CRwiki

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local storage

All computing nodes use central NFS shared directores ( /home, /workspace ). When running computation which require frequent storage access it maybe beneficial first to copy your input data to local disk on node ( to i.e /tmp ) and running computation on local files. Bellow few comparation :
mp5 compare

In this test each node was occupied only by one job. Times bellow are only computation time ( time to copy file to local storage is not included). As shown bellow using local storage is not beneficial.
node name 	cores 	NFS storage 	local storage (/tmp) 	diff as (avg1-avg2)/avg1
result1 [s] 	result2 [s] 	result3 [s] 	avg1 [s] 	result1 [s] 	result2 [s] 	result3 [s] 	avg2 [s]
ant002 	1 	1673.58 	1716.28 	1711.93 	1700.60 	1687.68 	1719.62 	1717.18 	1708.16 	-0.44%
ant003 	1 	1848.30 	1848.91 	1827.97 	1841.73 	1830.78 	1852.40 	1855.98 	1846.39 	-0.25%
ant004 	1 	1846.87 	1838.31 	1842.67 	1842.62 	1853.66 	1856.75 	1839.10 	1849.84 	-0.39%
ant005 	1 	1485.39 	1459.13 	1473.07 	1472.53 	1464.80 	1527.85 	1483.56 	1492.07 	-1.33%
ant006 	1 	1455.87 	1451.47 	1463.92 	1457.09 	1486.53 	1498.34 	1482.28 	1489.05 	-2.19%
ant007 	1 	743.93 	735.69 	745.45 	741.69 	740.62 	738.93 	737.61 	739.05 	0.36%
ant008 	1 	731.84 	731.60 	733.38 	732.27 	730.60 	731.14 	731.11 	730.95 	0.18%
ant009 	1 	803.87 	804.79 	805.43 	804.70 	810.02 	809.43 	806.13 	808.53 	-0.48%
ant011 	1 	610.29 	613.10 	611.29 	611.56 	611.03 	611.57 	612.51 	611.70 	-0.02%
ant012 	1 	601.49 	601.05 	599.79 	600.78 	600.63 	599.77 	600.92 	600.44 	0.06%
cdhit compare

