Skip to content

GitLab

B
BioEM

Planned maintenance on Wednesday, 2021-01-20, 17:00-18:00. Expect some interruptions during that time

Commit beebec5d authored by David Rohr's avatar David Rohr
Browse files
Options

fix segfault if rotated model point out of map, improve debug message and options, fix memory leaks

parent 05e7d589
Hide whitespace changes
Inline Side-by-side
Showing with 48 additions and 31 deletions
bioem.cpp
View file @ beebec5d
......@@ -68,6 +68,7 @@ ostream& operator<<(ostream& os, const vector<T>& v)
bioem::bioem()
{
FFTAlgo = getenv("FFTALGO") == NULL ? 0 : atoi(getenv("FFTALGO"));
DebugOutput = getenv("BIOEM_DEBUG_OUTPUT") == NULL ? 2 : atoi(getenv("BIOEM_DEBUG_OUTPUT"));
}
bioem::~bioem()
......@@ -219,8 +220,9 @@ int bioem::configure(int ac, char* av[])
if (getenv("BIOEM_DEBUG_BREAK"))
{
param.nTotGridAngles = atoi(getenv("BIOEM_DEBUG_BREAK"));
param.nTotCTFs = atoi(getenv("BIOEM_DEBUG_BREAK"));
const int cut = atoi(getenv("BIOEM_DEBUG_BREAK"));
if (param.nTotGridAngles > cut) param.nTotGridAngles = cut;
if (param.nTotCTFs > cut) param.nTotCTFs = cut;
}
pProb.init(RefMap.ntotRefMap, param.nTotGridAngles, *this);
......@@ -308,41 +310,44 @@ int bioem::run()
HighResTimer timer;
printf("\tMain Loop (GridAngles %d, CTFs %d, RefMaps %d, Shifts (%d/%d)²), Pixels %d²\n", param.nTotGridAngles, param.nTotCTFs, RefMap.ntotRefMap, 2 * param.param_device.maxDisplaceCenter + param.param_device.GridSpaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels);
if (DebugOutput >= 1) printf("\tMain Loop (GridAngles %d, CTFs %d, RefMaps %d, Shifts (%d/%d)²), Pixels %d²\n", param.nTotGridAngles, param.nTotCTFs, RefMap.ntotRefMap, 2 * param.param_device.maxDisplaceCenter + param.param_device.GridSpaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels);
// printf("\tInner Loop Count (%d %d %d) %lld\n", param.param_device.maxDisplaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels, (long long int) (param.param_device.NumberPixels * param.param_device.NumberPixels * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1) * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1)));
for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
{
// ***************************************************************************************
// ***** Creating Projection for given orientation and transforming to Fourier space *****
timer.ResetStart();
if (DebugOutput >= 1) timer.ResetStart();
createProjection(iOrient, proj_mapFFT);
printf("Time Projection %d: %f\n", iOrient, timer.GetCurrentElapsedTime());
if (DebugOutput >= 1) printf("Time Projection %d: %f\n", iOrient, timer.GetCurrentElapsedTime());
// ***************************************************************************************
// ***** **** Internal Loop over convolutions **** *****
for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
{
printf("\t\tConvolution %d %d\n", iOrient, iConv);
if (DebugOutput >= 2) printf("\t\tConvolution %d %d\n", iOrient, iConv);
// *** Calculating convolutions of projection map and crosscorrelations ***
timer.ResetStart();
if (DebugOutput >= 2) timer.ResetStart();
createConvolutedProjectionMap(iOrient, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
printf("Time Convolution %d %d: %f\n", iOrient, iConv, timer.GetCurrentElapsedTime());
if (DebugOutput >= 2) printf("Time Convolution %d %d: %f\n", iOrient, iConv, timer.GetCurrentElapsedTime());
// ***************************************************************************************
