Author Topic: Apploication bug  (Read 6477 times)

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Offline Kons

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Apploication bug
« on: December 11, 2014, 14:36 »
I have Ubuntu 12.04 LTS.

When I start VNL, and try to open Builder, application fails. Details:
non@non:~/ex/mp$ vnl
WARNING: Application calling GLX 1.3 function "glXCreatePbuffer" when GLX 1.3 is not supported!  This is an application bug!
X Error: GLXUnsupportedPrivateRequest 162
  Extension:    148 (Uknown extension)
  Minor opcode: 16 (Unknown request)
  Resource id:  0x10007
X Error: GLXUnsupportedPrivateRequest 162
  Extension:    148 (Uknown extension)
  Minor opcode: 17 (Unknown request)
  Resource id:  0x10008
X Error: GLXUnsupportedPrivateRequest 162
  Extension:    148 (Uknown extension)
  Minor opcode: 16 (Unknown request)
  Resource id:  0x10007
X Error: GLXBadDrawable 156
  Extension:    148 (Uknown extension)
  Minor opcode: 5 (Unknown request)
  Resource id:  0x4600212
Segmentation fault (core dumped)


It happens when I open existing project. When I'm trying to create "new project", builder doesn't crash.
« Last Edit: December 11, 2014, 14:47 by Kons »

Offline Umberto Martinez

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Re: Apploication bug
« Reply #1 on: December 11, 2014, 16:19 »
Please send more details. from the main window go to Help->About VNL.
does it only happens with a specific project?


Offline Kons

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Re: Apploication bug
« Reply #2 on: December 11, 2014, 16:47 »
System information
Build: 2014.1.eefa9df
Platform: Linux
Python 2.7.2
Qt 4.8.5
PyQt 4.10.3
3D graphics - OpenGL
Vendor: Mesa project: www.mesa3d.org
GPU: Mesa GLX Indirect
Version: OpenGL 1.2 (1.5 Mesa 6.4.1)
Shading language version: Unknown

HP DL585, VNC server + VNC viewer.

It actually happens to all projects. Even when I tried to create new and just created nanoribbon: builder->add->plugin->nanoribbon. Immediatelly after "OK" VNL fails.

Offline Anders Blom

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Re: Apploication bug
« Reply #3 on: December 11, 2014, 18:30 »
Try to switch off shaders, in Preferences (in the menu) in the main VNL window, on the Graphics tab. You need to restart VNL after this.

As a general note, your graphics driver is too old/simple to support high-performance graphics in VNL. If you want proper 3D graphics the machine should use vendor drivers (from NVidia or ATI or similar) rather than Mesa. That said, VNL should work anyway, we will look into why it fails - the shaders should have been automatically turned off.

Moreover, why are you running VNL over VNC? Why not run it on your own computer, that way the graphics will probably be a lot faster (a lot!!!).

Offline Kons

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Re: Apploication bug
« Reply #4 on: December 12, 2014, 11:34 »
Try to switch off shaders, in Preferences (in the menu) in the main VNL window, on the Graphics tab. You need to restart VNL after this.
This menu point is gray and unchecked. So, I assume it is off.

As a general note, your graphics driver is too old/simple to support high-performance graphics in VNL. If you want proper 3D graphics the machine should use vendor drivers (from NVidia or ATI or similar) rather than Mesa. That said, VNL should work anyway, we will look into why it fails - the shaders should have been automatically turned off.
In 99% scientists use remote servers for calculations, don't have physical access to them, and don't need high performance graphics. I don't care about graphics at ll. Actually, I have only two options: 1) ssh connection to hpc cluster (or dedicated server), or 2) VNC on request (VNC is more convenient). In the first case, I will construct system and run it from command line using batch system. In the second case, after constructions of the system I can either run it in VNC (using 1 server with 16-80 CPUs) or submit it using batch system (unlimited CPUs).

In my case, it is either dedicated HP DL585 with 4x16 cores, or HP SL230s with 2x8 cores. I even don't know what kind of graphics they have.

Moreover, why are you running VNL over VNC? Why not run it on your own computer, that way the graphics will probably be a lot faster (a lot!!!).
I don't need nice and fast graphics. I use VNL because it is convinient tools for the construction of nanodevoces. Running VNL locally on my laptop - is not a solution for many reasons.

Actually, I have more questions:
1. How many CPUs VNL can use effectively? When it was running on DL585 with 64 cores it was using 1, 10 or 32 CPUs in different moments of time. Why not all 64?
2. When running on cluster, I can specify as many CPUs as I want. But taking into account what I noticed about CPU usage on 1 server, it seems that running on cluster will just waste of computational time. So, can VNL run effectively on cluster?

Offline Umberto Martinez

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Re: Apploication bug
« Reply #5 on: December 12, 2014, 12:03 »
Quote
In 99% scientists use remote servers for calculations, don't have physical access to them, and don't need high performance graphics. I don't care about graphics at ll. Actually, I have only two options: 1) ssh connection to hpc cluster (or dedicated server), or 2) VNC on request (VNC is more convenient). In the first case, I will construct system and run it from command line using batch system. In the second case, after constructions of the system I can either run it in VNC (using 1 server with 16-80 CPUs) or submit it using batch system (unlimited CPUs).
In my case, it is either dedicated HP DL585 with 4x16 cores, or HP SL230s with 2x8 cores. I even don't know what kind of graphics they have.

