Comments (7)
I'm coming across the same issue using 2xA100 GPUs running segaling_repeat_masker on GCA_946052875.1
genome:
Chromosome block 2 interval 96/100 (2950000000:2960000000) with ref (720545186:1330545186) rc (70545185:80545185)
Chromosome block 2 interval 97/100 (2960000000:2970000000) with ref (720545186:1330545186) rc (60545185:70545185)
Chromosome block 2 interval 98/100 (2970000000:2980000000) with ref (720545186:1330545186) rc (50545185:60545185)
Chromosome block 2 interval 99/100 (2980000000:2990000000) with ref (720545186:1330545186) rc (40545185:50545185)
Chromosome block 2 interval 100/100 (2990000000:2999999981) with ref (720545186:1330545186) rc (30545204:40545185)
Sending block 3 ...
Chromosome block 3 interval 1/4 (3000000000:3010000000) with ref (0:330545186) rc (20545185:30545185)
Chromosome block 3 interval 2/4 (3010000000:3020000000) with ref (0:330545186) rc (10545185:20545185)
Error: cudaMemcpy of 4 bytes for num_anchors failed with error " invalid argument "
terminate called after throwing an instance of 'thrust::system::system_error'
what(): CUDA free failed: cudaErrorCudartUnloading: driver shutting down
[2023-06-02T23:43:08+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host nodeXXX
<=========
from segalign.
@RenzoTale88 This version of SegAlign (github.com/gsneha26/SegAlign) is broken and, sadly, doesn't seem to be maintained anymore. You may have more luck with the fork that Cactus uses, which can be found here: https://github.com/ComparativeGenomicsToolkit/SegAlign (in addition to the Cactus release GPU docker images). Even this fork has some overflow issues, but it works on most data.
from segalign.
@glennhickey thanks for the quick reply, I have been trying also with the second repository, but came across the same issue. I can open a second ticket on the cactus github page if you prefer?
from segalign.
Did you try the commit that cactus uses? I only just merged it into master. If you did not use that commit (or the current master as of 10 minutes ago), you would see the same error.
from segalign.
Just cloned the repo and currently compiling it. I'll come back on this, thanks!
from segalign.
@glennhickey still coming across this issue:
Chromosome block 2 interval 100/100 (2990000000:2999999981) with ref (794006738:1424006738) rc (114006756:124006737)
Sending block 3 ...
Chromosome block 3 interval 2/12 (3010000000:3020000000) with ref (0:424006738) rc (94006737:104006737)
Chromosome block 3 interval 1/12 (3000000000:3010000000) with ref (0:424006738) rc (104006737:114006737)
Chromosome block 3 interval 4/12 (3030000000:3040000000) with ref (0:424006738) rc (74006737:84006737)
Chromosome block 3 interval 3/12 (3020000000:3030000000) with ref (0:424006738) rc (84006737:94006737)
Chromosome block 3 interval 5/12 (3040000000:3050000000) with ref (0:424006738) rc (64006737:74006737)
Chromosome block 3 interval 6/12 (3050000000:3060000000) with ref (0:424006738) rc (54006737:64006737)
Chromosome block 3 interval 7/12 (3060000000:3070000000) with ref (0:424006738) rc (44006737:54006737)
Chromosome block 3 interval 8/12 (3070000000:3080000000) with ref (0:424006738) rc (34006737:44006737)
Chromosome block 3 interval 9/12 (3080000000:3090000000) with ref (0:424006738) rc (24006737:34006737)
Chromosome block 3 interval 10/12 (3090000000:3100000000) with ref (0:424006738) rc (14006737:24006737)
Chromosome block 3 interval 11/12 (3100000000:3110000000) with ref (0:424006738) rc (4006737:14006737)
Error: cudaMemcpy of 4 bytes for num_anchors failed with error " invalid argument "
terminate called after throwing an instance of 'thrust::system::system_error'
what(): CUDA free failed: cudaErrorCudartUnloading: driver shutting down
[2023-06-06T00:58:05+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host NODE
from segalign.
I will get it fixed by the end of the week.
from segalign.
Related Issues (20)
- couldn't find boost HOT 7
- Running on multi-fasta HOT 2
- "grep: *.err" and "m: cannot remove '*.segments'" errors HOT 2
- FAILURE: extra segments in file HOT 4
- SegAlign/progressivecactus errors on LSF HOT 1
- run_segalign_repeat_masker file HOT 2
- cudaErrorIllegalAddress: an illegal memory access was encountered HOT 1
- stdbuf: failed to run command ‘segalign’: No such file or directory HOT 2
- error during cmake HOT 1
- segalign_repeat_masker crashes HOT 3
- segalign crashes while aligning final against final reference block HOT 1
- run_segalign crashes on human-chimp (and exits 0!) HOT 2
- SegAlign crashes while running cactus on Terra HOT 3
- thrust::system::system_error | CUDA free failed: cudaErrorCudartUnloading
- Error: cudaMalloc of 256 bytes for sub_mat failed with error " the provided PTX was compiled with an unsupported toolchain. " HOT 1
- /usr/local/bin/run_segalign: line 60: segalign: command not found HOT 1
- AMD GPU support
- Output file size not correct HOT 1
- Support for linux-ppc64le?
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