// *** Comparing each calculated convoluted map with all experimental maps ***
timer.ResetStart();
if (DebugOutput >= 2) timer.ResetStart();
compareRefMaps(iOrient, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
const double compTime = timer.GetCurrentElapsedTime();
const int nShifts = 2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1;
const double nFlops = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 5. + 25.) / compTime;
const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 2. + 8.) * (double) sizeof(myfloat_t) / compTime;
const double nGBs2 = (double) RefMap.ntotRefMap * ((double) param.param_device.NumberPixels * (double) param.param_device.NumberPixels + 8.) * (double) sizeof(myfloat_t) / compTime;
printf("Time Comparison %d %d: %f sec (%f GFlops, %f GB/s (cached), %f GB/s)\n", iOrient, iConv, compTime, nFlops / 1000000000., nGBs / 1000000000., nGBs2 / 1000000000.);
if (DebugOutput >= 2)
{
const double compTime = timer.GetCurrentElapsedTime();
const int nShifts = 2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1;
const double nFlops = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 5. + 25.) / compTime;
const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 2. + 8.) * (double) sizeof(myfloat_t) / compTime;
const double nGBs2 = (double) RefMap.ntotRefMap * ((double) param.param_device.NumberPixels * (double) param.param_device.NumberPixels + 8.) * (double) sizeof(myfloat_t) / compTime;
printf("Time Comparison %d %d: %f sec (%f GFlops, %f GB/s (cached), %f GB/s)\n", iOrient, iConv, compTime, nFlops / 1000000000., nGBs / 1000000000., nGBs2 / 1000000000.);
}
}
}
//deallocating fftw_complex vector
......@@ -516,6 +521,12 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
i = floor(RotatedPointsModel[n].pos[0] / param.pixelSize + (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
j = floor(RotatedPointsModel[n].pos[1] / param.pixelSize + (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
if (i < 0 || j < 0 || i >= param.param_device.NumberPixels || j >= param.param_device.NumberPixels)
{
if (DebugOutput >= 3) cout << "Model Point out of map: " << i << ", " << j << "\n";
continue;
}
localproj[i * param.param_device.NumberPixels + j] += Model.densityPointsModel[n] / Model.NormDen;
}
......
bioem_cuda.cu
View file @ beebec5d
......@@ -450,6 +450,7 @@ int bioem_cuda::deviceFinishRun()
if (GPUWorkload < 100)
{
pProb.copyFrom(pProb_host, *this);
free_device_host(pProb_host->ptr);
delete[] pProb_host;
}
......
include/bioem.h
View file @ beebec5d
......@@ -55,6 +55,7 @@ protected:
int nProjectionMapsTotal; //Maps in total
int FFTAlgo;
int DebugOutput;
mycomplex_t** localCCT;
myfloat_t** lCC;
......
include/defs.h
View file @ beebec5d
......@@ -16,6 +16,7 @@ typedef float myfloat_t;
#define myfftw_plan_dft_r2c_2d fftwf_plan_dft_r2c_2d
#define myfftw_plan_dft_c2r_2d fftwf_plan_dft_c2r_2d
#define myfftw_plan fftwf_plan
#define myfftw_cleanup fftwf_cleanup
#define MY_CUFFT_C2R CUFFT_C2R
#define mycufftExecC2R cufftExecC2R
#define mycuComplex_t cuComplex
......@@ -32,6 +33,7 @@ typedef double myfloat_t;
#define myfftw_plan_dft_r2c_2d fftw_plan_dft_r2c_2d
#define myfftw_plan_dft_c2r_2d fftw_plan_dft_c2r_2d
#define myfftw_plan fftw_plan
#define myfftw_cleanup fftw_cleanup
#define mycufftExecC2R cufftExecZ2D
#define mycuComplex_t cuDoubleComplex
#define MY_CUFFT_C2R CUFFT_Z2D
......
model.cpp
View file @ beebec5d
......@@ -2,7 +2,7 @@
