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parallel: Fix --line-buffer problem with missing \n for last record. Passes testsuite.
This commit is contained in:
Ole Tange
parent
a3f11158b5
commit
94ce0d8f9f
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## Copyright (C) 2014 Ole Tange, David Rosenberg, and Free Software
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## Foundation, Inc.
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##
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## This program is free software; you can redistribute it and/or modify
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## it under the terms of the GNU General Public License as published by
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## the Free Software Foundation; either version 3 of the License, or
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## (at your option) any later version.
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##
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## This program is distributed in the hope that it will be useful, but
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## WITHOUT ANY WARRANTY; without even the implied warranty of
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## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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## General Public License for more details.
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##
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## You should have received a copy of the GNU General Public License
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## along with this program; if not, see <http://www.gnu.org/licenses/>
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## or write to the Free Software Foundation, Inc., 51 Franklin St,
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## Fifth Floor, Boston, MA 02110-1301 USA
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##
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##
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## LIBRARY FOR READING GNU PARALLEL RESULTS
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##
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## Example:
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## parallel --results my/results/dir --header : \
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## 'printf "FOO={foo}\\tBAR={bar}\\n";paste <(seq {bar}) <(seq {bar} -1 1)' \
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## :::: <(echo foo; seq 100) <(echo bar; seq 10)
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##
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## dir="my/results/dir"
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## filenametable <- load_parallel_results_filenames(dir);
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## raw <- load_parallel_results_raw(filenametable)
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## newlines <- load_parallel_results_split_on_newline(filenametable)
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## rawdt <- raw_to_data.table(raw)
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## rawdf <- raw_to_data.frame(raw)
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load_parallel_results_filenames <- function(resdir) {
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## Find files called .../stdout
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stdoutnames <- list.files(path=resdir, pattern="stdout", recursive=T);
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## Find files called .../stderr
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stderrnames <- list.files(path=resdir, pattern="stderr", recursive=T);
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if(length(stdoutnames) == 0) {
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## Return empty data frame if no files found
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return(data.frame());
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}
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## The argument names are every other dir level
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## The argument values are every other dir level
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## e.g. my/results/dir/age/18/chromosome/20/stdout
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m <- matrix(unlist(strsplit(stdoutnames, "/")),nrow = length(stdoutnames),byrow=T);
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filenametable <- as.table(m[,c(F,T)]);
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## Append the stdout and stderr filenames
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filenametable <- cbind(filenametable,
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paste(resdir,unlist(stdoutnames),sep="/"),
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paste(resdir,unlist(stderrnames),sep="/"));
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colnames(filenametable) <- c(strsplit(stdoutnames[1],"/")[[1]][c(T,F)],"stderr");
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return(filenametable);
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}
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load_parallel_results_raw <- function(filenametable) {
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## Read the files given in column stdout
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stdoutcontents <-
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lapply(filenametable[,c("stdout")],
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function(filename) {
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return(readChar(filename, file.info(filename)$size));
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} );
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## Read the files given in column stderr
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stderrcontents <-
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lapply(filenametable[,c("stderr")],
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function(filename) {
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return(readChar(filename, file.info(filename)$size));
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} );
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## Replace filenames with file contents
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filenametable[,c("stdout","stderr")] <-
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c(as.character(stdoutcontents),as.character(stderrcontents));
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return(filenametable);
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}
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load_parallel_results_split_on_newline <- function(filenametable,split="\n") {
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raw <- load_parallel_results_raw(filenametable);
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## Keep all columns except stdout and stderr
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varnames = setdiff(colnames(raw), c("stdout","stderr"))
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## Find the id of the non-stdout and non-stderr columns
