From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Aug 15 2014 - 00:39:36 CDT
Isn’t the right option +ppn?
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Maxime Boissonneault
Gesendet: Donnerstag, 14. August 2014 18:53
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: AW: AW: namd-l: Hybrid MPI + Multicore + Cuda build
I built charm with :
./build charm++ mpi-linux-x86_64 smp --with-production -j20
I then built namd with :
./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64-smp \
--with-fftw3 --fftw-prefix $(dirname $(dirname $(which fftw-wisdom)))
\
--with-cuda --cuda-prefix $(dirname $(dirname $(which nvcc)))
Yet, when I run mpiexec namd +p2 it tells me
mpiexec -np 8 --bind-to-socket --npernode 8 --npersocket 4 --report-bindings
namd2 +p2 +idlepoll apoa1.namd
Reason: FATAL ERROR: Unknown command-line option +p2
However, I see that without specifying +p2, it still uses more than 1 CPU
per MPI rank.
Shouldn't the +p option work with MPI + SMP ?
Maxime
Le 2014-08-14 09:14, Norman Geist a écrit :
Looks like, ./build is interactive if you start it without arguments.
Norman Geist.
-----Ursprüngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
Auftrag von Maxime Boissonneault
Gesendet: Donnerstag, 14. August 2014 14:20
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: AW: namd-l: Hybrid MPI + Multicore + Cuda build
Hi,
That should not be a problem, since if a job uses more than one node,
we
expect it will use the nodes to their full extent. In other words, I
don't see a use case where you would want to use two half nodes instead
of one full node.
I've been given the pointer that building charm++ with
./build charm++ mpi-linux-x86_64 smp ....
should do the trick. Is that correct ?
Maxime
Le 2014-08-14 03:13, Norman Geist a écrit :
Yes its possible, but the keyword isn't "multicore" which always
indicate a
single node build, but "SMP". So you need to build your charm++ with
network+smp support ;)
BUT, unfortunately namd threats the +devices list for each node.
Therefore
it's not possible to assign different gpus on different nodes for the
same
job. I hacked the code to allow the +devices list to be accessed by
the
process's global rank, rather than the local rank on the node. So
it's
possible to assign a individual GPU for every process, which wouldn't
also
require a smp build. I can send you the changes I made.
Norman Geist.
-----Ursprüngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
Auftrag von Maxime Boissonneault
Gesendet: Mittwoch, 13. August 2014 18:47
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Hybrid MPI + Multicore + Cuda build
Hi,
I am managing a GPU cluster. The configuration of the nodes is :
- 8 x K20 per node
- 2 x 10-core sockets per node.
The GPUs are run in exclusive process mode to prevent one user to
hijack
the GPU allocated to another user.
I would like to be able to run Namd with Cuda, with 1 MPI rank per
GPU
and 2 or 3 threads.
Is it possible to build namd with such hybrid support ? All I see on
the
website and documentation is either multicore or mpi, but never
both.
Thanks,
-- --------------------------------- Maxime Boissonneault Analyste de calcul - Calcul Québec, Université Laval Ph. D. en physique --- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com -- --------------------------------- Maxime Boissonneault Analyste de calcul - Calcul Québec, Université Laval Ph. D. en physique --- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com -- --------------------------------- Maxime Boissonneault Analyste de calcul - Calcul Québec, Université Laval Ph. D. en physique --- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:43 CST