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
......@@ -150,6 +150,7 @@ int bioem_model::readModel()
NormDen += densityPointsModel[numres];
numres++;
}
fclose(file);
nPointsModel = numres;
cout << "Protein structure read from Standard File\n";
}
......
param.cpp
View file @ beebec5d
......@@ -2,7 +2,7 @@
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
......@@ -66,7 +66,7 @@ int bioem_param::readParameters()
bool yesGSPEnv = false ;
bool yesGSPpha = false ;
bool yesMDC = false ;
bool yesGCen = false ;
bool yesGCen = false ;
ifstream input(fileinput);
if (!input.good())
......@@ -105,7 +105,7 @@ int bioem_param::readParameters()
token = strtok(NULL, " ");
param_device.NumberPixels = int(atoi(token));
if (param_device.NumberPixels < 0 ) { cout << "*** Error: Negative Number of Pixels "; exit(1);}
cout << "Number of Pixels " << param_device.NumberPixels << "\n";
cout << "Number of Pixels " << param_device.NumberPixels << "\n";
yesNumPix= true ;
}
else if (strcmp(token, "GRIDPOINTS_ALPHA") == 0)
......@@ -215,7 +215,7 @@ int bioem_param::readParameters()
}
input.close();
// Checks for ALL INPUT
// Checks for ALL INPUT
if( not ( yesPixSi ) ){ cout << "**** INPUT MISSING: Please provide PIXEL_SIZE\n" ; exit (1);};
if( not ( yesNumPix ) ){ cout << "**** INPUT MISSING: Please provide NUMBER_PIXELS \n" ; exit (1);};
if( not ( yesGPal ) ) { cout << "**** INPUT MISSING: Please provide GRIDPOINTS_ALPHA \n" ; exit (1);};
......@@ -233,15 +233,15 @@ int bioem_param::readParameters()
if( not ( yesGCen ) ) { cout << "**** INPUT MISSING: Please provide PIXEL_GRID_CENTER \n" ; exit (1);};
//if only one grid point for PSF kernel:
if( (myfloat_t) numberGridPointsCTF_amp == 1 ) gridCTF_amp = startGridCTF_amp;
if( (myfloat_t) numberGridPointsCTF_phase == 1 ) gridCTF_phase = startGridCTF_phase;
if( (myfloat_t) numberGridPointsEnvelop == 1 ) gridEnvelop = startGridEnvelop;
//if only one grid point for PSF kernel:
if( (myfloat_t) numberGridPointsCTF_amp == 1 ) gridCTF_amp = startGridCTF_amp;
if( (myfloat_t) numberGridPointsCTF_phase == 1 ) gridCTF_phase = startGridCTF_phase;
if( (myfloat_t) numberGridPointsEnvelop == 1 ) gridEnvelop = startGridEnvelop;
//More checks with input parameters
// Envelope should not have a standard deviation greater than Npix/2
// Envelope should not have a standard deviation greater than Npix/2
if(sqrt(1./( (myfloat_t) numberGridPointsDisplaceCenter * gridEnvelop + startGridEnvelop))> float(param_device.NumberPixels)/2.0) {
cout << "MAX Standar deviation of envelope is larger than Allowed KERNEL Length";
cout << "MAX Standard deviation of envelope is larger than Allowed KERNEL Length\n";
exit(1);
}
// Envelop param should be positive
......@@ -255,7 +255,7 @@ int bioem_param::readParameters()
exit(1);
}
cout << " +++++++++++++++++++++++++++++++++++++++++ \n";
cout << "Preparing FFTs\n";
......@@ -303,6 +303,7 @@ void bioem_param::releaseFFTPlans()
myfftw_destroy_plan(fft_plan_c2c_backward);
myfftw_destroy_plan(fft_plan_r2c_forward);
myfftw_destroy_plan(fft_plan_c2r_backward);
myfftw_cleanup();
}
fft_plans_created = 0;
}
......@@ -339,7 +340,7 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
}
nTotGridAngles = n;
// ********** Calculating normalized volumen element *********
param_device.volu = grid_alpha * grid_alpha * cos_grid_beta * (myfloat_t) param_device.GridSpaceCenter * pixelSize * (myfloat_t) param_device.GridSpaceCenter * pixelSize
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment