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Domain decomposition problem
- James Starlight
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Topic Author
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8 years 1 month ago #5445
by James Starlight
Domain decomposition problem was created by James Starlight
Hello,
I have faced with the problem of running CG simulation on cluster. In particular case I made Martini parametrization of the GPCR embedded within bilayer and successfully tested this system on my local machine with GMX 4.5 following tutorial.
Then I was tried to submit gromacs job on 64 nodes on mu local cluster using GMX 4.5 with mpiexec obtaining error
Program g_mdrun_openmpi, VERSION 4.5.7
Source code file:
/builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 64 nodes that is compatible with
the given box and a minimum cell size of 2.6255 nm
Change the number of nodes or mdrun option -rcon or your LINCS settings
Next I tried to increase size of the system putting twisely bigger bilayer
unfortunately I that sim also dint start
Program g_mdrun_openmpi, VERSION 4.5.7
Source code file:
/builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_con.c, line: 693
Fatal error:
DD cell 0 2 1 could only obtain 0 of the 1 atoms that are connected
via vsites from the neighbouring cells. This probably means your vsite
lengths are too long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells.
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
Is it possible to modify some mdp options for those runs or it will be better to switch to 5.0 GMX instead7
Thanks for help!
J.
Thanks!
I have faced with the problem of running CG simulation on cluster. In particular case I made Martini parametrization of the GPCR embedded within bilayer and successfully tested this system on my local machine with GMX 4.5 following tutorial.
Then I was tried to submit gromacs job on 64 nodes on mu local cluster using GMX 4.5 with mpiexec obtaining error
Program g_mdrun_openmpi, VERSION 4.5.7
Source code file:
/builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 64 nodes that is compatible with
the given box and a minimum cell size of 2.6255 nm
Change the number of nodes or mdrun option -rcon or your LINCS settings
Next I tried to increase size of the system putting twisely bigger bilayer
unfortunately I that sim also dint start
Program g_mdrun_openmpi, VERSION 4.5.7
Source code file:
/builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_con.c, line: 693
Fatal error:
DD cell 0 2 1 could only obtain 0 of the 1 atoms that are connected
via vsites from the neighbouring cells. This probably means your vsite
lengths are too long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells.
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
Is it possible to modify some mdp options for those runs or it will be better to switch to 5.0 GMX instead7
Thanks for help!
J.
Thanks!
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- mnmelo
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8 years 1 month ago #5451
by mnmelo
Replied by mnmelo on topic Domain decomposition problem
Hi!
One mdrun flag you probably need to set isThis will tell mdrun to communicate some more particles than the default across neighboring DD cells.
Let us know if this helps.
Manel
One mdrun flag you probably need to set is
-rdd 1.4Let us know if this helps.
Manel
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