BwUniCluster/Maintenance/2016-10

2016-10-20T06:26:16Z

M Neuer: /* Software Module Updates */

BwUniCluster/Maintenance/2016-10

2016-10-19T11:05:04Z

M Neuer: /* Software Modules which will be REMOVED */

2014-10-08T09:03:38Z

M Neuer:

{| style="width:100%; vertical-align:top; background:#f5fffa;border:1px solid #e7aa01;"
| style="padding:2px;" | <div style="margin:3px; background:#cef2e0; font-size:120%; font-weight:bold; border:1px solid #e7aa01; text-align:left; color:#000; padding:0.2em 0.4em;">Mathematica might not be available on all locations.</div>
|}


{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | Mathematica
|-
| module load
| math/mathematica

|-
| License
| Commercial
|-
|Citing
|
|-
| Links
| [http://www.wolfram.com/mathematica/ Homepage]; [http://www.wolfram.com/support/?source=nav Documentation];
|
|-
| Graphical Interface
| Yes (See [[VNC]]) 
|-
| Included in module
| 
|}

'''Mathematica''' is a software from Wolfram for symbolic and numerical computation with many features
such as powerful visualization and application specific functions.

== Loading ==
To check if Mathematica is available execute
$ module avail math/mathematica

If Mathematica is available you can load a specific version or you can load the default version with
$ module load math/mathematica

== General Usage ==
Mathematica can be used interactively on the command line or with a graphical front-end.
Alternatively Mathematica can run a script in batch mode which is useful when submitting batch jobs to the cluster.
After loading Mathematica the different modes can be used as follows.

*Interactive with GUI (needs [[X11 forwarding]] or [[VNC]]): <pre>$ mathematica</pre>

*Interactive with command line: <pre>$ math</pre>

*Non-Interactive. Looks like interactive with command line but input is taken from script.m: <pre>$ math < script.m</pre>

*Non-Interactive. You have to explicitly specify what you want to print <pre>$ math -script script.m</pre>However, the output is done in InputForm which is suitable for input in other Mathematica calculations but if you want pretty output you have to change the output format to OutputForm like this <pre>SetOptions[$Output, FormatType -> OutputForm]</pre>

For an introduction to Mathematica we refer to the online documentation ([http://reference.wolfram.com/mathematica/guide/Mathematica.html Mathematica Documentation Center]). Specific information on the use in a compute cluster is in the next section.

== Parallel Computation ==
Obviously parallel computation can be useful to speed up time-consuming computations, but it should also be used for multiple computations with different input data files (e.g. for parametric studies). The reason for this
is the license model from Wolfram. There are two types of licenses.
* Each time an instance of Mathematica starts, a so called MathKernel license is used up.
* Each time Mathematica spawns a subprocess, a license called SubMathKernel is used up.
Because usually there are much more SubMathKernel licenses than MathKernel licenses it is recommended to start multiple subprocesses instead of submitting multiple jobs.

Remember to request the correct amount of processors in your [[Batch Jobs]] script but note that Mathematica will not automatically use these processors.
In general you have to adjust your code to benefit from more cores.
To do this you first have to start a number of kernels which are then used by ParallelTable to run the computations in parallel.
This basic example computes the first eight square numbers in parallel.
<pre>
LaunchKernels[8]
f[i_] := i^2
DistributeDefinitions[f]
ParallelTable[f[i], {i,0,7}]
CloseKernels[]
</pre>
Note that the use of DistributeDefinitions is necessary for f is a user defined function and the definition of this function must be available to all kernels.

The next example is the computation of a numerical solution for the following initial value problem
x'(t) = x(t)^2 - x(t)^3
x(0) = d
It is difficult to solve this equation with high accuracy at the point 1/d.
We decrease the step size of the algorithm to see how the execution time and the relative error at the point 1/d change.

