So you have decided to install FIDASIM. Don't worry this should be relatively painless.
If you experiance problems installing FIDASIM you did something wrong and you should let us know so we can laugh at you (and also help you)
The following code snippets assumes you are using a BASH shell.
To figure out what shell you currently have run echo $SHELL to find out.
FIDASIM has the following dependencies:
The following commands will install the required dependencies (Tested on Ubuntu 16.04)
sudo apt-get update
sudo apt-get install build-essential
sudo apt-get install gfortran
sudo apt-get install zlib1g-dev
The followeing commands will install the required dependencies (Tested on Fedora 34)
sudo dnf update
sudo dnf install gcc-c++
sudo dnf install gfortran
sudo dnf install openmpi
sudo dnf install openmpi-devel
sudo dnf install zlib-devel
It's rather difficult to run software you haven't downloaded. There are two ways of getting the source code.
The most recent version of FIDASIM (3.0.0-dev) can be downloaded from here
Once you have downloaded the .tar.gz or .zip file unpack it using the following commands.
tar -zxf FIDASIM-3.0.0-dev.tar.gz
or if you downloaded the .zip file
unzip FIDASIM-3.0.0-dev.zip
There should now be a directory named FIDASIM-3.0.0-dev in your current directory. Enter the directory using
cd FIDASIM-3.0.0-dev
If you are planning to develop FIDASIM it is best to use git.
git clone https://github.com/D3DEnergetic/FIDASIM.git FIDASIM
cd FIDASIM
By default you will be on the master branch which may or may not be in a usable state. To use the release version run the command
git checkout v3.0.0-dev
FIDASIM needs to know where some things are so you have to set the following environmental variables in your .bashrc file located in your home directory.
export FIDASIM_DIR=/path/to/fidasim/install/directory
export FC=gfortran #use 'ifort' for Intel Fortran compiler
export CC=gcc #use 'icc' for Intel C compiler
export CXX=g++ #use 'icpc' for Intel C++ compiler
#For using helper routines
export PATH=$FIDASIM_DIR/deps/hdf5/bin:$FIDASIM_DIR/lib/scripts:$PATH
export PATH=$FIDASIM_DIR/deps/efit:$FIDASIM_DIR/test:$PATH
export IDL_PATH="+$FIDASIM_DIR:$IDL_PATH:<IDL_DEFAULT>"
export PYTHONPATH=$FIDASIM_DIR/lib/python:$PYTHONPATH
ulimit -s unlimited #Omit this if you like segfaults
## FEDORA and MPI ONLY
source /etc/profile.d/modules.sh
module load mpi/openmpi-x86_64
replacing /path/to/fidasim/install/directory with the real directory. To set the environmental variables in the current shell run
source ~/.bashrc
Once you are in the source directory (and have all the dependencies installed) run the following
make
This will build the fidasim executable using the default compiler options. Run make help to view all the available options.
Once running, go get a coffee since it will take a while because HDF5 is being built as well.
Once make has completed check if FIDASIM compiled correctly.
user@computer:~/FIDASIM-3.0.0-dev$ ./fidasim
____ ____ ___ ___ ____ ____ __ ___
/ __// _// _ \ / _ | / __// _// |/ /
/ _/ _/ / / // // __ | _\ \ _/ / / /|_/ /
/_/ /___//____//_/ |_|/___//___//_/ /_/
Version: 3.0.0-dev
FIDASIM is released as open source code under the MIT Licence.
For more information visit http://d3denergetic.github.io/FIDASIM/
Good job! You installed FIDASIM! But wait theres more.
Calculating reaction rates on the fly is time consuming so we need to pre-compute them to save time.
The following code snippit will generate the atomic tables using the default settings.
The default settings should be appropriate for most use cases, however, it may be necessary to generate custom atomic tables.
In that case edit the file tables/table_settings.dat before running the following command if FIDASIM was compiled with OpenMP (the default build)
./tables/generate_tables ./tables/table_settings.dat [num_threads]
or if FIDASIM was built with MPI
mpirun -np num_processes ./tables/generate_tables ./tables/table_settings.dat
This is computationally expensive so make sure you run this on a computer where you won't get angry emails for using up all the CPU's
Now would be a good time to get more coffee... or maybe a nap.
From the command line
run_tests.py, "/place/where/you/want/the/output"
Note: This requires python
Or from within IDL
IDL> run_tests, "/place/where/you/want/the/output"
Some stuff that will make sense later will flash by and when its done you should see something like
SUCCESS: FIDASIM pre-processing completed
To run FIDASIM use the following command
/u/lstagner/FIDASIM/fidasim /p/fida/lstagner/TEST/test_1a_inputs.dat
Now do what the computer says. Think of as good practice for when the robots take over.
It should print out the following.
[lstagner@dawson061]% /u/lstagner/FIDASIM/fidasim /p/fida/lstagner/TEST/test_1a_inputs.dat
____ ____ ___ ___ ____ ____ __ ___
/ __// _// _ \ / _ | / __// _// |/ /
/ _/ _/ / / // // __ | _\ \ _/ / / /|_/ /
/_/ /___//____//_/ |_|/___//___//_/ /_/
Version: 3.0.0-dev
FIDASIM is released as open source code under the MIT Licence.
