Comments (2)
If anyone else is having this issue, my workaround is to set the OMP_THREAD_LIMIT
environment variable before running SegAlign as documented here
from segalign.
I usually run via WDL/Terra on the cloud where it makes sense to give SegAlign all cores on the node. But not being able to specify the CPU count can cause trouble on other environments Toil supports. Ex : ComparativeGenomicsToolkit/cactus#709
@gsneha26 Could you please add a command-line option to run_segalign
as well as segalign_repeat_masker
to specify the number of cpus?
I remember you mentioning taskset
but from what I've (just) read, I don't think this will work in general. The reason is that it requires specific CPUs to be specified, and not the number of CPUs. This distinction is important, as it's not within Toil's scope to know which CPUs are free or not free -- it only cares about the total counts.
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
- segaling_repeat_masker still crashes HOT 7
- 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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from segalign.