<pre>
d = 0.00001

y[t_] := 1/(ProductLog[(1/d-1)*Exp[1/d-1-t]]+1) (* analytical solution *)
relerr[t_, s_] := Abs[(y[t] - x[t]/.s)/y[t]] (* relative error of solution s at time t *)
g[v_] := {v[[1]], v[[2]][[1]], relerr[1/d, v[[2]][[2]][[1]]]} (* helper function *)

(* compute numerical solutions for 6 different step sizes *)
LaunchKernels[6]
tbl = ParallelTable[{step, Timing[NDSolve[{x'[t] == x[t]^2 - x[t]^3, x[0] == d}, x, {t, 0, 2/d}, MaxStepSize->step, MaxSteps->10000000]]}, {step,5,3,-0.4}]
CloseKernels[]

SetOptions[$Output, FormatType -> OutputForm] (* better output when called with -script *)
Print[ Grid[Join[{{"Stepsize", "Time", "Error at 1/d"}}, Map[g, tbl]]] ] (* print the result *)
</pre>
Mathematica features some further functions similar to ParallelTable which are documented on the [http://reference.wolfram.com/mathematica/guide/ParallelComputing.html Mathematica parallel computing webpage] from Wolfram. One such function is ParallelSubmit which can be used to start two (or more) completely unrelated functions in parallel. But bear in mind that the functions should have similar running times because the scheduler reserves the requested resources for the runtime of the whole job. The following code shows how to pack two 1-core jobs into one 2-core job.
<pre>
f[r_] := (
d = 0.000001;
{time, sol} = Timing[NDSolve[{x'[t] == r*x[t]^2 - x[t]^3, x[0] == d}, x, {t, 0, 2/d}, MaxStepSize->3, MaxSteps->10000000]];
{time, x[1/d]/.sol[[1]]}
)

g[r_] := (
{time, sol} = Timing[NDSolve[{y''[t] + (r+1)*y'[t] + r*y[t] == 0, y[0] == 1, y'[0] == 0}, y, {t, 0, 30}, MaxStepSize->0.000002, MaxSteps->10000000000]];
{time, y[30]/.sol[[1]]}
)

kernel1 := (
file = OpenWrite["out1.txt", FormatType -> OutputForm];
$Output = {file};
Print[f[1.2]];
Close[file];
)

kernel2 := (
file = OpenWrite["out2.txt", FormatType -> OutputForm];
$Output = {file};
Print[g[1000]];
Close[file];
)

LaunchKernels[2]
DistributeDefinitions[kernel1, kernel2]
e = {ParallelSubmit[kernel1], ParallelSubmit[kernel2]}
WaitAll[e]
</pre>
The helper functions kernel1 and kernel2 get started in different threads and then they execute f and g. The output of these functions is redirected to different files so the results can clearly be distinguished and examined as soon as one function is done.
[[Category:Mathematics software]]

BwUniCluster2.0/Software/Mathematica

2014-08-27T08:20:29Z

M Neuer:

BwUniCluster2.0/Software/Mathematica

2014-07-17T12:18:31Z

M Neuer: /* Parallel Computation */

{| style="width:100%; vertical-align:top; background:#f5fffa;border:1px solid #e7aa01;"
| style="padding:2px;" | <div style="margin:3px; background:#cef2e0; font-size:120%; font-weight:bold; border:1px solid #e7aa01; text-align:left; color:#000; padding:0.2em 0.4em;">Mathematica might not be available on all locations.</div>
|}


{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | Mathematica
|-
| module load
| math/mathematica

|-
| License
| Commercial
|-
|Citing
|
|-
| Links
| [http://www.wolfram.com/mathematica/ Homepage]; [http://www.wolfram.com/support/?source=nav Documentation];
|
|-
| Graphical Interface
| Yes (See [[VNC]]) 
|-
| Included in module
| 
|}

'''Mathematica''' is a software from Wolfram for symbolic and numerical computation with many features
such as powerful visualization and application specific functions.