In this test each node was occupied only by one job. Times bellow are only computation time ( time to copy file to local storage is not included). File : uniprot_sprot.fasta . Memory allocated for each job : 2048 MB.
node name 	cores 	NFS storage 	local storage (/tmp) 	diff as (avg1-avg2)/avg1
result1 [s] 	result2 [s] 	result3 [s] 	avg1 [s] 	result1 [s] 	result2 [s] 	result3 [s] 	avg2 [s]
ant001 	1 	365.94 	371.68 	367.26 	368.29 	- 	- 	- 	- 	-
ant001 	2 	244.42 	240.67 	242.41 	242.50 	- 	- 	- 	- 	-
ant002 	1 	409.78 	369.57 	368.46 	382.60 	396.02 	386.15 	392.98 	391.72 	-2.38%
ant002 	2 	243.23 	238.74 	244.39 	242.12 	248.04 	243.36 	245.42 	245.61 	-1.44%
ant003 	1 	360.88 	361.21 	365.22 	362.44 	367.28 	404.73 	395.84 	389.28 	-7.41%
ant003 	2 	245.87 	251.52 	245.33 	247.57 	244.08 	254.47 	252.73 	250.43 	-1.15%
ant003 	4 	202.77 	205.50 	203.77 	204.01 	199.02 	203.76 	202.36 	201.71 	1.13%
ant004 	1 	357.43 	364.11 	372.73 	364.76 	390.87 	379.48 	391.56 	387.30 	-6.18%
ant004 	2 	239.34 	239.92 	236.58 	238.61 	245.38 	243.99 	236.85 	242.07 	-1.45%
ant004 	4 	189.77 	194.00 	194.24 	192.67 	190.79 	194.33 	188.09 	191.07 	0.83%
ant005 	1 	334.39 	331.71 	318.99 	328.36 	317.27 	318.02 	317.50 	317.60 	3.28%
ant005 	2 	238.52 	234.26 	239.69 	237.49 	238.53 	237.55 	234.73 	236.94 	0.23%
ant005 	4 	196.94 	199.28 	198.59 	198.27 	190.92 	195.83 	194.65 	193.80 	2.25%
ant005 	8 	175.24 	178.24 	173.24 	175.57 	152.13 	176.71 	154.17 	161.00 	8.30%
ant006 	1 	318.60 	330.38 	330.18 	326.39 	331.14 	331.60 	318.12 	326.95 	-0.17%
ant006 	2 	239.27 	238.46 	240.01 	239.25 	231.82 	238.91 	240.22 	236.98 	0.95%
ant006 	4 	192.16 	191.58 	196.91 	193.55 	198.30 	194.13 	198.21 	196.88 	-1.72%
ant006 	8 	156.69 	176.7 	178.24 	170.54 	179.06 	175.82 	169.99 	174.96 	-2.59%
ant007 	1 	149.80 	140.85 	147.45 	146.03 	138.59 	148.81 	143.30 	143.57 	1.69%
ant007 	2 	114.65 	112.76 	118.23 	115.21 	115.10 	115.38 	117.53 	116.00 	-0.69%
ant007 	4 	98.15 	96.56 	98.67 	97.79 	92.23 	95.88 	93.78 	93.96 	3.91%
ant007 	8 	90.63 	89.64 	88.38 	89.55 	80.74 	80.45 	90.72 	83.97 	6.23%
ant007 	14 	85.28 	87.12 	83.37 	85.26 	75.94 	87.64 	86.04 	83.21 	2.41%
ant007 	16 	82.46 	86.69 	86.67 	85.27 	86.34 	82.84 	76.55 	81.91 	3.94%
ant007 	28 	75.35 	87.45 	85.33 	82.71 	83.88 	81.89 	88.64 	84.80 	-2.53%
ant008 	1 	140.42 	147.09 	142.25 	143.25 	145.01 	140.70 	140.92 	142.21 	0.73%
ant008 	2 	113.35 	116.83 	118.27 	116.15 	117.19 	117.35 	113.49 	116.01 	0.12%
ant008 	4 	99.10 	91.73 	90.12 	93.65 	97.40 	96.11 	95.96 	96.49 	-3.03%
ant008 	8 	88.89 	80.20 	89.31 	86.13 	87.13 	88.33 	88.83 	88.10 	-2.28%
ant008 	14 	76.03 	85.79 	86.91 	82.91 	85.26 	73.94 	84.47 	81.22 	2.03%
ant008 	16 	86.97 	82.77 	85.11 	84.95 	73.62 	84.37 	85.96 	81.32 	4.28%
ant008 	28 	83.19 	89.83 	89.45 	87.49 	73.10 	73.12 	85.27 	77.16 	11.80%
ant009 	1 	135.40 	135.35 	140.31 	137.02 	133.06 	134.52 	134.26 	133.95 	2.24%
ant009 	2 	108.71 	111.89 	108.27 	109.62 	110.77 	108.15 	105.28 	108.07 	1.42%
ant009 	4 	85.06 	90.44 	84.27 	86.59 	90.08 	90.17 	89.77 	90.01 	-3.95%
ant009 	8 	72.98 	78.29 	77.61 	76.29 	73.05 	79.16 	78.6 	76.94 	-0.85%
ant009 	14 	71.93 	72.95 	67.78 	70.89 	73.74 	68.62 	68.87 	70.41 	0.68%
ant009 	16 	67.35 	71.71 	72.00 	70.35 	67.04 	72.01 	72.19 	70.41 	-0.09%
ant011 	1 	104.71 	105.06 	104.5 	104.76 	104.6 	104.64 	104.29 	104.51 	0.24%
ant011 	2 	89.57 	90.33 	89.65 	89.85 	89.72 	89.87 	90.10 	89.90 	-0.05%
ant011 	4 	72.20 	71.92 	72.22 	72.11 	71.84 	71.69 	71.63 	71.72 	0.54%
ant012 	1 	106.92 	106.50 	107.06 	106.83 	105.24 	106.59 	104.92 	105.58 	1.17%
ant012 	2 	93.41 	93.48 	93.27 	93.39 	94.07 	94.13 	93.18 	93.79 	-0.43%
ant012 	4 	75.24 	75.16 	75.23 	75.21 	74.82 	74.82 	74.83 	74.82 	0.51%