Comments (3)
yuk12
commented on May 24, 2024
I tried with latest commit on the given input. It executes to completion.
Could you try with the latest commit.
Run info:
Compiler used: icc-18, gcc.
Command line same as mentioned above.
make CXX=icpc multi
./bwa-mem2 mem -t 8 /scratch/omics/genomes-indexes-reads/human/ref/hs38DH/hs38DH.fa /scratch/omics/genomes-indexes-reads/human/reads/ERR3242459_1.fastq.gz /scratch/omics/genomes-indexes-reads/human/reads/ERR3242459_2.fastq.gz -K 100000000 -Y -R '@RG\tID:ERR3242459_1\tPL:ILLUMINA\tPU:ERR3242459_1\tLB:ERR3242459\tSM:ERR3242459' > /scratch/mvasimud/sam_out/tmpv.sa
Here is the log (icc-18):
-----------------------------
Executing in AVX512 mode!!
-----------------------------
* Ref file: /scratch/omics/genomes-indexes-reads/human/ref/hs38DH/hs38DH.fa
* Entering FMI_search
* Reference seq len for bi-index = 6418915857
* Count:
0, 1
1, 1877984092
2, 3209457929
3, 4540931766
4, 6418915857
* Reading other elements of the index from files /scratch/omics/genomes-indexes-reads/human/ref/hs38DH/hs38DH.fa
* Index prefix: /scratch/omics/genomes-indexes-reads/human/ref/hs38DH/hs38DH.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = /scratch/omics/genomes-indexes-reads/human/ref/hs38DH/hs38DH.fa.0123
* Reference genome size: 6418915856 bp
* Done reading reference genome !!
- Memory pre-allocation for Chaining: 1393.3971 MB
- Memory pre-allocation for BSW: 1916.9362 MB
- Memory pre-allocation for BWT: 618.5134 MB
- Threads used (compute): 8
- No. of pipeline threads: 2
[0000] read_chunk: 100000000, work_chunk_size: 100000200, nseq: 666668
[0000][ M::kt_pipeline] read 666668 sequences (100000200 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 100000000, work_chunk_size: 100000200, nseq: 666668
[0000][ M::kt_pipeline] read 666668 sequences (100000200 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209457928, n: 666668
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[0000][PE] skip orientation FF as there are not enough pairs
[0000][PE] skip orientation FR as there are not enough pairs
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 666668 reads in 79.952 CPU sec, 10.282 real sec
[[Skipped intermediate logs]]
[0000] Calling mem_process_seqs.., task: 1097
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 100000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209457928, n: 346624
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[0000][PE] skip orientation FF as there are not enough pairs
[0000][PE] skip orientation FR as there are not enough pairs
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 346624 reads in 23.609 CPU sec, 2.976 real sec
[0000] read_chunk: 100000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
from bwa-mem2.
yihchii
commented on May 24, 2024
Hi @yuk12 with the latest binary (should be 20 days old by now) we have, bwa-mem2 failed with Segmentation fault.
- Ran on AWS c5d.18xlarge (144GiB memory) with Linux 4.4.0-1099-aws and Ubuntu 16.04.6 LTS
- Executing in AVX512 mode
See log and clip of error message below:
⟫ bwa-mem2 mem -t 36 genome/hs38DH.fa /home/dnanexus/in/reads_fastqgzs/0/ERR3242459_1.fastq.gz /home/dnanexus/in/reads2_fastqgzs/0/ERR3242459_2.fastq.gz -K 100000000 -Y -R '@RG\tID:ERR3242459_1\tPL:ILLUMINA\tPU:ERR3242459_1\tLB:ERR3242459\tSM:ERR3242459' > test.sam
-----------------------------
Executing in AVX512 mode!!
-----------------------------
* Ref file: genome/hs38DH.fa
* Entering FMI_search
* Index file found. Loading index from genome/hs38DH.fa.bwt.8bit.32
* Reference seq len for bi-index = 6434693835
* Count:
0, 1
1, 1882204624
2, 3217346918
3, 4552489212
4, 6434693835
* Reading other elements of the index from files genome/hs38DH.fa
* Index prefix: genome/hs38DH.fa
* Read 3171 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = genome/hs38DH.fa.0123
...
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 666668 reads in 106.872 CPU sec, 3.558 real sec
[0000] Calling mem_process_seqs.., task: 366
[0000] 1. Calling kt_for - worker_bwt
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3217346917, n: 666668
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (13, 317237, 2, 0)
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (242, 405, 1463)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 3905)
[0000][PE] mean and std.dev: (703.23, 720.10)
[0000][PE] low and high boundaries for proper pairs: (1, 5126)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (359, 420, 495)
[0000][PE] low and high boundaries for computing mean and std.dev: (87, 767)
[0000][PE] mean and std.dev: (430.15, 100.14)
[0000][PE] low and high boundaries for proper pairs: (1, 903)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000][PE] skip orientation FF
[0000] 3. Calling kt_for - worker_sam
[0000] read_chunk: 100000000, work_chunk_size: 100000200, nseq: 666668
[0000][ M::kt_pipeline] read 666668 sequences (100000200 bp)...
