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On 2/04/2012 7:13 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopx_5RE+AdrExRtuf2mTA5OKCa=MT8YjJ+esqHdEx59jPA@mail.gmail.com"
type="cite">Mark,<br>
<br>
As I've told previously I have problems with the running
simulation in multi-node mode.<br>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAALQopx_5RE+AdrExRtuf2mTA5OKCa=MT8YjJ+esqHdEx59jPA@mail.gmail.com"
type="cite"><br>
I checked logs of such simulations and fond like this<br>
<br>
Will use 10 particle-particle and 6 PME only nodes<br>
This is a guess, check the performance at the end of the log file<br>
Using 6 separate PME nodes<br>
<br>
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.</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAALQopx_5RE+AdrExRtuf2mTA5OKCa=MT8YjJ+esqHdEx59jPA@mail.gmail.com"
type="cite"> Might it be that some special options for the PME
nodes are needed in the mdp file to be defined ?<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopx_5RE+AdrExRtuf2mTA5OKCa=MT8YjJ+esqHdEx59jPA@mail.gmail.com"
type="cite">
<br>
James<br>
<br>
<div class="gmail_quote">20 марта 2012 г. 18:02 пользователь Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb">
<div class="h5">On 20/03/2012 10:35 PM, James Starlight
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Could someone tell me what tell the below error<br>
<br>
Getting Loaded...<br>
Reading file MD_100.tpr, VERSION 4.5.4 (single
precision)<br>
Loaded with Money<br>
<br>
<br>
Will use 30 particle-particle and 18 PME only nodes<br>
This is a guess, check the performance at the end of the
log file<br>
[ib02:22825] *** Process received signal ***<br>
[ib02:22825] Signal: Segmentation fault (11)<br>
[ib02:22825] Signal code: Address not mapped (1)<br>
[ib02:22825] Failing at address: 0x10<br>
[ib02:22825] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xf030)
[0x7f535903e03$<br>
[ib02:22825] [ 1] /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x7e23)
[0x7f535$<br>
[ib02:22825] [ 2] /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x8601)
[0x7f535$<br>
[ib02:22825] [ 3] /usr/lib/openmpi/lib/openmpi/mca_pml_ob1.so(+0x8bab)
[0x7f535$<br>
[ib02:22825] [ 4] /usr/lib/openmpi/lib/openmpi/mca_btl_sm.so(+0x42af)
[0x7f5353$<br>
[ib02:22825] [ 5] /usr/lib/libopen-pal.so.0(opal_progress+0x5b)
[0x7f535790506b]<br>
[ib02:22825] [ 6] /usr/lib/libmpi.so.0(+0x37755)
[0x7f5359282755]<br>
[ib02:22825] [ 7] /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so(+0x1c3a)
[0x7f$<br>
[ib02:22825] [ 8] /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so(+0x7fae)
[0x7f$<br>
[ib02:22825] [ 9] /usr/lib/libmpi.so.0(ompi_comm_split+0xbf)
[0x7f535926de8f]<br>
[ib02:22825] [10] /usr/lib/libmpi.so.0(MPI_Comm_split+0xdb)
[0x7f535929dc2b]<br>
[ib02:22825] [11] /usr/lib/libgmx_mpi_d.openmpi.so.6(gmx_setup_nodecomm+0x19b)
$<br>
[ib02:22825] [12] mdrun_mpi_d.openmpi(mdrunner+0x46a)
[0x40be7a]<br>
[ib02:22825] [13] mdrun_mpi_d.openmpi(main+0x1256)
[0x407206]<br>
[ib02:22825] [14] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)
[0x7f$<br>
[ib02:22825] [15] mdrun_mpi_d.openmpi() [0x407479]<br>
[ib02:22825] *** End of error message ***<br>
--------------------------------------------------------------------------<br>
mpiexec noticed that process rank 36 with PID 22825 on
node ib02 exited on sign$<br>
--------------------------------------------------------------------------<br>
<br>
<br>
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?<br>
</blockquote>
<br>
</div>
</div>
The trace back suggests your MPI system is not configured
correctly for your hardware.<span class="HOEnZb"><font
color="#888888"><br>
<br>
Mark</font></span>
<div class="HOEnZb">
<div class="h5"><br>
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