Genome Networking

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====== FDT Results ======

Below we list a simple experiment that transfers a  478M file from a server with hostname "net-server-2" to a client with hostname "net-server-1" over a 1Gbps link.

We assume FDT is installed on both machines in directory "~/fdt". 



Create the file and host the FDT server:
<code>
[net-test-2]# cd ~/fdt
[net-test-2]# dd if=/dev/zero of=500-file.data bs=1MB count=500
[net-test-2]# md5sum 500-file.data
[net-test-2]# ./fdtServer.sh
</code>

Use the client to copy the file from the server:
<code>
[net-test-1]# cd ~/fdt
[net-test-1]# ./fdtClient.sh -pull -c net-test-2 500-file.data -d .
[net-test-1]# md5sum 500-file.data
</code>

For this test with RTT of **0.010ms**, we have a transfer period of **16s**, or a throughput of **239Mbps**. Note that there is a BDP of 0.010ms * 1Gbps = **1.31072KB**. We had a Net In average of **450.251Mbps** and Avg: **450.251Mbps**, with Avg disk write of: **225.103Mbps**.

Using the dummynet with a RTT set to **100ms**, we have a transfer period of **20s**, or a throughput of **191.2Mbps**. Note that there is a BDP of 100ms * 1Gbps = **12.8MB**. We had a Net In average of **309.842Mbps** and Avg: **398.217Mbps**, with Avg disk write of: **265.46Mbps**.

By default FDT uses 4 parallel streams, now we will test the transfer with 8 parallel streams:
<code>
[net-test-1]# cd ~/fdt
[net-test-1]# ./fdtClient.sh -pull -c net-test-2 500-file.data -d . -P 8
[net-test-1]# md5sum 500-file.data
</code>

Using the dummynet with a RTT set to **100ms**, we have a transfer period of **19s**, or a throughput of **201.3Mbps**. Note that there is a BDP of 100ms * 1Gbps = **12.8MB**. We had a Net In average of **796.343Mbps** and Avg: **796.343Mbps**, with Avg disk write of: **398.052Mbps**.

====== felCat4.2bit 806192 bytes, Mem-mem, 100ms RTT, 0 pkt loss ======

{{http://chart.apis.google.com/chart?chxl=1:%7c4%7c6%7c8%7c10%7c12&chxr=0,0,25&chxt=y,x&chbh=a&chs=300x225&cht=bvg&chco=A2C180&chds=0,25&chd=t:21.6,17.67,17,17.34,18&chtt=FDT+mem-mem%2C+806192+bytes&.png?}}


<code>
through dummynet wan2 788mb cat (4 streams)
1.
22/04 21:28:58  Net In: 501.667 Mb/s    Avg: 501.667 Mb/s
22/04 21:29:03  Net In: 575.637 Mb/s    Avg: 538.659 Mb/s
Transfer period:   22s

2.
22/04 21:29:51  Net In: 558.462 Mb/s    Avg: 558.462 Mb/s
22/04 21:29:56  Net In: 605.479 Mb/s    Avg: 581.919 Mb/s
22/04 21:30:01  Net In: 150.615 Mb/s    Avg: 438.170 Mb/s 100.00% ( 00s )
Transfer period:   21s

3.
22/04 21:30:59  Net In: 437.020 Mb/s    Avg: 437.020 Mb/s
22/04 21:31:04  Net In: 567.302 Mb/s    Avg: 502.161 Mb/s
22/04 21:31:09  Net In: 310.019 Mb/s    Avg: 438.113 Mb/s1
Transfer period:   22s

through dummynet wan2 788mb cat (6 streams)
1.
22/04 21:42:21  Net In: 784.635 Mb/s    Avg: 784.635 Mb/s
22/04 21:42:26  Net In: 529.316 Mb/s    Avg: 656.897 Mb/s
Transfer period:   17s

2.
22/04 21:43:24  Net In: 723.623 Mb/s    Avg: 723.623 Mb/s
22/04 21:43:29  Net In: 589.816 Mb/s    Avg: 656.640 Mb/s
Transfer period:   19s

3.
22/04 21:44:10  Net In: 814.112 Mb/s    Avg: 814.112 Mb/s
22/04 21:44:15  Net In: 500.012 Mb/s    Avg: 656.949 Mb/s
Transfer period:   17s


through dummynet wan2 788mb cat (8 streams)
1.
22/04 18:41:07  Net In: 805.100 Mb/s    Avg: 805.100 Mb/s
22/04 18:41:12  Net In: 510.615 Mb/s    Avg: 657.828 Mb/s
Transfer period:   17s

2.
22/04 21:26:38  Net In: 818.788 Mb/s    Avg: 818.788 Mb/s
22/04 21:26:43  Net In: 496.035 Mb/s    Avg: 657.298 Mb/s
Transfer period:   17s

