int bi_entry(void * mdpv, int iproblemsize, double * dresults) { /* dstart, dend: the start and end time of the measurement */ /* dtime: the time for a single measurement in seconds */ double dstart = 0.0, dend = 0.0, dtime = 0.0, dinit = 0.0; /* flops stores the calculated FLOPS */ double flops = 0.0; /* ii is used for loop iterations */ myinttype ii, jj, imyproblemsize, numberOfRuns; /* cast void* pointer */ mydata_t* pmydata = (mydata_t*)mdpv; int invalid = 0; long status, len[3]; /* calculate real problemsize */ imyproblemsize = (int)(pmydata->problemsizes[iproblemsize - 1]); len[0] = imyproblemsize; len[1] = imyproblemsize; len[2] = imyproblemsize; /* store the value for the x axis in results[0] */ dresults[0] = (double)imyproblemsize; /*** in place run ***/ /* malloc */ pmydata->inout = (double*)malloc(sizeof(double) * imyproblemsize * imyproblemsize * imyproblemsize * 2); /* create FFT plan */ status = DftiCreateDescriptor(&pmydata->my_desc_handle, DFTI_DOUBLE, DFTI_COMPLEX, 3, len); status = DftiCommitDescriptor(pmydata->my_desc_handle); /* init stuff */ initData_ip(pmydata, imyproblemsize); numberOfRuns = 1; dstart = bi_gettime(); /* fft calculation */ status = DftiComputeForward(pmydata->my_desc_handle, pmydata->inout); dend = bi_gettime(); /* calculate the used time*/ dtime = dend - dstart; dtime -= dTimerOverhead; /* loop calculation if accuracy is insufficient */ while (dtime < 100 * dTimerGranularity) { numberOfRuns = numberOfRuns * 2; dstart = bi_gettime(); for (jj = 0; jj < numberOfRuns; jj++) { /* fft calculation */ status = DftiComputeForward(pmydata->my_desc_handle, pmydata->inout); } dend = bi_gettime(); dtime = dend - dstart; dtime -= dTimerOverhead; } /* check for overflows */ for (ii = 0; ii < imyproblemsize * imyproblemsize * imyproblemsize; ii++) { if (isnan(pmydata->inout[2 * ii]) || isnan(pmydata->inout[2 * ii + 1])) invalid = 1; if (isinf(pmydata->inout[2 * ii]) || isinf(pmydata->inout[2 * ii + 1])) invalid = 1; } /* if loop was necessary */ if (numberOfRuns > 1) dtime = dtime / numberOfRuns; /* calculate the used FLOPS */ flops = (double)(5.0 * imyproblemsize * imyproblemsize * imyproblemsize * (log2(1.0 * imyproblemsize * imyproblemsize * imyproblemsize)) / dtime); /* store the FLOPS in results[1] */ if (invalid == 1) dresults[1] = INVALID_MEASUREMENT; else dresults[1] = flops; status = DftiFreeDescriptor(&pmydata->my_desc_handle); /* free data */ free(pmydata->inout); /*** out of place run ***/ /* malloc */ pmydata->in = (double*)malloc(sizeof(double) * imyproblemsize * imyproblemsize * imyproblemsize * 2); pmydata->out = (double*)malloc(sizeof(double) * imyproblemsize * imyproblemsize * imyproblemsize * 2); /* create FFT plan */ status = DftiCreateDescriptor(&pmydata->my_desc_handle, DFTI_DOUBLE, DFTI_COMPLEX, 3, len); status = DftiSetValue(pmydata->my_desc_handle, DFTI_PLACEMENT, DFTI_NOT_INPLACE); status = DftiCommitDescriptor(pmydata->my_desc_handle); /* init stuff */ initData_oop(pmydata, imyproblemsize); numberOfRuns = 1; dstart = bi_gettime(); /* fft calculation */ status = DftiComputeForward(pmydata->my_desc_handle, pmydata->in, pmydata->out); dend = bi_gettime(); /* calculate the used time*/ dtime = dend - dstart; dtime -= dTimerOverhead; /* loop calculation if accuracy is insufficient */ while (dtime < 100 * dTimerGranularity) { numberOfRuns = numberOfRuns * 2; dstart = bi_gettime(); for (ii = 0; ii < numberOfRuns; ii++) { /* fft calculation */ status = DftiComputeForward(pmydata->my_desc_handle, pmydata->in, pmydata->out); } dend = bi_gettime(); /* calculate the used time*/ dtime = dend - dstart; dtime -= dTimerOverhead; } /* if loop was necessary */ if (numberOfRuns > 1) dtime = dtime / numberOfRuns; /* check for overflows */ for (ii = 0; ii < imyproblemsize * imyproblemsize * imyproblemsize; ii++) { if (isnan(pmydata->out[2 * ii]) || isnan(pmydata->out[2 * ii + 1])) invalid = 1; if (isinf(pmydata->out[2 * ii]) || isinf(pmydata->out[2 * ii + 1])) invalid = 1; } /* calculate the used FLOPS */ flops = (double)(5.0 * imyproblemsize * imyproblemsize * imyproblemsize * (log2(1.0 * imyproblemsize * imyproblemsize * imyproblemsize)) / dtime); /* store the FLOPS in results[2] */ if (invalid == 1) dresults[2] = INVALID_MEASUREMENT; else dresults[2] = flops; status = DftiFreeDescriptor(&pmydata->my_desc_handle); /* free data */ free(pmydata->in); free(pmydata->out); return 0; }
int gmx_fft_init_1d_real(gmx_fft_t * pfft, int nx, gmx_fft_flag gmx_unused flags) { gmx_fft_t fft; int d; int status; if (pfft == NULL) { gmx_fatal(FARGS, "Invalid opaque FFT datatype pointer."); return EINVAL; } *pfft = NULL; if ( (fft = (gmx_fft_t)malloc(sizeof(struct gmx_fft))) == NULL) { return ENOMEM; } /* Mark all handles invalid */ for (d = 0; d < 3; d++) { fft->inplace[d] = fft->ooplace[d] = NULL; } fft->ooplace[3] = NULL; status = DftiCreateDescriptor(&fft->inplace[0], GMX_DFTI_PREC, DFTI_REAL, 1, (MKL_LONG)nx); if (status == 0) { status = DftiSetValue(fft->inplace[0], DFTI_PLACEMENT, DFTI_INPLACE); } if (status == 0) { status = DftiCommitDescriptor(fft->inplace[0]); } if (status == 0) { status = DftiCreateDescriptor(&fft->ooplace[0], GMX_DFTI_PREC, DFTI_REAL, 1, (MKL_LONG)nx); } if (status == 0) { status = DftiSetValue(fft->ooplace[0], DFTI_PLACEMENT, DFTI_NOT_INPLACE); } if (status == 0) { status = DftiCommitDescriptor(fft->ooplace[0]); } if (status == DFTI_UNIMPLEMENTED) { gmx_fatal(FARGS, "The linked Intel MKL version (<6.0?) cannot do real FFTs."); gmx_fft_destroy(fft); return status; } if (status != 0) { gmx_fatal(FARGS, "Error initializing Intel MKL FFT; status=%d", status); gmx_fft_destroy(fft); return status; } fft->ndim = 1; fft->nx = nx; fft->real_fft = 1; fft->work = NULL; *pfft = fft; return 0; }
struct fft_plan_3d *fft_3d_create_plan( MPI_Comm comm, int nfast, int nmid, int nslow, int in_ilo, int in_ihi, int in_jlo, int in_jhi, int in_klo, int in_khi, int out_ilo, int out_ihi, int out_jlo, int out_jhi, int out_klo, int out_khi, int scaled, int permute, int *nbuf, int usecollective) { struct fft_plan_3d *plan; int me,nprocs; int flag,remapflag; int first_ilo,first_ihi,first_jlo,first_jhi,first_klo,first_khi; int second_ilo,second_ihi,second_jlo,second_jhi,second_klo,second_khi; int third_ilo,third_ihi,third_jlo,third_jhi,third_klo,third_khi; int out_size,first_size,second_size,third_size,copy_size,scratch_size; int np1,np2,ip1,ip2; // query MPI info MPI_Comm_rank(comm,&me); MPI_Comm_size(comm,&nprocs); // compute division of procs in 2 dimensions not on-processor bifactor(nprocs,&np1,&np2); ip1 = me % np1; ip2 = me/np1; // allocate memory for plan data struct plan = (struct fft_plan_3d *) malloc(sizeof(struct fft_plan_3d)); if (plan == NULL) return NULL; // remap from initial distribution to layout needed for 