VMD-L Mailing List

From: Lenz Fiedler (l.fiedler_at_hzdr.de)
Date: Mon Apr 04 2022 - 09:39:17 CDT

Dear VMD users and developers,

I am facing a problem in running VMD using MPI.

I compiled VMD from source (alongside Tachyon, which I would like to use
for rendering). I had first checked everything in serial, there it
worked. Now, after parallel compilation, I struggle to run VMD.

E.g. I am allocating 8 CPUs on a cluster node that has 24 CPUs in total.
Afterwards, I am trying to do:

mpirun -np 8 vmd

and I get this output:

Info) VMD for LINUXAMD64, version 1.9.3 (April 4, 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 8 VMD MPI nodes containing a total of 384 CPUs and 0 GPUs:
Info)    0:  48 CPUs, 324.9GB (86%) free mem, 0 GPUs, Name: gv002.cluster
Info)    1:  48 CPUs, 324.9GB (86%) free mem, 0 GPUs, Name: gv002.cluster
Info)    2:  48 CPUs, 324.9GB (86%) free mem, 0 GPUs, Name: gv002.cluster
Info)    3:  48 CPUs, 324.9GB (86%) free mem, 0 GPUs, Name: gv002.cluster
Info)    4:  48 CPUs, 324.9GB (86%) free mem, 0 GPUs, Name: gv002.cluster
Info)    5:  48 CPUs, 324.9GB (86%) free mem, 0 GPUs, Name: gv002.cluster
Info)    6:  48 CPUs, 324.9GB (86%) free mem, 0 GPUs, Name: gv002.cluster
Info)    7:  48 CPUs, 324.9GB (86%) free mem, 0 GPUs, Name: gv002.cluster
--------------------------------------------------------------------------
Open MPI has detected that this process has attempted to initialize
MPI (via MPI_INIT or MPI_INIT_THREAD) more than once.  This is
erroneous.
--------------------------------------------------------------------------
[gv002:139339] *** An error occurred in MPI_Init
[gv002:139339] *** reported by process [530644993,2]
[gv002:139339] *** on a NULL communicator
[gv002:139339] *** Unknown error
[gv002:139339] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
will now abort,
[gv002:139339] ***    and potentially your MPI job)

 From the output it seems to me that each of the 8 MPI ranks assumes it
is rank zero? At least the fact that each rank gives 48 CPUs (24*2 I
assume?) makes me believe that.

Could anyone give me a hint on what I might be doing wrong? The OpenMPI
installation I am using has been used for many other programs on this
cluster, so I would assume it is working correctly.

Kind regards,

Lenz 

-- 
Lenz Fiedler, M. Sc.
PhD Candidate | Matter under Extreme Conditions
Tel.: +49 3581 37523 55
E-Mail: l.fiedler_at_hzdr.de
https://www.casus.science
CASUS - Center for Advanced Systems Understanding
Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)
Untermarkt 20
02826 Görlitz
Vorstand: Prof. Dr. Sebastian M. Schmidt, Dr. Diana Stiller
Vereinsregister: VR 1693 beim Amtsgericht Dresden