Re: [AMBER] Amber scaling on culster

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 25 Jun 2014 10:29:56 -0300

Ross, Adrian

Many thanks for the advice. My prior experience with Amber MD was running a Mac 2 x 3.06 GHz 6-Core Intel Xeon. The performance on such machine for the same system is ~ 18ns/day. I thought that the system would scale better on the cluster. In retrospect, a rather naive assumption.

Once again thank you for the prompt and helpful response

George



On Jun 24, 2014, at 6:11 PM, Ross Walker <ross.rosswalker.co.uk> wrote:

> One further note - you can improve things a little bit by using ntt=1 or 2
> rather than 3. The langevin thermostat can hurt scaling in parallel. You
> could also try leaving some of the cores idle on the machine - sometimes
> this helps. As in request say 4 nodes but only 8 cores per node and set
> mpirun -np 32. Make sure it does indeed run only 8 mpi tasks per node.
>
> All the best
> Ross
>
>
> On 6/24/14, 1:48 PM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
>
>> That sounds normal to me - scaling over multiple nodes is mostly an
>> exercise in futility these days. Scaling to multiple cores normally
>> improves with system size - chances are your system is too small (12,000
>> atoms?) to scale to more than about 16 or 24 MPI tasks so that's probably
>> about where you will top out. Unfortunately the latencies and bandwidths
>> of 'modern' interconnects just aren't up to the job.
>>
>> Better use a single GTX-780 GPU in a single node and you should get
>> 180ns/day+ - < $2500 for a node with 2 of these:
>> http://ambermd.org/gpus/recommended_hardware.htm#diy
>>
>> All the best
>> Ross
>>
>>
>> On 6/24/14, 1:39 PM, "Roitberg,Adrian E" <roitberg.ufl.edu> wrote:
>>
>>> Hi
>>>
>>> I am not sure those numbers are indicative of a bad performance. Why do
>>> you say that ?
>>>
>>> If I look at the amber benchmarks in the amber webpage for JAC (25K
>>> atoms, roughly double yours), it seems that 45 ns/day is not bad at all
>>> for cpus.
>>>
>>>
>>> Dr. Adrian E. Roitberg
>>>
>>> Colonel Allan R. and Margaret G. Crow Term Professor.
>>> Quantum Theory Project, Department of Chemistry
>>> University of Florida
>>> roitberg.ufl.edu
>>> 352-392-6972
>>>
>>> ________________________________________
>>> From: George Tzotzos [gtzotzos.me.com]
>>> Sent: Tuesday, June 24, 2014 4:19 PM
>>> To: AMBER Mailing List
>>> Subject: [AMBER] Amber scaling on culster
>>>
>>> Hi everybody,
>>>
>>> This is a plea for help. I'm running production MD on a cluster of a
>>> relatively small system (126 residues, ~ 4,000 HOH molecules). Despite
>>> all sorts of tests using different number of nodes and processors, I
>>> never managed to get the system running faster than 45ns/day, which seems
>>> to me a rather bad performance. The problem seems to be beyond the
>>> knowledge range of our IT people, therefore, your help will be greatly
>>> appreciated.
>>>
>>>
>>> Im running Amber 12 and AmberTools 13
>>>
>>> My input script is:
>>>
>>> production Agam(3n7h)-7octenoic acid (OCT)
>>> &cntrl
>>> imin=0,irest=1,ntx=5,
>>> nstlim=10000000,dt=0.002,
>>> ntc=2,ntf=2,
>>> cut=8.0, ntb=2, ntp=1, taup=2.0,
>>> ntpr=5000, ntwx=5000,
>>> ntt=3, gamma_ln=2.0, ig=-1,
>>> temp0=300.0,
>>> /
>>>
>>> The Cluster configuration is:
>>>
>>>
>>> SGI Specs SGI ICE X
>>> OS - SUSE Linux Enterprise Server 11 SP2
>>> Kernel Version: 3.0.38-0.5
>>> 2x6-Core Intel Xeon
>>>
>>> 16 blades 12 cores each
>>>
>>> The cluster uses Xeon E5-2630 . 2.3 GHz; Infiniband FDR 70 Gbit/sec
>>>
>>>
>>>
>>> [root.service0 ~]# mpirun -host r1i0n0,r1i0n2 -np 2 /mnt/IMB-MPI1
>>> PingPong
>>> benchmarks to run PingPong
>>> #---------------------------------------------------
>>> # Intel (R) MPI Benchmark Suite V3.2.4, MPI-1 part
>>> #---------------------------------------------------
>>> # Date : Wed May 21 19:52:41 2014
>>> # Machine : x86_64
>>> # System : Linux
>>> # Release : 2.6.32-358.el6.x86_64
>>> # Version : #1 SMP Tue Jan 29 11:47:41 EST 2013
>>> # MPI Version : 2.2
>>> # MPI Thread Environment:
>>>
>>> # New default behavior from Version 3.2 on:
>>>
>>> # the number of iterations per message size is cut down # dynamically
>>> when a certain run time (per message size sample) # is expected to be
>>> exceeded. Time limit is defined by variable # "SECS_PER_SAMPLE" (=>
>>> IMB_settings.h) # or through the flag => -time
>>>
>>> ======================================================
>>> Tests resulted in the following output
>>>
>>> # Calling sequence was:
>>>
>>> # /mnt/IMB-MPI1 PingPong
>>>
>>> # Minimum message length in bytes: 0
>>> # Maximum message length in bytes: 4194304 #
>>> # MPI_Datatype : MPI_BYTE
>>> # MPI_Datatype for reductions : MPI_FLOAT
>>> # MPI_Op : MPI_SUM
>>> #
>>> #
>>>
>>> # List of Benchmarks to run:
>>>
>>> # PingPong
>>>
>>> #---------------------------------------------------
>>> # Benchmarking PingPong
>>> # #processes = 2
>>> #---------------------------------------------------
>>> #bytes #repetitions t[usec] Mbytes/sec
>>> 0 1000 0.91 0.00
>>> 1 1000 0.94 1.02
>>> 2 1000 0.96 1.98
>>> 4 1000 0.98 3.90
>>> 8 1000 0.97 7.87
>>> 16 1000 0.96 15.93
>>> 32 1000 1.09 28.07
>>> 64 1000 1.09 55.82
>>> 128 1000 1.28 95.44
>>> 256 1000 1.27 192.46
>>> 512 1000 1.44 338.48
>>> 1024 1000 1.64 595.48
>>> 2048 1000 1.97 992.49
>>> 4096 1000 3.10 1261.91
>>> 8192 1000 4.65 1681.57
>>> 16384 1000 8.56 1826.30
>>> 32768 1000 15.84 1972.98
>>> 65536 640 17.73 3525.00
>>> 131072 320 32.92 3797.43
>>> 262144 160 55.51 4504.01
>>> 524288 80 115.21 4339.80
>>> 1048576 40 256.11 3904.54
>>> 2097152 20 537.72 3719.39
>>> 4194304 10 1112.70 3594.86
>>>
>>>
>>> # All processes entering MPI_Finalize
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Received on Wed Jun 25 2014 - 07:00:03 PDT
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