That easy strategy wouldn't work, for instance two successive calls to MulticoreParam() would get the same port assigned, rather than the contract of a 'random' port in a specific range; the port can be assigned by the manager.port= argument if the user wants to avoid random assignment. I could maintain a separate random number stream in BiocParallel for what amounts to a pretty trivial and probably dubious strategy [choosing random ports in hopes that one is not in use], but that starts to sound like a more substantial feature.
Martin On 4/11/19, 7:06 PM, "Pages, Herve" <[email protected]> wrote: Hi Steffi, Any code that gets called between your calls to set.seed() and runif() could potentially use the random number generator. So the sequence set.seed(123); runif(1) is only guaranteed to be deterministic if no other code is called in between, or if the code called in between does not use the random number generator (but if that code is not under your control it could do anything). @Martin: I'll look at your suggestion for DelayedArray. An easy workaround would be to avoid changing the RNG state in BiocParallel by having .snowPort() make a copy of .Random.seed (if it exists) before calling runif() and restoring it on exit. H. On 4/11/19 15:25, Martin Morgan wrote: > This is actually from a dependency DelayedArray which, on load, calls DelayedArray::setAutoBPPARAM, which calls BiocParallel::MulticoreParam(), which uses the random number generator to select a random port for connection. > > A different approach would be for DelayedArray to respect the user's configuration and use bpparam(), or perhaps look at the class of bpparam() and tell the user they should, e.g., BiocParallel::register(SerialParam()) if that's appropriate, or use registered("MulticoreParam") or registered("SerialParam") if available (they are by default) rather than creating an ad-hoc instance. > > Martin > > On 4/11/19, 10:17 AM, "Bioc-devel on behalf of Steffi Grote" <[email protected] on behalf of [email protected]> wrote: > > Hi all, > I found out that example code for my package GOfuncR yields a different result the first time it's executed, despite setting a seed. All the following executions are identical. > It turned out that loading the database package 'Homo.sapiens' changed the random numbers: > > set.seed(123) > runif(1) > # [1] 0.2875775 > > set.seed(123) > suppressWarnings(suppressMessages(require(Homo.sapiens))) > runif(1) > # [1] 0.7883051 > > set.seed(123) > runif(1) > # [1] 0.2875775 > > Is that known or expected behaviour? > Should I not load a package inside a function that later uses random numbers? > > Thanks in advance, > Steffi > > _______________________________________________ > [email protected] mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8XXamcpEeef966i7IGk_3aE9GMJodKAzXwWW4fL_hrI&s=KoHGLM0HbP4whRZLG4ol66_q1qkg9E0LjFHObDqgNuo&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: [email protected] Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
