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#!/bin/bash
#PBS -N RayRay-ERS006494-__SAMPLE__-2013-05-24-2
#PBS -o RayRay-ERS006494-__SAMPLE__-2013-05-24-2.o
#PBS -e RayRay-ERS006494-__SAMPLE__-2013-05-24-2.e
#PBS -A nne-790-ac
#PBS -l walltime=48:00:00
#PBS -l nodes=8:ppn=8
#PBS -q default

cd $PBS_O_WORKDIR

sebhtml

INSTANCE	i-87a385f7	ami-08249861	ec2-54-235-234-68.compute-1.amazonaws.com	ip-10-58-91-103.ec2.internal	running	GoldThor	0		cc2.8xlarge	2013-02-10T00:57:30+0000	us-east-1c				monitoring-disabled	54.235.234.68	10.58.91.103			ebs	spot	sir-28e26e11			hvm	xen	474bed44-adc0-46df-95b4-48b88f6dfda2	sg-6aa44c02	default	false	
BLOCKDEVICE	/dev/sda1	vol-a31283d2	2013-02-10T00:57:33.000Z	true		
TAG	instance	i-87a385f7	Project	ray-in-cloud-cc2.8xlarge
RESERVATION	r-04506b7f	584851907886	default
INSTANCE	i-85a385f5	ami-08249861	ec2-107-22-54-169.compute-1.amazonaws.com	ip-10-58-173-137.ec2.internal	running	GoldThor	0		cc2.8xlarge	2013-02-10T00:57:30+0000	us-east-1c				monitoring-disabled	107.22.54.169	10.58.173.137			ebs	spot	sir-29bb7611			hvm	xen	6e3f6557-20b5-4dfd-9e0a-0caa9868c5b2	sg-6aa44c02	default	false	
BLOCKDEVICE	/dev/sda1	vol-aa1283db	2013-02-10T00:57:35.000Z	true		
TAG	instance	i-85a385f5	Project	ray-in-cloud-cc2.8xlarge
RESERVATION	r-fa506b81	584851907886	default
INSTANCE	i-89a385f9	ami-08249861	ec2-54-242-68

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Instances:

i-f8de5a88
i-e2e26692
i-87a385f7
i-85a385f5
i-89a385f9
i-8ba385fb
i-8da385fd
i-71a08601

sebhtml

Hi Nick Loman,

Can you run these 3 tests and tweet the average and standard deviation reported in NetworkTest on Twitter ?



# Test with no virtual network

mpiexec -n 64 Ray -test-network-only -o test-default

sebhtml

diff --git a/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp b/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp
index e9d80f6..7a42732 100644
--- a/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp
+++ b/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp
@@ -1107,7 +1107,6 @@ void GenomeNeighbourhood::resolveSymbols(ComputeCore*core){
 	m_parameters=(Parameters*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/Parameters.ray");
 	m_contigLengths=(map<PathHandle,int>*)core->getObjectFromSymbol(m_plugin,"/RayAssembler/ObjectStore/ContigLengths.ray");
 
-
 	m_virtualCommunicator=core->getVirtualCommunicator();

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Table 1: Comparison of MPI ranks with mini-ranks on the Colosse
super-computer at Laval University. 
+-------+---------------------------------------------------+
| Cores | Average round-trip latency (us)                   |
+-------+-----------------------+---------------------------+
|       | MPI ranks             | mini-ranks                |
|       | (pure MPI)            | (MPI + pthread)           |
+-------+-----------------------+---------------------------+
| 8     | 11.25 +/- 0           | 24.1429 +/- 0             |
| 16    | 35.875 +/- 6.92369    | 43.0179 +/- 8.76275       |

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# average and mode round trip latency in microseconds (10^-6 seconds) when requesting a reply for a message of 4000 bytes
# MessagePassingInterfaceRank	Name	ModeLatencyInMicroseconds	AverageLatencyInMicroseconds	NumberOfExchanges
# AverageForAllRanks: 1369.78
# StandardDeviation: 281.242
0	cp2157	71	78	1000
1	cp2147	71	2089	1000
2	cp2145	70	2101	1000
3	cp2129	64	1968	1000
4	cp2128	73	2238	1000
5	cp2127	74	2100	1000

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# average and mode round trip latency in microseconds (10^-6 seconds) when requesting a reply for a message of 4000 bytes
# MessagePassingInterfaceRank	Name	ModeLatencyInMicroseconds	AverageLatencyInMicroseconds	NumberOfExchanges
# AverageForAllRanks: 1393.85
# StandardDeviation: 275.696
0	cp2157	68	69	1000
1	cp2147	70	2195	1000
2	cp2145	67	2198	1000
3	cp2129	73	1506	1000
4	cp2128	69	2319	1000
5	cp2127	79	1407	1000

sebhtml

6 vertices, alphabetSize= 3, diameter= 2
12 vertices, alphabetSize= 3, diameter= 3
12 vertices, alphabetSize= 4, diameter= 2
20 vertices, alphabetSize= 5, diameter= 2
24 vertices, alphabetSize= 3, diameter= 4
30 vertices, alphabetSize= 6, diameter= 2
36 vertices, alphabetSize= 4, diameter= 3
42 vertices, alphabetSize= 7, diameter= 2
48 vertices, alphabetSize= 3, diameter= 5
56 vertices, alphabetSize= 8, diameter= 2

sebhtml

seb@fault ~ $ cat kautz.py 
#!/usr/bin/env python

minimumAlphabetSize=1
maximumAlphabetSize=100
minimumDiameter=2
maximumDiameter=100
minimumVertices=3
maximumVertices=10000