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header_cols = which(colnames(raw) %in% varnames)
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## Split stdout on \n
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splits = strsplit(raw[,"stdout"], split)
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## Compute lengths of all the lines
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lens = sapply(splits, length)
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## The arguments should be repeated as many times as there are lines
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reps = rep(1:nrow(raw), lens)
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## Merge the repeating argument and the lines into a matrix
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m = cbind(raw[reps, header_cols], unlist(splits))
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return(m)
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}
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raw_to_data.table <- function(raw, ...) {
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require(data.table)
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## Keep all columns except stdout and stderr
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varnames = setdiff(colnames(raw), c("stdout","stderr"))
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## after data.table feature request the as.data.frame can be skipped
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## and will thus be much faster
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ddt = as.data.table(as.data.frame(raw,stringsAsFactors=FALSE))
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## ensure fread knows stdout is string and not filename by appending \n
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ddt[, stdout := paste0(stdout,"\n")]
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## drop files with empty stdout
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ddd = ddt[nchar(stdout)>1,fread(stdout, header=FALSE, ...), by=varnames]
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return(ddd)
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}
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raw_to_data.frame <- function(raw, ...) {
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require(plyr)
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## Convert to data.frame without factors
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raw = as.data.frame(raw, stringsAsFactors = FALSE)
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## Keep all columns except stdout and stderr
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varnames = setdiff(colnames(raw), c("stdout","stderr"))
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dd = ddply(raw, .variables=varnames, function(row) {
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## Ignore empty stdouts
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if (nchar(row[,"stdout"]) == 0) {
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return(NULL)
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}
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## Read stdout with read.table
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con <- textConnection(row[,"stdout"], open = "r")
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d = read.table(con, header=FALSE, ...)
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return(d)
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})
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return(dd)
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}
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22
src/parallel
22
src/parallel
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@ -316,8 +316,10 @@ sub spreadstdin {
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if(not $anything_written and not eof($in)) {
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# Nothing was written - maybe the block size < record size?
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# Increase blocksize exponentially
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my $old_blocksize = $blocksize;
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$blocksize = ceil($blocksize * 1.3 + 1);
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::warning("A full record was not matched in a block. Increasing to --blocksize ".$blocksize."\n");
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::warning("A record was longer than $old_blocksize. " .
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"Increasing to --blocksize $blocksize\n");
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}
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}
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# If there is anything left in the buffer write it
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@ -626,7 +628,7 @@ sub get_options_from_array {
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sub parse_options {
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# Returns: N/A
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# Defaults:
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$Global::version = 20140222;
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$Global::version = 20140315;
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$Global::progname = 'parallel';
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$Global::infinity = 2**31;
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$Global::debug = 0;
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@ -5025,16 +5027,8 @@ sub print {
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# Remove the printed part
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substr($$partial,0,$i+1)="";
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}
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}
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if(defined $self->{'exitstatus'}) {
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# The job is finished, there might be line with no \n left
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print $out_fd $$partial;
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}
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if($self->fh($fdno,"rpid") and CORE::kill 0, $self->fh($fdno,"rpid")) {
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# decompress still running
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} elsif(defined $self->{'exitstatus'}) {
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# If the job is dead: print the remaining partial line
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# read remaining
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if($$partial and ($opt::tag or defined $opt::tagstring)) {
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@ -5044,8 +5038,12 @@ sub print {
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print $out_fd $$partial;
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# Release the memory
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$$partial = undef;
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# then close fh
