VMD-L Mailing List

From: Chris Taylor (cht_at_imipolex-g.com)
Date: Sun Apr 09 2023 - 22:07:14 CDT

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 ***