1st set of 1d FFTs // not needed if all procs own entire fast axis initially // first indices = distribution after 1st set of FFTs if (in_ilo == 0 && in_ihi == nfast-1) flag = 0; else flag = 1; MPI_Allreduce(&flag,&remapflag,1,MPI_INT,MPI_MAX,comm); if (remapflag == 0) { first_ilo = in_ilo; first_ihi = in_ihi; first_jlo = in_jlo; first_jhi = in_jhi; first_klo = in_klo; first_khi = in_khi; plan->pre_plan = NULL; } else { first_ilo = 0; first_ihi = nfast - 1; first_jlo = ip1*nmid/np1; first_jhi = (ip1+1)*nmid/np1 - 1; first_klo = ip2*nslow/np2; first_khi = (ip2+1)*nslow/np2 - 1; plan->pre_plan = remap_3d_create_plan(comm,in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi, first_ilo,first_ihi,first_jlo,first_jhi, first_klo,first_khi,2,0,0,FFT_PRECISION,0); if (plan->pre_plan == NULL) return NULL; } // 1d FFTs along fast axis plan->length1 = nfast; plan->total1 = nfast * (first_jhi-first_jlo+1) * (first_khi-first_klo+1); // remap from 1st to 2nd FFT // choose which axis is split over np1 vs np2 to minimize communication // second indices = distribution after 2nd set of FFTs second_ilo = ip1*nfast/np1; second_ihi = (ip1+1)*nfast/np1 - 1; second_jlo = 0; second_jhi = nmid - 1; second_klo = ip2*nslow/np2; second_khi = (ip2+1)*nslow/np2 - 1; plan->mid1_plan = remap_3d_create_plan(comm, first_ilo,first_ihi,first_jlo,first_jhi, first_klo,first_khi, second_ilo,second_ihi,second_jlo,second_jhi, second_klo,second_khi,2,1,0,FFT_PRECISION, usecollective); if (plan->mid1_plan == NULL) return NULL; // 1d FFTs along mid axis plan->length2 = nmid; plan->total2 = (second_ihi-second_ilo+1) * nmid * (second_khi-second_klo+1); // remap from 2nd to 3rd FFT // if final distribution is permute=2 with all procs owning entire slow axis // then this remapping goes directly to final distribution // third indices = distribution after 3rd set of FFTs if (permute == 2 && out_klo == 0 && out_khi == nslow-1) flag = 0; else flag = 1; MPI_Allreduce(&flag,&remapflag,1,MPI_INT,MPI_MAX,comm); if (remapflag == 0) { third_ilo = out_ilo; third_ihi = out_ihi; third_jlo = out_jlo; third_jhi = out_jhi; third_klo = out_klo; third_khi = out_khi; } else { third_ilo = ip1*nfast/np1; third_ihi = (ip1+1)*nfast/np1 - 1; third_jlo = ip2*nmid/np2; third_jhi = (ip2+1)*nmid/np2 - 1; third_klo = 0; third_khi = nslow - 1; } plan->mid2_plan = remap_3d_create_plan(comm, second_jlo,second_jhi,second_klo,second_khi, second_ilo,second_ihi, third_jlo,third_jhi,third_klo,third_khi, third_ilo,third_ihi,2,1,0,FFT_PRECISION,usecollective); if (plan->mid2_plan == NULL) return NULL; // 1d FFTs along slow axis plan->length3 = nslow; plan->total3 = (third_ihi-third_ilo+1) * (third_jhi-third_jlo+1) * nslow; // remap from 3rd FFT to final distribution // not needed if permute = 2 and third indices = out indices on all procs if (permute == 2 && out_ilo == third_ilo && out_ihi == third_ihi && out_jlo == third_jlo && out_jhi == third_jhi && out_klo == third_klo && out_khi == third_khi) flag = 0; else flag = 1; MPI_Allreduce(&flag,&remapflag,1,MPI_INT,MPI_MAX,comm); if (remapflag == 0) plan->post_plan = NULL; else { plan->post_plan = remap_3d_create_plan(comm, third_klo,third_khi,third_ilo,third_ihi, third_jlo,third_jhi, out_klo,out_khi,out_ilo,out_ihi, out_jlo,out_jhi,2,(permute+1)%3,0,FFT_PRECISION,0); if (plan->post_plan == NULL) return NULL; } // configure plan memory pointers and allocate