HATCHet check failing for Gurobi
Answered
We are trying to run HATCHet with Gurobi as the default Solver. However, hatchet check is failing. As per https://raphael-group.github.io/hatchet/README.html#usingasolver
Gurobi is the default Solver in HATCHet. I followed the instruction in the above URL and installed hatchet and loaded gurobi module file in a conda environment. However, hatchet fails at solver check.
Are there any known issues with Gurobi and HATCHet that is causing this issue? I
We have a floating license for Gurobi Optimizer. The license appears to be working with Gurobi. When I run gurobi_cl from the compute node, I see "grb" entries in the token server logs. However, when we run hatchet check, there are no “grb” entries in token server logs.
(hatchet) [jws@node116 ~]$ module list
Currently Loaded Modulefiles:
1) conda3/202311(default) 2) gurobi/12.0.1
(hatchet) [jws@node101 ~]$ hatchet check
======================
Running HATCHet checks
======================
----------------------
Command: count-reads
----------------------
tabix check SUCCESSFUL.
samtools check SUCCESSFUL.
mosdepth check SUCCESSFUL.
----------------------
Command: genotype-snps
----------------------
samtools check SUCCESSFUL.
bcftools check SUCCESSFUL.
----------------------
Command: count-alleles
----------------------
samtools check SUCCESSFUL.
bcftools check SUCCESSFUL.
----------------------
Command: combine-counts
----------------------
bedtools check SUCCESSFUL.
----------------------
Command: compute-cn
----------------------
solver check FAILED.
See http://compbio.cs.brown.edu/hatchet/README.html#using-a-solver
----------------------
Command: phase-snps
----------------------
bcftools check SUCCESSFUL.
picard check SUCCESSFUL.
shapeit check SUCCESSFUL.
bgzip check SUCCESSFUL.
-
-
Gurobi Staff
Hi Soubhadra,
I don't expect anyone at Gurobi will have heard of hatchet (with only 86k downloads in 6 years this is not a popular package).
My only advice is to have a read of the following article, move your license file to a default location (if it is not already) and set the GRB_LICENSE_FILE environment variable.
Otherwise, perhaps you can open an issue with the creators of hatchet:
https://github.com/raphael-group/hatchet
- Riley
0 -
Please sign in to leave a comment.
Comments
1 comment