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Commit 011ee4e2 authored by Gaurav Saxena's avatar Gaurav Saxena
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In create_point_sources() and create_point_sinks() in the main() 

function, when we calculate the coordinates of the MPI process
corresponding to the (x,y,z) position of the Basic Agent, we were not
subtracting the initial starting coordinates of the physical domain from
the tempPoint[] array. This will not work when the physical domain
starts from a non-zero value. Thus added
tempPoint[0] = tempPoint[0] - lower_x_boundary_coordinate_of_domain;
similary for the y, z dimensions.
Have not compiled it but committing it.
parent df0bb860
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Showing with 35 additions and 1627 deletions
BioFVM_parallel.cpp
View file @ 011ee4e2
......@@ -192,7 +192,7 @@ void Cartesian_Mesh::resize( double x_start, double x_end, double y_start, doubl
for( int i=0; i < connected_voxel_indices.size() ; i++ )
{
connected_voxel_indices[i].clear();
connected_voxel_indices[i].clear();
}
......
HOW_TO_COMPILE 0 → 100644
View file @ 011ee4e2
Just do:
$ make tutorial1
If we change N in tutorial1.cpp, then only tutorial1.cpp is recompiled.
When we do $ make clean, it completely removes all .o files and hence doing
$ make tutorial1
will again recompile ALL the .cpp files.
error-7513445 deleted 100644 → 0
View file @ df0bb860
[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).
--------------------------------------------------------------------------
error-7584197 deleted 100644 → 0
View file @ df0bb860
[s06r1b59:192760] MCW rank 0 bound to socket 0[core 0[hwt 0]], socket 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], socket 0[core 3[hwt 0]], socket 0[core 4[hwt 0]], socket 0[core 5[hwt 0]], socket 0[core 6[hwt 0]], socket 0[core 7[hwt 0]], socket 0[core 8[hwt 0]], socket 0[core 9[hwt 0]], socket 0[core 10[hwt 0]], socket 0[core 11[hwt 0]], socket 0[core 12[hwt 0]], socket 0[core 13[hwt 0]], socket 0[core 14[hwt 0]], socket 0[core 15[hwt 0]], socket 0[core 16[hwt 0]], socket 0[core 17[hwt 0]], socket 0[core 18[hwt 0]], socket 0[core 19[hwt 0]], socket 0[core 20[hwt 0]], socket 0[core 21[hwt 0]], socket 0[core 22[hwt 0]], socket 0[core 23[hwt 0]]: [B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B][./././././././././././././././././././././././.]
[s06r1b59:192760] MCW rank 1 bound to socket 1[core 24[hwt 0]], socket 1[core 25[hwt 0]], socket 1[core 26[hwt 0]], socket 1[core 27[hwt 0]], socket 1[core 28[hwt 0]], socket 1[core 29[hwt 0]], socket 1[core 30[hwt 0]], socket 1[core 31[hwt 0]], socket 1[core 32[hwt 0]], socket 1[core 33[hwt 0]], socket 1[core 34[hwt 0]], socket 1[core 35[hwt 0]], socket 1[core 36[hwt 0]], socket 1[core 37[hwt 0]], socket 1[core 38[hwt 0]], socket 1[core 39[hwt 0]], socket 1[core 40[hwt 0]], socket 1[core 41[hwt 0]], socket 1[core 42[hwt 0]], socket 1[core 43[hwt 0]], socket 1[core 44[hwt 0]], socket 1[core 45[hwt 0]], socket 1[core 46[hwt 0]], socket 1[core 47[hwt 0]]: [./././././././././././././././././././././././.][B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B]
[s06r1b61:272153] MCW rank 2 bound to socket 0[core 0[hwt 0]], socket 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], socket 0[core 3[hwt 0]], socket 0[core 4[hwt 0]], socket 0[core 5[hwt 0]], socket 0[core 6[hwt 0]], socket 0[core 7[hwt 0]], socket 0[core 8[hwt 0]], socket 0[core 9[hwt 0]], socket 0[core 10[hwt 0]], socket 0[core 11[hwt 0]], socket 0[core 12[hwt 0]], socket 0[core 13[hwt 0]], socket 0[core 14[hwt 0]], socket 0[core 15[hwt 0]], socket 0[core 16[hwt 0]], socket 0[core 17[hwt 0]], socket 0[core 18[hwt 0]], socket 0[core 19[hwt 0]], socket 0[core 20[hwt 0]], socket 0[core 21[hwt 0]], socket 0[core 22[hwt 0]], socket 0[core 23[hwt 0]]: [B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B][./././././././././././././././././././././././.]