Segmentation fault
from bwa-mem2.
yihchii
commented on May 24, 2024
When I reduced the threads usage to 36, it went Segmentation fault as well:
⟫ bwa-mem2 mem -t 36 genome/hs38DH.fa /home/dnanexus/in/reads_fastqgzs/0/ERR3242459_1.fastq.gz /home/dnanexus/in/reads2_fastqgzs/0/ERR3242459_2.fastq.gz -K 100000000 -Y -R '@RG\tID:ERR3242459_1\tPL:ILLUMINA\tPU:ERR3242459_1\tLB:ERR3242459\tSM:ERR3242459' > test.sam
-----------------------------
Executing in AVX512 mode!!
-----------------------------
* Ref file: genome/hs38DH.fa
* Entering FMI_search
* Index file found. Loading index from genome/hs38DH.fa.bwt.8bit.32
* Reference seq len for bi-index = 6434693835
* Count:
0, 1
1, 1882204624
2, 3217346918
3, 4552489212
4, 6434693835
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 666668 reads in 106.872 CPU sec, 3.558 real sec
[0000] Calling mem_process_seqs.., task: 366
[0000] 1. Calling kt_for - worker_bwt
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3217346917, n: 666668
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (13, 317237, 2, 0)
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (242, 405, 1463)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 3905)
[0000][PE] mean and std.dev: (703.23, 720.10)
[0000][PE] low and high boundaries for proper pairs: (1, 5126)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (359, 420, 495)
[0000][PE] low and high boundaries for computing mean and std.dev: (87, 767)
[0000][PE] mean and std.dev: (430.15, 100.14)
[0000][PE] low and high boundaries for proper pairs: (1, 903)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000][PE] skip orientation FF
[0000] 3. Calling kt_for - worker_sam
[0000] read_chunk: 100000000, work_chunk_size: 100000200, nseq: 666668
[0000][ M::kt_pipeline] read 666668 sequences (100000200 bp)...
Segmentation fault
When I further lowered the thread usage to 18 on this same instance, the mapping finished successfully:
⟫ bwa-mem2 mem -t 18 genome/hs38DH.fa /home/dnanexus/in/reads_fastqgzs/0/ERR3242459_1.fastq.gz /home/dnanexus/in/reads2_fastqgzs/0/ERR3242459_2.fastq.gz -K 100000000 -Y -R '@RG\tID:ERR3242459_1\tPL:ILLUMINA\tPU:ERR3242459_1\tLB:ERR3242459\tSM:ERR3242459' > test.sam
-----------------------------
Executing in AVX512 mode!!
-----------------------------
* Ref file: genome/hs38DH.fa
* Entering FMI_search
* Index file found. Loading index from genome/hs38DH.fa.bwt.8bit.32
* Reference seq len for bi-index = 6434693835
* Count:
0, 1
1, 1882204624
2, 3217346918
3, 4552489212
4, 6434693835
...
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 346624 reads in 38.236 CPU sec, 2.619 real sec
[0000] read_chunk: 100000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 18
Processor is runnig @3000.175212 MHz
Runtime profile:
Time taken for main_mem function: 8803.08 sec
IO times (sec) :
Reading IO time (reads) avg: 1085.79, (1085.79, 1085.79)
Writing IO time (SAM) avg: 906.82, (906.82, 906.82)
Reading IO time (Reference Genome) avg: 3.97, (3.97, 3.97)
Index read time avg: 33.06, (33.06, 33.06)
Overall time (sec) (Excluding Index reading time):
PROCESS() (Total compute time + (read + SAM) IO time) : 8760.86
MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 8757.87, (8757.87, 8757.87)
SAM Processing time (sec):
--WORKER_SAM avg: 2894.57, (2894.57, 2894.57)
Kernels' compute time (sec):
Total kernel (smem+sal+bsw) time avg: 5724.08, (5724.08, 5724.08)
SMEM compute avg: 2122.51, (2139.92, 2114.91)
SAL compute avg: 776.54, (782.75, 744.07)
BSW time, avg: 2179.92, (2185.53, 2176.70)
Total re-allocs: 1766946271 out of total requests: -721685421, Rate: -2.45
Important parameter settings:
BATCH_SIZE: 512
MAX_SEQ_LEN_REF: 256
MAX_SEQ_LEN_QER: 128
MAX_SEQ_LEN8: 128
SEEDS_PER_READ: 500
SIMD_WIDTH8 X: 64
SIMD_WIDTH16 X: 32
AVG_SEEDS_PER_READ: 64
Feel free to close this thread.
from bwa-mem2.
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