== Loading ==
To check if Mathematica is available execute
$ module avail math/mathematica

If Mathematica is available you can load a specific version or you can load the default version with
$ module load math/mathematica

== General Usage ==
Mathematica can be used interactively on the command line or with a graphical front-end.
Alternatively Mathematica can run a script in batch mode which is useful when submitting batch jobs to the cluster.
After loading Mathematica the different modes can be used as follows.

Interactive with command line:
$ math

Interactive with GUI (needs [[X11 forwarding]] or [[VNC]]):
$ mathematica

Non-Interactive:
$ math < script.m

For an introduction to Mathematica we refer to the online documentation ([http://reference.wolfram.com/mathematica/guide/Mathematica.html Mathematica Documentation Center]). Specific information on the use in a compute cluster is in the next section.

== Parallel Computation ==
Obviously parallel computation can be useful to speed up time-consuming computations, but it should also be used for multiple computations with different input data files (e.g. for parametric studies). The reason for this
is the license model from Wolfram. There are two types of licenses.
* Each time an instance of Mathematica starts, a so called MathKernel license is used up.
* Each time Mathematica spawns a subprocess, a license called SubMathKernel is used up.
Because usually there are much more SubMathKernel licenses than MathKernel licenses it is recommended to start multiple subprocesses instead of submitting multiple jobs.

Remember to request the correct amount of processors in your [[Batch Jobs]] script but note that Mathematica will not automatically use these processors.
In general you have to adjust your code to benefit from more cores.
To do this you first have to start a number of kernels which are then used by ParallelTable to run the computations in parallel.
This basic example computes the first eight square numbers in parallel.
<pre>
LaunchKernels[8]
f[i_] := i^2
DistributeDefinitions[f]
ParallelTable[f[i], {i,0,7}]
CloseKernels[]
</pre>
Note that the use of DistributeDefinitions is necessary for f is a user defined function and the definition of this function must be available to all kernels.

The next example is the computation of a numerical solution for the following initial value problem
x'(t) = x(t)^2 - x(t)^3
x(0) = d
It is difficult to solve this equation with high accuracy at the point 1/d.
We decrease the step size of the algorithm to see how the execution time and the relative error at the point 1/d change.

<pre>
d = 0.00001

y[t_] := 1/(ProductLog[(1/d-1)*Exp[1/d-1-t]]+1) (* analytical solution *)
relerr[t_, s_] := Abs[(y[t] - x[t]/.s)/y[t]] (* relative error of solution s at time t *)
g[v_] := {v[[1]], v[[2]][[1]], relerr[1/d, v[[2]][[2]][[1]]]} (* helper function *)

(* compute numerical solutions for 6 different step sizes *)
LaunchKernels[6]
tbl = ParallelTable[{step, Timing[NDSolve[{x'[t] == x[t]^2 - x[t]^3, x[0] == d}, x, {t, 0, 2/d}, MaxStepSize->step, MaxSteps->10000000]]}, {step,5,3,-0.4}]
CloseKernels[]

Grid[Join[{{"Stepsize", "Time", "Error at 1/d"}}, Map[g, tbl]]] (* print the result *)
</pre>
Mathematica features some further functions similar to ParallelTable which are documented on the [http://reference.wolfram.com/mathematica/guide/ParallelComputing.html Mathematica parallel computing webpage] from Wolfram.

[[Category:Mathematics software]]

BwUniCluster2.0/Software/Mathematica

2014-07-11T08:57:03Z

M Neuer:

{| style="width:100%; vertical-align:top; background:#f5fffa;border:1px solid #e7aa01;"
| style="padding:2px;" | <div style="margin:3px; background:#cef2e0; font-size:120%; font-weight:bold; border:1px solid #e7aa01; text-align:left; color:#000; padding:0.2em 0.4em;">Mathematica might not be available on all locations.</div>
|}


{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | Mathematica
|-
| module load
| math/mathematica

|-
| License
| Commercial
|-
|Citing
|
|-
| Links
| [http://www.wolfram.com/mathematica/ Homepage]; [http://www.wolfram.com/support/?source=nav Documentation];
|
|-
| Graphical Interface
| Yes (See [[VNC]]) 
|-
| Included in module
| 
|}

'''Mathematica''' is a software from Wolfram for symbolic and numerical computation with many features
such as powerful visualization and application specific functions.

