G3NAV not finishing alignment

[wpoehlm]

I am able to get G3NAV to start running, but it hangs and runs for over an hour without finishing.

Environment:

qsub -I -l select=1:ngpus=1:ncpus=16:mem=32gb,walltime=02:00:00
module load gcc/4.8.1 cuda-toolkit/7.5.18
export DISPLAY=:0

command:

./G3NAV.exe input.json

Output:

1
File Opened successfully!!!. Reading data from file into array
Parsed Successful {type=[7], size=2}string(graph1)
<------------>ID : 1
Name : Maize
Loc: ./data/M.tab
Cluster : ./data/M.tab.cluster
Ont: ./data/Maize_info.txt
X: -100
Y: 0
Z: 0
W: 200
H: 200
Reading Maize Filename : ./data/M.tab
--Total Nodes : 2073
--Total Edges : 33398
Count = 33398 vs 33398
Graph Size :2073 for GPU
Malloc Edge Matrix
Malloc Node Position
Malloc Node Prop
Mem Cpy Node Position
Mem Cpy Node Prop
Mem Cpy Edge
Setup Complete
Load Complete
string(graph2)
<------------>ID : 2
Name : Rice
Loc: ./data/R.tab
Cluster : ./data/R.tab.cluster
Ont: ./data/Rice_info.txt
X: 100
Y: 0
Z: 0
W: 200
H: 200
Reading Rice Filename : ./data/R.tab
--Total Nodes : 2259
--Total Edges : 32821
Count = 32821 vs 32821
Graph Size :2259 for GPU
Malloc Edge Matrix
Malloc Node Position
Malloc Node Prop
Mem Cpy Node Position
Mem Cpy Node Prop
Mem Cpy Edge
Setup Complete
Load Complete
string(alignment1)
Perform Alignment on 1 2 using ./data/magma0.5.output
--Total Alignment Edges : 20732073,2073
Matrix Alloc Complete
---><--Edge Count Verified : 2073 vs 2073
Malloc Align Edge Matrix
Mem Cpy Edge Align
Setup Complete
Edges Moved: 2073

It seems to hang after the last "Edges Moved" line, without finishing or producing an error message

[wpoehlm]

Need to use TurboVNC, can't run G3NAV standalone