[s06r1b65:389755] MCW rank 6 bound to socket 0[core 0[hwt 0]], socket 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], socket 0[core 3[hwt 0]], socket 0[core 4[hwt 0]], socket 0[core 5[hwt 0]], socket 0[core 6[hwt 0]], socket 0[core 7[hwt 0]], socket 0[core 8[hwt 0]], socket 0[core 9[hwt 0]], socket 0[core 10[hwt 0]], socket 0[core 11[hwt 0]], socket 0[core 12[hwt 0]], socket 0[core 13[hwt 0]], socket 0[core 14[hwt 0]], socket 0[core 15[hwt 0]], socket 0[core 16[hwt 0]], socket 0[core 17[hwt 0]], socket 0[core 18[hwt 0]], socket 0[core 19[hwt 0]], socket 0[core 20[hwt 0]], socket 0[core 21[hwt 0]], socket 0[core 22[hwt 0]], socket 0[core 23[hwt 0]]: [B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B][./././././././././././././././././././././././.]
[s06r1b61:272153] MCW rank 3 bound to socket 1[core 24[hwt 0]], socket 1[core 25[hwt 0]], socket 1[core 26[hwt 0]], socket 1[core 27[hwt 0]], socket 1[core 28[hwt 0]], socket 1[core 29[hwt 0]], socket 1[core 30[hwt 0]], socket 1[core 31[hwt 0]], socket 1[core 32[hwt 0]], socket 1[core 33[hwt 0]], socket 1[core 34[hwt 0]], socket 1[core 35[hwt 0]], socket 1[core 36[hwt 0]], socket 1[core 37[hwt 0]], socket 1[core 38[hwt 0]], socket 1[core 39[hwt 0]], socket 1[core 40[hwt 0]], socket 1[core 41[hwt 0]], socket 1[core 42[hwt 0]], socket 1[core 43[hwt 0]], socket 1[core 44[hwt 0]], socket 1[core 45[hwt 0]], socket 1[core 46[hwt 0]], socket 1[core 47[hwt 0]]: [./././././././././././././././././././././././.][B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B]
[s06r1b65:389755] MCW rank 7 bound to socket 1[core 24[hwt 0]], socket 1[core 25[hwt 0]], socket 1[core 26[hwt 0]], socket 1[core 27[hwt 0]], socket 1[core 28[hwt 0]], socket 1[core 29[hwt 0]], socket 1[core 30[hwt 0]], socket 1[core 31[hwt 0]], socket 1[core 32[hwt 0]], socket 1[core 33[hwt 0]], socket 1[core 34[hwt 0]], socket 1[core 35[hwt 0]], socket 1[core 36[hwt 0]], socket 1[core 37[hwt 0]], socket 1[core 38[hwt 0]], socket 1[core 39[hwt 0]], socket 1[core 40[hwt 0]], socket 1[core 41[hwt 0]], socket 1[core 42[hwt 0]], socket 1[core 43[hwt 0]], socket 1[core 44[hwt 0]], socket 1[core 45[hwt 0]], socket 1[core 46[hwt 0]], socket 1[core 47[hwt 0]]: [./././././././././././././././././././././././.][B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B]
[s06r1b64:351888] MCW rank 4 bound to socket 0[core 0[hwt 0]], socket 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], socket 0[core 3[hwt 0]], socket 0[core 4[hwt 0]], socket 0[core 5[hwt 0]], socket 0[core 6[hwt 0]], socket 0[core 7[hwt 0]], socket 0[core 8[hwt 0]], socket 0[core 9[hwt 0]], socket 0[core 10[hwt 0]], socket 0[core 11[hwt 0]], socket 0[core 12[hwt 0]], socket 0[core 13[hwt 0]], socket 0[core 14[hwt 0]], socket 0[core 15[hwt 0]], socket 0[core 16[hwt 0]], socket 0[core 17[hwt 0]], socket 0[core 18[hwt 0]], socket 0[core 19[hwt 0]], socket 0[core 20[hwt 0]], socket 0[core 21[hwt 0]], socket 0[core 22[hwt 0]], socket 0[core 23[hwt 0]]: [B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B][./././././././././././././././././././././././.]
