Commit 975859a6 authored by Gaurav Saxena's avatar Gaurav Saxena

Working version till 4 processes. It doesn't work with 8 processes because of...

Working version till 4 processes. It doesn't work with 8 processes because of (99.99% sure) divisibility problem. The reason: domain size in Z-dimension: (1000-0)=1000, since voxel size=10 then voxels in Z-direction = 1000/10 = 100. Since there are 8 processes we have to divide 100 by 8 --> not perfectly divisible. Hence change domain size. Further the order in which the SERIAL program was generating sources and sinks was it was alternating between sources and sinks but the PARALLEL version was genearting all sources first then generating all sinks. Although random numbers generated were the same but they were alternating between sources and sinks in SERIAL version but going all to sources first then all sinks next in the PARALLEL version. Repairing this made the output the same !
parent 9e7df55f
......@@ -778,7 +778,7 @@ void Microenvironment::simulate_bulk_sources_and_sinks( double dt )
void Microenvironment::simulate_cell_sources_and_sinks( std::vector<Basic_Agent*>& basic_agent_list , double dt )
{
#pragma omp parallel for
//#pragma omp parallel for
for( int i=0 ; i < basic_agent_list.size() ; i++ )
{
basic_agent_list[i]->simulate_secretion_and_uptake( this , dt );
......
[s01r1b47:254716] *** Process received signal ***
[s01r1b47:254716] Signal: Segmentation fault (11)
[s01r1b47:254716] Signal code: Address not mapped (1)
[s01r1b47:254716] Failing at address: 0xd1
[s01r1b47:254716] [ 0] /lib64/libpthread.so.0(+0x10b10)[0x7f1531a87b10]
[s01r1b47:254716] [ 1] ./examples/tutorial1[0x407ade]
[s01r1b47:254716] [ 2] ./examples/tutorial1[0x405594]
[s01r1b47:254716] [ 3] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f15316f46e5]
[s01r1b47:254716] [ 4] ./examples/tutorial1[0x405cf9]
[s01r1b47:254716] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 254716 on node s01r1b47 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
No preview for this file type
......@@ -452,7 +452,7 @@ int main( int argc, char* argv[] )
mpi_Dims[0] = 1;
mpi_Dims[1] = 1;
mpi_Dims[2] = 4;
mpi_Dims[2] = mpi_Size;
//MPI_Dims_create(mpi_Size,3,mpi_Dims);
mpi_Is_periodic[0]=0;
......
Total MPI processes = 8
Thread level provided = 1
Total Voxels = 1
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 0 microns^2 / minutes
decay rate: 0 minutes^-1
diffusion length scale: 0 microns
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 0 microns^2 / minutes
decay rate: 0 minutes^-1
diffusion length scale: 0 microns
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 0 microns^2 / minutes
decay rate: 0 minutes^-1
diffusion length scale: 0 microns
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 0 microns^2 / minutes
decay rate: 0 minutes^-1
diffusion length scale: 0 microns
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 0 microns^2 / minutes
decay rate: 0 minutes^-1
diffusion length scale: 0 microns
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 0 microns^2 / minutes
decay rate: 0 minutes^-1
diffusion length scale: 0 microns
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 0 microns^2 / minutes
decay rate: 0 minutes^-1
diffusion length scale: 0 microns
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 0 microns^2 / minutes
decay rate: 0 minutes^-1
diffusion length scale: 0 microns
Total voxels are = 120000
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 1000 microns^2 / minutes
decay rate: 0.01 minutes^-1
diffusion length scale: 316.228 microns
Total voxels are = 120000
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 1000 microns^2 / minutes
decay rate: 0.01 minutes^-1
diffusion length scale: 316.228 microns
Total voxels are = 120000
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 1000 microns^2 / minutes
decay rate: 0.01 minutes^-1
diffusion length scale: 316.228 microns
Total voxels are = 120000
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 1000 microns^2 / minutes
decay rate: 0.01 minutes^-1
diffusion length scale: 316.228 microns
Total voxels are = 120000
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 1000 microns^2 / minutes
decay rate: 0.01 minutes^-1
diffusion length scale: 316.228 microns
Total voxels are = 120000
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 1000 microns^2 / minutes
decay rate: 0.01 minutes^-1
diffusion length scale: 316.228 microns
Total voxels are = 120000
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 1000 microns^2 / minutes
decay rate: 0.01 minutes^-1
diffusion length scale: 316.228 microns
Total voxels are = 120000
Microenvironment summary: substrate scale:
Mesh information:
type: uniform Cartesian
Domain: [0,1000] microns x [0,1000] microns x [0,1000] microns
resolution: dx = 10 microns
voxels: 120000
voxel faces: 0
volume: 1e+09 cubic microns
Densities: (1 total)
substrate1:
units: dimensionless
diffusion coefficient: 1000 microns^2 / minutes
decay rate: 0.01 minutes^-1
diffusion length scale: 316.228 microns
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------
......@@ -8,4 +8,4 @@
# set application and parameters
export OMP_NUM_THREADS=1
ddt mpiexec -n 2 ./examples/tutorial1
ddt mpiexec -n 1 ./examples/tutorial1
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1
#SBATCH -t 00:05:00
#SBATCH -o output-%j
......
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