@@ -10,102 +10,111 @@ Graphical Installation
1010 out of date and there might be small differences between what you read here and
1111 watch there.
1212
13- SEAMM should be installed in the **seamm ** conda environment. Open a terminal
14- and run the following commands::
13+ SEAMM should be installed in the **seamm ** conda environment. The steps are:
1514
16- conda create -n seamm -c conda-forge seamm seamm-installer seamm-dashboard python=3.9
15+ #. Download :download: `seamm.yml <./seamm.yml >` and save it in a known location.
16+ #. Open a terminal and run the following commands::
1717
18- If you do not intend to run the SEAMM Dashboard in this installation, you can leave it
19- off the command line::
18+ conda env create --file <path to seamm.yml>
2019
21- conda create -n seamm -c conda-forge seamm seamm-installer python=3.9
20+ #. Once the environment is in place, activate it::
2221
23- Once the environment is in place, you can activate it as prompted::
22+ conda activate seamm
2423
25- conda activate seamm
24+ #. Now run the SEAMM Installer to install both the SEAMM environment and the available
25+ plug-ins::
2626
27- You can choose a different name for your SEAMM environment by replacing
28- the ``<name> `` argument in the ``-n <name> `` option with your preferred title.
27+ seamm-installer
2928
30- Now run the SEAMM Installer to install both the SEAMM environment and the available
31- plug-ins::
29+ You will see a window like this:
3230
33- seamm-installer
34-
35- You will see a window like this:
36-
37- .. figure :: images/initial.png
38- :align: center
39- :alt: The initial Installer window
31+ .. figure :: images/initial.png
32+ :align: center
33+ :alt: The initial Installer window
4034
41- The initial window of the Installer
35+ The initial window of the Installer
4236
43- Click on the second tab **Components **. The Installer needs to examine the installation
44- and sometimes -- like this first time you use it -- needs to search the Internet to find
45- the plug-ins for SEAMM. This can take a few minutes, so be patient! A small dialog will
46- come up in front of the Installer to let you know about progress. When the Installer has
47- examined everthing it will fill out the window, like this:
37+ #. Click on the second tab **Components **. The Installer needs to examine the
38+ installation. This can take a few minutes, so be patient! A small dialog will
39+ come up in front of the Installer to let you know about progress. When the Installer has
40+ examined everthing it will fill out the window, like this:
4841
49- .. figure :: images/components.png
50- :align: center
51- :alt: The initial Components tab.
42+ .. figure :: images/components.png
43+ :align: center
44+ :alt: The initial Components tab.
45+
46+ The initial Components tab.
47+
48+ The lines in green show components or plug-ins that are installed and
49+ up-to-date. Black indicates that the item is not installed, and red indicates
50+ items that are installed but out-of-date. The first time that you run the
51+ Installer most of the core packages will be installed and up-to-date because you
52+ just installed them as you created the Conda environment.
53+
54+ You can select the plug-ins that you want, or select everything using the ``Select
55+ all `` button. Once you are happy with your selection, click the ``Install
56+ selected `` button. Don't worry if you have selected some of the packages that are
57+ already installed: they will be ignored. Depending on your internet connection,
58+ computer, and the plug-ins selected, the installation can take up to 10 or 20
59+ minutes. This is because many of the plug-ins also install additional software
60+ such as LAMMPS, Psi4, Packmol, and DFTB+, and some of these packages are quite
61+ large and take time to install.
62+
63+ When the installation is done, the window will update with the current status. If
64+ you wish you can select more packages to install and repeat the process.
65+
66+ .. note ::
67+ If you plan to only use the GUI on this machine, and submit jobs to other machines,
68+ you can select the **GUI only ** checkbox. This will install only the components for
69+ the GUI of SEAMM. None of the background software, like LAMMPS, be installed. This is
70+ both faster and keeps the installation smaller.
71+
72+ #. Once you are happy with the installation, go to the next tab, **Shortcuts ** to install
73+ shortcuts for starting SEAMM and the Installer. It looks like this:
74+
75+ .. figure :: images/shortcuts.png
76+ :align: center
77+ :alt: The initial Shortcuts tab.
5278
53- The initial Components tab.
79+ The initial Shortcuts tab.
