VMD-L Mailing List

From: Chris Taylor (cht_at_imipolex-g.com)
Date: Wed May 04 2022 - 22:46:28 CDT

> On May 4, 2022 1:11 PM John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> Chris,
> Can you show me your VMD startup messages? It should help clarify
> if your binary was properly compiled and how MPI startup proceeded.

Thank you- I hope this isn't too hard to read. I have this sbatch script:

$ cat vmd-text.sbatch
#!/bin/bash

#SBATCH --nodes=3
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4

module load ffmpeg
module load ospray
module load mpich
module load vmd-mpi

srun vmd -dispdev text -e noderank-parallel-render.tcl

When I run it:

$ cat slurm-101.out
Info) VMD for LINUXAMD64, version 1.9.4a55 (April 12, 2022)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_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) VMD for LINUXAMD64, version 1.9.4a55 (April 12, 2022)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_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) Initializing parallel VMD instances via MPI...
Info) Found 1 VMD MPI node containing a total of 4 CPUs and 0 GPUs:
Info) 0: 4 CPUs, 15.0GB (96%) free mem, 0 GPUs, Name: node001
Info) VMD for LINUXAMD64, version 1.9.4a55 (April 12, 2022)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_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) Initializing parallel VMD instances via MPI...
Info) Found 1 VMD MPI node containing a total of 4 CPUs and 0 GPUs:
Info) 0: 4 CPUs, 15.0GB (96%) free mem, 0 GPUs, Name: node002
Info) Initializing parallel VMD instances via MPI...
Info) Found 1 VMD MPI node containing a total of 4 CPUs and 0 GPUs:
Info) 0: 4 CPUs, 15.0GB (96%) free mem, 0 GPUs, Name: node003
0
0
1
Starting, nodecount is 1
1
Starting, nodecount is 1
node 0 is running ...
node 0 is running ...
0
1
Starting, nodecount is 1
node 0 is running ...
Info) Using plugin pdb for structure file 5ire_merged.pdb
Info) Using plugin pdb for structure file 5ire_merged.pdb
Info) Using plugin pdb for structure file 5ire_merged.pdb
Info) Using plugin pdb for coordinates from file 5ire_merged.pdb
Info) Using plugin pdb for coordinates from file 5ire_merged.pdb
Info) Using plugin pdb for coordinates from file 5ire_merged.pdb
Info) Determining bond structure from distance search ...
Info) Determining bond structure from distance search ...
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file 5ire_merged.pdb.
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) Finished with coordinate file 5ire_merged.pdb.
Info) Analyzing structure ...
Info) Atoms: 1578060
Info) Finished with coordinate file 5ire_merged.pdb.
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) Bonds: 1690676
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Segments: 540
Info) Fragments: 720 Protein: 360 Nucleic: 0
Info) Residues: 104040
Info) Waters: 0
Info) Residues: 104040
Info) Waters: 0
Info) Segments: 540
Info) Segments: 540
Info) Fragments: 720 Protein: 360 Nucleic: 0
Info) Fragments: 720 Protein: 360 Nucleic: 0
0
node 0 has loaded data
Info) Rendering current scene to 'test_node_0.ppm' ...
0
node 0 has loaded data
0
node 0 has loaded data
Info) Rendering current scene to 'test_node_0.ppm' ...
Info) Rendering current scene to 'test_node_0.ppm' ...
OSPRayDisplayDevice) Total rendering time: 1.01 sec
Info) Rendering complete.
node 0 has rendered a frame
1
Ending, nodecount is 1
OSPRayDisplayDevice) Total rendering time: 1.01 sec
Info) Rendering complete.
node 0 has rendered a frame
1
Ending, nodecount is 1
OSPRayDisplayDevice) Total rendering time: 1.02 sec
Info) Rendering complete.
node 0 has rendered a frame
1
Ending, nodecount is 1
Info) VMD for LINUXAMD64, version 1.9.4a55 (April 12, 2022)
Info) Exiting normally.
Info) All nodes have reached the MPI shutdown barrier.
Info) VMD for LINUXAMD64, version 1.9.4a55 (April 12, 2022)
Info) Exiting normally.
Info) VMD for LINUXAMD64, version 1.9.4a55 (April 12, 2022)
Info) Exiting normally.
Info) All nodes have reached the MPI shutdown barrier.
Info) All nodes have reached the MPI shutdown barrier.

Also I have tried:

$ sbatch --export=VMDOSPRAYMPI vmd-text.sbatch

And I get:

$ cat slurm-102.out
srun: error: node001: task 0: Exited with exit code 2
srun: error: node003: task 2: Exited with exit code 2
srun: error: node002: task 1: Exited with exit code 2
slurmstepd: error: execve(): vmd: No such file or directory
slurmstepd: error: execve(): vmd: No such file or directory
slurmstepd: error: execve(): vmd: No such file or directory

If look at the executable I see (highlights follow):

[cht_at_node001 VMD]$ ldd /cm/shared/apps/vmd-mpi/1.9.4/vmd/vmd_LINUXAMD64
        linux-vdso.so.1 (0x0000155555551000)
        libGL.so.1 => /lib64/libGL.so.1 (0x00001555550a1000)
        libGLU.so.1 => /lib64/libGLU.so.1 (0x00001555554cd000)
        libfltk_gl.so.1.3 => /lib64/libfltk_gl.so.1.3 (0x0000155554e83000)
        libmpi.so.12 => /cm/shared/apps/mpich/ge/gcc/64/3.3.2/lib/libmpi.so.12 (0x0000155554937000)
        libospray.so.0 => /cm/shared/apps/ospray/1.8.0/lib/libospray.so.0 (0x0000155555459000)
        libospray_common.so.0 => /cm/shared/apps/ospray/1.8.0/lib/libospray_common.so.0 (0x00001555553f7000)
        libembree3.so.3 => /cm/shared/apps/ospray/1.8.0/lib/libembree3.so.3 (0x00001555520a5000)
        libtbb.so.2 => /cm/shared/apps/ospray/1.8.0/lib/libtbb.so.2 (0x0000155551e47000)
        libtbbmalloc.so.2 => /cm/shared/apps/ospray/1.8.0/lib/libtbbmalloc.so.2 (0x0000155551bf0000)
..
..
etc etc