Commit 38287fde authored by gsaxena's avatar gsaxena

Update readme.txt

parent fd4bc4ce
####################################
BioFVM_X is based on BioFVM v 1.1.6.
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+ BioFVM (http://BioFVM.MathCancer.org) supports only on-node shared memory
parallelism using OpenMP.
......@@ -22,6 +24,24 @@ BioFVM_X is based on BioFVM v 1.1.6.
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
Example output:
bsc99102@login1:~/GS_BioFVM_X/GS_BioFVM> make tutorial1
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_vector.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_matlab.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_utilities.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_mesh.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_microenvironment.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_solvers.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_basic_agent.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_agent_container.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_MultiCellDS.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c BioFVM_parallel.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -c pugixml.cpp
mpic++ -march=native -O2 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11 -g -o ./examples/tutorial1 ./examples/tutorial1_BioFVM.cpp BioFVM_vector.o BioFVM_matlab.o BioFVM_utilities.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_basic_agent.o BioFVM_agent_container.o BioFVM_MultiCellDS.o BioFVM_parallel.o pugixml.o
bsc99102@login1:~/GS_BioFVM_X/GS_BioFVM>
(5) For the SLURM scheduler, the following script can be used:
============================================================================
......@@ -65,8 +85,9 @@ total Voxels in X (or Y or Z) direction as (maxX-minX)/mesh_resolution =
must be perfectly divisible by total number of MPI processes (in this case P=2).
Thus, we have 100/2 = 50 Voxels per process.
BioFVM: Finite Volume Solver for Biological Problems.
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BioFVM: Finite Volume Solver for Biological Problems.
####################################################
Version: 1.1.6
Release date: 19 August 2017
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