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  • PhysiCell X user guide

PhysiCell X user guide · Changes

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Update PhysiCell X user guide authored Mar 31, 2022 by Arnau Montagud's avatar Arnau Montagud
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PhysiCell-X-user-guide.md
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...@@ -47,8 +47,8 @@ The current version of PhysiCell-X is 0.1 and it is based on PhysiCell version 1 ...@@ -47,8 +47,8 @@ The current version of PhysiCell-X is 0.1 and it is based on PhysiCell version 1
PhysiCell-X can be visualized as being made up of two layers. The first layer BioFVM-X \[4\] solves the diffusion equations of substrates in the micro-environment. The second layer is PhysiCell-X itself and takes care of the movement, growth, decay, division, chemical and mechanical interaction and death of cells (agents) etc. BioFVM-X has been released separately and is available at: PhysiCell-X can be visualized as being made up of two layers. The first layer BioFVM-X \[4\] solves the diffusion equations of substrates in the micro-environment. The second layer is PhysiCell-X itself and takes care of the movement, growth, decay, division, chemical and mechanical interaction and death of cells (agents) etc. BioFVM-X has been released separately and is available at:
1. [Zenodo](https://zenodo.org/record/5044998#.YfjVwi8RppQ) and 1. [Zenodo](https://zenodo.org/record/5044998#.YfjVwi8RppQ)
2. [GitLab](https://gitlab.bsc.es/gsaxena/biofvm_x) (a detailed tutorial $^1$ to run examples can be found here) 2. [GitLab](https://gitlab.bsc.es/gsaxena/biofvm_x). A detailed tutorial to run examples can be found here. We encourage you to read this tutorial as it will _also_ help you understand how to run examples in PhysiCell-X.
The latest version of BioFVM-X also forms part of PhysiCell-X. It can kindly be noted that the stand-alone version of BioFVM-X available at the links above is _different_ from the version of BioFVM-X that comes bundled with PhysiCell-X. This is because the design of BioFVM-X has evolved as PhysiCell-X evolved. The latest version of BioFVM-X also forms part of PhysiCell-X. It can kindly be noted that the stand-alone version of BioFVM-X available at the links above is _different_ from the version of BioFVM-X that comes bundled with PhysiCell-X. This is because the design of BioFVM-X has evolved as PhysiCell-X evolved.
...@@ -60,7 +60,7 @@ We describe the high level parallel design with the help of a non-technical anal ...@@ -60,7 +60,7 @@ We describe the high level parallel design with the help of a non-technical anal
### Domain Partitioning ### Domain Partitioning
Figure [\[fig:domain_partitioning\]](#fig:domain_partitioning){reference-type="ref" reference="fig:domain_partitioning"} formally illustrates the aforementioned analogy. It shows a 3-D domain and the directions of the axes. The domain is divided in the X-direction _only_ among the MPI processes i.e. the 3-D domain is partitioned in a single dimension only (1-D domain partitioning - imagine slices of a bread). It is important to note that the direction of the axes of BioFVM-X/PhysiCell-X is different from the directions of the axes of MPI Cartesian Topology $^2$. In this specific case, the whole 3-D domain is partitioned among 4 MPI processes (shown in gray, green, blue and red). This Cartesian Topology is $1 \\times 4 \\times 1$, indicating that we have 1 MPI process in the X-direction, 4 in the Y-direction and 1 in the Z-direction. Please note we have 4 processes in the Y-direction of the MPI Cartesian Topology because _the X-axis of BioFVM-X/PhysiCell-X is equivalent to the Y-axis of the MPI Topology_. Each of these sub-partitions (formally called sub-domains) can be located with the help of MPI Cartesian coordinates. Process 0 (formally called Rank 0) has coordinates $(0,0,0)$, process 1 (Rank 1) has $(0,1,0)$, process 2 (Rank 2) has $(0,2,0)$ and process 4 (Rank 3) has coordinates $(0,3,0)$. Within each sub-domain managed by a single MPI process, the wavy, dark, solid lines indicate OpenMP threads. Figure [\[fig:domain_partitioning\]](#fig:domain_partitioning){reference-type="ref" reference="fig:domain_partitioning"} formally illustrates the aforementioned analogy. It shows a 3-D domain and the directions of the axes. The domain is divided in the X-direction _only_ among the MPI processes i.e. the 3-D domain is partitioned in a single dimension only (1-D domain partitioning - imagine slices of a bread). It is important to note that the direction of the axes of BioFVM-X/PhysiCell-X is different from the directions of the axes of MPI Cartesian Topology (An MPI Cartesian Topology is a _virtual_ arrangement of processes.). In this specific case, the whole 3-D domain is partitioned among 4 MPI processes (shown in gray, green, blue and red). This Cartesian Topology is $1 \\times 4 \\times 1$, indicating that we have 1 MPI process in the X-direction, 4 in the Y-direction and 1 in the Z-direction. Please note we have 4 processes in the Y-direction of the MPI Cartesian Topology because _the X-axis of BioFVM-X/PhysiCell-X is equivalent to the Y-axis of the MPI Topology_. Each of these sub-partitions (formally called sub-domains) can be located with the help of MPI Cartesian coordinates. Process 0 (formally called Rank 0) has coordinates $(0,0,0)$, process 1 (Rank 1) has $(0,1,0)$, process 2 (Rank 2) has $(0,2,0)$ and process 4 (Rank 3) has coordinates $(0,3,0)$. Within each sub-domain managed by a single MPI process, the wavy, dark, solid lines indicate OpenMP threads.
### Mapping to Hardware ### Mapping to Hardware
...@@ -611,12 +611,6 @@ PhysiCell-X is project that is being actively developed as the distributed-paral ...@@ -611,12 +611,6 @@ PhysiCell-X is project that is being actively developed as the distributed-paral
The research leading to these results has received funding from EU H2020 Programme under the PerMedCoE project, grant agreement number 951773 and the INFORE project, grant agreement number 825070. The research leading to these results has received funding from EU H2020 Programme under the PerMedCoE project, grant agreement number 951773 and the INFORE project, grant agreement number 825070.
## Footnotes:
$^1$: We encourage you to read this tutorial as it will _also_ help you understand how to run examples in PhysiCell-X
$^2$: An MPI Cartesian Topology is a _virtual_ arrangement of processes.
# References: # References:
\[1\] A. Ghaffarizadeh, S. H. Friedman, and P. Macklin. BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. Bioinformatics, 32(8):1256–8, 2016. doi: 10.1093/bioinformatics/btv730. URL <http://dx.doi.org/10.1093/bioinformatics/btv730>. \[1\] A. Ghaffarizadeh, S. H. Friedman, and P. Macklin. BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. Bioinformatics, 32(8):1256–8, 2016. doi: 10.1093/bioinformatics/btv730. URL <http://dx.doi.org/10.1093/bioinformatics/btv730>.
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