For more information visit http://d3denergetic.github.io/FIDASIM/
---- Shot settings ----
Shot: 1
Time: 1000 [ms]
Runid: test
---- Input files ----
Tables file: /p/fida/FIDASIM/tables/atomic_tables.h5
Geometry file: /p/fida/lstagner/TEST/test_geometry.h5
Equilibrium file: /p/fida/lstagner/TEST/test_equilibrium.h5
Distribution file: /p/fida/lstagner/TEST/test_distribution.h5
---- OpenMP settings ----
Number of threads: 16
---- Atomic tables settings ----
Maximum n/m: 6
Beam/Fast-ion mass: 2.014 [amu]
Thermal/Bulk-ion mass: 2.014 [amu]
Impurity mass: 12.011 [amu]
---- Interpolation grid settings ----
Nr: 70
Nz: 100
Nphi: 1
dA: 4.00 [cm^2]
---- Beam grid settings ----
Nx: 50
Ny: 60
Nz: 70
dV: 8.00 [cm^3]
alpha: 0.00 [rad]
beta: 0.00 [rad]
gamma: 0.00 [rad]
origin: [ 0.00, 0.00, 0.00] [cm]
Number of cells in plasma: 184494
---- Neutral beam settings ----
Beam: test_beam
Power: 1.70 [MW]
Voltage: 72.50 [keV]
---- Passive grid settings ----
Nr: 70
Nz: 100
Nphi: 10
R range = [100.00,238.00]
Z range = [-100.00, 98.00]
Phi range = [ 4.25, 5.15]
dA: 4.00 [cm^3]
---- Fast-ion distribution settings ----
Distribution type: Fast-ion Density Function F(energy,pitch,R,Z,Phi)
Nenergy = 75
Npitch = 50
Nr = 70
Nz = 100
Nphi = 1
Energy range = [ 0.81,120.87]
Pitch range = [-0.98, 0.98]
R range = [100.00,238.00]
Z range = [-100.00, 98.00]
Phi range = [ 0.00, 0.00]
Ntotal = 1.214E+19
---- FIDA/BES settings ----
FIDA/BES System: SPECTRAL
Number of channels: 3
---- NPA settings ----
NPA System: NPA
Number of channels: 3
nbi: 19:06:28 --- elapsed: 0:00:23
# of markers: 50000
birth profile written to: /p/fida/lstagner/TEST/test_birth.h5
dcx: 19:06:42 --- elapsed: 0:00:37
# of markers: 500000
halo: 19:07:13 --- elapsed: 0:01:08
# of markers: 527175 --- Seed/DCX: 1.000
# of markers: 672040 --- Seed/DCX: 0.600
# of markers: 792640 --- Seed/DCX: 0.366
# of markers: 873160 --- Seed/DCX: 0.225
# of markers: 900615 --- Seed/DCX: 0.139
# of markers: 913130 --- Seed/DCX: 0.086
# of markers: 919085 --- Seed/DCX: 0.053
# of markers: 921060 --- Seed/DCX: 0.033
# of markers: 921935 --- Seed/DCX: 0.020
# of markers: 922180 --- Seed/DCX: 0.013
write neutrals: 19:14:31 --- elapsed: 0:08:26
neutral density written to: /p/fida/lstagner/TEST/test_neutrals.h5
cold: 19:14:35 --- elapsed: 0:08:30
bremsstrahlung: 19:14:36 --- elapsed: 0:08:31
fida: 19:14:36 --- elapsed: 0:08:31
# of markers: 5000000
pfida: 19:15:19 --- elapsed: 0:09:14
# of markers: 50000000
write spectra: 19:20:47 --- elapsed: 0:14:42
Spectra written to: /p/fida/lstagner/TEST/test_spectra.h5
npa: 19:20:47 --- elapsed: 0:14:42
# of markers: 5000000
Number of Active NPA particles that hit a detector: 40733
pnpa: 19:21:21 --- elapsed: 0:15:16
# of markers: 50000000
Number of Passive NPA particles that hit a detector: 116510
write npa: 19:26:47 --- elapsed: 0:20:42
NPA data written to: /p/fida/lstagner/TEST/test_npa.h5
neutron rate: 19:26:47 --- elapsed: 0:20:42
Rate: 5.97592E+14 [neutrons/s]
write neutrons: 19:28:16 --- elapsed: 0:22:11
Neutrons written to: /p/fida/lstagner/TEST/test_neutrons.h5
fida weight function: 19:28:25 --- elapsed: 0:22:20
Number of Channels: 3
Nlambda: 1000
Nenergy: 50
Npitch: 50
Ngyro: 100
Maximum Energy: 100.00
LOS averaged: True
Channel: 1
Radius: 200.00
Mean Fast-ion Density: 5.00757E+11
Channel: 2
Radius: 170.00
Mean Fast-ion Density: 5.00757E+11
Channel: 3
Radius: 140.00
Mean Fast-ion Density: 5.00757E+11
write fida weights: 19:28:41 --- elapsed: 0:22:36
FIDA weights written to: /p/fida/lstagner/TEST/test_fida_weights.h5
npa weight function: 19:28:48 --- elapsed: 0:22:43
Number of Channels: 3
Nenergy: 50
Npitch: 50
Maximum energy: 100.00
Channel: 1
Radius: 200.000
Flux: 0.00000E+00
Weight: 3.48351E+03
Channel: 2
Radius: 170.000
Flux: 0.00000E+00
Weight: 1.41572E+03
Channel: 3
Radius: 140.000
Flux: 0.00000E+00
Weight: 8.38209E+02
write npa weights: 19:33:50 --- elapsed: 0:27:45
NPA weights written to: /p/fida/lstagner/TEST/test_npa_weights.h5
END: hour:minute:second 19:33:50 --- elapsed: 0:27:45
Congratulations! You followed the instructions.
Most likely you wont be satisfied by just running a test case. Click here to learn how to make the input files used by FIDASIM.