How to use the cluster
From PERFORM Wiki
HPC Cluster usage
Connection Steps:
- Ensure that you have an internet connection to Concordia (via Ethernet / Wifi), or that you are on Concordia's VPN: https://www.concordia.ca/it/services/vpn.html
- To login to the cluster:
ssh <concordia_netname>@perform-hpc
Please note that if this is your first time trying to login, you might receive a permission denied error, and then you will have to try the process 5 minutes later. - After you login it might ask you for your password a second time to create a keytab that allows you access the storage server - please do so.
- Once that is complete you can now start using the cluster. The login node (perform-hpc) should only be used for the uploading and downloading of data. In order to process data or use scientific packages, you'll need to ssh to a server. You can do this by typing:
goto_execution_node
Usage Steps:
- Before you begin working or submit a job, you'll need to load the appropriate paths ("modules") of each program you wish to use. To see what modules are available you can type:
module avail------------------------------------------------------ /util/modules/repo ------------------------------------------------------ AFNI/16.2.18 matlab/R2017a AFNI/19.0.21 matlab/R2017b Anaconda/4.2.0_using_python2.7.12 matlab/R2018b Anaconda/4.2.0_using_python3.5.2 matlab/R2018b_local Anaconda/5.0.1_using_python3.6.3 minc-stuffs/0.1.16_built_with_minc-1.0.08 Anaconda/5.2.0_using_python2.7.15 minc-stuffs/0.1.16_built_with_minc-1.9.11 ANTs/2016-09-19 minc-toolkit/1.0.08 ANTs/2.2.0 minc-toolkit/1.9.11 ANTs/2.3.1 minc-toolkit/1.9.15(default) ARPACK/96 minc-toolkit/1.9.16 ARPACK-NG/3.4.0 mipav/7.3.0(default) brainstorm/3 mipav/7.4.0 brain-view2/0.1.1_built_with_minc-1.9.11 mni_cortical_statistics/0.9.4 BrainVISA/4.2.1 MRIcroGL/2016-10-10 BrainVISA/4.4.0 MRIcron/2016-10-12 BrainVISA/4.5.0 MRtrix3/2018-05-16 dcm2niix/1.0.20171017 NIAK/1.1.4 dcm2niix/1.0.20171215 NIAK/1.1.4_dep dcm2niix/1.0.20181125 octave/4.2.0 dicom-toolkit/3.6.1 OpenCV/3.1.0 FID-A/1.0 oxford_asl/3.9.15 FID-A/2017-06-07 ParaView/5.2.0 FID-A/2017-08-02 pyminc/0.48 FreeSurfer/5.3.0 R/3.1.3 FreeSurfer/6.0.0 R/3.3.1 FSL/5.0.10(default) R/3.5.1 FSL/5.0.11 REST/1.8 FSL/5.0.9 RMINC/1.4.2.1_built_with_R-3.3.1_and_minc_1.0.08 Gannet/2.0 RMINC/1.4.2.1_built_with_R-3.3.1_and_minc_1.9.11 ITK/4.9.1 SCT/3.2.7 Mango/4.0.1 SPM/12_r6685 matlab/R2015a surfstat/2008-09-26 matlab/R2016a VTK/6.2.0 matlab/R2016b(default) VTK/7.1.0 matlab/R2016b2 xjView/9 matlab/R2016b_local
- Load your desired module: (note that the command below defaults to the latest version of the package. If you want a specific version, you need to specify it - i.e. module load minc-toolkit/1.0.08 . You should also take note of what version you use, so you can use the same one in a future analysis.
Also, don't type the (default) suffix"):
module load minc-toolkit - You can uload modules with:
module unload <module_name> - You can remove all loaded modules with:
module purge - If you forget which ones are loaded, you can List the ones your have loaded with:
module list - If your module requires other modules to function, it will inform you to load them:
user@perf-hpc01:/util/modules$ module load spm spm/12_r6685(3):ERROR:151: Module 'spm/12_r6685' depends on one of the module(s) 'matlab/R2016b matlab/R2016a' spm/12_r6685(3):ERROR:102: Tcl command execution failed: prereq matlab
- Similarly, if a module conflicts with another module, they can't both be loaded at the same time:
user@perf-hpc01:/util/modules$ module load minc-toolkit user@perf-hpc01:/util/modules$ module load freesurfer freesurfer/5.3.0(5):ERROR:150: Module 'freesurfer/5.3.0' conflicts with the currently loaded module(s) 'minc-toolkit/1.9.11' freesurfer/5.3.0(5):ERROR:102: Tcl command execution failed: conflict minc-toolkit