[s06r1b64:351888] MCW rank 5 bound to socket 1[core 24[hwt 0]], socket 1[core 25[hwt 0]], socket 1[core 26[hwt 0]], socket 1[core 27[hwt 0]], socket 1[core 28[hwt 0]], socket 1[core 29[hwt 0]], socket 1[core 30[hwt 0]], socket 1[core 31[hwt 0]], socket 1[core 32[hwt 0]], socket 1[core 33[hwt 0]], socket 1[core 34[hwt 0]], socket 1[core 35[hwt 0]], socket 1[core 36[hwt 0]], socket 1[core 37[hwt 0]], socket 1[core 38[hwt 0]], socket 1[core 39[hwt 0]], socket 1[core 40[hwt 0]], socket 1[core 41[hwt 0]], socket 1[core 42[hwt 0]], socket 1[core 43[hwt 0]], socket 1[core 44[hwt 0]], socket 1[core 45[hwt 0]], socket 1[core 46[hwt 0]], socket 1[core 47[hwt 0]]: [./././././././././././././././././././././././.][B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B/B]
OPENMP DISPLAY ENVIRONMENT BEGIN
_OPENMP = '201511'
OPENMP DISPLAY ENVIRONMENT BEGIN
_OPENMP = '201511'
OMP_DYNAMIC = 'FALSE'
OMP_NESTED = 'FALSE'
OMP_NUM_THREADS = '24'
OMP_SCHEDULE = 'DYNAMIC'
OMP_PROC_BIND = 'SPREAD'
OMP_PLACES = '{ OMP_DYNAMIC = 'FALSE'
OMP_NESTED = 'FALSE'
OMP_NUM_THREADS = '24'
OMP_SCHEDULE = 'DYNAMIC'
OMP_PROC_BIND = 'SPREAD'
OMP_PLACES = '{024},{25},{26},{27},{28},{29},{30},{},{1},{2},{3},{4},{5},{6},{31},{32},{33},{34},{35},{36},{37},{38},{7},{8},{9},{10},{11},{12},{13},39},{40},{41},{42},{43},{44},{45},{46},{47}{14},{15},{16},{17},{18},{19},{20},{21},{22},'
OMP_STACKSIZE = '0'
OMP_WAIT_POLICY = 'PASSIVE'
OMP_THREAD_LIMIT = '4294967295'
OMP_MAX_ACTIVE_LEVELS = '2147483647'
OMP_CANCELLATION = 'FALSE'
OMP_DEFAULT_DEVICE = '0'
OMP_MAX_TASK_PRIORITY = '0'
OPENMP DISPLAY ENVIRONMENT END
{23}'
OMP_STACKSIZE = '0'
OMP_WAIT_POLICY = 'PASSIVE'
OMP_THREAD_LIMIT = '4294967295'
OMP_MAX_ACTIVE_LEVELS = '2147483647'
OMP_CANCELLATION = 'FALSE'
OMP_DEFAULT_DEVICE = '0'
OMP_MAX_TASK_PRIORITY = '0'
OPENMP DISPLAY ENVIRONMENT END
OPENMP DISPLAY ENVIRONMENT BEGIN
_OPENMP = '201511'
OMP_DYNAMIC = 'FALSE'
OMP_NESTED = 'FALSE'
OMP_NUM_THREADS = '24'
OMP_SCHEDULE = 'DYNAMIC'
OMP_PROC_BIND = 'SPREAD'
OMP_PLACES = '{0},{1},{2},{3},{4},{5},{6},{
OPENMP DISPLAY ENVIRONMENT BEGIN
_OPENMP = '201511'
OMP_DYNAMIC = 'FALSE'
7},{8},{9},{10},{11},{
OPENMP DISPLAY ENVIRONMENT BEGIN
_OPENMP = '201511'
OMP_DYNAMIC = 'FALSE'
OMP_NESTED = 'FALSE'
OMP_NUM_THREADS = '24'
OMP_SCHEDULE = 'DYNAMIC'
OMP_PROC_BIND = 'SPREAD'
OMP_PLACES = '{12},{13},{14},{15},{16},{ OMP_NESTED = 'FALSE'
OMP_NUM_THREADS = '24'
OMP_SCHEDULE = 'DYNAMIC'
OMP_PROC_BIND = 'SPREAD'
OMP_PLACES = '{17},{18},{19},{20},{21},{0},{1},{222},{23}'
OMP_STACKSIZE = '0'
OMP_WAIT_POLICY = 'PASSIVE'
OMP_THREAD_LIMIT = '4294967295'
OMP_MAX_ACTIVE_LEVELS = '2147483647'
OMP_CANCELLATION = 'FALSE'
},{3},{4},{5},{6 OMP_DEFAULT_DEVICE = '0'
OMP_MAX_TASK_PRIORITY = '0'
OPENMP DISPLAY ENVIRONMENT END
24},{25},{26},{27},{28
OPENMP DISPLAY ENVIRONMENT BEGIN
_OPENMP = '201511'
OMP_DYNAMIC = 'FALSE'
OMP_NESTED = 'FALSE'
OMP_NUM_THREADS = '24'
OMP_SCHEDULE = 'DYNAMIC'
OMP_PROC_BIND = 'SPREAD'