3.
22/04 21:28:04  Net In: 843.213 Mb/s    Avg: 843.213 Mb/s
22/04 21:28:09  Net In: 471.038 Mb/s    Avg: 657.004 Mb/s
Transfer period:   17s

through dummynet wan2 788mb cat (10 streams)

1.
22/04 21:46:16  Net In: 794.490 Mb/s    Avg: 794.490 Mb/s
22/04 21:46:21  Net In: 521.501 Mb/s    Avg: 657.982 Mb/s
Transfer period:   18s

2.
22/04 21:47:18  Net In: 799.751 Mb/s    Avg: 799.751 Mb/s
22/04 21:47:23  Net In: 515.986 Mb/s    Avg: 657.826 Mb/s
Transfer period:   17s

3.
22/04 21:49:16  Net In: 815.398 Mb/s    Avg: 815.398 Mb/s
22/04 21:49:21  Net In: 500.277 Mb/s    Avg: 657.790 Mb/s
Transfer period:   17s

through dummynet wan2 788mb cat (12 streams)

1.
22/04 21:39:35  Net In: 759.637 Mb/s    Avg: 759.637 Mb/s
22/04 21:39:40  Net In: 557.083 Mb/s    Avg: 658.340 Mb/s
Transfer period:   18s

2.
22/04 21:40:31  Net In: 778.779 Mb/s    Avg: 778.779 Mb/s
22/04 21:40:36  Net In: 537.939 Mb/s    Avg: 658.335 Mb/s
Transfer period:   18s

3.
22/04 21:41:19  Net In: 775.203 Mb/s    Avg: 775.203 Mb/s
22/04 21:41:24  Net In: 541.706 Mb/s    Avg: 658.354 Mb/s
Transfer period:   18s
</code>


====== Homo sapien, mem-mem, 100ms RTT 0% pkt loss ======

We used the following tcp settings:
<code>
# Static Common Parameters
net.ipv4.ip_forward = 0
net.ipv4.conf.default.rp_filter = 1
net.ipv4.conf.default.accept_source_route = 0
kernel.sysrq = 0
kernel.core_uses_pid = 1
net.ipv4.tcp_syncookies = 1
kernel.msgmnb = 65536
kernel.msgmax = 65536
kernel.shmmax = 68719476736
kernel.shmall = 4294967296

# Custom Parameters set by modSysctl
net.core.rmem_max=16777216
net.core.wmem_max=16777216
net.ipv4.tcp_rmem=4096 87380 16777216
net.ipv4.tcp_wmem=4096 87380 16777216
net.core.netdev_max_backlog=30000
net.ipv4.tcp_congestion_control=htcp
net.ipv4.tcp_window_scaling=1
</code>

4 parallel streams
<code>
INFO: Requested window size -1. Using window size: 43690
25/04 19:05:45  Net In: 638.997 Mb/s    Avg: 638.997 Mb/s
25/04 19:05:50  Net In: 919.210 Mb/s    Avg: 779.096 Mb/s
25/04 19:05:55  Net In: 901.718 Mb/s    Avg: 819.910 Mb/s
25/04 19:06:00  Net In: 848.939 Mb/s    Avg: 827.166 Mb/s 53.26% ( 17s )
25/04 19:06:05  Net In: 877.686 Mb/s    Avg: 837.269 Mb/s 67.37% ( 12s )
25/04 19:06:10  Net In: 911.560 Mb/s    Avg: 849.649 Mb/s 82.05% ( 06s )
25/04 19:06:15  Net In: 928.149 Mb/s    Avg: 860.863 Mb/s 97.00% ( 01s )
25/04 19:06:20  Net In: 184.508 Mb/s    Avg: 776.310 Mb/s 100.00% ( 00s )
Transfer period:   46s
</code>

<code>
$ fdtClient.sh -pull -c wan1 xenoMrna.fa -d . -P 4 -ss 16M &> output
INFO: Requested window size 16777216. Using window size: 16777216
25/04 19:12:30  Net In: 553.170 Mb/s    Avg: 553.170 Mb/s
25/04 19:12:35  Net In: 913.072 Mb/s    Avg: 733.157 Mb/s
25/04 19:12:40  Net In: 882.125 Mb/s    Avg: 782.761 Mb/s
25/04 19:12:45  Net In: 891.221 Mb/s    Avg: 809.874 Mb/s 52.16% ( 18s )
25/04 19:12:50  Net In: 937.617 Mb/s    Avg: 835.426 Mb/s 67.24% ( 12s )
25/04 19:12:55  Net In: 887.844 Mb/s    Avg: 844.163 Mb/s 81.51% ( 06s )
25/04 19:13:05  Net In: 250.629 Mb/s    Avg: 776.319 Mb/s 100.00% ( 00s )
Transfer period:   46s
</code>
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