Commit 2186f6b0 authored by Éamonn Murray's avatar Éamonn Murray

Update details with new server

parent 13630e38
......@@ -20,12 +20,12 @@ a lab workstation. If you'd prefer to use your own laptop to connect, you'll
need to download and install the x2go client that's freely available via
[their website](https://wiki.x2go.org/doku.php/download:start).
If there is not already a session named "mt-studentx" visible in the
If there is not already a session named "mt-studenty" visible in the
right-hand list on x2go when you start it up, you will need to create it.
- The shortcut to create a new session is "Ctrl+n".
- In this menu, you should name the session "mt-studentx".
- Set the Host as "mt-studentx.mt.ic.ac.uk".
- In this menu, you should name the session "mt-studenty".
- Set the Host as "mt-studenty.mt.ic.ac.uk".
- Select "XFCE" as the session type in the bottom drop down menu.
- An image of this is given below:
......@@ -185,7 +185,7 @@ directory that contains it.
- `rm -f` can be used to force deletion without prompting. Combine with the
previous option with caution. **There is no recycle bin** when using `rm`.
When you use it to delete a file it is gone, unless you have a backup.
(On mt-studentx there are daily snapshots you can recover deleted files from
(On mt-studenty there are daily snapshots you can recover deleted files from
in ~/.snapshots)
### rmdir
......@@ -567,7 +567,7 @@ it sets whatever environment variables are required automatically. This lets
many different and possibly conflicting software versions be installed on the
same system. Environment modules are almost always used on HPC systems to make
various versions of common version of computational software packages
available. The version installed on mt-studentx is called
available. The version installed on mt-studenty is called
[Lmod](https://www.tacc.utexas.edu/research-development/tacc-projects/lmod).
- The main command is `module`.
......@@ -575,21 +575,19 @@ available. The version installed on mt-studentx is called
- To see what modules are currently available type `module avail`. (some
groups of modules which require a compiler module to be loaded will not be
visible).
- To load the module making the Intel compilers available type `module load
intel`. This makes some additional modules available.
- To load the module making software compiled using the gcc compilers
available type `module load gcc`. This makes some additional modules
available.
- To see a complete list of all modules type `module spider`.
- The particular module implementation we use allows us to easily switch
between versions of codes compiled with different compilers.
- For example to load the quantum espresso module, you'll first need to
have the "intel" and "mkl" modules loaded. You can load everything in a
have the "gcc" and "mkl" modules loaded. You can load everything in a
single command though provided the order is correct:
```bash
module load intel mkl espresso
module load gcc mkl espresso
```
- If you load the gcc module after this, you'll see a notice that the
espresso module has automatically switched to the version compiled with
gcc.
- Throughout the course, when running on the undergrad server you'll need to
remember to load the modules above before you'll be able to use the codes
in the quantum espresso package.
......@@ -605,9 +603,9 @@ module load intel mkl espresso
Now you know enough to run your first DFT calculation.
- First we need to load the quantum espresso module. An optimized compilation
of this is available on the system compiled with the Intel compilers and
Math Kernel Libraries. Type the following in your terminal to load
everything you need in one go `module load intel mkl espresso` to load
of this is available on the system compiled with the GCC compilers and
Intel Math Kernel Libraries. Type the following in your terminal to load
everything you need in one go `module load gcc mkl espresso` to load
everything you need.
- Now you'll be able to use the various quantum espresso package executables
directly. Go to the silicon folder you copied earlier
......@@ -663,7 +661,7 @@ To run the DFT example in this lab you will need to do the following:
- Make a link to the espresso documentation directory in your home directory:
`cd ~/MSE404`, `ln -s /opt/share/quantum-espresso/doc-6.3 ./qe-doc`.
- Load the modules needed to run quantum espresso:
`module load intel mkl espresso`.
`module load gcc mkl espresso`.
- Go to the directory with the input files you copied and use these with
`pw.x` saving the output in a file:
`cd ~/MSE404/lab01/silicon; pw.x < Si.in > Si.out`.
......
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  • 2-up
  • Swipe
  • Onion skin
......@@ -79,14 +79,14 @@ which will let us go through the input in more detail. Let's look at this now.