You are confusing Virtual NanoLab, the GUI, with ATK, the calculation engine (including DFT, SE, Calssical packages).
Sure you run ATK on your remote cluster for your big systems and you are absolutely right, most of these machines do not have any graphic acceleration.
However, we offer you the possibility of using VNL to create your input files (both configurations from the Builder and scripts from the Scripter) and analyze your output files with all the dedicate plugins that the graphical interface offers you.
Unless you have a very good reason to do otherwise (do you?) you should do these operations from your local machine copying the files to and from your remote cluster.

It seems you are an expert user so if you have to modify your input files it won't be a problem to do that directly from the server without going through VNL.

Also, if you do not care about graphics at all why do you run VNL?

Quote
Actually, I have more questions:
1. How many CPUs VNL can use effectively? When it was running on DL585 with 64 cores it was using 1, 10 or 32 CPUs in different moments of time. Why not all 64?
2. When running on cluster, I can specify as many CPUs as I want. But taking into account what I noticed about CPU usage on 1 server, it seems that running on cluster will just waste of computational time. So, can VNL run effectively on cluster?

yes, of course. It seems you actually run in serial.
Please have a look to the Parallel Guide here http://quantumwise.com/support/manuals

Offline Kons

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Re: Apploication bug
« Reply #6 on: December 12, 2014, 13:34 »
However, we offer you the possibility of using VNL to create your input files (both configurations from the Builder and scripts from the Scripter) and analyze your output files with all the dedicate plugins that the graphical interface offers you. Unless you have a very good reason to do otherwise (do you?) you should do these operations from your local machine copying the files to and from your remote cluster.
Cluster has a license - I don't have, and I can't use cluster's license on my PC.
It seems you are an expert user so if you have to modify your input files it won't be a problem to do that directly from the server without going through VNL.
My area of expertise is a bit different, h-bar for me is mainly 0.
Also, if you do not care about graphics at all why do you run VNL?
Quote
I use VNL because it is convinient tools for the construction of nanodevoces. I like it.
Quote
1. How many CPUs VNL can use effectively? Why not all 64?
yes, of course. It seems you actually run in serial. Please have a look to the Parallel Guide here http://quantumwise.com/support/manuals
What I saw in the guide: "MKL will detect the presence of a multi-core processor and enable OpenMP automatically. It is recommended to let the software figure out itself how many threads to use optimally." So, I asume that when I run calculations from GUI ("locally"), all available processors should be used. If not (this is what I see now), should I use
Code
mpiexec -localonly -n 64 ... 
to force usage of all 64 cores?

Offline Umberto Martinez

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Re: Apploication bug
« Reply #7 on: December 12, 2014, 14:56 »
Quote
Cluster has a license - I don't have, and I can't use cluster's license on my PC.

Yes you can. I guess a license server is running on your cluster, then you just need to configure properly the license tools on your local machine.
Please, check the installation guide and in particular the licensin section http://quantumwise.com/documents/manuals/latest/InstallationGuide/index.html/chap.licensing.html#sect1.licensing.managing

I am very sorry I bring up this only know! I assumed you were aware about that.

Quote
What I saw in the guide: "MKL will detect the presence of a multi-core processor and enable OpenMP automatically. It is recommended to let the software figure out itself how many threads to use optimally."

So, I asume that when I run calculations from GUI ("locally"), all available processors should be used.

If not (this is what I see now), should I use
mpiexec -localonly -n 64 ...
to force usage of all 64 cores?

yes. Check http://quantumwise.com/documents/tutorials/latest/ParallelGuide/index.html/chap.strategy.html
When you run from VNL you don't use any MPI parallelization but only OpenMP which will behave as you quote.
We are working on a job manager (GUI part) which will allow you to specify also the number of MPI processes (plus many more things).


We are a bit off topic here, so if you still have license or parallelization problems please open a new thread.

Offline Anders Blom

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Re: Apploication bug
« Reply #8 on: December 14, 2014, 00:22 »
To summarize the origin of this thread:

1) It seems to be a bug that VNL can't run on the cluster - we have opened a ticket and will attempt to fix it. We may call on your for more exact details on the hardware and software on the machine.

2) You should be able to run VNL on your laptop, by simply telling VNL to get the license from the cluster. This is the whole point of a floating licenses scheme, that you don't need a separate license for each machine that will run VNL or ATK. Now, there may be firewalls in the way, but because of 1) this is anyway your only option at the moment.

As for the parallel part, it's important to understand the difference between threading and MPI parallelization. ATK gives a nice performance boost over MPI using mpiexec, which can only be done from the command line. For additional questions on that it might indeed be prudent to open a separate thread.

Offline Anders Blom

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Re: Apploication bug
« Reply #9 on: December 14, 2014, 19:53 »
I only now noticed one crucial point in the "About box" report you included. You can see there that only OpenGL 1.2 is supported by the driver on the cluster. This falls short of the system requirements for VNL - you must have a driver that supports OpenGL 1.3 to run VNL. The specific driver your cluster uses is from November 2005 (http://www.mesa3d.org/) so it's time to update it...

Offline Kons

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Re: Apploication bug
« Reply #10 on: December 15, 2014, 13:31 »
I requested to update video driver, I will notify will it solve issue or not.