1 Background

GDx at OUSAMG is planning to upscale the WGS production to 4 x 48 samples or 2 x 48 + 1 x 96 samples per week. Do we have enough capacity in IT and bioinformatics pipelines for this upscaling?

The capacity of IT & bioinformatics pipelines can be evaluated from following three aspects:

Data transfer speed
Data storage
Pipeline capacity

2 Data transfer speed

Both sequencing data and NSC pipeline results are stored at the NSC. So the volume of data that needs to be transferred from NSC to TSD is huge. The data transfer is done by the nsc-exporter. The nsc-exporter uses TSD s3api which in turn uses s3cmd under the hood. The nsc-exporter will check for new data to transfer every 10 minutes and uses s3cmd put to transfer the data.

flowchart LR
    subgraph dt[nsc-exporter]
    check-new-data(((New data?))) --> |Yes| transfer(Transfer to TSD) 
    transfer --> sleep(Sleep 10 minutes)
    sleep --> check-new-data
    check-new-data --> |No| sleep
    end
    subgraph dp[data producer]
    lims-exporter[lims-exporter]  ---> |produce| check-new-data
    pipeline[NSC pipeline] ---> |produce| check-new-data
    end
    style dt fill:#e4eda6,stroke-width:3px
    style dp fill:#aab0a2

2.1 Data Collection

To evaluate the data transfer speed from NSC to TSD, we collected the historical data transfer records between 2023-09-01 08:41:40 and 2023-11-30 20:14:10 from the nsc-exporter log.

expand to see some examples of collected transfer records

         [,1]                                     
datetime "2023-10-28 13:57:15"                    
project  "wgs324"                                 
filename "Diag-wgs324-HG13227027-DR.alignedMT.bam"
bytes    "43159658"                               
seconds  "0.6"                                    
speed    "65780000"                               
         [,1]                                                
datetime "2023-11-27 07:38:38"                               
project  "wgs336"                                            
filename "HG01766173-FremSegment-KIT-wgs_S16_R2_001.fastq.gz"
bytes    "36961964841"                                       
seconds  "402.9"                                             
speed    "87490000"                                          
         [,1]                               
datetime "2023-09-01 22:57:48"              
project  "wgs308"                           
filename "merged_Diag-wgs308-HG60069601.vcf"
bytes    "6611439"                          
seconds  "0.2"                              
speed    "29380000"                         
         [,1]                              
datetime "2023-09-10 22:08:29"             
project  "wgs311"                          
filename "Diag-wgs311-HG38424441-PK.sample"
bytes    "1649"                            
seconds  "0"                               
speed    "54010"                           
         [,1]                                                                                
datetime "2023-10-14 12:26:24"                                                               
project  "EKG231012"                                                                         
filename "231013_NDX551382_RUO_0020_AHN7YKAFX5.HG39397526-KREFT-KIT-CuCaV3_S24_R2_001.qc.pdf"
bytes    "134905"                                                                            
seconds  "0"                                                                                 
speed    "3940000"

The nsc-exporter log files and the sequencer overview html files were ignored for simplicity. ¹

2.2 Data Overview

The size of transferred files ranges from 0.0 B to 100.9 GiB. The average file size is 1.5 GiB. The median file size is 9.3 KiB. The standard deviation is 8.1 GiB.

         filesize
Min.        0.0 B
1st Qu.   421.0 B
Median    9.3 KiB
Mean      1.5 GiB
3rd Qu. 968.0 KiB
Max.    100.9 GiB

The transfer speed ranges from 1.0 B/s to 93.1 MiB/s. The average transfer speed is 12.2 MiB/s. The median transfer speed is 286.7 KiB/s. The standard deviation is 23.4 MiB/s. Transfer speed for small files is usually very low, so the average transfer speed is not a good indicator for actual transfer speed, see Section 2.3.1.

        speed(/s)
Min.        1.0 B
1st Qu.  11.9 KiB
Median  286.7 KiB
Mean     12.2 MiB
3rd Qu.   8.4 MiB
Max.     93.1 MiB

The transfer time ranges from 0 seconds to 2084.4 seconds. The average transfer time is 19.5 seconds. The median transfer time is 0 seconds. The standard deviation is 104 seconds.

    seconds       
 Min.   :   0.00  
 1st Qu.:   0.00  
 Median :   0.00  
 Mean   :  19.47  
 3rd Qu.:   0.10  
 Max.   :2084.40

2.3 Correlation

Next, we would like to know the how does file size affect transfer speed and transfer time.