== Loading ==
To check if Mathematica is available execute
$ module avail math/mathematica

If Mathematica is available you can load a specific version or you can load the default version with
$ module load math/mathematica

== General Usage ==
Mathematica can be used interactively on the command line or with a graphical front-end.
Alternatively Mathematica can run a script in batch mode which is useful when submitting batch jobs to the cluster.
After loading Mathematica the different modes can be used as follows.

Interactive with command line:
$ math

Interactive with GUI (needs [[X11 forwarding]] or [[VNC]]):
$ mathematica

Non-Interactive:
$ math < script.m

For an introduction to Mathematica we refer to the online documentation ([http://reference.wolfram.com/mathematica/guide/Mathematica.html Mathematica Documentation Center]). Specific information on the use in a compute cluster is in the next section.

== Parallel Computation ==
Obviously parallel computation can be useful to speed up time-consuming computations, but it should also be used for multiple computations with different input data files (e.g. for parametric studies). The reason for this
is the license model from Wolfram. There are two types of licenses.
* Each time an instance of Mathematica starts, a so called MathKernel license is used up.
* Each time Mathematica spawns a subprocess, a license called SubMathKernel is used up.
Because usually there are much more SubMathKernel licenses than MathKernel licenses it is recommended to start multiple subprocesses instead of submitting multiple jobs.

Remember to request the correct amount of processors in your [[Batch Jobs]] script but note that Mathematica will not automatically use these processors.
In general you have to adjust your code to benefit from more cores.
To do this you first have to start a number of kernels which are then used by ParallelTable to run the computations in parallel.
This basic example computes the first eight square numbers in parallel.
<pre>
LaunchKernels[8]
f[i_] := i^2
DistributeDefinitions[f]
ParallelTable[f[i], {i,0,7}]
CloseKernels[]
</pre>
Note that the use of DistributeDefinitions is necessary for f is a user defined function and the definition of this function must be available to all kernels.

The next example is the computation of a numerical solution for the following initial value problem
x'(t) = x(t)^2 - x(t)^3
x(0) = d
It is difficult to solve this equation with high accuracy at the point 1/d.
We decrease the step size of the algorithm to see how the execution time and the relative error at the point 1/d change.

<pre>
d = 0.00001

y[t_] := 1/(ProductLog[(1/d-1)*Exp[1/d-1-t]]+1) (* analytical solution *)
relerr[t_, s_] := Abs[(y[t] - x[t]/.s)/y[t]] (* relative error of solution s at time t *)
g[v_] := {v[[1]], v[[2]][[1]], relerr[1/d, v[[2]][[2]][[1]]]} (* helper function *)

(* compute numerical solutions for 6 different step sizes *)
LaunchKernels[6]
tbl = ParallelTable[{step, Timing[NDSolve[{x'[t] == x[t]^2 - x[t]^3, x[0] == d}, x, {t, 0, 2/d}, MaxStepSize->step, MaxSteps->10000000]]}, {step,5,3,-0.2}]
CloseKernels[]

Grid[Join[{{"Stepsize", "Time", "Error at 1/d"}}, Map[g, tbl]]] (* print the result *)
</pre>
Mathematica features some further functions similar to ParallelTable which are documented on the [http://reference.wolfram.com/mathematica/guide/ParallelComputing.html Mathematica parallel computing webpage] from Wolfram.

