We are studying the PhD thesis of Zubair Nawaz titled “Recursive Variable Expansion: A Transformation for Reconfigurable Computing” at TU Delft, because the following claim caught our attention.
We show that our technique can reduce the memory bandwidth requirement from 49.36 Gb/sec to 8 Kb/sec even for existing approaches.
As we mentioned many times, memory bandwidth has become the biggest bottleneck in the kind of developments we are doing. The best analogy was ten cooks getting eggs from the fridge at the kitchen of Intel ex-CEO.
In our case, the fridge is the memory and cooks are the processors. We read the recently published SOAP3-dp paper carefully and found the authors to struggle with the same problem. Of course, they were there years before us, and came up with three clever tricks -
1. Optimization of parallel access to the GPU global memory
SOAP3 makes use of the 2way-BWT indexing technique  and involves random access to the indexing data structures in the main memory. The original design of 2way-BWT  was based on two-level sampling. The design works well for CPU but not in the highly parallel environment of GPU. The data structures are too large and must be placed into the global memory of GPU, causing serious memory contention among the processors inside the GPU. For this purpose, in SOAP3, the index is redesigned to use one-level sampling instead, which greatly reduces the number of memory accesses by half.
Apart from reducing the number of global memory accesses, we also optimize the time of individual access to the global memory. This is achieved by coalescing simultaneous global memory accesses.
In SOAP3-dp, we try to coalesce as many memory accesses as possible. The global memory of GPU device holds two large data structures the 2way-BWT index, and the set of reads. To enable coalesced access. the set of reads is partitioned into groups of 32 (equals the warp size). …..These coalesced accesses could be done in a single memory transaction with only one time of memory address interpretation, achieving excellent memory throughput.
2. Divergence control and 3-level stratified alignment pipeline
GPU works in a single-instruction multiple-thread (SIMT) mode. Processors in the same SM must execute the same instruction at one time. When mismatches are allowed, a read can have more than one branch during alignment. Too many diverging branches however would lower the efficiency of GPU drastically, because most processors (with few branches) may become idle and wait for a few others. For this purpose, we derive a suffix array (SA) ranges count based parameter, which can be determined at runtime, whether a read would generate too many branches, and reads are classified into different levels of complexity according to this parameter. The basic idea is that reads of different levels should be aligned separately. In SOAP3-dp’s implementation, we have designed three levels of complexity. For the all best output parameter, which outputs all alignment results equally the best, if 2 mismatches are allowed, the SA ranges count dividing the three levels are 4 and 32 respectively (it means that, during alignment, a read with SA ranges count exceeding a threshold after extending a base, will be stopped and scheduled for next level, thresholds for other mismatch allowances and output parameters are included in the definition.h file in the source code). In particular, we let the GPU handle the first two levels, and use the CPU to take care of the most complicated reads (which account for a small percentage only). Furthermore, to fully utilize both GPU and CPU processing power, SOAP3 overlaps the alignment of complicated reads from the previous batch in CPU with the alignment of the next batch in GPU (as shown in the Figure S4 in File S1).
3. GPU-accelerated dynamic programming
Here they rewrote Smith-Waterman.
**4. Effort Limit for Dynamic Programming
5. Paired-end alignment
6. Scoring functions**
We do not understand all solutions yet, but we are happy to at least reach the same problem as them.
Getting back to recursive variable expansion, how does it reduce the memory bandwidth requirement so much? Apparently by not sending data and back and forth between processor and FPGA.
In the last chapter, we saw that there are two stages in Smith-Waterman (SW) algorithm namely matrix fill and traceback. First, we fill the matrix with
optimal score found, then we find the maximum of the optimal score. Finally we perform the traceback starting from the maximum value. This procedure is performed for all the sequences in the database. Since the matrix fill stage takes 98.6% of the overall time , all FPGA implementations use FPGAs for accelerating the matrix fill stage.
There are two methods to perform the sequence alignment on a reconfigurable system. In the first method, the matrix is filled on an FPGA and then the matrix data is sent to the GPP, where the traceback is performed. This method creates a memory bottleneck in any off-the-shelf FPGA board. In the second method, a sequence is shortlisted by finding the maximum value after performing the matrix fill stage for the whole database. Later, that maximum value and the index of the corresponding sequence is transferred to the GPP. The matrix fill stage for the shortlisted sequences is repeated on the GPP and the traceback is performed to get the optimal alignment.
In this chapter, we propose a parallel FPGA design of the SW traceback, which performs the alignment immediately after completing the matrix fill for all the sequences in the database. This way, we can avoid the second matrix fill stage for the shortlisted sequences at the expense of more area consumption.
Parallel implementation of bioinformatics algorithms is a fascinating exercise. As we continue, we seem to find ourselves more compelled to view the algorithms as spatio-temporal dynamics of data moving between processing blocks and memory. In that mode of operation, algorithms are not static mathematical construct, but are highly dependent on the relative sizes of various ‘pipes’ through with data is moving from one place to another.