VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 10 2023 - 00:58:11 CDT

Hi,
  How much RAM do the GPUs you're running on actually have?
While I wouldn't expect a 1.5M-atom structure to be a big
challenge for QuickSurf, it does need some decent GPU memory,
and if you've restricted it to anything less than several gigabytes,
I would perhaps start out with no restriction at all and work back
the other direction.

If your next goal is to do some GPU ray tracing, that'll need even
more memory, so I would again recommend letting VMD use all of the
available GPU memory...

If this doesn't work out, tell me more about the hardware and I can
give you some things to try out.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Apr 09, 2023 at 08:07:14PM -0700, Chris Taylor wrote:
> Hi- I built 1.9.4a55 with OpenMPI and the NVIDIA-OptiX-SDK-5.1.1-linux64 package. I'm rendering a scene from a script on the command line and I get this error. I've tried adjusting the memory-per-GPU in my SLURM script but it doesn't seem to do anything. I tried some other materials and get the same error. My configure.options:
> ```LINUXAMD64 CUDA MPI LIBOPTIX LIBPNG ZLIB TCL PTHREADS```
> Thanks,
> Chris
>
> Info) Creating CUDA device pool and initializing hardware...
> Info) Initializing parallel VMD instances via MPI...
> Info) Found 3 VMD MPI nodes containing a total of 12 CPUs and 3 GPUs:
> Info) 0: 4 CPUs, 30.2GB (96%) free mem, 1 GPUs, Name: node001
> Info) 1: 4 CPUs, 30.2GB (96%) free mem, 1 GPUs, Name: node002
> Info) 2: 4 CPUs, 30.2GB (96%) free mem, 1 GPUs, Name: node003
> Info) Analyzing structure ...
> Info) Atoms: 1578060
> Info) Bonds: 1690676
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 104040
> Info) Waters: 0
> Info) Segments: 540
> Info) Fragments: 720 Protein: 360 Nucleic: 0
> Info) Finished with coordinate file 5ire_merged.pdb.
>
> node 0 is running ...
> node 2 is running ...
> node 1 is running ...
>
> CUDA error: an illegal memory access was encountered, CUDAQuickSurf.cu line 1453
> CUDA error: an illegal memory access was encountered, CUDAQuickSurf.cu line 1453
> CUDA error: an illegal memory access was encountered, CUDAQuickSurf.cu line 1453
> Info) Rendering current scene to 'frames/test_node_1.ppm' ...
> [node001:18899] *** Process received signal ***
> [node001:18899] Signal: Segmentation fault (11)
> [node001:18899] Signal code: Address not mapped (1)
> [node001:18899] Failing at address: 0x18
> [node001:18899] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x155551088cf0]
> [node001:18899] [ 1] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZNK7Matrix411multpoint3dEPKfPf+0x7d)[0x53214d]
> [node001:18899] [ 2] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZN13OptiXRenderer19trimesh_c4u_n3b_v3fER7Matrix4PKhPKaPKfii+0xe5)[0x4ac9a5]
> [node001:18899] [ 3] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZN18OptiXDisplayDevice19trimesh_c4u_n3b_v3fEPhPaPfi+0xe5)[0x493915]
> [node001:18899] [ 4] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZN12FileRenderer6renderEPK14VMDDisplayList+0x289c)[0x51b49c]
> [node001:18899] [ 5] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZNK11Displayable4drawEP13DisplayDevice+0x74)[0x4de534]
> [node001:18899] [ 6] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZNK11Displayable4drawEP13DisplayDevice+0x50)[0x4de510]
> [node001:18899] [ 7] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZNK11Displayable4drawEP13DisplayDevice+0x50)[0x4de510]
> [node001:18899] [ 8] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZN5Scene8filedrawEP12FileRendererPKcP13DisplayDevice+0x174)[0x5b3d94]
> [node001:18899] [ 9] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZN14FileRenderList6renderEPKcS1_S1_+0xd6)[0x514026]
> [node001:18899] [10] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZN6VMDApp17filerender_renderEPKcS1_S1_+0x29)[0x5d6919]
> [node001:18899] [11] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_Z15text_cmd_renderPvP10Tcl_InterpiPPKc+0x6f1)[0x65d011]
> [node001:18899] [12] /lib64/libtcl8.6.so(TclInvokeStringCommand+0x7b)[0x155550adba3b]
> [node001:18899] [13] /lib64/libtcl8.6.so(+0x47ff3)[0x155550ae3ff3]
> [node001:18899] [14] /lib64/libtcl8.6.so(TclNRRunCallbacks+0x4f)[0x155550ae0b1f]
> [node001:18899] [15] /lib64/libtcl8.6.so(Tcl_RecordAndEvalObj+0xfc)[0x155550b81bcc]
> [node001:18899] [16] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZN13TclTextInterp8evalFileEPKc+0xaf)[0x63984f]
> [node001:18899] [17] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_ZN6VMDApp12logfile_readEPKc+0xd)[0x5d8fed]
> [node001:18899] [18] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_Z14VMDreadStartupP6VMDApp+0x18e)[0x61757e]
> [node001:18899] [19] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(main+0xab)[0x48d31b]
> [node001:18899] [20] /lib64/libc.so.6(__libc_start_main+0xe5)[0x15554f930d85]
> [node001:18899] [21] /cm/shared/apps/vmd-openmpi-cuda/current/vmd/vmd_LINUXAMD64(_start+0x2e)[0x49311e]
> [node001:18899] *** End of error message *** 

-- 
Research Affiliate, NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           
http://www.ks.uiuc.edu/Research/vmd/