[[Category:Mathematics software]]

BwUniCluster2.0/Software/Mathematica

2014-07-08T08:15:37Z

M Neuer:

{| style="width:100%; vertical-align:top; background:#f5fffa;border:1px solid #e7aa01;"
| style="padding:2px;" | <div style="margin:3px; background:#cef2e0; font-size:120%; font-weight:bold; border:1px solid #e7aa01; text-align:left; color:#000; padding:0.2em 0.4em;">Mathematica might not be available on all locations.</div>
|}


{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | Mathematica
|-
| module load
| math/mathematica

|-
| License
| Commercial
|-
|Citing
|
|-
| Links
| [http://www.wolfram.com/mathematica/ Homepage]; [http://www.wolfram.com/support/?source=nav Documentation];
|
|-
| Graphical Interface
| Yes (See [[VNC]]) 
|-
| Included in module
| 
|}

'''Mathematica''' is a software from Wolfram for symbolic and numerical computation with many features
such as powerful visualization and application specific functions.

== Loading ==
To check if Mathematica is available execute
$ module avail math/mathematica

If Mathematica is available you can load a specific version or you can load the default version with
$ module load math/mathematica

== General Usage ==
Mathematica can be used interactively on the command line or with a graphical front-end.
Alternatively Mathematica can run a script in batch mode which is useful when submitting batch jobs to the cluster.
After loading Mathematica the different modes can be used as follows.

Interactive with command line:
$ math

Interactive with GUI (needs [[X11 forwarding]] or [[VNC]]):
$ mathematica

Non-Interactive:
$ math < script.m

For an introduction to Mathematica we refer to the online documentation ([http://reference.wolfram.com/mathematica/guide/Mathematica.html Mathematica Documentation Center]). Specific information on the use in a compute cluster is in the next section.

== Parallel Computation ==
Obviously parallel computation can be useful to speed up a long running computation but it should also be used
when multiple computations with different input data are needed (e.g. for parametric studies). The reason for this
is the license model from Wolfram. There are two types of licenses.
* Each time an instance of Mathematica starts, a so called MathKernel license is used up.
* Each time Mathematica spawns a subprocess, a license called SubMathKernel is used up.
Because usually there are much more SubMathKernel licenses than MathKernel licenses it is recommended to start multiple subprocesses instead of submitting multiple jobs.

Remember to request the right amount of processors in your job script but note that Mathematica will not automatically use these processors.
In general you have to change your code to benefit from more cores.
To do this you first have to start a number of kernels which are then used by ParallelTable to run the computations in parallel.
This basic example computes the first eight square numbers in parallel.
<pre>
LaunchKernels[8]
f[i_] := i^2
DistributeDefinitions[f]
ParallelTable[f[i], {i,0,7}]
CloseKernels[]
</pre>
Note that the use of DistributeDefinitions is necessary for f is a user defined function and the definition of this function must be available to all kernels.

The next example is the computation of the numerical solution of the following initial value problem
x'(t) = x(t)^2 - x(t)^3
x(0) = d
It is difficult to solve this equation with high accuracy at the point 1/d.
We decrease the step size of the algorithm to see how the execution time and the relative error at the point 1/d change.

<pre>
d = 0.00001

y[t_] := 1/(ProductLog[(1/d-1)*Exp[1/d-1-t]]+1) (* analytical solution *)
relerr[t_, s_] := Abs[(y[t] - x[t]/.s)/y[t]] (* relative error of solution s at time t *)
g[v_] := {v[[1]], v[[2]][[1]], relerr[1/d, v[[2]][[2]][[1]]]} (* helper function *)

(* compute numerical solutions for 6 different step sizes *)
LaunchKernels[6]
tbl = ParallelTable[{step, Timing[NDSolve[{x'[t] == x[t]^2 - x[t]^3, x[0] == d}, x, {t, 0, 2/d}, MaxStepSize->step, MaxSteps->10000000]]}, {step,5,3,-0.2}]
CloseKernels[]

Grid[Join[{{"Stepsize", "Time", "Error at 1/d"}}, Map[g, tbl]]] (* print the result *)
</pre>
There are other functions similar to ParallelTable which are documented on the site
http://reference.wolfram.com/mathematica/guide/ParallelComputing.html which provides general information on parallel computing with Mathematica.

