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SEP-stochastic

Fortran numerical integrator for SEP stochastic model

Setting up virtual env

To set up virtual env

$ module load python/3.9.0
$ python -m pip install virtualenv
$ # if venv-python doesn't already exist
$ python -m virtualenv venv-python
$ source venv-python/bin/activate

Compiling

To compile, run make all, or just make. If there are some dependency errors, you can use make modules to compile the modules first before redoing make all. If errors still persist, use make clean to start from scratch. Current versions of Fortran compilers don't support automatic dependency generation, so some dependencies, like for mtrx.o and dxx.o have to be defined manually.

To compile using GFortran/GCC, set the environment variable $toolset to gcc. By default the Makefile will assme a PGI toolset is being used.

$ export toolset=gcc
$ make clean
$ make modules
$ make all

Running

INVALID. Does not work for the python script.

First, run export SHTC_URL=<url from GONG here> to set the environment variable to the URL, the URL from which the spherical harmonic transform coefficients will be downloaded. Then, run ./master-runner.sh and sit back and wait for it to email you. That is,

$ export SHTC_URL=https://gong.nso.edu/data/magmap/QR/bqc/202004/mrbqc200421/mrbqc200421t0054c2230_348.dat
$ ./master-runner.sh

This can also be combined into one line by setting the variable in the same line right before the script invocation, like so:

$ SHTC_URL=https://gong.nso.edu/data/magmap/QR/bqc/202004/mrbqc200421/mrbqc200421t0054c2230_348.dat ./master-runner.sh

where a SHTC file from 2020 April is used as an example.

If you are Florida Tech faculty/staff, you will want to change the line containing the variable $MAIL_ADDRESS from

MAIL_ADDRESS="[email protected]"

to

MAIL_ADDRESS="[email protected]"

i.e., remove the 'my.' domain, to ensure you receive emails. This could be automated by checking if $HOME contains /udrive/faculty, /udrive/student, or /udrive/staff, but the author is not familiar enough with the email address protocols of Florida Tech to reliably automate that in a future-proof fashion.

Cleaning

There are three cleaning targets within the Makefile, clean, clean-logs, and clean-objs. make clean will remove all object files, module files, and compiled executables. make clean-objs will only remove object (.o) files, leaving the executables and module (.mod) files intact. Finally, make clean-logs will only remove the output and error files within the logs/ directory.

TODO

  • Get rid of control through environment variables and implement a conf file reader, a la Finer
  • Figure out what 2damrhistss is trying to do, and redirect I/O accordingly.