[maker-devel] Fatal error in PMPI_Send

[Carson Holt]

Set --debugmpi as a command line option to maker.  It will produce a bunch of extra output that could help. You will want to capture the output to a file.

Example:
maker --debugmpi &> all_output

That might help track down exactly where it happens. From the error below I gather that there is too much data to transfer over MPI. The size of the data message causes the count variable to overflow the max positive value which loops back around to a negative value as a result.  It makes me think something is odd with your data input, i.e. you are trying to align raw mRNA-seq reads as evidence instead of assembled read, you set the max_dna_len to a value that is way too large in the control files, or you have an odd contig and evidence dataset resulting in alignment depth in the tens of thousands for a single locus. If that’s the case, set all of the depth_blast parameters in maker_bopts (20 is a good number).

—Carson


> On Aug 30, 2021, at 2:45 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> Hi,
> 
> I have this strange error that kill my job and tthat seems to occur randomly:
> 
> running  est2genome search.
> #--------- command -------------#
> Widget::exonerate::est2genome:
> exonerate  -q /tmp/maker_JZ_DUt/12/MSTRG%2E13631%2E1.for.154952409-154955259.12.fasta -t /tmp/maker_JZ_DUt/12/Tps_LRv5b_scf2.154952409-154955259.12.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 100000 --showcigar --percent 20 > /tmp/maker_JZ_DUt/12/Tps_LRv5b_scf2.154952409-154955259.MSTRG%2E13631%2E1.e.exonerate
> #-------------------------------#
> Fatal error in PMPI_Send: Invalid count, error stack:
> PMPI_Send(159): MPI_Send(buf=0x7f526282e010, count=-1326766804, MPI_CHAR, dest=22, tag=9999, MPI_COMM_WORLD) failed
> PMPI_Send(99).: Negative count, value is -1326766804
> 
> 
> 
> Do you know what could be the problem ?
> 
> Best,
> 
> Patrick Tran Van
> 
> Bioinformatician: Lab Chapuisat & Schwander 
> Department of Ecology and Evolution
> University of Lausanne
> Lausanne - Switzerland
> Office 3206
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