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## How to connect to the login node / hpc cluster ## How to connect to the login node / hpc cluster
### From a Linux workstation ### From a Linux workstation
You are free to choose your Linux version, but we recommend the following distributions: You are free to choose your Linux distribution, but we recommend the following distributions:
- [Ubuntu Desktop 18.04 or 19.10](https://ubuntu.com/) - [Ubuntu Desktop 18.04 or 19.10](https://ubuntu.com/)
- [Fedora 31 workstation](https://getfedora.org/) - [Fedora 31 workstation](https://getfedora.org/)
Other distributions: Other distributions:
- [CentOS 8](https://www.centos.org/) - [CentOS 8](https://www.centos.org/)
- [Debian 10.2.0](https://www.debian.org/CD/)
- [Red Hat 8](https://www.redhat.com/en/technologies/linux-platforms/enterprise-linux) Commercial license required - [Red Hat 8](https://www.redhat.com/en/technologies/linux-platforms/enterprise-linux) Commercial license required
- [Arch Linux](https://www.archlinux.org/download/) Rolling distribution - [Arch Linux](https://www.archlinux.org/download/) Rolling distribution
...@@ -228,6 +229,10 @@ The setup is already described with the Linux client. ...@@ -228,6 +229,10 @@ The setup is already described with the Linux client.
## Module environment ## Module environment
When you will be working on the cluster, you probably the to load the correct the module, which will set the correct environment for you library, compiler or program.
Here below are some useful commands and examples:
- List all available modules - List all available modules
``` ```
...@@ -321,10 +326,10 @@ hello1.c:2:10: fatal error: mpi.h: No such file or directory ...@@ -321,10 +326,10 @@ hello1.c:2:10: fatal error: mpi.h: No such file or directory
compilation terminated. compilation terminated.
``` ```
So we need to load the correct module: So we need to load the correct module and use the correct compiler
``` ```
$ module add pmi/openpmix/4.0.0/gcc-8.2.1 $ module add mpi/openmpi/4.0.2/gcc-8.2.1
``` ```
- mpicc hello.c -o hello - mpicc hello.c -o hello
...@@ -341,6 +346,9 @@ Handy reference: ...@@ -341,6 +346,9 @@ Handy reference:
Hello world from process 000 out of 001, processor name res-hpc-lo01.researchlumc.nl Hello world from process 000 out of 001, processor name res-hpc-lo01.researchlumc.nl
``` ```
Here you can see that we ran the program only on 1 core of the cpu.
To make use of the MPI capabilitues of the program, we have to run the program with the "mpirun" which comes with the loaded module mpi/openmpi/4.0.2/gcc-8.2.1
- mpirun ./hello - mpirun ./hello
``` ```
...@@ -361,6 +369,7 @@ Hello world from process 008 out of 016, processor name res-hpc-lo01.researchlum ...@@ -361,6 +369,7 @@ Hello world from process 008 out of 016, processor name res-hpc-lo01.researchlum
Hello world from process 009 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 009 out of 016, processor name res-hpc-lo01.researchlumc.nl
Hello world from process 014 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 014 out of 016, processor name res-hpc-lo01.researchlumc.nl
``` ```
Here you can see that it is using all the cores of the local machine.
## Submitting jobs ## Submitting jobs
......