phydev / angio

Developing a 3D phase-field modelling for tumor angiogenesis

Welcome

Hi,

I am a computational physicist by training currently working as researcher on biostatistics, data science and machine learning. My main projects are in the development of prediction models for head and neck cancer. I have experience in several programming languages such as Python, R, Fortran90-20xx, C++, and many data science tools.

You may notice that my previous field was on developing and implementing mathematical models for biological systems, where I used modern Fortran for high performance computing.

My gists: https://gist.github.com/phydev

"When software is done right, it requires a fraction of the human resources to create and maintain." - Robert C. Martin

angio's Issues

Docker configuration file needed

To improve reporducibility and help others to compile the code we should add a docker configuration file to the repository.

compiling issues

Dear Authors,

Thank you for sharing this interesting project. I was trying to run this code, but also got error either from pulling the docker file or compile the src. The error messages are attached. Could you please provide some suggestions. Thanks,

 docker build --platform linux/x86_64 -t angio docker/
ERROR: permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get "http://%2Fvar%2Frun%2Fdocker.sock/_ping"                           : dial unix /var/run/docker.sock: connect: permission denied

./compile.sh
ifort: command line remark #10412: option '-mkl' is deprecated and will be removed in a future release. Please use the replacement option '-qmkl'
./src/run_angio.F90(171): error #6633: The type of the actual argument differs from the type of the dummy argument.   [PERIODIC]
     vegf_c, nstep, vegf_grad_min, np, cell_radius, n_max_tipc, np_tip_s, periodic)
---------------------------------------------------------------------------^
./src/run_angio.F90(170): error #6631: A non-optional actual argument must be present when invoking a procedure with an explicit interface.   [VEGF_XYZ]
     call etc_search(cell, tipc, gg, Lsize, lxyz, lxyz_inv, notch_distance, n_tipcell, tip_s, &
-----------^
./src/run_angio.F90(170): error #6631: A non-optional actual argument must be present when invoking a procedure with an explicit interface.   [NDIM]
     call etc_search(cell, tipc, gg, Lsize, lxyz, lxyz_inv, notch_distance, n_tipcell, tip_s, &
-----------^
./src/run_angio.F90(170): error #6631: A non-optional actual argument must be present when invoking a procedure with an explicit interface.   [PERIODIC]
     call etc_search(cell, tipc, gg, Lsize, lxyz, lxyz_inv, notch_distance, n_tipcell, tip_s, &
-----------^
./src/run_angio.F90(171): error #7976: An allocatable dummy argument may only be argument associated with an allocatable actual argument.   [PERIODIC]
     vegf_c, nstep, vegf_grad_min, np, cell_radius, n_max_tipc, np_tip_s, periodic)
---------------------------------------------------------------------------^
./src/run_angio.F90(170): error #8284: If the actual argument is scalar, the dummy argument shall be scalar unless the actual argument is of type character or is an element of an array that is not assumed shape, pointer, or polymorphic.   [GRID_CELL_DOMAIN]
     call etc_search(cell, tipc, gg, Lsize, lxyz, lxyz_inv, notch_distance, n_tipcell, tip_s, &
-----------^
./src/run_angio.F90(171): error #6634: The shape matching rules of actual arguments and dummy arguments have been violated.   [PERIODIC]
     vegf_c, nstep, vegf_grad_min, np, cell_radius, n_max_tipc, np_tip_s, periodic)
---------------------------------------------------------------------------^
compilation aborted for ./src/run_angio.F90 (code 1)
./src/main.F90(3): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [RUN_ANGIO_M]
 use run_angio_m
------^
compilation aborted for ./src/main.F90 (code 1)