User: lee.tibbert

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lee.tibbert20
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Posts by lee.tibbert

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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... Dr. Morgan, Is this a good place for a design discussion? Would another venue, such as an issue on GitHub,  be better? Please advise. I have taken some time to parse through the issues & run a few benchmarks.  I considered  a trifecta of   1) an audience which is much more interested in biolo ...
written 3.4 years ago by lee.tibbert20
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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... [ 2016-03-25 21:36 -0400 Post was blocked because I exceeded my max allowed   posts per 6 hours.]   OK, I think I have identified the problem. The key is in the trace above: [1] "ssh -l lee YYY.local /usr/lib/R/bin/Rscript /home/lee/R/i686-pc-linux-gnu-library/3.2/BiocParallel/snow/RSOCKnode.R MAST ...
written 3.4 years ago by lee.tibbert20
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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... [ 2016-03-25 21:36 -0400 Post was blocked because I exceeded my max allowed   posts per 6 hours.]   Progress.... 1) The location of the Rscript turned out to be a non-issue. On Ubuntu 15.10 (and probably other versions), /usr/bin/Rscript is a full copy (not link) of /usr/lib/R/bin/Rscript.  An ssh ...
written 3.4 years ago by lee.tibbert20
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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... I may have a clue.  On XXX, Rscript is in /usr/bin/Rscript. The ssh command expects it in /usr/lib/R/bin/Rscript. I will check node YYY, but I expect it to have the same setup. I need to go off line for a while, but will report back. (Both nodes are Ubuntu 15.10, using Ubuntu .deb packages). ...
written 3.4 years ago by lee.tibbert20
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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... Ah, the trace command gives me someplace to start. At least, it puts me down into SSH land. I will study the R scripts to see if they are doing port forwarding or fancy SSH stuff.   From a fresh invocation of R: if (!("BiocParallel") %in% .packages()) +   library("BiocParallel") # implied & n ...
written 3.4 years ago by lee.tibbert20
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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... Using bpstart() I get essentially the same results: XXX is local, YYY is remote node.  SSH from XXX to YYY works, R is installed & available to SSH'd user on YYY (I have believed the error message about XXX and have _not_ yet checked for  firewall/port_blocked issues on YYY. ) > library("Bi ...
written 3.4 years ago by lee.tibbert20
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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... My package version seems to match: packageVersion("BiocParallel") [1] ‘1.5.21’ What I am doing. I hope/believe  that I have copied the example correctly: if (!("BiocParallel") %in% .packages()) library("BiocParallel") # implied & necessary, not in text # Continues to not work, BiocParall ...
written 3.4 years ago by lee.tibbert20 • updated 3.4 years ago by Martin Morgan ♦♦ 23k
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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... NAK on 1.5.21, sorry... Given XXX.local as the local host and YYY.local as the remote host I continue to be unable to execute the example on the remote host. host <- c("YYY.local")  gives execution on the local node XXX, BTW: I discovered during my testing that host <- c("") also executes o ...
written 3.4 years ago by lee.tibbert20
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Comment: C: BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers
... Thank you for the rapid turnaround (and the heads up on typo'ed hostnames).  When, if the fullness of time, 1.5.21 becomes available in 'devel', I will try this out again and report back (close.)  As always, thank you for biocParallel, it is saving me a _lot_ of time (and is interesting & well ...
written 3.4 years ago by lee.tibbert20
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BiocParallel 1.5.20: Another error following example 4.2.1: all "remote" workers on localhost
... Using BiocParallel 1.5.20, I am trying to follow example 4.2.1 in the "Introduction to BiocParallel" vignette. Thanks to a fix in 1.5.20, I can now use hostnames/IP_addresses in the workers= argument to SnowParam. So far so good. The problem I seem to be encountering is that the workers are all cre ...
biocparallel written 3.4 years ago by lee.tibbert20 • updated 3.4 years ago by Martin Morgan ♦♦ 23k

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