OMP_PLACES = '{24},{25},{26},{27},{28},{29},{30},{31},{32},{33},{34},{35},{36},{37},{38},{39},{40},{41},{42},{43},{44},{45},{},{7},{8},{9},{10},{11},{12},{1346},{47}'
OMP_STACKSIZE = '0'
OMP_WAIT_POLICY = 'PASSIVE'
OMP_THREAD_LIMIT = '4294967295'
OMP_MAX_ACTIVE_LEVELS = '2147483647'
OMP_CANCELLATION = 'FALSE'
OMP_DEFAULT_DEVICE = '0'
OMP_MAX_TASK_PRIORITY = '0'
OPENMP DISPLAY ENVIRONMENT END
},{29},{30},{31},{32},{33},{34},{35},{36},},{14},{15},{16},{17},{18},{19},{20},{21},{22},{23}'
OMP_STACKSIZE = '0'
OMP_WAIT_POLICY = 'PASSIVE'
OMP_THREAD_LIMIT = '4294967295'
OMP_MAX_ACTIVE_LEVELS = '2147483647'
OMP_CANCELLATION = 'FALSE'
OMP_DEFAULT_DEVICE = '0'
{37},{38},{39},{40},{41},{42},{43},{44},{45},{46},{47}'
OMP_STACKSIZE = '0'
OMP_WAIT_POLICY = 'PASSIVE'
OMP_THREAD_LIMIT = '4294967295'
OMP_MAX_ACTIVE_LEVELS = '2147483647'
OMP_CANCELLATION = 'FALSE'
OMP_DEFAULT_DEVICE = '0'
OMP_MAX_TASK_PRIORITY = '0'
OPENMP DISPLAY ENVIRONMENT END
OMP_MAX_TASK_PRIORITY = '0'
OPENMP DISPLAY ENVIRONMENT END
OPENMP DISPLAY ENVIRONMENT BEGIN
_OPENMP = '201511'
OMP_DYNAMIC = 'FALSE'
OMP_NESTED = 'FALSE'
OMP_NUM_THREADS = '24'
OMP_SCHEDULE = 'DYNAMIC'
OMP_PROC_BIND = 'SPREAD'
OMP_PLACES = '{0},{1},{2},{3},{4},{5},{6},{7},{8},{9},{10},{11},{12},{13},{14},{15},{16},
OPENMP DISPLAY ENVIRONMENT BEGIN
_OPENMP = '201511'
OMP_DYNAMIC = 'FALSE'
OMP_NESTED = 'FALSE'
OMP_NUM_THREADS = '24'
OMP_SCHEDULE = 'DYNAMIC'
OMP_PROC_BIND = 'SPREAD'
OMP_PLACES = '{24},{25},{26},{27{17},{18},{19},{20},{21},{22},{23}'
OMP_STACKSIZE = '0'
OMP_WAIT_POLICY = 'PASSIVE'
OMP_THREAD_LIMIT = '4294967295'
OMP_MAX_ACTIVE_LEVELS = '2147483647'
OMP_CANCELLATION = 'FALSE'
OMP_DEFAULT_DEVICE = '0'
OMP_MAX_TASK_PRIORITY = '0'
OPENMP DISPLAY ENVIRONMENT END
},{28},{29},{30},{31},{32},{33},{34},{35},{36},{37},{38},{39},{40},{41},{42},{43},{44},{45},{46},{47}'
OMP_STACKSIZE = '0'
OMP_WAIT_POLICY = 'PASSIVE'
OMP_THREAD_LIMIT = '4294967295'
OMP_MAX_ACTIVE_LEVELS = '2147483647'
OMP_CANCELLATION = 'FALSE'
OMP_DEFAULT_DEVICE = '0'
OMP_MAX_TASK_PRIORITY = '0'
OPENMP DISPLAY ENVIRONMENT END
examples/tutorial1
View file @ 011ee4e2
No preview for this file type
examples/tutorial1_BioFVM.cpp
View file @ 011ee4e2
......@@ -68,7 +68,7 @@ using namespace BioFVM;
//int omp_num_threads = 48; // set number of threads for parallel computing, set this to # of CPU cores x 2 (for hyperthreading)
#define N 3840
#define N 1000
double pi= 3.1415926535897932384626433832795;
double UniformRandom()
......@@ -134,6 +134,15 @@ void create_point_sources(double cell_radius, double dt, int num_sources, Microe
/* Use the floor() function, as type promotion was creating a problem in proc_x_coord expression */
/*------------------------------------------------------------------------------------------------*/
/*------------------------------------------------------------------------------------------------------------------------------------------------------*/
/* When the starting point of domain is not zero i.e. minX != 0, minY != 0 and minZ != 0, then we should subtract these starting points from tempPoints */