5480
55- The lines in green show components or plug-ins that are installed and up-to-date. Black
56- indicates that the item is not installed, and red indicates items that are installed but
57- out-of-date. The first time that you run the Installer most of the core packages will be
58- installed and up-to-date because you just installed them as you created the Conda
59- environment.
81+ Select the applications that you want, and click ``Create selected apps `` to create the
82+ shortcuts. On a Mac, the shortcuts will be in ``~/Applications ``, i.e. the Applications folder
83+ under your home directory, not the main ``/Applications `` folder. On Linux, they will be
84+ in ``~/.local/share/Applications ``. You can usually drag the shortcuts to the desktop,
85+ dock, launcher or similar place for easy access; however, the details depend on the your
86+ OS and desktop so check the documentation if need be.
6087
61- You can select the plug-ins that you want, or select everything using the ``Select all ``
62- button. Once you are happy with your selection, click the ``Install selected ``
63- button. Don't worry if you have selected some of the packages that are already
64- installed: they will be ignored. Depending on your internet connection, computer, and
65- the plug-ins selected, the installation can take up to 10 or 20 minutes. This is
66- because many of the plug-ins also install additional software such as LAMMPS, Psi4,
67- Packmol, and DFTB+, and some of these packages are quite large and take time to install.
88+ #. If you want to run jobs locally, go to the last tab, **Services **, to install the
89+ Dashboard and JobServer as services so that they are always available. This tab looks
90+ like this:
6891
69- When the installation is done, the window will update with the current status. If you
70- wish you can select more packages to install and repeat the process.
92+ .. figure :: images/services.png
93+ :align: center
94+ :alt: The initial Services tab.
7195
72- .. note ::
73- If you plan to only use the GUI on this machine, and submit jobs to other machines,
74- you can select the **GUI only ** checkbox. This will install only the components for
75- the GUI of SEAMM. Neither the Dashboard or JobServer will be installed, nor will any
76- of the background software, like LAMMPS, be installed. This is both faster and keeps
77- the installation smaller.
78-
79- Once you are happy with the installation, go to the next tab, **Shortcuts ** to install
80- shortcuts for starting SEAMM and the Installer. It looks like this:
81-
82- .. figure :: images/shortcuts.png
83- :align: center
84- :alt: The initial Shortcuts tab.
85-
86- The initial Shortcuts tab.
96+ The initial Services tab.
8797
88- Select the applications that you want, and click ``Create selected apps `` to create the
89- shortcuts. On a Mac, the shortcuts will be in ``~/Applications ``, i.e. the Applications folder
90- under your home directory, not the main ``/Applications `` folder. On Linux, they will be
91- in ``~/.local/share/Applications ``. You can usually drag the shortcuts to the desktop,
92- dock, launcher or similar place for easy access; however, the details depend on the your
93- OS and desktop so check the documentation if need be.
98+ Select both the Dashboard and JobServer and click on ``Create selected
99+ services ``. A small dialog will pop up allowing you to set the name of the Dashboard
100+ and the port. The default port is 55055, but you can change it to any port > 1024
101+ that does not conflict with another service on your machine. Large numbers, like
102+ 55055, are generally safe:
94103
95- Finally, go to the last tab, **Services **, to install the Dashboard and JobServer as
96- services so that they are always available. This tab looks like this:
104+ .. figure :: images/name_port.png
105+ :align: center
106+ :alt: The Dashboard Parameters
97107
98- .. figure :: images/services.png
99- :align: center
100- :alt: The initial Services tab.
101-
102- The initial Services tab.
108+ The dialog for setting the name and port of the Dashboard
103109
104- If you want to run jobs locally, select both the Dashboard and JobServer and click on
105- ``Create selected services ``. This will install the services and start them. Note the
106- other two buttons, which let you stop and start the services if you need.
110+ Click ``OK ``. This will install the services and start them.
107111
112+ .. note:
113+ Note the other two buttons, which let you stop and start the services if you need.
108114
115+
116+ :doc: `../tutorials/index ` is a good place to start.
117+
109118.. Link shortcuts and cross-referencing labels
110119Miniconda : https://docs.conda.io/en/latest/miniconda.html
111120.. _Anaconda : https://www.anaconda.com/distribution
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