[[Category:Mathematics software]]

JUSTUS2/Visualization

2014-07-08T08:09:39Z

M Neuer:

= TigerVNC =
{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | TigerVNC
|-
| module load
| vis/tigervnc
|-
| License
| GPL
|-
| Links
| [http://www.tigervnc.org TigerVNC Homepage]
|}
'''TigerVNC''' is a high-performance implementation of VNC (Virtual Network Computing), a client/server application that allows
users to launch and interact with graphical applications on remote machines. It should be faster than standard X11 forwarding and thus can
be used if a graphical software feels slow and has bad responsiveness.

== Instructions ==

First, you need to start the VNC server on the bwUniCluster. Therefore you must log into the bwUniCluster with your username and password as usual.
You should not start the server on a login node but request an interactive job using for example the following command.
$ msub -v HOME,TERM,USER,DISPLAY -S /bin/bash -I -l nodes=1:ppn=1 -l walltime=0:02:00:00
On your assigned compute node start the VNC server with
$ module load vis/tigervnc
$ run_vncserver
If you start a VNC server for the first time you will be asked to set a password which will be required for clients trying to access your VNC desktop. '''Use a strong password because otherwise an attacker could take control of your VNC session.'''
The script prints detailed instructions on how to establish the connection to the VNC server from your local computer. They depend on whether you
use Windows or Linux and if you work with TightVNC Java Viewer which is a tool that can simplify the process a little bit but needs at least Java version 1.6 to run. Therefore the next steps are
divided into 3 cases. Each command should be issued on the local computer.

* '''Login with TightVNC Java Viewer''' Needed Software: [http://www.tightvnc.com/download.php TightVNC Java Viewer], Java Open TightVNC Java Viewer (the executable is called tightvnc-jviewer.jar), check "Use SSH tunneling" and fill in the parameters provided by the ''run_vncserver'' script. Now you can click on the "Connect" button and enter your passwords.

* '''Login without TightVNC Java Viewer for Linux users''' Needed Software: A VNC viewer such as tigervnc, gvncviewer or tightvnc A tunnel must be created with the ssh command given by the ''run_vncserver'' script. Open a new terminal, start a VNC viewer and connect to localhost:n, where n is the display number printed by ''run_vncserver'', using a command such like this <pre>$ vncviewer localhost:1</pre>

* '''Login without TightVNC Java Viewer for Windows users''' Needed Software: [http://sourceforge.net/projects/tigervnc/files/tigervnc/1.3.0 tigervnc], [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html Putty] You need to start Putty and go to Connection -> SSH -> Tunnels. Choose "IPv4" and fill in the parameters provided by ''run_vncserver''. After you clicked "Add" you must navigate to Session and connect to the bwUniCluster with your username and password. Once the connection is established start the tigervnc client and connect to localhost:n where n is the display number printed by ''run_vncserver''.

== Shutdown ==
If you want to exit your VNC session don't just close the window because then the VNC server won't terminate and you will run into problems
when you try to start a new VNC session later. If you log out of Gnome properly the VNC server will terminate automatically.
[[Category:visualization]][[Category:bwUniCluster]]

BwUniCluster2.0/Software/Mathematica

2014-07-08T08:07:46Z

M Neuer:

2014-03-05T12:36:07Z

M Neuer:

= TigerVNC =
{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | TigerVNC
|-
| module load
| vis/tigervnc
|-
| License
| GPL
|-
| Links
| [http://www.tigervnc.org TigerVNC Homepage]
|
|-
| Graphical Interface
| No
|}
'''TigerVNC''' is a high-performance implementation of VNC (Virtual Network Computing), a client/server application that allows
users to launch and interact with graphical applications on remote machines. It should be faster than standard X11 forwarding and thus can
be used if a graphical software feels slow and has bad responsiveness.

== Instructions ==

First, you need to start the VNC server on the bwunicluster. Therefore you must log into the bwunicluster with your username and password as usual.
You should not start the server on a login node but request an interactive job using for example the following command.
$ msub -v HOME,TERM,USER,DISPLAY -S /bin/bash -I -l nodes=1:ppn=1 -l walltime=0:02:00:00
On your assigned compute node start the VNC server with
$ module load vis/tigervnc
$ run_vncserver
The script prints detailed instructions on how to establish the connection to the VNC server with your computer. They depend on whether you
use Windows or Linux and if you work with ssvnc which is a tool that can simplify the process a little bit. Therefore the next steps are
divided into 3 cases. Each command should be issued on the local computer.

