Poudlard

Bonjour,

J'ai un petit souci avec l'utilisation des cartes graphique lors des sessions openondemand sur poudlard.
En utilisant le logiciel de visualisation vmd sur curta, avec un job openondemand, les cartes sont reconnues comme accélérateur cuda et le rendu graphique passe par la carte graphique.

sur CURTA¶

[paurel@visu01 ~]$ vglrun vmd ~/ADN.pdb
/gpfs/softs/contrib/apps/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no version information available (required by /gpfs/softs/contrib/apps/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/                         
Info) Email questions and bug reports to vmd@ks.uiuc.edu           
Info) Please include this reference in published work using VMD:   
Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   
Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 32 CPUs detected.
Info)   CPU features: SSE2 AVX AVX2 FMA KNL:AVX-512F+CD+ER+PF 
Info) Free system memory: 170GB (90%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 2 available CUDA accelerators:
Info) [0] Quadro P4000       14 SM_6.1 @ 1.48 GHz, 7.9GB RAM, KTO, AE2, ZCP
Info) [1] Quadro P4000       14 SM_6.1 @ 1.48 GHz, 7.9GB RAM, KTO, AE2, ZCP
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option.  Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: Quadro P4000/PCIe/SSE2
Info)   Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS) 
Info)   Full GLSL rendering mode is available.
Info)   Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture (4)
Info) Detected 2 available TachyonL/OptiX ray tracing accelerators
Info)   Compiling 1 OptiX shaders on 2 target GPUs...
Info) Dynamically loaded 2 plugins in directory:
Info) /gpfs/softs/contrib/apps/vmd/1.9.3/lib/vmd/plugins/LINUXAMD64/molfile
Info) File loading in progress, please wait.
Info) Using plugin pdb for structure file /gpfs/home/paurel/ADN.pdb
Info) Using plugin pdb for coordinates from file /gpfs/home/paurel/ADN.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file /gpfs/home/paurel/ADN.pdb.
Info) Analyzing structure ...
Info)    Atoms: 779
Info)    Bonds: 872
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
Info)    Residues: 38
Info)    Waters: 0
Info)    Segments: 1
Info)    Fragments: 2   Protein: 0   Nucleic: 2
vmd > 

avec nvidia-smi mon appli apparaît bien en C+G sur une carte et C uniquement sur l'autre

[paurel@visu01 ~]$ nvidia-smi
Fri Nov 14 13:34:48 2025       
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 550.67                 Driver Version: 550.67         CUDA Version: 12.4     |
|-----------------------------------------+------------------------+----------------------+
| GPU  Name                 Persistence-M | Bus-Id          Disp.A | Volatile Uncorr. ECC |
| Fan  Temp   Perf          Pwr:Usage/Cap |           Memory-Usage | GPU-Util  Compute M. |
|                                         |                        |               MIG M. |
|=========================================+========================+======================|
|   0  Quadro P4000                   Off |   00000000:2F:00.0 Off |                  N/A |
| 46%   36C    P0             28W /  105W |     157MiB /   8192MiB |      0%      Default |
|                                         |                        |                  N/A |
+-----------------------------------------+------------------------+----------------------+
|   1  Quadro P4000                   Off |   00000000:86:00.0 Off |                  N/A |
| 46%   28C    P0             27W /  105W |     114MiB /   8192MiB |      0%      Default |
|                                         |                        |                  N/A |
+-----------------------------------------+------------------------+----------------------+
                                                                                         
+-----------------------------------------------------------------------------------------+
| Processes:                                                                              |
|  GPU   GI   CI        PID   Type   Process name                              GPU Memory |
|        ID   ID                                                               Usage      |
|=========================================================================================|
|    0   N/A  N/A      2789      G   /usr/libexec/Xorg                              47MiB |
|    0   N/A  N/A      5738      G   /usr/bin/gnome-shell                            2MiB |
|    0   N/A  N/A   2055005    C+G   ...ps/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64        102MiB |
|    1   N/A  N/A      2789      G   /usr/libexec/Xorg                               8MiB |
|    1   N/A  N/A   2055005      C   ...ps/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64        100MiB |
+-----------------------------------------------------------------------------------------+

sur POUDLARD¶

[paurel@gpu02 ~]$ vglrun vmd ~/molecules/pdb/ADN.pdb 
/nfs/softs/contrib/apps/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no version information available (required by /nfs/softs/contrib/apps/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/                         
Info) Email questions and bug reports to vmd@ks.uiuc.edu           
Info) Please include this reference in published work using VMD:   
Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   
Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info)   CPU features: SSE2 AVX 
Info) Free system memory: 60GB (96%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option.  Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
XRequest.152: BadValue (integer parameter out of range for operation) 0x0
ERROR) Could not create OpenGL rendering context-> Exiting...
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) Unable to create OpenGL window.

si je décide de passer par le llvmpipe pour la partie graphique

[paurel@gpu02 ~]$ vmd ~/molecules/pdb/ADN.pdb 
/nfs/softs/contrib/apps/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no version information available (required by /nfs/softs/contrib/apps/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/                         
Info) Email questions and bug reports to vmd@ks.uiuc.edu           
Info) Please include this reference in published work using VMD:   
Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   
Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info)   CPU features: SSE2 AVX 
Info) Free system memory: 60GB (96%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option.  Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: llvmpipe (LLVM 17.0.6, 256 bits)
Info)   Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS) 
Info)   Full GLSL rendering mode is available.
Info)   Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /nfs/softs/contrib/apps/vmd/1.9.3/lib/vmd/plugins/LINUXAMD64/molfile
Info) File loading in progress, please wait.
Info) Using plugin pdb for structure file /nfs/home/paurel/molecules/pdb/ADN.pdb
Info) Using plugin pdb for coordinates from file /nfs/home/paurel/molecules/pdb/ADN.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file /nfs/home/paurel/molecules/pdb/ADN.pdb.
Info) Analyzing structure ...
Info)    Atoms: 779
Info)    Bonds: 872
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
Info)    Residues: 38
Info)    Waters: 0
Info)    Segments: 1
Info)    Fragments: 2   Protein: 0   Nucleic: 2
vmd > 

J'ai l'affichage mais pas le compute.
Un nvidia-smi me dit "No devices were found"

Il me semble que la limitation d'utilisation des cartes graphiques en compute et graphique sur poudlard vient des droits sur les fichiers de périphérique.
Sur curta les droits sur les cartes sont :

paurel@visu01 ~]$ ls -l /dev/dri/
total 0
drwxr-xr-x  2 root root      140 Jun 13 09:00 by-path
crw-rw-rw-+ 1 root root 226,   0 Jun 13 09:00 card0
crw-rw-rw-+ 1 root root 226,   1 Jun 13 09:00 card1
crw-rw-rw-+ 1 root root 226,   2 Jun 13 09:00 card2
crw-rw-rw-  1 root root 226, 128 Jun 13 09:00 renderD128
crw-rw-rw-  1 root root 226, 129 Jun 13 09:00 renderD129

finalement tout le monde à l'air d'avoir le droit

Sur poudlard

[paurel@gpu02 ~]$ ls -l /dev/dri
total 0
drwxr-xr-x  2 root root        100 12 août  23:59 by-path
crw-rw----+ 1 root video  226,   0 12 août  23:59 card0
crw-rw----+ 1 root video  226,   1 12 août  23:59 card1
crw-rw-rw-  1 root render 226, 128 12 août  23:59 renderD128

est-il possible de faire parti du group video et render sur poudlard, ou créer un groupe vglusers des fois que l'on veuille que certaine personnes n'aient pas accès aux cartes.