VMD-L Mailing List

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Thu Mar 30 2023 - 02:28:18 CDT

Hi,

I am trying to get the VMD MPI rendering working.

I successfully compiled VMD with MPI (mpich) and am trying to use srun
to start the parallel render script found on the mailing list.

single node execution works resulting in

Info) Initializing parallel VMD instances via MPI...
Info) Found 1 VMD MPI node containing a total of 48 CPUs and 0 GPUs:
Info)    0:  48 CPUs, 374.3GB (99%) free mem, 0 GPUs, Name: node098
Info) No CUDA accelerator devices available.
ERROR) invalid command name "lmap"

.. (running as intended)

but using the following srun flags with 2 tasks (i.e. one per node)

srun  -v -n2  --ntasks-per-node=1 -c48 vmd194a57patched7MPI -dispdev
text -e render_movie_parallel_test.tcl

I just get the startup message twice instead of the nodes being detected
properly as shown below.

Does anyone had this case that required more arguments to be set for
srun to spawn this correctly?

srun: defined options
srun: -------------------- --------------------
srun: cpus-per-task       : 48
srun: ntasks              : 2
srun: ntasks-per-node     : 1
srun: verbose             : 1
srun: -------------------- --------------------
srun: end of defined options
srun: Waiting for nodes to boot (delay looping 3600 times @ 0.100000
secs x index)
srun: Nodes node[097-098] are ready for job
srun: jobid 443709: nodes(2):`node[097-098]', cpu counts: 48(x2)
srun: Implicitly setting --exact, because -c/--cpus-per-task given.
srun: launch/slurm: launch_p_step_launch: CpuBindType=(null type)
srun: launching StepId=443709.0 on host node097, 1 tasks: 0
srun: launching StepId=443709.0 on host node098, 1 tasks: 1
srun: route/default: init: route default plugin loaded
srun: launch/slurm: _task_start: Node node097, 1 tasks started
srun: launch/slurm: _task_start: Node node098, 1 tasks started
Info) VMD for LINUXAMD64, version 1.9.4a57 (March 10, 2023)
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 48 CPUs and 0 GPUs:
Info)    0:  48 CPUs, 374.3GB (99%) free mem, 0 GPUs, Name: node097
Info) No CUDA accelerator devices available.
ERROR) invalid command name "lmap"
Info) VMD for LINUXAMD64, version 1.9.4a57 (March 10, 2023)
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 48 CPUs and 0 GPUs:
Info)    0:  48 CPUs, 374.3GB (99%) free mem, 0 GPUs, Name: node098
Info) No CUDA accelerator devices available.
ERROR) invalid command name "lmap"
ERROR) invalid command name "lmap"
after#0

Kind regards

René 

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany