srun<\/code><\/li>\nsinteractive<\/code><\/li>\n<\/ul>\nIf you need a Graphical User Interface (GUI), this can be done using X or VNC (Virtual Network Computing). For more graphical intensive programs (MATLAB (is<\/b>\u00a0a fourth-generation programming\u00a0<\/span>language<\/b>\u00a0and numerical analysis environment. Uses for\u00a0<\/span>MATLAB<\/b>\u00a0include matrix calculations, developing and running algorithms, creating user interfaces (UI) and data visualization)<\/span>, etc), we suggest to use VNC as X is not designed to be used over a slow SSH (Secure Shell) tunnel.<\/p>\n\nsinteractive<\/code>\u00a0<\/span>(X)<\/li>\nsinteractive-vnc<\/code>\u00a0<\/span>(VNC)<\/li>\n<\/ul>\nThe intended use of ABACUS2.0 is for batch scripts to be submitted using\u00a0<\/span>sbatch<\/code>. During periods of heavy loads on the system, you may have to wait for quite some time for your interactive session to start.<\/p>\nWe suggest you run interactive sessions with a run time of less than 24 hours, e.g.,\u00a0<\/span>--time 4:00:00<\/code>, as this makes it more likely that the interactive session\/job can be fit into the Slurm job schedule.<\/p>\nSoftware<\/h4>\n
If you only need to run interactive\u00a0<\/span>text<\/em>\u00a0<\/span>sessions, you do not need any additional software on your own computer on top of what you already use for SSH access.<\/p>\nFor GUI interactive jobs, what you need depends on the operating system, you are using:<\/p>\n
\n- For Windows users, we recommend using\u00a0<\/span>MobaXterm<\/a>\u00a0<\/span>as this includes both X and VNC as part of the installation. Further details can be found on our page on\u00a0<\/span>SSH installation for Windows<\/a>.<\/li>\n
- For Mac users, you’ll need two pieces of software:\n
\n- XQuartz<\/a>\u00a0<\/span>can be used for X sessions (
sinteractive<\/code>)<\/li>\n- TurboVNC<\/a>\u00a0<\/span>can be used for VNC sessions (
sinteractive-vnc<\/code>). The\u00a0<\/span>download page<\/a>\u00a0<\/span>is available here<\/a>. You should download and install the .dmg file.<\/li>\n<\/ul>\n<\/li>\n- For Linux users, support for X is already installed by default. For VNC support, we suggest to check whether your system already has a VNC viewer installed, e.g., Ubuntu installs\u00a0<\/span>Remmina Remote Desktop Client<\/em>. If not, we suggest you install TurboVNC:\n
\n- TurboVNC<\/a>\u00a0<\/span>can be downloaded\u00a0<\/span>here<\/a>.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n
srun: Text-only interactive jobs<\/h4>\n
The simplest solution when you want to run an interactive job is to use the\u00a0<\/span>srun<\/code>\u00a0<\/span>command with a few options. This preserves your current environment including e.g. loaded modules, but does not setup X nor VNC:<\/p>\n\ntestuser@fe1:~$<\/span> srun -A sdutest_gpu --time 1:00:00 --pty bash -i\ntestuser@s32p19:~$<\/span>\n<\/code><\/pre>\n<\/div>\nExactly as you do for\u00a0<\/span>sbatch<\/code>, you can add extra options, if you need multiple nodes, etc.:<\/p>\n\ntestuser@fe1:~$<\/span> srun -A sdutest_gpu --time 1:00:00 --nodes 8<\/span> --pty bash -i\ntestuser@s32p19:~$<\/span> #<\/span>\n<\/code><\/pre>\n<\/div>\nsinteractive: Text-only or GUI\/X interactive jobs<\/h4>\n
If you need a graphical interface, it becomes slightly more complicated. First, when connecting to ABACUS2.0, you must setup X forwarding using the\u00a0<\/span>-X<\/code>\u00a0<\/span>option (If your are using MobaXterm on Windows, X support is turned on by default):<\/p>\n\npeter@laptop:~$<\/span> ssh -X testuser@fe.deic.sdu.dk\n<\/code><\/pre>\n<\/div>\nNext, on the frontend node use the command\u00a0<\/span>sinteractive<\/code>. Note that\u00a0<\/span>sinteractive<\/code>\u00a0<\/span>clears most environment variables, i.e., to make everything work, you have to reload software modules, etc. when you are “inside” the interactive job.