Running the calculation
-----------------------
The quantum espresso package has been compiled as a module on mt-studentx. As
discussed in the previous lab, modules are often used on HPC systems to make
different versions of various packages as compiled with different compilers
available to users. To add quantum espresso to your environment, along with
its dependencies type the following in a terminal:
The quantum espresso package has been compiled as a module on the mt-student
server. As discussed in the previous lab, modules are often used on HPC
systems to make different versions of various packages as compiled with
different compilers available to users. To add quantum espresso to your
environment, along with its dependencies type the following in a terminal:
```bash
module load intel mkl espresso
module load gcc mkl espresso
```
Now to run the code: make sure you are in the `01_carbon_diamond` directory
......
......@@ -194,7 +194,7 @@ This calculation has five steps:
- `q2r.x` doesn't have a help file like the other codes. You need to inspect
the source file in `PHonon/PH/q2r.f90` if you download a copy of the
quantum espresso source code. The inputs are all described in a comment
at the top of this file. On mt-studentx you can see this file at
at the top of this file. On the mt-student server you can see this file at
`/opt/build/quantum-espresso/q-e-qe-6.3/PHonon/PH/q2r.f90`.
- Take a look at the `q2r.x` input file
[`03_CD_q2r.in](02_CarbonDiamond/03_CD_q2r.in). The contents are as follows:
......@@ -221,8 +221,8 @@ This calculation has five steps:
- Finally we want to use this to generate our normal mode dispersion. We'll be
doing this with the `matdyn.x` code. As with `q2r.x` this doesn't have a doc
file describing its input variables. But you can check the comments at the
top of its source file to get their details. On mt-studentx this is at
`/opt/build/quantum-espresso/q-e-qe-6.3/PHonon/PH/matdyn.f90`.
top of its source file to get their details. On the mt-student server this
is at `/opt/build/quantum-espresso/q-e-qe-6.3/PHonon/PH/matdyn.f90`.
- Take a look at our input file
[`04_CD_matdyn-bands.in`](02_CarbonDiamond/04_CD_matdyn-bands.in). The
content is as follows:
......
......@@ -45,7 +45,7 @@ look at many photon energies and including many empty states in our DFT
calculation.
The paper outlining the methods it uses is distributed with the quantum
espresso package. You can find it on mt-studentx in
espresso package. You can find it on the mt-student server in
`/opt/share/quantum-espresso/doc-6.1/turboTDDFT-CPC.pdf`. There are also
slides on the quantum espresso website outlining the approach and making
a comparison to the more basic TDDFT method at
......@@ -116,9 +116,9 @@ this calculation for a methane molecule.
- `ipol = 4` which tells it to calculate the response in all 3
directions: x, y and z.
- Run `turbo_lanczos.x` with this input file. It will likely take somewhere
around five minutes on mt-studentx. If you follow the output as it is
generated, you will see it calculating each of the 400 requested iterations
in turn for each of the three polarization directions.
around five minutes on the mt-student server. If you follow the output as it
is generated, you will see it calculating each of the 400 requested
iterations in turn for each of the three polarization directions.
- Finally take a look at the `turbo_spectrum.x` input file
[`03_CH4_ts.in`](CH4/03_CH4_ts.in). We need to set a few more things here.
As before, you can see a full description of all the input parameters that
......@@ -208,10 +208,10 @@ Then we have added an addition section `LR_POST`, which is needed whenever
- `plot_type = 3` which selects the output file to be in the gaussian cube
format. This can be opened with xcrysden.
- Note: it seems there may a bug with this output for the version compiled
on mt-studentx such that for particular choices of energy cut-off,
box-size and output format, the output file is cut off before the end
and can't be plot. For the values chosen here, it should work hopefully
work correctly.
on the mt-student server such that for particular choices of energy
cut-off, box-size and output format, the output file is cut off before
the end and can't be plot. For the values chosen here, it should work
hopefully work correctly.
Run `turbo_lanczos.x` with this input file. It'll take a couple of minutes
to finish. Once completed you'll see either a pair of files named
......
......@@ -65,9 +65,9 @@ also prompt you for your college password):
```bash
sudo mkdir -p /opt/share
sudo rsync -auz USER@mt-studentx.mt.ic.ac.uk:/opt/share/quantum-espresso /opt/share
sudo rsync -auz USER@mt-studenty.mt.ic.ac.uk:/opt/share/quantum-espresso /opt/share
sudo mkdir /opt/Courses
sudo rsync -auvz USER@mt-studentx.mt.ic.ac.uk:/opt/Courses/MSE404 /opt/Courses
sudo rsync -auvz USER@mt-studenty.mt.ic.ac.uk:/opt/Courses/MSE404 /opt/Courses
```
Then you should have everything necessary in place. I would suggest
......
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