2.3.1 Transfer speed and time VS file size (all files)

Small files have lower transfer speed. A good transfer speed around 80 MB/s can be achieved for large files (>2 GB). However, the best speed is observed for files with size around 200 MB (zoom in or see Figure 5).

Figure 1: Transfer speed VS file size (all files)

Figure 2: Transfer time VS file size (all files)

2.3.2 Transfer speed and time VS file size (small files)

Although the transfer speed of small files are very low; the transfer time is usually very short. So small files are not the bottleneck of the data transfer. See also Section 2.5.1.

Figure 3: Transfer speed VS file size (small files)

Figure 4: Transfer time VS file size (small files)

2.3.3 Maximum transfer reached around 200MB file size?

Small files have lower transfer speed. Large files have higher transfer speed. But it looks like best transfer speed is observed for files with sizearound 200 MB file size.

Figure 5: maximum transfer speed reached around 200MB file size

2.4 Idle Time

To evaluate whether there is capacity for upscaling, we need to know the idle time of the nsc-exporter. The nsc-exporter is idle when it is not transferring data.

All transfer records are plotted with starting time of each transfer on x-axis and the time used to finished the transfer on y-axis. The gaps represents idle periods of nsc-exporter. The color represents projects, e.g. wgs123, EKG20230901 etc.. The shape represents project type, e.g. wgs, EKG etc. You can turn off a project by clicking it in the legend to the right of the figure.

For easier visualization, the data is grouped in months.

2.4.1 September

Figure 6: Transfer time of all files in September

Figure 7: Idle time in September (transfer gaps)

Figure 8: Time used for md5sum check in September ²

Attention

Total absolute time used for transferring files in September is 8 days, 20 hours, 35 minutes and 57.20 seconds. In total 62.9 TB data was transferred including 8 new wgs projects.
The nsc-exporter will sleep 10 minutes before checking for new data to transfer. In September, nsc-exporter slept 173 times, totally 1 day, 4 hours and 50 minutes. ³
Another type of time used is the md5sum checking by s3cmd put command which is not counted in the absolute transfer time. ⁴ The total time used for md5sum checking in September is 2 days, 7 hours, 12 minutes and 44.50 seconds.

2.4.2 October

Figure 9: Transfer time of all files in October

Figure 10: Idle time in October (transfer gaps)

Figure 11: Time used for md5sum check in October

Attention

Total absolute time used for transferring files in October is 9 days, 16 hours, 5 minutes and 58.40 seconds. In total 71.4 TB data was transferred including 10 new wgs projects.
The nsc-exporter will sleep 10 minutes before checking for new data to transfer. In October, nsc-exporter slept 319 times, totally 2 days, 5 hours and 10 minutes.
The total time used for md5sum checking in October is 2 days, 14 hours, 50 minutes and 37.70 seconds.

2.4.3 November

Figure 12: Transfer time of all files in November

Figure 13: Idle time in November (transfer gaps)

Figure 14: Time used for md5sum check in November

Attention

Total absolute time used for transferring files in November is 11 days, 12 hours, 49 minutes and 45 seconds. In total 83.5 TB data was transferred including 12 new wgs projects.
The nsc-exporter will sleep 10 minutes before checking for new data to transfer. In November, nsc-exporter slept 180 times, totally 1 day and 6 hours.
The total time used for md5sum checking in November is 3 days, 17 minutes and 58.60 seconds.

2.5 Discussion

Obviously, with a 10Gbps switch connecting NSC and TSD, the current transfer speed is not optimal. There can be many reasons for this, e.g. network components, software and protocol used to transfer data, the storage system I/O, CPU performance o both ends etc.

2.5.1 Do we transfer too many small files?

Figure 15 show the number of small files and the number of large files using different boundaries. Figure 16 shows that the time used to transfer small files is neglectable.

Figure 15: total number of small files vs large files

Figure 16: total time used for transferring small files

Total time (seconds) used to transfer small vs larger files (raw data)

	threshold	small files total time(s)	large files total time(s)
1	<100 kB	1940	2595561
2	<1 MB	4158	2593343
3	<10 MB	6746	2590755
4	<100 MB	10596	2586905
5	<1 GB	38479	2559021

2.5.2 Possibility Of an additional 48-sample run each week?

The nsc-exporter is idle for quite a portion of the time Section 2.4.
- September’s effective transfer time⁵ is 12 days, 8 hours, 38 minutes and 41 seconds to transfer 62.9 TB data including that of 8 wgs projects.
- October’s effective transfer time is 14 days, 12 hours, 6 minutes and 36 seconds to transfer 71.4 TB data including that of 10 wgs projects.
- November’s effective transfer time is 15 days, 19 hours, 7 minutes and 43 seconds to transfer 83.5 TB data including that of 12 wgs projects.
The maximum transfer speed is reached around 200 MB file size. Figure 5 This interestingly is the configured chunk size of s3cmd which is the tool used by nsc-exporter for data transfer. We might want to increase the chunk size to improve the transfer speed of large files?
The current transfer speed is not optimal considering the 10Gbps switch connecting NSC and TSD. We need to investigate the reason for the low transfer speed.

2.5.3 Calculator

import {textcolor} from "@observablehq/text-color-annotations-in-markdown"

formatBytes = function formatBytes(bytes,decimals) {
   if(bytes == 0) return '0 Bytes';
   var k = 1024,
       dm = decimals || 2,
       sizes = ['Bytes', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB', 'ZB', 'YB'],
       i = Math.floor(Math.log(bytes) / Math.log(k));
   return parseFloat((bytes / Math.pow(k, i)).toFixed(dm)) + ' ' + sizes[i];
}

volume_hour= formatBytes(speed*60*60*1000*1000, 1)
volume_day= formatBytes(speed*24*60*60*1000*1000 , 1)
volume_week = formatBytes(speed*7*24*60*60*1000*1000, 1)
volume_month = formatBytes(speed*30*24*60*60*1000*1000, 1)
md`${textcolor(volume_hour, 'MediumSeaGreen')} data can be transferred per **hour**.`

md`${textcolor(volume_day, 'SlateBlue')} data can be transferred per **day**.`

md`${textcolor(volume_week, 'Chocolate')} data can be transferred per **week**.`

md`${textcolor(volume_month, 'Crimson')} data can be transferred per **month**.`

2.5.4 Debugging

Does tacl transfer data at a higher speed?

The tacl tool transfers speed is actually lower than s3cmd. The tacl tool transfers data at around 65 MB/s.

CPU performance on NSC side

CPU usage on NSC side (sleipnir) is high during data transfer. It can reach 90% of a single core.

Does increasing the chunk size of s3cmd improve the transfer speed?

The 200MB chunk size is almost the optimal size for the current setup. 2500MB chunk size is slightly better (+10%) than 200MB chunk size for very large files.

Does parallelizing the transfer improve the transfer speed?

With two parallel nsc-exporter processes, we can achieve around 1.6x - 1.8x the transfer speed of a single process.

2.6 Conclusion

We can run 4 x 48 or 2 x 48 + 1 x 96 samples per week. Then the allowance for downtime is reduced to 2 days per week.
200MB chunk size is almost the optimal size for the current setup.
With 2 parallel nsc-exporter processes, we can achieve around 1.6x - 1.8x the transfer speed of a single process with current setup.
We are waiting or the investigation of the low transfer speed on TSD side, e.g. TCP Proxy, MinIO performance, storage I/O etc.

3 Data storage

WGS produces large amount of data. The data storage capacity is critical for the upscaling.

3.1 NSC

On NSC side, the data is stored in on boston at /boston/diag. Boston has a total capacity of 1.5 PB, and the usable capacity is 320TB at the moment.

3.2 TSD

On TSD side, the data is stored in /cluster/projects/p22. The total capacity is 1.8 PB, and the usable capacity is 1.2 PB at the moment.

4 Pipeline capacity (Illumina DRAGEN)

Illunima DRAGEN is a bioinformatics pipeline server that can be used to process WGS data. It takes around 1 hours to process a 30x WGS sample.

To be extended …

5 Discussion

To be added…

6 Conclusion

To be added…

Footnotes

The nsc-exporter log and sequencer overview html files are very small files and do not belong to any projects. They are always transferred in a very short time. They will not affect the transfer speed of other files. Therefore, they are ignored for simplicity.↩︎
Skipped wgs records where md5sum check time equals/close to zero, so project types with small files/folders such as EKG are shown.↩︎
Data comes in a continuous manner. The nsc-exporter normally takes a snapshot of new data and transfer it. It then sleeps for 10 minutes before checking for new data. The slept times counted here are where next sleep is more than the sleeping interval (10 minutes) later, signifying that new data comes right after the sleep. This is contrary to long idle time where no new data comes after the sleep.↩︎
To make sure files are transferred intact, s3cmd put checks the md5sum of the files. This takes time and is not reported as transfer time by s3cmd The md5sum check is done before starting the transfer. We estimate the md5sum check time by subtracting the transfer time from the time gap between two transfers. The md5sum check time is usually less than 10 minutes, so a gap larger than 10 minutes is not considered as md5sum check time.↩︎
Effective transfer time is calculated as “absolute transfer time” + “sleep time between 2 transfers” + “md5sum check time”.↩︎