Commit 9e270b80 authored by Arnau Montagud's avatar Arnau Montagud

Update readme.txt with some minor edits.

parent 42e51baa
......@@ -21,7 +21,7 @@ BioFVM_X is based on BioFVM v 1.1.6.
(1) git clone the repository
(2) Change to the top level directory i.e. $ cd GS_BioFVM_X/GS_BioFVM
(3) Make sure GCC 8.1 (or other version) and OpenMPI 3.1.1 (or other version)
present (or the modules are loaded in a module environment)
are present (or the modules are loaded in a module environment)
(4) Execute $ make tutorial1
This results in an executable file "tutorial1" in the directory ./examples
......@@ -69,7 +69,7 @@ export OMP_PLACES=threads
mpiexec --map-by ppr:1:socket:pe=24 --report-bindings ./examples/tutorial1
============================================================================
This script implies :
This script :
(a) uses 1 single node
(b) spawns 2 MPI processes in that node (Since we have 2 sockets per node, we
......@@ -152,9 +152,9 @@ TIME FOR WRITING FINAL FILE = 0.170324
TOTAL PROGRAM EXECUTION TIME = 3.99776
========================================================
(7) The simulation can produce .mat files and we produce at least 2 .mat files,
one at the beginning of the simulation and 1 at the end of the simulation. The
location where the files are produced can be controlled from inside the
(7) The simulation can produce .mat files as outputs. We produce at least 2 .mat files,
one at the beginning and 1 at the end of the simulation. The
location where the files are produced can be controlled from the
./examples/tutorial1_BioFVM.cpp file.
For example:
......@@ -167,8 +167,8 @@ microenvironment.write_to_matlab( "/gpfs/projects/initial_concentration.mat", mp
=================================================================================================================
(8) This .mat file can be plotted using the Matlab software (or Octave -
we used Octave). The .m help scripts for plotting can be found in ./GS_BioFVM_X/
GS_BioFVM/matlab. Any of the scripts can be tried - we plotted using
as in our case). The .m help scripts for plotting can be found in ./GS_BioFVM_X/
GS_BioFVM/matlab. Any of the scripts can be tried; we plotted using
(a) cross_section_colormap.m
(b) cross_section_surface.m
......@@ -187,7 +187,7 @@ In order to load Octave, we needed to load the following modules as well:
1) gcc/7.2.0 2) impi/2018.2 3) mkl/2018.2 4) suitesparse/5.2.0
5) octave/4.2.2
The octave
The octave #something is missing here.
####################################################
BioFVM: Finite Volume Solver for Biological Problems.
......
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