On 2/04/2012 7:13 PM, James Starlight wrote:
Mark,
As I've told previously I have problems with the running simulation in
multi-node mode.
Yup, and my bet is you can't run any other software on multiple MPI
nodes either, because your MPI system is not set up correctly, or maybe
is too old. We can't help with that, since it's nothing to do with GROMACS.
I checked logs of such simulations and fond like this
Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file
Using 6 separate PME nodes
This simulation was run on the 2 nodes ( 2*8 CPUs). And I've never
obtain the same notions about PME nodes when I've launch my systems on
the singe node.
Not surprising. Running in parallel is a lot more tricky than running in
serial, and so there's lots of software engineering that supports it.
See manual 3.15 and 3.17.5. Running at near-maximum efficiency in
parallel requires you understand some of that, but by default it will
"just run" almost all the time.
Might it be that some special options for the PME nodes are needed in
the mdp file to be defined ?
Not in the sense you mean. There are not normally any .mdp changes
necessary to support parallelism, and you get told about them when they
arise. The trace back below clearly indicates that the problem occurs as
GROMACS goes to set up the parallel communication infrastructure, which
has nothing directly to do with the .mdp contents.
Mark
James
20 ????? 2012 ?. 18:02 ???????????? Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> ???????:
On 20/03/2012 10:35 PM, James Starlight wrote:
Could someone tell me what tell the below error
Getting Loaded...
Reading file MD_100.tpr, VERSION 4.5.4 (single precision)
Loaded with Money
Will use 30 particle-particle and 18 PME only nodes
This is a guess, check the performance at the end of the log file
[ib02:22825] *** Process received signal ***
[ib02:22825] Signal: Segmentation fault (11)
[ib02:22825] Signal code: Address not mapped (1)
[ib02:22825] Failing at address: 0x10
[ib02:22825] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xf030) [0x7f535903e03$
[ib02:22825] [ 1]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x7e23) [0x7f535$
[ib02:22825] [ 2]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x8601) [0x7f535$
[ib02:22825] [ 3]
/usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x8bab) [0x7f535$
[ib02:22825] [ 4]
/usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x42af) [0x7f5353$
[ib02:22825] [ 5]
/usr/lib/libopen-pal.so.0(opal_progress+0x5b) [0x7f535790506b]
[ib02:22825] [ 6] /usr/lib/libmpi.so.0(+0x37755) [0x7f5359282755]
[ib02:22825] [ 7]
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so(+0x1c3a) [0x7f$
[ib02:22825] [ 8]
/usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so(+0x7fae) [0x7f$
[ib02:22825] [ 9] /usr/lib/libmpi.so.0(ompi_comm_split+0xbf)
[0x7f535926de8f]
[ib02:22825] [10] /usr/lib/libmpi.so.0(MPI_Comm_split+0xdb)
[0x7f535929dc2b]
[ib02:22825] [11]
/usr/lib/libgmx_mpi_d.openmpi.so.6(gmx_setup_nodecomm+0x19b) $
[ib02:22825] [12] mdrun_mpi_d.openmpi(mdrunner+0x46a) [0x40be7a]
[ib02:22825] [13] mdrun_mpi_d.openmpi(main+0x1256) [0x407206]
[ib02:22825] [14]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [0x7f$
[ib02:22825] [15] mdrun_mpi_d.openmpi() [0x407479]
[ib02:22825] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 36 with PID 22825 on node
ib02 exited on sign$
--------------------------------------------------------------------------
I've obtained it when I've tried to use my system on
multi-node station ( there is no problem on single node). Does
this problem with the cluster system or something wrong with
parameters of my simulation?
The trace back suggests your MPI system is not configured
correctly for your hardware.
Mark
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