work space // out_size = amount of memory given to FFT by user // first/second/third_size = // amount of memory needed after pre,mid1,mid2 remaps // copy_size = amount needed internally for extra copy of data // scratch_size = amount needed internally for remap scratch space // for each remap: // out space used for result if big enough, else require copy buffer // accumulate largest required remap scratch space out_size = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) * (out_khi-out_klo+1); first_size = (first_ihi-first_ilo+1) * (first_jhi-first_jlo+1) * (first_khi-first_klo+1); second_size = (second_ihi-second_ilo+1) * (second_jhi-second_jlo+1) * (second_khi-second_klo+1); third_size = (third_ihi-third_ilo+1) * (third_jhi-third_jlo+1) * (third_khi-third_klo+1); copy_size = 0; scratch_size = 0; if (plan->pre_plan) { if (first_size <= out_size) plan->pre_target = 0; else { plan->pre_target = 1; copy_size = MAX(copy_size,first_size); } scratch_size = MAX(scratch_size,first_size); } if (plan->mid1_plan) { if (second_size <= out_size) plan->mid1_target = 0; else { plan->mid1_target = 1; copy_size = MAX(copy_size,second_size); } scratch_size = MAX(scratch_size,second_size); } if (plan->mid2_plan) { if (third_size <= out_size) plan->mid2_target = 0; else { plan->mid2_target = 1; copy_size = MAX(copy_size,third_size); } scratch_size = MAX(scratch_size,third_size); } if (plan->post_plan) scratch_size = MAX(scratch_size,out_size); *nbuf = copy_size + scratch_size; if (copy_size) { plan->copy = (FFT_DATA *) malloc(copy_size*sizeof(FFT_DATA)); if (plan->copy == NULL) return NULL; } else plan->copy = NULL; if (scratch_size) { plan->scratch = (FFT_DATA *) malloc(scratch_size*sizeof(FFT_DATA)); if (plan->scratch == NULL) return NULL; } else plan->scratch = NULL; // system specific pre-computation of 1d FFT coeffs // and scaling normalization #if defined(FFT_MKL) DftiCreateDescriptor( &(plan->handle_fast), FFT_MKL_PREC, DFTI_COMPLEX, 1, (MKL_LONG)nfast); DftiSetValue(plan->handle_fast, DFTI_NUMBER_OF_TRANSFORMS, (MKL_LONG)plan->total1/nfast); DftiSetValue(plan->handle_fast, DFTI_PLACEMENT,DFTI_INPLACE); DftiSetValue(plan->handle_fast, DFTI_INPUT_DISTANCE, (MKL_LONG)nfast); DftiSetValue(plan->handle_fast, DFTI_OUTPUT_DISTANCE, (MKL_LONG)nfast); DftiCommitDescriptor(plan->handle_fast); DftiCreateDescriptor( &(plan->handle_mid), FFT_MKL_PREC, DFTI_COMPLEX, 1, (MKL_LONG)nmid); DftiSetValue(plan->handle_mid, DFTI_NUMBER_OF_TRANSFORMS, (MKL_LONG)plan->total2/nmid); DftiSetValue(plan->handle_mid, DFTI_PLACEMENT,DFTI_INPLACE); DftiSetValue(plan->handle_mid, DFTI_INPUT_DISTANCE, (MKL_LONG)nmid); DftiSetValue(plan->handle_mid, DFTI_OUTPUT_DISTANCE, (MKL_LONG)nmid); DftiCommitDescriptor(plan->handle_mid); DftiCreateDescriptor( &(plan->handle_slow), FFT_MKL_PREC, DFTI_COMPLEX, 1, (MKL_LONG)nslow); DftiSetValue(plan->handle_slow, DFTI_NUMBER_OF_TRANSFORMS, (MKL_LONG)plan->total3/nslow); DftiSetValue(plan->handle_slow, DFTI_PLACEMENT,DFTI_INPLACE); DftiSetValue(plan->handle_slow, DFTI_INPUT_DISTANCE, (MKL_LONG)nslow); DftiSetValue(plan->handle_slow, DFTI_OUTPUT_DISTANCE, (MKL_LONG)nslow); DftiCommitDescriptor(plan->handle_slow); if (scaled == 0) plan->scaled = 0; else { plan->scaled = 1; plan->norm = 1.0/(nfast*nmid*nslow); plan->normnum = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) * (out_khi-out_klo+1); } #elif