martijnpieters / mcgpu Goto Github PK

Hi!

Is there a possibility to use PENELOPE 2008 to generate new material files for 
MC-GPU.
I'm currently stuck in modifying the MC-GPU_create_material_data.f file.
I managed it to get the MFP values for the interactions, but in PENELOPE 2008 
there is no GRAaD1 method. And using the existing GRAaD method gives false 
results for the maximum Rayleigh cumulative probabilities.
Also all "SAMPLING DATA FROM COMMON/CGRA" values are zero.

Any suggestion?

Best regards
Markus

Hello,

I would like to perform simulation with new C1 C2 WCC WCR parameters.
If I change the file MC-GPU_create_material_data.f with the new parameter, it 
is impossible to compile the file. There are some errors

`graai_linear_energy__':
/home/dt229232/mcgpu/MC-GPU_material_files/MC-GPU_create_material_data.f:315: 
undefined reference to `graad1_'
/home/dt229232/mcgpu/MC-GPU_material_files/MC-GPU_create_material_data.f:315: 
undefined reference to `ritai0_'
/home/dt229232/mcgpu/MC-GPU_material_files/MC-GPU_create_material_data.f:356: 
undefined reference to `simpsu_'

I am a "new be" with Penelope where ould I find the missing function ?

Thank you 

Regards

David

I want to use MC-GPU to simulate CT projections, but encounter a problem.
The attachment is the input file which is modified from the sample file. The 
main changes are "SECTION CT SCAN TRAJECTORY" part. With these modification, I 
expect the projections of the scanned object locating at the center of the 
detector. But the results are not as expected. 
I looked at the coordinates of the source and detector after rotation. The 
coordinates of the source and the center of the detector are the same as 
expected, but the values of "new detector low corner (at +Y)" are not the same 
as expected. I do not quite understand the meaning of these values. Is this the 
coordinates of the low corner of the detector?

I'm wondering if I can run your code to simulate high energy interaction 
between photons and objects? 
For treatment purpose, 6 and 18 MV x-rays are commonly used. According to your 
published paper, the code can simulate photons with energy up to 1 GeV. 

Does this mean I can use it to simulate the high-energy treatment beams (6 and 
18 MV)?

Hello,

I am trying to simulated X-ray spectra of 28 kV with filtering for a study on 
mammography. I am encountering a few difficulties with the tools that I have 
available so I am looking for a already made spectrum. In the spectrum files 
that came with MCGPU it says that the source is IPEM Report 78. I want to ask 
you if you have an idea if this will be helpful for me (I could not find an 
abstract or resume of the content). Thank for your help.

Hello,

I noticed, that the total speed varies widely from one simulation to another. I 
have a Geforce GTX 770 and if I change the phantom or choose different 
source/detector settings my speed varies from about 1 million x-ray/s to 13 
million x-rays/s.
Could you explain this? Could I do any changes (e.g. in the Input-File) to 
optimize the simulation speed? I've tried to change the "GPU-Threads per 
Cuda-Block" and the "simulated histories per GPU-Thread", but I can only make 
it slower.

Best regards
Jenny

While running multiple scans sequentially using MC-GPU, the program will 
randomly hang when trying to initialize the voxels. 

I have let the program sit at this phase overnight with no change, but when I 
reset the computer the program runs right away.

This is happening on a Dell Precision T7500 using a Quadro 6000 for computing 
and Quadro 600 for display running Ubuntu 12.04 and using Cuda v5.0 and MC-GPU 
v1.3. 

I checked the nvidia-smi output and even though in the terminal the program is 
running and the output recognizes the mc-gpu job is there, the Quadro 6000 
never leaves the P12 idle state to start computing like it would on a normal 
run. I don't believe it is a memory leak or overheating because the card shows 
almost all memory free and all reasonable temperatures.

Has anyone encountered similar problems of the program hanging until a restart?

-Dave

I am writing to ask where I can find the database of PENELOPE (V. 2006).
I have searched the web for a long time and find only the version v 2011.

Thanks!

