I'm running hhblits for over 7000 sequences on Uniref DB. When using hhblist_omp using 128 threads the process gets killed after reaching ~600 sequences after it consumes the whole RAM memory (the machine has 256GB). As I observe the RAM consumption increases slowly with time as some processes did not clean the memory after dumping the alignment to output an a3m file (a bug?).
The command
hhblits_omp -i indb -d UniRef30_2020_06 -oa3m out_a3m -n 5 -cpu 128
I can split the file into ~500-sequence chunks but that is not efficient as hhblits_omp would not balance it optimally. mpirun also seems to consume a lot of RAM as the threads seem not to share common database files in memory.
Any suggestions on how to make profiles for thousands of sequences at once?
I'm running hhblits for over 7000 sequences on Uniref DB. When using hhblist_omp using 128 threads the process gets killed after reaching ~600 sequences after it consumes the whole RAM memory (the machine has 256GB). As I observe the RAM consumption increases slowly with time as some processes did not clean the memory after dumping the alignment to output an a3m file (a bug?). The command
hhblits_omp -i indb -d UniRef30_2020_06 -oa3m out_a3m -n 5 -cpu 128I can split the file into ~500-sequence chunks but that is not efficient as hhblits_omp would not balance it optimally. mpirun also seems to consume a lot of RAM as the threads seem not to share common database files in memory.Any suggestions on how to make profiles for thousands of sequences at once?