<\/p>\n\ntestuser@fe1:~$<\/span> sinteractive -A sdutest_slim --time 1:00:00\nWaiting for JOBID 8476 to start<\/span>\ntestuser@s22p22:~$<\/span>\n<\/code><\/pre>\n<\/div>\nIn both cases, by default you get 1 node. Exactly as you do using\u00a0<\/span>sbatch<\/code>\/sinteractive<\/code>, you can add extra options, if you need multiple nodes, etc.:<\/p>\n\ntestuser@fe1:~$<\/span> sinteractive -A sdutest_gpu --time 1:00:00 --nodes 4\nWaiting for JOBID 8477 to start<\/span>\ntestuser@s32p19:~$<\/span> #<\/span>\n<\/code><\/pre>\n<\/div>\nsinteractive-vnc: GUI\/VNC interative jobs<\/h4>\n
Some GUI applications, in particular COMSOL (Multiphysics\u00a0<\/span>is<\/em>\u00a0a cross-platform finite element analysis, solver and multiphysics simulation software. It allows conventional physics-based user interfaces and coupled systems of partial differential equations (PDEs))<\/span> and MATLAB, do not either\u00a0 work correctly when using “simple” X forwarding over SSH as shown above or alternatively run very slow. In these cases, you should consider looking at VNC.<\/p>\nRunning a VNC session is a three step procedure:<\/p>\n
1: Start a VNC server on one of the ABACUS2.0 compute nodes<\/h4>\n
First, login to a frontend node and run the command\u00a0<\/span>sinteractive-vnc<\/code>\u00a0<\/span>and follow the instructions:<\/p>\n\ntestuser@fe1:~$<\/span> sinteractive-vnc --time 2:00:00 --account sdutest_slim\n<\/code><\/pre>\n<\/div>\nThis starts a two hour job. You may want to request more\/less hours. You can also add extra options to get more than one node, etc. Exactly as you do for\u00a0<\/span>sbatch<\/code>\u00a0<\/span>or\u00a0<\/span>sinteractive<\/code>.<\/p>\nThe first time you run\u00a0<\/span>sinteractive-vnc<\/code>\u00a0<\/span>you are asked to setup a VNC password, which you later use when you connect your VNC viewer to the server (in Step 2.a\/2.b)<\/p>\n\ntestuser@fe1:~$<\/span> sinteractive-vnc --time 2:00:00 --account sdutest_slim\n==========================================================================<\/span>\nInteractive VNC session on Abacus<\/span>\n==========================================================================<\/span>\n\n------------<\/span>\nVNC password<\/span>\n------------<\/span>\n\/home\/testuser\/.vnc\/passwd does not exist<\/span>\n\nYou are required to setup a VNC password for accessing your VNC session.<\/span>\n\nYou should not reuse a password from elsewhere, as the password is not<\/span>\nencrypted securely.<\/span>\n\nAnswer no to whether you want to enter a 'view-only password'.<\/span>\n\nPassword:<\/span>\nVerify:<\/span>\nWould you like to enter a view-only password (y\/n)? n<\/span>\n\n\/home\/testuser\/.vnc\/passwd exists and is probably ok.<\/span>\n\nIf you forget your VNC password, use the command 'vncpassword' to reset it,<\/span>\ni.e., run<\/span>\n module add turbovnc ; vncpasswd<\/span>\n\n--------------------------------<\/span>\nSubmit interactive VNC slurm job<\/span>\n--------------------------------<\/span>\nWaiting for JOBID 95387 to start.<\/span>\nIf this step is interrupted, you may have to cancel the job yourself using<\/span>\n scancel 95387<\/span>\n\n--------------------------<\/span>\nVNC server ready on s12p34<\/span>\n--------------------------<\/span>\nNow run a VNC viewer on your own computer.<\/span>\n\nIf you are using TurboVNC on a Mac\/Linux computer, the following should work<\/span>\n peter@laptop:~$ \/opt\/TurboVNC\/bin\/vncviewer -via testuser@fe.deic.sdu.dk -ExtSSH=1 s12p34<\/span>\n\nOtherwise first setup an SSH tunnel<\/span>\n peter@laptop:~$ ssh -L 5900:s12p34:5900 testuser@fe.deic.sdu.dk<\/span>\nNext, while the above is running, start a vncviewer on your own computer<\/span>\nin another terminal window<\/span>\n peter@laptop:~$ vncviewer localhost<\/span>\n\nRemember to cancel\/shutdown the VNC server when you are done using<\/span>\n scancel 95387<\/span>\n<\/code><\/pre>\n<\/div>\nNote that the output from\u00a0<\/span>sinteractive-vnc<\/code>\u00a0<\/span>includes the name of the compute node your interactive VNC session is running. In the output above, the node is\u00a0<\/span>s12p34<\/code>.<\/p>\n2: Start a VNC viewer on your own computer<\/h4>\n