[deleted issue]

Hallo,

I have installed debain wheezy 7.0. I would like run  the SAMPLE SIMULATION FOR 
MC-GPU v1.3 USING THE ZUBAL PHANTOM. The voxelizied geometery of the Zubal 
phatnow has been downloaded from the adress http://noodle.med.yale.edu/zubal/.

 The MCGPU was obtained with the command:
 gcc -O3 zubal2mcgpu.c -o zubal2mcgpu.x 

The exceution of the next command showed an error  Memory access erorr

./zubal2mcgpu.x zubal2mcgpu_conversion_table.in voxel_man.dat

The used System for the MCGPU has the following specfications:  

-Processor

Intel® Pentium® 4 Processor 641   • 3.20 GHz, 2 MB L2 cache, 800 MHz front 
side bus 

- Standard memory 

512 MB (256 MB x 2)

- Graphic Subsystem Video Card Memory

Graphics memory is shared with system memory. Graphics memory usage can vary 
from 8 to 128 MB depending on the amount of system memory installed and system 
load

Thank you

Regards 
Ghassan 

Hello,

I am currently trying to get MC-GPU up and running so that I am able to change 
the code to simulate inverse geometry systems. I am new to linux and running 
into a few problems. I understand that these may be trivial, but it never hurts 
to ask. 

First off, let me explain my situation.

Using a Lenovo y400 Laptop with Nvidia 650m
Running Ubuntu 12.10
Installed Cuda-5.0, all samples compiled and I ran quite a few to test that 
they worked
Using Proprietary driver, not dev-driver that came with Cuda-5.0
Wrote a quick "Hello world" cuda program that compiled and ran
I am compiled with the given lines in the code to create the MC-GPU_v1.3.x and 
run the simple geometry using ../MC-GPU_v1.3.x MC-GPU_v1.3_6voxels.in | tee 
MC-GPU_v1.3_6voxels.out

I can compile and run the simple geometery code using the CPU compilation but 
the GPU part I cannot get to work.

I switch to console, disable the Xserver by calling service lightdm stop and 
init 3
When I try to run the code after doing this, I get all print outs to the point 
of where it states: starting the Monte Carlo Loop Phase and then it tells me 
that I am executing 7813 blocks of 128 threads with 100 histories in each 
thread for a total of 100006400 histories in total. After this output, I get an 
error from line 891 in MC-GPU_v1.3.cu that !!Kernel execution failed while 
simulating particle tracks!!  : (4) unspecified launch failure.

I am assuming that I am getting the error from where the code first tries to 
access the memory of the GPU, but unsure why I am getting these errors. Since I 
am running a sample I am hoping that this is a simple problem of not compiling 
something correctly or missing a step in attempting the simulation. Please let 
me know if anyone has time to help or if I should share any other information.

Thanks,

Dave

[deleted issue]

I need a MC-GPU material file for iodine (or if anyone has one for some typical 
iodine based x-ray contrast agents that would be better). I tired using the 
cross section files from GEANT but the lack of documentation on those files 
made converting them into MC-GPU format difficult. Please advise! Thanks!!!!

-tim szczykutowicz (University of Wisconsin Madison)

Hello,

I am searching some way, to edit a phantom, maybe one of the Virtual Family. Do 
you know some way to do this? It's not possible to import them into Autocad or 
SolidWorks. 

Regards
Jenny

Hallo Andreu,

I would like to ask two question:

1. Is it possible to run mcpgu with the new versions of NVIDIA GeForce like  
GTX 760 2048MB GDDR5  GDDR5?

2. What are the specifications for the Hardware to run the mcgpu?

With best regards 
Ghassan 

[deleted issue]

It might be useful to be able to input as an x-ray source a phase space file, 
where a phase space file is defined as a file containing photons  scored at a 
specific plane with the each particle's location, energy and direction encoded 
in the file/.

An example use would be to simulate an x-ray tube starting with the electrons 
striking the tungsten anode generating photons and then tracking the photons 
all the way to the collimator using a separate MC simulation (e.g. BEAMnrc, 
Geant4, etc) and scoring the photons at the exit of the collimators  in a phase 
space file.

The phase space file could then be used as an input the mcgpu as a source. 
Potentially a database of phase space files for some common x-ray tubes could 
be generated and available similar to the effort to create a common source of 
phase space files for external beam radiation therapy. 
(http://www-nds.iaea.org/phsp/phsp.htmlx)

[deleted issue]

I have been installed mcgup v1.3 

1. I tried to start the simulation, with the following commands:

a. gcc -x c -O3 MC-GPU_v1.3.cu -o MC-GPU_v1.3_CPU.x -I./ -lm -lz

Here, I have no problem.

b. ./MC-GPU_v1.3.x MC-GPU_v1.3.in | tee MC-GPU_v1.3.out

After the second command, I got the following error 

bash: ./MC-GPU_V1.3.x: cannot execute binary file

why cannot binary file be executed? 

Thank you very much for your help

Best regards, 

Seonkyu

Hi,

I just want to confirm that the source always rotates around the axis x=0, y=0 
(i.e. z-axis)?  And due to the way the program is setup, this z-axis is always 
at the edge of the voxel volume?

This seems to cause trouble if one wants to produce CT datasets.  In the ".in" 
file, to get the voxel volume to project to the center of the detector on the 
first projection one must offset the source's coordinates in the ".in" file to 
be half of the voxel volume size in each dimension.  However, since the source 
continues to rotate around the z-axis and not the axis parallel to the z-axis 
that runs through the center of the volume.  Thus, the object rotates 
eccentrically relative to the detector and tends to "fall off" the detector at 
most angles when the field of view is small.

Is this the case, or do I understand the ".in" file incorrectly?  Is one 
supposed to fix this problem by changing the source cosines?  Or should I edit 
the source trajectory function (void set_CT_trajectory(...)) to try to make it 
so the voxel volume is centered in the field of view throughout a CT 
acquisition.

Thanks!

Jared

A user of MC-GPU observed some obvious correlations in the simulated CT 
projections, that appeared as vertical lines in the sinogram and as circular 
artifacts in the reconstructed CT.

As he suggested, the artifacts were caused by the use of the same starting 
random seed for each projection. 

The code in the Source section has been updated to use uncorrelated seeds for 
each projection, using the same leap frog algorithm used to avoid correlations 
among GPU threads.

Please, submit more bug reports, it will be better for all.
Thank you for the feed back! 

MC-GPU_create_material_data.f

line 140
function PHMFP returns.....

where are the codes of PHMFP function located? 

What steps will reproduce the problem?
1. Compile MC-GPU v.1.3.x on my operating system (see below)
2. Run the simple 6-voxel sample simulation
3. Watch program exit with CUDA error 13 during device initialization

What is the expected output? What do you see instead?
Expected output is the simple image of six squares in given for the 6-voxel 
sample simulation.  

What version of the product are you using? On what operating system?
I'm using MC-GPU version 1.3 on Ubuntu 13.10 with Cuda 5.5.  My graphics card 
is an NVIDIA Quadro FX3700.  The drivers and CUDA libraries seem to be 
correctly installed (they can compile and run other CUDA programs correctly.)

Please provide any additional information below.
I've tracked the error down to the line 
checkCudaErrors(cudaMemcpyToSymbol(voxel_data_CONST,     voxel_data,     
sizeof(struct voxel_struct))); and similar function calls in the file 
MC-GPU_v1.3.cu around line 2555.  The problem seems to be that the input 
arguments are of the wrong type, but I don't know how to fix this.  CUDA 
documentation suggests the input arguments have changed type since CUDA 4.1, 
but I have been unable to figure out how to modify the code to make it work.

Hello.

Currently, I am using MC-GPU v1.3 version.

In linux command, I made a running the script "make.sh"
, but had a massage the below. 

'nvcc' has been the problem...

please, solve the problem..

Thank you 






root@CentOS MC-GPU_v1.3_RELEASE_2012-12-12]# "./make_MC-GPU_v1.3.sh"

 -- Compiling MC-GPU v1.3 with CUDA 5.0 for both compute capability 2.0 and 3.0 (64 bits), with MPI:
    To run a simulation in parallel with openMPI execute:
      $ time mpirun --tag-output -v -x LD_LIBRARY_PATH -hostfile hostfile_gpunodes -n 22 /GPU_cluster/MC-GPU_v1.3.x /GPU_cluster/MC-GPU_v1.3.in | tee MC-GPU_v1.3.out

- /usr/local/cuda-6.5/bin/nvcc
nvcc MC-GPU_v1.3.cu -o MC-GPU_v1.3.x -m64 -O3 -use_fast_math -DUSING_CUDA 
-DUSING_MPI -I. -I/usr/local/cuda/include 
-I/usr/local/cuda-6.5/samples/common/inc 
-I/usr/local/cuda-6.5/samples/shared/inc/ -I/usr/include/openmpi -L/usr/lib/ 
-lmpi -lz --ptxas-options=-v -gencode=arch=compute_20,code=sm_20 
-gencode=arch=compute_30,code=sm_30
./make_MC-GPU_v1.3.sh: line 29: nvcc: command not found
.

Could you please to place / point out more complex voxel geometry files in 
order to check the program ? 

In particularly, is it possible to transfer the data from
http://noodle.med.yale.edu/zubal/index.htm
to penEasy 2008 format ? 

I compile the source code with nvcc but get the following prompts:

MC-GPU_v1.2.cu(2367): error: identifier "_ConvertSMVer2Cores" is undefined

MC-GPU_v1.2.cu(2523): error: identifier "_ConvertSMVer2Cores" is undefined

So I looked the source code of "cutil_inline_runtime.h". I found that in CUDA 
release 4.2 the function " _ConvertSMVer2Cores" has been renamed to " 
_ConvertSMVer2Cores_local". 

Hello Andreu,

I would to ask about two issues:

1. I tried to start the simulation, which is described in MCGPU v1.3. with the 
following commands:

a. gcc -x c -O3 MC-GPU_v1.3.cu -o MC-GPU_v1.3_CPU.x -I./ -lm -lz

b. ./MC-GPU_v1.3.x MC-GPU_v1.3.in | tee MC-GPU_v1.3.out

after the second command i got the following error

fopen ERROR load_voxels!! File 
/GPU_cluster/voxelized_phantoms/Duke_34y_V5_5mm.raw.vox.gz does not exist!!

2. I tried to run Zubalphatom Data with the follwoing commands :
gcc -O3 zubal2mcgpu.c -o zubal2mcgpu.x

a. ./zubal2mcgpu.x zubal2mcgpu_conversion_table.in voxel_man.dat

b.   gzip voxel_man.dat.vox

c. ../MC-GPU_v1.3.x MC-GPU_v1.3_Zubal.in | tee MC-GPU_v1.3_Zubal.out

the following last erorr came after running the last command:

-- Reading voxel file 'Zubal_voxel_man.vox.gz':


!!Reading ERROR load_voxels!! File is not readable or does not contain the 
string '[SECTION VOXELS HEADER'!!

Thank you very much for your help

Best regards
Ghassan 

I am trying to create a new material for MC-GPU simulation and failed.
I copied the "penelope.f" (2006 version) to the "MC-GPU_material_files" 
directory,
and typed "g77 -O MC-GPU_create_material_data.f"
This produced an error as follows:

$ g77 -O MC-GPU_create_material_data.f
/tmp/cccYAEhq.o: In function `MAIN__':
MC-GPU_create_material_data.f:(.text+0x4b0): undefined reference to `peinit_'
MC-GPU_create_material_data.f:(.text+0x8cd): undefined reference to `phmfp_'
 ...

Can you give me more detail information how to compile the 
"MC-GPU_create_material_data.f" file and how to use the executable file to 
create a new material?
Does your code use "pendbase" database? then, where should I locate this 
"pendbase" folder in your MC-GPU directory?