diff --git a/docs/software/eog.md b/docs/software/eog.md index 8ce56d1e9..2897a56eb 100644 --- a/docs/software/eog.md +++ b/docs/software/eog.md @@ -2,7 +2,6 @@ ![Example use of eog](./img/eog.png) - `eog` is a tool to view images on an UPPMAX cluster. To be able to see the images, @@ -12,13 +11,13 @@ or [login to a remote desktop](../getting_started/login.md) Usage: -``` +```bash eog [filename] ``` for example: -``` +```bash eog my.png ``` @@ -26,7 +25,7 @@ eog my.png In the terminal, do: - ``` + ```bash convert -size 32x32 xc:transparent my.png ``` diff --git a/docs/software/finishedjobinfo.md b/docs/software/finishedjobinfo.md index 7883ce1ad..380b3c277 100644 --- a/docs/software/finishedjobinfo.md +++ b/docs/software/finishedjobinfo.md @@ -6,13 +6,13 @@ To show the help of `finishedjobinfo`, in a terminal , do: -``` +```bash finishedjobinfo -h ``` ???- question "How does that look like?" - ``` + ```bash [sven@rackham3 ~]$ finishedjobinfo -h Usage: finishedjobinfo [-h] [-M cluster_name] [-j jobid[,jobid...]] [-m|-y|-s YYYY-MM-DD[/hh:mm:ss]] [-e YYYY-MM-DD[/hh:mm:ss]] [project_or_user]... -h Ask for help @@ -44,7 +44,7 @@ for example `finishedjobinfo -j 44981366`. Here is an example output: - ``` + ```bash [richel@rackham3 ~]$ finishedjobinfo -j 44981366 2024-02-09 12:30:37 jobid=44981366 jobstate=TIMEOUT username=richel account=staff nodes=r35 procs=1 partition=core qos=normal jobname=run_beast2.sh maxmemory_in_GiB=0.1 maxmemory_node=r35 timelimit=00:01:00 submit_time=2024-02-09T12:27:29 start_time=2024-02-09T12:29:18 end_time=2024-02-09T12:30:37 runtime=00:01:19 margin=-00:00:19 queuetime=00:01:49 ``` diff --git a/docs/software/games_us.md b/docs/software/games_us.md index 8a9dd1784..a6b3a327c 100644 --- a/docs/software/games_us.md +++ b/docs/software/games_us.md @@ -5,10 +5,13 @@ GAMESS-US versions 20170930 is installed on Rackham. Newer versions can be insta ## Running GAMESS Load the module using + ```bash module load gamess/20170930 ``` + Below is an example submit script for Rackham, running on 40 cores (2 nodes with 20 cores each). It is essential to specify the project name: + ```slurm #!/bin/bash -l #SBATCH -J jobname @@ -22,14 +25,17 @@ rungms gms >gms.out ``` ## Memory specification + GAMESS uses two kinds of memory: replicated memory and distributed memory. Both kinds of memory should be given in the $SYSTEM specification. Replicated memory is specified using the MWORDS keyword and distributed memory with the MEMDDI keyword. It is very important that you understand the uses of these keywords. Check the GAMESS documentation for further information. If your job requires 16MW (mega-words) of replicated memory and 800MW of distributed memory, as in the example below, the memory requirements per CPU core varies as 16+800/N where N is the number of cores. Each word is 8 bytes of memory, why the amount of memory per core is (16+800/N)*8. The amount of memory per node depends on the number of cores per node. Rackham has 20 cores per node, most nodes have 128 GB of memory, but 30 nodes have 512 GB and 4 nodes at 1 TB. ## Communication + For intra-node communication shared memory is used. For inter-node communication MPI is used which uses the Infiniband interconnect. ## Citing GAMESS papers + It is essential that you read the GAMESS manual thoroughly to properly reference the papers specified in the instructions. All publications using GAMESS should cite at least the following paper: ```bibtex @@ -43,4 +49,5 @@ pages={1347}, year=1993, comment={The GAMESS program}} ``` -If you need to obtain GAMESS yourself, please visit the GAMESS website for further instructions. \ No newline at end of file + +If you need to obtain GAMESS yourself, please visit the GAMESS website for further instructions. diff --git a/docs/software/gaussian.md b/docs/software/gaussian.md index 9b182b1df..045ce1d96 100644 --- a/docs/software/gaussian.md +++ b/docs/software/gaussian.md @@ -76,7 +76,7 @@ Gaussian can be run in parallel on a single node using shared memory. This is th The `dimer4.inp` input: -``` +```text %Mem=3800MB %NProcShared=4 #P MP2 aug-cc-pVTZ SCF=Tight