The next step is to start a VNC viewer on your own computer. The VNC viewer connects to the VNC server running on the compute node, e.g.\u00a0<\/span>s12p34<\/code>, via a gateway, i.e. a frontend node\u00a0<\/span>fe.deic.sdu.dk<\/code>.<\/p>\nWhat you need to do depends on exactly which VNC viewer your are using — see below for a few examples.<\/p>\n
In all cases, as part of establishing the connection you are asked for a password. This is the VNC password you entered earlier in Step 1:<\/p>\n
![\"VNC](\"https:\/\/deic-info.sdu.dk\/content\/doc\/images\/win-moba-vnc-5.png\")
\u00a0<\/span>![\"VNC](\"https:\/\/deic-info.sdu.dk\/content\/doc\/images\/vnc-2.png\")
<\/p>\n2.a: MobaXterm as a VNC Viewer (Windows)<\/h4>\n
In Step 2.a.3, replace\u00a0<\/span>s12p34<\/code>\u00a0<\/span>with the node name written in the output of\u00a0<\/span>sinteractive-vnc<\/code>:<\/p>\n\n- Click Session (top left corner).<\/li>\n
- Click VNC.<\/li>\n
- Enter the compute node name in the middle, e.g.,\u00a0<\/span>
s12p34<\/code>.<\/li>\n- Click the\u00a0<\/span>Network settings<\/em>\u00a0<\/span>tab, and select\u00a0<\/span>
fe.deic.sdu.dk<\/code>\u00a0<\/span>as the gateway server.<\/li>\n- Enter your username, e.g.,\u00a0<\/span>
testuser<\/code>.<\/li>\n- Click\u00a0<\/span>Use private key<\/em>\u00a0<\/span>and select your SSH private key.<\/li>\n
- Click OK<\/li>\n
- Next, enter your VNC password in the box that appears.<\/li>\n<\/ul>\n
![\"VNC](\"https:\/\/deic-info.sdu.dk\/content\/doc\/images\/win-moba-vnc-4b.png\")
<\/p>\n
2.b: TurboVNC as a VNC Viewer (Mac\/Linux)<\/h4>\n
If you are using TurboVNC on Mac\/Linux, run the following command on your own computer replacing\u00a0<\/span>s12p34<\/code>\u00a0<\/span>with the node name written in the output of\u00a0<\/span>sinteractive-vnc<\/code>.<\/p>\n\npeter@laptop:~$<\/span> \/opt\/TurboVNC\/bin\/vncviewer -via testuser@fe1.deic.sdu.dk -ExtSSH=<\/span>1<\/span> s12p34\n<\/code><\/pre>\n<\/div>\n2.c: Other VNC Viewers (Linux)<\/h4>\n
If you neither use MobaXterm nor TurboVNC, starting VNC is a two step process:<\/p>\n
First, setup a SSH tunnel using a command similar to this (replacing\u00a0<\/span>s12p34<\/code>\u00a0<\/span>with the node name written in the output of\u00a0<\/span>sinteractive-vnc<\/code>).<\/p>\n\npeter@laptop:~$<\/span> ssh -L 5900:s12p34:5900 testuser@fe1.deic.sdu.dk\n<\/code><\/pre>\n<\/div>\nNext,\u00a0<\/span>while the above is running<\/em>, start the vncviewer on your computer and ask the viewer to connect to\u00a0<\/span>localhost:9000<\/code>. For some viewers, this can be done using a command similar to this:<\/p>\n\npeter@laptop:~$<\/span> vncviewer localhost:5900\n<\/code><\/pre>\n<\/div>\n3: Start applications inside the VNC session<\/h4>\n
Inside the VNC window, you can start applications by first clicking the iceWM logo in the lower-left corner, and then starting an xterm window.<\/p>\n
Next, inside the xterm window, you can run anything you want, e.g. MATLAB:<\/p>\n
\ntestuser@s12p34:~$<\/span> module add matlab\ntestuser@s12p34:~$<\/span> matlab\n<\/code><\/pre>\n<\/div>\nSome applications do not work correctly, in particular, if they use 3D X11 library calls. Usually this can be fixed by adding the\u00a0<\/span>turbovnc<\/code>\u00a0<\/span>module which includes the Mesa 3D software library.<\/p>\n\ntestuser@s12p34:~$<\/span> module add turbovnc photoscan\n