* '''Login with ssvnc''' Needed Software: [http://www.karlrunge.com/x11vnc/ssvnc.html ssvnc] Open ssvnc and fill in the parameters provided by the run_vncserver script. Check "Use SSH" and click on the "Connect" button.

* '''Login without ssvnc for Linux users''' Needed Software: A VNC viewer such as tigervnc, gvncviewer or tightvnc A tunnel must be created with the command given by the run_vncserver script. Open a new terminal, start a VNC viewer and connect to localhost:1 using a command such like this <pre>$ vncviewer localhost:1</pre>

* '''Login without ssvnc for Windows users''' Needed Software: [http://sourceforge.net/projects/tigervnc/files/tigervnc/1.3.0 tigervnc], [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html Putty] You need to start Putty and add a tunnel in Connection -> SSH -> Tunnels with the parameters provided by run_vncserver. Now you can start tigervnc and connect to localhost:1

== Shutdown ==
If you want to exit your VNC session don't just close the window because then the VNC server won't terminate and you will run into problems
when you try to start a new VNC session later. If you log out of Gnome properly the VNC server will terminate automatically.

JUSTUS2/Visualization

2014-03-05T12:33:04Z

M Neuer:

{|{{Softwarebox}}
|-
! colspan="2" style="text-align:center" | TigerVNC
|-
| module load
| vis/tigervnc
|-
| License
| GPL
|-
| Links
| [http://www.tigervnc.org TigerVNC Homepage]
|
|-
| Graphical Interface
| No
|}
= TigerVNC =

'''TigerVNC''' is a high-performance implementation of VNC (Virtual Network Computing), a client/server application that allows
users to launch and interact with graphical applications on remote machines. It should be faster than standard X11 forwarding and thus can
be used if a graphical software feels slow and has bad responsiveness.

== Instructions ==

First, you need to start the VNC server on the bwunicluster. Therefore you must log into the bwunicluster with your username and password as usual.
You should not start the server on a login node but request an interactive job using for example the following command.
$ msub -v HOME,TERM,USER,DISPLAY -S /bin/bash -I -l nodes=1:ppn=1 -l walltime=0:02:00:00
On your assigned compute node start the VNC server with
$ module load vis/tigervnc
$ run_vncserver
The script prints detailed instructions on how to establish the connection to the VNC server with your computer. They depend on whether you
use Windows or Linux and if you work with ssvnc which is a tool that can simplify the process a little bit. Therefore the next steps are
divided into 3 cases. Each command should be issued on the local computer.

* '''Login with ssvnc''' Needed Software: [http://www.karlrunge.com/x11vnc/ssvnc.html ssvnc] Open ssvnc and fill in the parameters provided by the run_vncserver script. Check "Use SSH" and click on the "Connect" button.

* '''Login without ssvnc for Linux users''' Needed Software: A VNC viewer such as tigervnc, gvncviewer or tightvnc A tunnel must be created with the command given by the run_vncserver script. Open a new terminal, start a VNC viewer and connect to localhost:1 using a command such like this <pre>$ vncviewer localhost:1</pre>

* '''Login without ssvnc for Windows users''' Needed Software: [http://sourceforge.net/projects/tigervnc/files/tigervnc/1.3.0 tigervnc], [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html Putty] You need to start Putty and add a tunnel in Connection -> SSH -> Tunnels with the parameters provided by run_vncserver. Now you can start tigervnc and connect to localhost:1

== Shutdown ==
If you want to exit your VNC session don't just close the window because then the VNC server won't terminate and you will run into problems
when you try to start a new VNC session later. If you log out of Gnome properly the VNC server will terminate automatically.