defined(FFT_FFTW2) plan->plan_fast_forward = fftw_create_plan(nfast,FFTW_FORWARD,FFTW_ESTIMATE | FFTW_IN_PLACE); plan->plan_fast_backward = fftw_create_plan(nfast,FFTW_BACKWARD,FFTW_ESTIMATE | FFTW_IN_PLACE); if (nmid == nfast) { plan->plan_mid_forward = plan->plan_fast_forward; plan->plan_mid_backward = plan->plan_fast_backward; } else { plan->plan_mid_forward = fftw_create_plan(nmid,FFTW_FORWARD,FFTW_ESTIMATE | FFTW_IN_PLACE); plan->plan_mid_backward = fftw_create_plan(nmid,FFTW_BACKWARD,FFTW_ESTIMATE | FFTW_IN_PLACE); } if (nslow == nfast) { plan->plan_slow_forward = plan->plan_fast_forward; plan->plan_slow_backward = plan->plan_fast_backward; } else if (nslow == nmid) { plan->plan_slow_forward = plan->plan_mid_forward; plan->plan_slow_backward = plan->plan_mid_backward; } else { plan->plan_slow_forward = fftw_create_plan(nslow,FFTW_FORWARD,FFTW_ESTIMATE | FFTW_IN_PLACE); plan->plan_slow_backward = fftw_create_plan(nslow,FFTW_BACKWARD,FFTW_ESTIMATE | FFTW_IN_PLACE); } if (scaled == 0) plan->scaled = 0; else { plan->scaled = 1; plan->norm = 1.0/(nfast*nmid*nslow); plan->normnum = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) * (out_khi-out_klo+1); } #elif defined(FFT_FFTW3) plan->plan_fast_forward = FFTW_API(plan_many_dft)(1, &nfast,plan->total1/plan->length1, NULL,&nfast,1,plan->length1, NULL,&nfast,1,plan->length1, FFTW_FORWARD,FFTW_ESTIMATE); plan->plan_fast_backward = FFTW_API(plan_many_dft)(1, &nfast,plan->total1/plan->length1, NULL,&nfast,1,plan->length1, NULL,&nfast,1,plan->length1, FFTW_BACKWARD,FFTW_ESTIMATE); plan->plan_mid_forward = FFTW_API(plan_many_dft)(1, &nmid,plan->total2/plan->length2, NULL,&nmid,1,plan->length2, NULL,&nmid,1,plan->length2, FFTW_FORWARD,FFTW_ESTIMATE); plan->plan_mid_backward = FFTW_API(plan_many_dft)(1, &nmid,plan->total2/plan->length2, NULL,&nmid,1,plan->length2, NULL,&nmid,1,plan->length2, FFTW_BACKWARD,FFTW_ESTIMATE); plan->plan_slow_forward = FFTW_API(plan_many_dft)(1, &nslow,plan->total3/plan->length3, NULL,&nslow,1,plan->length3, NULL,&nslow,1,plan->length3, FFTW_FORWARD,FFTW_ESTIMATE); plan->plan_slow_backward = FFTW_API(plan_many_dft)(1, &nslow,plan->total3/plan->length3, NULL,&nslow,1,plan->length3, NULL,&nslow,1,plan->length3, FFTW_BACKWARD,FFTW_ESTIMATE); if (scaled == 0) plan->scaled = 0; else { plan->scaled = 1; plan->norm = 1.0/(nfast*nmid*nslow); plan->normnum = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) * (out_khi-out_klo+1); } #else plan->cfg_fast_forward = kiss_fft_alloc(nfast,0,NULL,NULL); plan->cfg_fast_backward = kiss_fft_alloc(nfast,1,NULL,NULL); if (nmid == nfast) { plan->cfg_mid_forward = plan->cfg_fast_forward; plan->cfg_mid_backward = plan->cfg_fast_backward; } else { plan->cfg_mid_forward = kiss_fft_alloc(nmid,0,NULL,NULL); plan->cfg_mid_backward = kiss_fft_alloc(nmid,1,NULL,NULL); } if (nslow == nfast) { plan->cfg_slow_forward = plan->cfg_fast_forward; plan->cfg_slow_backward = plan->cfg_fast_backward; } else if (nslow == nmid) { plan->cfg_slow_forward = plan->cfg_mid_forward; plan->cfg_slow_backward = plan->cfg_mid_backward; } else { plan->cfg_slow_forward = kiss_fft_alloc(nslow,0,NULL,NULL); plan->cfg_slow_backward = kiss_fft_alloc(nslow,1,NULL,NULL); } if (scaled == 0) plan->scaled = 0; else { plan->scaled = 1; plan->norm = 1.0/(nfast*nmid*nslow); plan->normnum = (out_ihi-out_ilo+1) * (out_jhi-out_jlo+1) * (out_khi-out_klo+1); } #endif return plan; }