|
162 | 162 | \--zmin and \--zmax are ignored. |
163 | 163 |
|
164 | 164 | Python-Specific Options |
165 | | -^^^^^^^^^^^^^^^^^^^^^^^^ |
| 165 | +^^^^^^^^^^^^^^^^^^^^^^^ |
166 | 166 | --py-lmod |
167 | 167 | If running on a cluster which uses the |Lmod| module system, |
168 | 168 | specify here which file to source (relative to the :file:`lmod` |
|
173 | 173 | the python executable of the |virtual_Python_environment| in which |
174 | 174 | MDTools is installed. Default: ``'python3'``. |
175 | 175 | --mdt-path |
176 | | - Path to the MDTools installation. Default: |
177 | | - ``'${HOME}/.local/lib/python3.9/site-packages/mdtools'``. |
| 176 | + Path to the *cloned* MDTools repository. Note that you really need |
| 177 | + to clone MDTools |
| 178 | + (:bash:`git clone https://github.com/andthum/mdtools.git`) and |
| 179 | + install MDTools from the clone repository. For the last step refer |
| 180 | + to MDTools' `documentation |
| 181 | + <https://mdtools.readthedocs.io/en/latest/doc_pages/general_docs/installation.html>`_. |
| 182 | + The reason for this is that the Slurm job scripts (that are launched |
| 183 | + by this Python submit script) use the path to MDTools' |
| 184 | + :file:`scripts/` directory to call the MDTools scripts. Default: |
| 185 | + ``'${HOME}/git/github/mdtools'``. |
178 | 186 |
|
179 | 187 | Sbatch Options |
180 | 188 | ^^^^^^^^^^^^^^ |
@@ -857,8 +865,8 @@ def _submit(sbatch_opts, job_script): |
857 | 865 | "--mdt-path", |
858 | 866 | type=str, |
859 | 867 | required=False, |
860 | | - default="gmx", |
861 | | - help="Path to the MDTools installation. Default: %(default)s.", |
| 868 | + default="${HOME}/git/github/mdtools", |
| 869 | + help="Path to the cloned MDTools repository. Default: %(default)s.", |
862 | 870 | ) |
863 | 871 | opts = opthandler.get_opts( |
864 | 872 | argparser=parser, |
|
0 commit comments