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--- services:cluster:important [2025/02/07 15:13] – [Submit jobs from /scratch/username] update scratch information behrmj87
+++ services:cluster:important [2025/02/07 16:43] (current) – Add note on modules behrmj87
@@ Line 1: / Line 1: @@
 ====== Important notes on cluster usage ======
+==== ''/home'' on the cluster ====
+The ''/home'' directories on the cluster are separate for each cluster and separate from our regular home directories, so you will need to copy over config you may need, such as SSH keys.
 ==== Submit jobs from ''/scratch/username'' ====
@@ Line 12: / Line 17: @@
 When submitting a job you absolutely must specify an amount of memory to be allocated for your job.
-By default, a job get's ''1MB'' of memory per allocated CPU. This is a ridiculously value, which we set to make sure that some thought goes into how much memory you need. If more memory is allocated than you actually need, your job might wait longer than needed for a free spot in the cluster.
+By default, a job gets ''1MB'' of memory per allocated CPU. This is a ridiculously small value, which we set to make sure that some thought goes into how much memory you need. If more memory is allocated than you actually need, your job might wait longer than needed for a free spot in the cluster.
-If you specifiy less memory than needed, your program will automatically be killed.
+If you specify less memory than needed, your program will be killed automatically by Slurm.
@@ Line 23: / Line 28: @@
-<note important>
+<note tip>
-Usable space below ''/tmp'' and ''/dev/shm'' counts towards your job's memory usage and thus is limited by the ''--mem'' option
+Usable space below ''/tmp'' and ''/dev/shm'' counts towards your job's memory usage and thus is limited by the ''%%--%%mem'' option
 </note>
+==== SSH access ====
+The login node allows password-based login only from within the university network. We generally recommend SSH access with key files. To get your SSH key on the login node, when you are not at the university, you have two options:
+  - Use the VPN.
+  - Use an SSH proxy jump via login,physik.fu-berlin.de
+The latter is done via
+<code bash>
+ssh-copy-id \
+    -i ~/.ssh/id_sheldon \
+    -o ProxyJump=username@login.physik.fu-berlin.de \
+    username@headnode.physik.fu-berlin.de
+</code>
+Assuming a key file ''id_sheldon''. You will need to change ''username'' to your username and ''headnode'' to the name of the head node (login node) of the cluster.
+==== Modules ====
+Modules are a staple in the HPC world. They are a way to change your environment to include paths that are not normally in your binary (~PATH~) or library search paths (~LD_LIBRARY_PATH~) so that you can use a wider variety/other/different versions of programs
+<code>
+These are the most important commands
+#+BEGIN_SRC bash
+# show available modules
+module avail
+# load a module
+module load name_of_module
+# e.g. module load gromacs/double/2020.4
+#
+# unload a module (usually not necessary in a job script, but you can use
+# modules interactively, too)
+module unload name_of_module
+</code>
+Somebody has to build the software. This is done by us and interested users, e.g. the GROMACS packages are mostly built by users in AG Netz. The software modules can be found in ~/net/opt~. If you want to contribute, let us know!