Option --db-load-mode can be modified for msa-server's mmseqs calls.
Current Behavior
--db-load-mode is hardcoded in msa-server's sources
Steps to Reproduce (for bugs)
Run colabfold_batch with a locally installed msa server and check server's logs. --dbload-mode is always 2. There is no option to set it on msa-server level.
ColabFold Output (for bugs)
Example server output:
search jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/prof_res ./databases/pdb70_220313 jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/res_pdb jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/tmp2 --db-load-mode 2 -s 7.5 -a -e 0.1
convertalis jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/prof_res ./databases/pdb70_220313.idx jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/res_pdb jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/pdb70.m8 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2
Context
Running a local msa server on a shared application server with remote networked filesystems (NFS/gpfs). The idea is to improve performance by using a different --db-load-mode
Your Environment
RHEL7-9.0, 512G RAM, remote networed file systems (NFS/gpfs)
MMSEQS_COMMIT=${1:-4589151554eb83a70ff0c4d04d21b83cabc203e4}
BACKEND_COMMIT=${2:-14e087560f309f989a5e1feb54fd1f9c988076d5}
Abhishaike
commented
1 year ago
Expected Behavior
Option --db-load-mode can be modified for msa-server's mmseqs calls.
Current Behavior
--db-load-mode is hardcoded in msa-server's sources
Steps to Reproduce (for bugs)
Run colabfold_batch with a locally installed msa server and check server's logs. --dbload-mode is always 2. There is no option to set it on msa-server level.
ColabFold Output (for bugs)
Example server output: search jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/prof_res ./databases/pdb70_220313 jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/res_pdb jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/tmp2 --db-load-mode 2 -s 7.5 -a -e 0.1 convertalis jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/prof_res ./databases/pdb70_220313.idx jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/res_pdb jobs/JthYkd9UZxhngcAQox-SOHM1ltLiGIP4wDZbwA/pdb70.m8 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2
Context
Running a local msa server on a shared application server with remote networked filesystems (NFS/gpfs). The idea is to improve performance by using a different --db-load-mode
Your Environment
RHEL7-9.0, 512G RAM, remote networed file systems (NFS/gpfs) MMSEQS_COMMIT=${1:-4589151554eb83a70ff0c4d04d21b83cabc203e4} BACKEND_COMMIT=${2:-14e087560f309f989a5e1feb54fd1f9c988076d5}