I have been using my Amazon Web Servies account and the directions on http://www.bioconductor.org/help/bioconductor-cloud-ami/#parallel to bootstrap a cluster of Bioconductor AMIs. After running the lines of code below, it hangs on the makePSOCKcluster call. This error happens quite frequently to me, but not always. Any ideas for how to get reliable results or is there workaround? Thanks for your time and consideration. library(parallel) lines <- readLines("/usr/local/Rmpi/hostfile.plain") hosts <- character() for (line in lines) { x <- (strsplit(line[[1]], " ")) hosts <- c(hosts, rep.int(x[[1]][1], as.integer(x[[1]][2]))) } #THIS LINE HANGS #HOSTS IS A CHARACTER VECTORS OF IP ADDRESSES FOR BIOCONDUCTOR AMIs CREATED FROM STACK TEMPLATE cl <- makePSOCKcluster(hosts) Steven Mortimer Data Scientist II, Performance Technologies The Advisory Board Company 202-266-6487 direct | 202-266-5700 fax mortimes@advisory.com<mailto:mortimes@advisory.com> | www.advisory.com<http: www.advisory.com=""> Create your road map for long-term profitability. Run your custom margin analysis today. www.advisory.com/MarginScenarioPlanner<http: www.advisory.com="" researc="" h="" health-care-advisory-board="" tools="" 2012="" margin-scenario-="" planner?wt.mc_id="eMail|Signature|Tool|HCAB|MBE|Oct232012|"> [[alternative HTML version deleted]]

On Sat, Dec 1, 2012 at 7:59 PM, Mortimer, Steven <mortimes at="" advisory.com=""> wrote: > I have been using my Amazon Web Servies account and the directions on http://www.bioconductor.org/help/bioconductor-cloud-ami/#parallel to bootstrap a cluster of Bioconductor AMIs. After running the lines of code below, it hangs on the makePSOCKcluster call. This error happens quite frequently to me, but not always. Any ideas for how to get reliable results or is there workaround? Thanks for your time and consideration. > > library(parallel) > lines <- readLines("/usr/local/Rmpi/hostfile.plain") > hosts <- character() > for (line in lines) > { > x <- (strsplit(line[[1]], " ")) > hosts <- > c(hosts, rep.int(x[[1]][1], as.integer(x[[1]][2]))) > } > #THIS LINE HANGS > #HOSTS IS A CHARACTER VECTORS OF IP ADDRESSES FOR BIOCONDUCTOR AMIs CREATED FROM STACK TEMPLATE > cl <- makePSOCKcluster(hosts) > Hi Steven, Use this command instead: cl <- makePSOCKcluster(hosts, master=system("hostname -i", intern=TRUE)) I've updated the AMI web page to reflect this change. Thanks, Dan > > Steven Mortimer > Data Scientist II, Performance Technologies > The Advisory Board Company > 202-266-6487 direct | 202-266-5700 fax > mortimes at advisory.com<mailto:mortimes at="" advisory.com=""> | www.advisory.com<http: www.advisory.com=""> > > Create your road map for long-term profitability. > Run your custom margin analysis today. > www.advisory.com/MarginScenarioPlanner<http: www.advisory.com="" resea="" rch="" health-care-advisory-board="" tools="" 2012="" margin-scenario-="" planner?wt.mc_id="eMail|Signature|Tool|HCAB|MBE|Oct232012|"> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor