1. ZFS test with VM on PC

2. Alignment test
• Commands
– cp ~/r100609_1_thy__coreRag1__Rag1_E1.fastq .
– ~/src/bowtie2-2.1.0/bowtie2 -x ~/indexes/mm9 -
U r100609_1_thy__coreRag1__Rag1_E1.fastq -S
r100609_1_thy__coreRag1__Rag1_E1.sam --
threads 2
• Check the process status (execution time
,CPU, memory) with “ps” command for each
10 seconds

3. Alignment test
Uncompressed Compressed
resident set size, the non-swapped physical memory that a task has used (in kiloBytes)
% CPU
Memory

4. I/O performance
• Copy 1GB divided by 1 – 10 blocks
• Command
– for count in $(seq 1 10); do for directory in
uncompressed compressed; do dd if=/dev/zero
of=/mnt/$directory/foovar count=$count bs=`perl
-e "print int(1000000000 / $count - 0.5) + 1"`
2>&1 | tail -n1 | sed 's/^.*, //'; done; done | paste
- - > dd.txt &

5. I/O performance
Blocks Uncompressed Compressed
1 50.1 MB/s 59.1 MB/s
2 56.0 MB/s 54.5 MB/s
3 56.0 MB/s 57.8 MB/s
4 57.6 MB/s 52.7 MB/s
5 53.9 MB/s 58.9 MB/s
6 57.2 MB/s 61.4 MB/s
7 52.3 MB/s 60.0 MB/s
8 43.9 MB/s 60.7 MB/s
9 58.2 MB/s 57.3 MB/s
10 48.1 MB/s 61.3 MB/s

6. File system disk space usage (df)
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/mapper/fedora-root 64247652 25341508 35635900 42% /
devtmpfs 1017952 0 1017952 0% /dev
tmpfs 1025732 80 1025652 1% /dev/shm
tmpfs 1025732 708 1025024 1% /run
tmpfs 1025732 0 1025732 0% /sys/fs/cgroup
tmpfs 1025732 12 1025720 1% /tmp
/dev/sda1 487652 67503 394549 15% /boot
129.112.138.227:/mnt/zfs1 203341312 8697920 194643392 5% /mnt/uncompressed
129.112.138.227:/mnt/zfs2 203341376 3823808 199517568 2% /mnt/compressed

7. File system disk space usage (df)
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/mapper/fedora-root 64247652 25341508 35635900 42% /
devtmpfs 1017952 0 1017952 0% /dev
tmpfs 1025732 80 1025652 1% /dev/shm
tmpfs 1025732 708 1025024 1% /run
tmpfs 1025732 0 1025732 0% /sys/fs/cgroup
tmpfs 1025732 12 1025720 1% /tmp
/dev/sda1 487652 67503 394549 15% /boot
129.112.138.227:/mnt/zfs1 203341312 2181504 201159808 2% /mnt/uncompressed
129.112.138.227:/mnt/zfs2 203341376 2181376 201160000 2% /mnt/compressed
After gzipping of data files

8. ZFS test with Amazon EC2

9. Alignment test 1
• Commands (4 processes using 4 CPU cores)
– ~/src/bowtie2-2.1.0/bowtie2 -x indexes/mm9 -U
r100609_1_thy__coreRag1__Rag1_E1.fastq -S
r100609_1_thy__coreRag1__Rag1_E1.1.sam --threads 1 &
– ~/src/bowtie2-2.1.0/bowtie2 -x indexes/mm9 -U
r100609_1_thy__coreRag1__Rag1_E1.fastq -S
r100609_1_thy__coreRag1__Rag1_E1.2.sam --threads 1 &
– ~/src/bowtie2-2.1.0/bowtie2 -x indexes/mm9 -U
r100609_1_thy__coreRag1__Rag1_E1.fastq -S
r100609_1_thy__coreRag1__Rag1_E1.3.sam --threads 1 &
– ~/src/bowtie2-2.1.0/bowtie2 -x indexes/mm9 -U
r100609_1_thy__coreRag1__Rag1_E1.fastq -S
r100609_1_thy__coreRag1__Rag1_E1.4.sam --threads 1 &

10. Alignment test 1
• The test processes were terminated with memory error.
Out of memory allocating the offs[] array for the Bowtie index.
Please try again on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/ec2-user/src/bowtie2-2.1.0/bowtie2-align --
wrapper basic-0 -x indexes/mm9 -S
r100609_1_thy__coreRag1__Rag1_E1.1.sam --threads 1 -U
r100609_1_thy__coreRag1__Rag1_E1.fastq
bowtie2-align exited with value 1

11. Alignment test 2
• Commands (2 processes using 4 CPU cores)
– ~/src/bowtie2-2.1.0/bowtie2 -x indexes/mm9 -U
r100609_1_thy__coreRag1__Rag1_E1.1.fastq -S
r100609_1_thy__coreRag1__Rag1_E1.1.sam --
threads 2 &
– ~/src/bowtie2-2.1.0/bowtie2 -x indexes/mm9 -U
r100609_1_thy__coreRag1__Rag1_E1.2.fastq -S
r100609_1_thy__coreRag1__Rag1_E1.2.sam --
threads 2 &

12. Alignment test 2
Uncompressed
resident set size, the non-swapped physical memory that a task has used (in kiloBytes)
% CPU
Memory

13. Alignment test 2
Compressed
resident set size, the non-swapped physical memory that a task has used (in kiloBytes)
% CPU
Memory

14. Alignment test 3
• Checking the total memory usage
• Commands (1 process using 2 CPU cores)
– free -t -s 1
– ~/src/bowtie2-2.1.0/bowtie2 -x indexes/mm9 -U
r100609_1_thy__coreRag1__Rag1_E1.fastq -S
r100609_1_thy__coreRag1__Rag1_E1.sam --
threads 4 &

15. Alignment test 3
Uncompressed Compressed

16. I/O performance (Read rate)
Blocks Uncompressed Compressed
1 1.1 GB/s 1.1 GB/s
2 1.6 GB/s 1.6 GB/s
3 1.9 GB/s 2.0 GB/s
4 2.2 GB/s 2.2 GB/s
5 2.3 GB/s 2.4 GB/s
6 2.4 GB/s 2.4 GB/s
7 2.5 GB/s 2.5 GB/s
8 2.6 GB/s 2.6 GB/s
9 2.6 GB/s 2.6 GB/s
10 2.6 GB/s 2.7 GB/s

17. I/O performance (Write rate 1)
Blocks Uncompressed Compressed
1 43.6 MB/s 324 MB/s
2 1.1 GB/s 1.1 GB/s
3 1.2 GB/s 43.9 MB/s
4 42.8 MB/s 1.3 GB/s
5 46.0 MB/s 165 MB/s
6 57.1 MB/s 46.3 MB/s
7 374 MB/s 1.4 GB/s
8 1.1 GB/s 45.4 MB/s
9 42.5 MB/s 44.8 MB/s
10 510 MB/s 1.4 GB/s

18. I/O performance (Write rate 2)
Blocks Uncompressed Compressed
1 814 MB/s 812 MB/s
2 1.1 GB/s 45.5 MB/s
3 43.3 MB/s 50.4 MB/s
4 233 MB/s 1.3 GB/s
5 1.3 GB/s 45.5 MB/s
6 41.8 MB/s 1.3 GB/s
7 98.6 MB/s 176 MB/s
8 60.4 MB/s 599 MB/s
9 47.3 MB/s 38.0 MB/s
10 1.5 GB/s 1.4 GB/s

19. File system disk space usage (df)
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/xvde1 6193088 2393636 3736840 40% /
none 7619740 0 7619740 0% /dev/shm
tank/compressed 79563136 12784384 66778752 17% /mnt/compressed
tank/uncompressed 89918080 23139328 66778752 26% /mnt/uncompressed
tank 66778752 0 66778752 0% /tank
100GB disk pooling (64G + 13G + 23G)

20. Conclusion
• We adopted a short-read alignment step with bowtie2
to the tests of ZFS, as it would mainly utilize the
computational resource including storage disk.
• The tests show that there is no considerable difference
of resource usage between on uncompressed and
compressed disk partitions of ZFS.
– Execution time, CPU, memory, I/O performance
– But it may need more tests in more computational burden
to recognize the stability of ZFS.
• The adoption of compressed system makes more
efficient usage of our storage, especially with unzipped
data files. (refer slide 6-7)