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View Code? Open in Web Editor NEWGWAS third-level epistatic search tool for cluster architectures
License: GNU General Public License v3.0
GWAS third-level epistatic search tool for cluster architectures
License: GNU General Public License v3.0
Currently uses 50% of GPU memory for output array and contingency table allocation. When increasing memory usage, segmentation fault occurs.
Depending on the MPI implementation, a library warning may appear. Use --mca mpi_cuda_support 0
to suppress the message.
Hello. I tried to run mpi3snp on the example.zip file in the plink teaching material section [1]
I get the error:
Error in example/wgas1.tped:1: invalid nucleotide value '0' at position 265
I also created a jupyter notebook that can run on google colab to illustrate the issue [2]
Is this a problem from my side?
[1] https://www.cog-genomics.org/plink/1.9/resources#teach
[2] https://gist.github.com/shadiakiki1986/366a61df58475e667aa84101ff337b1a
It is recommended to use --bind-to
flag with socket
or none
argument depending on your needs.
On a MPI context, system() forks a new process to satisfy the call. This messes with MPI, and should be avoided.
The solution could be reading the files using the I/O library and parsing the results with regular expressions.
Number of analysis on GPU build always returns 0.
Currently uses Statistics class, should call IOMpi instead.
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