Hi,
we're using the 6.1.5 Pipeline Pilot version and have encountered a problem with our Protocol for creating Decoysets. Due to utilizing a large intial database (15-20 million compounds, SDF format) and a complex, vast protocol architecture the protocol won't run to the end because of limited (physical) memory errors. We've already implemented memory saving components (e.g. the merge component from this forum) and tried to optimize the overall structure, however no change has siginficantly improved the memory limitation.
So now we're looking for some command or component, which makes it possible to clear or reduce the amount of occupied physical memory during the protocol-run. There should be also no problem with data loss as we save data to HDD by using text writers after each intermediate step. We'd welcome any suggestion, thanks in advance.
Matthias B.
PhD student, LMU
we're using the 6.1.5 Pipeline Pilot version and have encountered a problem with our Protocol for creating Decoysets. Due to utilizing a large intial database (15-20 million compounds, SDF format) and a complex, vast protocol architecture the protocol won't run to the end because of limited (physical) memory errors. We've already implemented memory saving components (e.g. the merge component from this forum) and tried to optimize the overall structure, however no change has siginficantly improved the memory limitation.
So now we're looking for some command or component, which makes it possible to clear or reduce the amount of occupied physical memory during the protocol-run. There should be also no problem with data loss as we save data to HDD by using text writers after each intermediate step. We'd welcome any suggestion, thanks in advance.
Matthias B.
PhD student, LMU
