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The Join approach is always better in terms of overhead, especially as the number of map processes increases. For example, sorting D3 takes only 1.5 minutes with 128 mappers (join only), which means a speedup of 8.7 with respect to SortHDFS. It can also be observed that sorting the RDDs by key consumes extra time. In particular, the overhead means on average doubling the time required by the sorting process when only the join transformation is performed.

Table 4 summarizes the results of SparkBWA in terms of performance for all the datasets. It shows the minimum time required by SparkBWA to perform the alignment on our hardware platform, the number of mappers used, the speed measured as the number of pairs aligned per second and also the corresponding speedup with respect to the sequential execution of BWA. The sequential times are respectively 258, 496 and 5,940 minutes for D1, D2 and D3. In the particular case of D3 it means more than 4 days of computation. It is worth noting that using SparkBWA this time was reduced to less than an hour reaching speedups higher than 125.

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Next, a performance comparison among different BWA-based aligners and SparkBWA is shown. The evaluated tools are enumerated in Table 3 together with their corresponding parallelization technology. Some of them take advantage of classical parallel paradigms, as Pthreads or MPI, while the others are based on big data technologies as Hadoop. All the experiments were performed using SparkBWA in regular mode. For comparison purposes all the graphs in this subsection include the corresponding results considering ideal speedup with respect to the sequential execution of BWA.

The corresponding speedups obtained by the aligners for BWA-backtrack are displayed in Fig 10. As reference we have used the BWA sequential time. Results confirm the good behavior of SparkBWA with respect to SEAL and pBWA. For instance, SparkBWA reaches speedups up to 57 and 77 for D1 and D2 respectively. The maximum speedups achieved by SEAL are only about 31 and 42, while the corresponding values for pBWA are 46 and 59. In this way, SparkBWA is on average 1.9 and 1.4 faster than SEAL and pBWA respectively.

Performance results in terms of speedup with respect to the sequential execution of BWA are shown in Fig 12. The scalability problems of BWA are clearly revealed in the graphs. Hadoop-based tools show a better scalability but it is not enough to get closer to SparkBWA. The average speedup is respectively 50 and 49.2 for BigBWA and Halvade using 128 workers. This value increases up to 72.5 for SparkBWA. Note that the scalability of SparkBWA is especially good when considering the biggest dataset (Fig 12(c)), reaching a maximum speedup of 85.6. In other words, the parallel efficiency is 0.67.

The behavior of SparkBWA was evaluated in terms of performance, scalability and memory consumption. In addition, a thorough comparison between SparkBWA and several state of the art BWA-based aligners was performed. Those tools take advantage of different parallel approaches as Pthreads, MPI, and Hadoop to improve the performance of BWA. The evaluation shows that when considering the algorithm to align shorter reads (BWA-backtrack), SparkBWA is on average 1.9 and 1.4 faster than SEAL and pBWA. For longer reads and the BWA-MEM algorithm, the average speedup achieved by SparkBWA with respect to BigBWA and Halvade tools is 1.4.

Hmm, I tried to find an example, but besides the benchmark sites that have already been posted, I couldn't find any public descriptions of one. My experience mainly comes from people telling me about their experiences rewriting projects in Rust, and the people who get large speedups are generally rewriting something written in a language with a garbage collector.

Cons: the insurance, that I bought seems that has 100% coverage, but the car rental amigo told me, thats not true. In the conditiones was a lot of excentions! so i must buy another one insurance directly from Amigo!

The throughput of BWASpark reached its highest point at seven nodes and started decreasing. This was because the speedup brought by using more nodes was less than the overhead caused by additional nodes.

Relative speed of PipeMEM to BWASpark (GATK) and PipeMEM to SparkBWA. At every different node environment, PipeMEM maintains a higher performance compared with BWASpark and SparkBWA. PipeMEM is at least 2.2 times faster than SparkBWA and at least 1.5 times faster than BWASpark. The relative performance between PipeMEM and SparkBWA is relatively stable. The relative speedup of PipeMEM to SparkBWA is increasing as the number of nodes increases. It achieves about 2.66 speedup at the 10-node environment. On average, PipeMEM is 2.33 times faster than SparkBWA and 2.27 times faster than BWASpark.

Relative speedup of PipeMEM compared with SparkBWA (including the pre-processing and the main computation). Relative speedup of PipeMEM to SparkBWA as a whole. There is a flatter trend in this line. The relative speedup ends at about 1.2.

Yes, as my amigo Mountainbike stated, driving the vehicle in this condition is certainly not helping it to achieve a long life. If my car was revving at 4k and only able to go 50 mph, it would be on a flatbed trailer very quickly.

President Bush Welcomes President Uribe of Colombia to the White House

Oval Office

President's Remarks

view In Focus: Global Diplomacy

12:06 P.M. EDTPRESIDENT BUSH: Thank you all for coming. It's my honor to welcome backto the Oval Office mi amigo, el Presidente. Mr. President, we're gladyou're here. This is my first chance to be able to congratulate thePresident for a very strong victory. I asked him what it's like to winwith a lot of votes. He was obviously a good campaigner that had a messagethat the Colombian people appreciated.So first of all, congratulationsfor a grand victory.President Uribe is a personal friend. I'm able to talk very frankly withhim about a variety of subjects. I told him that one of the things Iadmire is he's a strong believer in democracy, human rights, human dignity. He's got a tough job in dealing with narco-terrorist groups in hiscountry, but he's committed to dealing firmly with narco-terrorism. He'scommitted to helping reconcile past differences. He's committed to helpingpeople get back into society. And I appreciate those commitments. He'scommitted to human rights.We talked about trade.We negotiated a free trade agreement. We've stillgot some details to work out, but we committed ourselves to working outthose details and try to get this done as quickly as we can. I will submitthe agreement to Congress once it gets done, and I would hope members ofboth political parties understand the importance of a free trade agreementwith this vital ally of ours.We talked about the neighborhood. We talked about -- he came from ameeting with some of the Andean neighbors and he brought messages and heshared some thoughts with me. I appreciate strategizing with the Presidentabout how to make sure our neighborhood is a peaceful and hopeful place.I told President Uribe that one of the things I will do a better job of iscommunicating to the people of South America and Central America mycountry's desire to promote justice and education and health. We spendabout $1.6 billion a year in Central and South America. I want the peopleto understand that money is meant to help them, to help improve theirlives.I want the people to understand America is a considerate country,that we care about justice.And so, Mr. President, I am really pleased you're here. It's good to seeyou again. And, again, congratulations on a great victory.PRESIDENT URIBE: Thank you, Mr. President. I want to repeat my gratitudeto your government, to you personally, to your Congress, to the U.S. publicopinion, for the permanent support of my country. I appreciate yourfriendship, your permanent advice, and we have many challenges before us.One challenge is that Colombia can overcome this long nightmare ofterrorism. I understand the mandate my fellow country citizens have givenme to work harder, and with better results, for my country to get peace,and the United States cooperation is necessary.In the last two years we have not gotten the (inaudible) result in droppingthe areas with illegal drugs. One point we have studied this morning withPresident Bush is how to speed up the eradication of drugs, because we needto show better results in this area.And of course, as President Bush has informed to you, we spoke about ourfree trade agreement, and some pending points.And we spoke about thenecessity in Colombia and to all the Central American and South Americancountries to improve social cohesion. For I thank President Bush, he'swilling to bring (inaudible) and determination to help us in education, insocial issues, because we need to conduct hand-in-hand our fight againstterrorism with our fight to create social cohesion, not only in Colombia,but in the whole region, as well.PRESIDENT BUSH: Gracias, amigo. Thank you very much.END 12:12 P.M. EDT Printer-Friendly Version Email this page to a friend IssuesBudget ManagementEducationEnergyHealth CareHomeland SecurityHurricanesImmigrationJobs & Economy Judicial NominationsMedicareMiddle EastNational SecurityPandemic FluPatriot ActRenewal in IraqSocial SecurityMore Issues e24fc04721