/* otherwise the strategy below fails */
/*------------------------------------------------------------------------------------------------------------------------------------------------------*/
tempPoint[0] = tempPoint[0] - microenvironment.mesh.bounding_box[0];
tempPoint[1] = tempPoint[1] - microenvironment.mesh.bounding_box[1];
tempPoint[2] = tempPoint[2] - microenvironment.mesh.bounding_box[2];
proc_y_coord = tempPoint[0]/(local_x_voxels * dx); //Can use floor() here but no need
proc_x_coord = (mpi_Dims[0] - 1) - floor(tempPoint[1]/(local_y_voxels * dy)); //Automatic promotion to double was creating problems
proc_z_coord = tempPoint[2]/(local_z_voxels * dz); //Can use floor() here but no need
......@@ -304,6 +313,15 @@ void create_point_sinks(double cell_radius, double dt, int num_sinks, Microenvir
/* MPI Process X direction is top to bottom */
/*------------------------------------------------------------------------------------------------*/
/*------------------------------------------------------------------------------------------------------------------------------------------------------*/
/* When the starting point of domain is not zero i.e. minX != 0, minY != 0 and minZ != 0, then we should subtract these starting points from tempPoints */
/* otherwise the strategy below fails */
/*------------------------------------------------------------------------------------------------------------------------------------------------------*/
tempPoint[0] = tempPoint[0] - microenvironment.mesh.bounding_box[0];
tempPoint[1] = tempPoint[1] - microenvironment.mesh.bounding_box[1];
tempPoint[2] = tempPoint[2] - microenvironment.mesh.bounding_box[2];
proc_y_coord = tempPoint[0]/(local_x_voxels * dx);
proc_x_coord = (mpi_Dims[0] - 1) - floor(tempPoint[1]/(local_y_voxels * dy));
proc_z_coord = tempPoint[2]/(local_z_voxels * dz);
......
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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.
-------------------------------------------------------
output-7584197 deleted 100644 → 0
View file @ df0bb860
TIME FOR RESIZING MICROENVIRONMENT = 0.758827
TIME FOR GENERATING GAUSSIAN PROFILE = 0.00794553
TIME FOR WRITING INITIAL CONCENTRATION FILE = 0.34451
TIME FOR CREATING ALL BASIC AGENTS = 0.000949931
TIME FOR SIMULATING (SOURCES+SINKS+DIFFUSION) = 8.48919
TIME FOR WRITING FINAL FILE = 0.280464
TOTAL PROGRAM EXECUTION TIME = 9.88661
script_ddt.sh
View file @ 011ee4e2
#!/bin/bash
#SBATCH --nodes=16
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=2
#SBATCH -t 08:00:00
#SBATCH --cpus-per-task=1
......@@ -9,6 +9,7 @@
#SBATCH --exclusive
# set application and parameters
export OMP_NUM_THREADS=24
export OMP_NUM_THREADS=1
export OMP_PROC_BIND=spread
ddt mpiexec --map-by socket --bind-to socket ./examples/tutorial1
#ddt mpiexec --map-by socket --bind-to socket ./examples/tutorial1
ddt srun ./examples/tutorial1
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