasColMajor, CblasNoTrans, CblasNoTrans, n, n, n,
> - 1.0, A, n, B, n, 1.0, C, n);
> - get_ticks(end_tick);
> - duration = min(duration, (double)(ticks2sec(end_tick, start_tick)));
> - int a = 0;
> - for (int j = 0; j < n * n ; j++)
> - {
> - a += A[j] + B[j] + C[j];
> - }
> - b += a;
> - }
> - //!2nnn - nn + 2nn (from+c)
> - GFLOPS = gemm_flops(n, n, n, 0);
> -
> - cout << b;
> -
> - delete []A;
> - delete []B;
> - delete []C;
> -}
> -
> -
> float getTvalue(float pval)
> {
> // cout << pval << endl;
>
> Modified: pkg/OmicABELnoMM/src/Utility.h
> ===================================================================
> --- pkg/OmicABELnoMM/src/Utility.h 2014-10-28 09:59:23 UTC (rev 1860)
> +++ pkg/OmicABELnoMM/src/Utility.h 2014-10-28 10:20:35 UTC (rev 1861)
> @@ -25,10 +25,7 @@
>
> type_precision* replicate_vec(type_precision*old, int size);
> void matlab_print_matrix(string name, int m, int n, type_precision* A);
> -void cpu_benchmark(int n, int samples, double &duration, double &gflops);
>
> -void re_random_vec_nan(type_precision* vec, int size);
> -
> void replace_with_zeros(list<long int>* indexs, type_precision* vec,
> int n, int r, int block_count);
>
>
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--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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