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close $in_fh;
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if($self->fh($fdno,"rpid") and CORE::kill 0, $self->fh($fdno,"rpid")) {
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# decompress still running
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} else {
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# decompress done: close fh
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close $in_fh;
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}
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}
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} else {
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my $buf;
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@ -3328,7 +3328,7 @@ this. To see this in action try:
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parallel -kP4 -n1 grep 1 > out.par ::: a b c d e f
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echo a b c d e f | xargs -P4 -n1 grep 1 > out.xargs-unbuf
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echo a b c d e f | xargs -P4 -n1 grep --line-buffered 1 > out.xargs-linebuf
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echo a b c d e f | xargs -n1 grep --line-buffered 1 > out.xargs-serial
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echo a b c d e f | xargs -n1 grep 1 > out.xargs-serial
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ls -l out*
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md5sum out*
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@end verbatim
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@ -21,7 +21,7 @@ echo '### niceload with no arguments should give no output'
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echo '### Test -t and -s'
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niceload -v -t 1 -s 2 sleep 4.5
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echo 'bug #38908: niceload: Ctrl-C/TERM should resume jobs if using -p'
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echo 'bug #38908: niceload: Ctrl-C/TERM should resume jobs if using -p - Order may change, but not output'
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# This should take 10 seconds to run + delay from niceload
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# niceload killed after 1 sec => The delay from niceload should be no more than 1 second
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stdout /usr/bin/time -f %e perl -e 'for(1..100) { select(undef, undef, undef, 0.1); } print "done\n"' | int &
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@ -29,7 +29,8 @@ echo 'bug #38908: niceload: Ctrl-C/TERM should resume jobs if using -p'
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export A=$!;
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sleep 2;
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kill -s TERM $A;
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wait
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wait;
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echo Finished
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echo 'bug #38908: niceload: Ctrl-C should resume jobs if using -p'
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# This should take 10 seconds to run + delay from niceload
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@ -11,25 +11,51 @@ echo 'bug #41613: --compress --line-buffer no newline';
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echo 'bug #41613: --compress --line-buffer no --tagstring';
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diff
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<(perl -e 'for("x011".."x110"){print "$_\t", (map { rand } (1..100000)),"\n"}'|
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<(nice perl -e 'for("x011".."x110"){print "$_\t", ("\n", map { rand } (1..100000)) }'|
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parallel -N10 -L1 --pipe -j6 --block 20M --compress
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pv -qL 3000000 | perl -pe 's/(....).*/$1/')
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<(perl -e 'for("x011".."x110"){print "$_\t", (map { rand } (1..100000)),"\n"}'|
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<(nice perl -e 'for("x011".."x110"){print "$_\t", ("\n", map { rand } (1..100000)) }'|
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parallel -N10 -L1 --pipe -j6 --block 20M --compress --line-buffer
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pv -qL 3000000 | perl -pe 's/(....).*/$1/')
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>/dev/null
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|| echo 'Good: --line-buffer matters'
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|| (echo 'Good: --line-buffer matters'; false) && echo 'Bad: --line-buffer not working'
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echo 'bug #41613: --compress --line-buffer with --tagstring';
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diff
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<(perl -e 'for("x011".."x110"){print "$_\t", (map { rand } (1..100000)),"\n"}'|
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<(nice perl -e 'for("x011".."x110"){print "$_\t", ("\n", map { rand } (1..100000)) }'|
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parallel -N10 -L1 --pipe -j6 --block 20M --compress --tagstring {#}
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pv -qL 3000000 | perl -pe 's/(....).*/$1/')
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<(perl -e 'for("x011".."x110"){print "$_\t", (map { rand } (1..100000)),"\n"}'|
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<(nice perl -e 'for("x011".."x110"){print "$_\t", ("\n", map { rand } (1..100000)) }'|
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parallel -N10 -L1 --pipe -j6 --block 20M --compress --tagstring {#} --line-buffer
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pv -qL 3000000 | perl -pe 's/(....).*/$1/')
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>/dev/null
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|| echo 'Good: --line-buffer matters'
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|| (echo 'Good: --line-buffer matters'; false) && echo 'Bad: --line-buffer not working'
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echo 'bug #41613: --compress --line-buffer - no newline';
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echo 'pipe compress tagstring'
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perl -e 'print "O"'| parallel --compress --tagstring {#} --pipe --line-buffer cat
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echo "K"
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echo 'pipe compress notagstring'
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perl -e 'print "O"'| parallel --compress --pipe --line-buffer cat
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echo "K"
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echo 'pipe nocompress tagstring'
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perl -e 'print "O"'| parallel --tagstring {#} --pipe --line-buffer cat
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echo "K"
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echo 'pipe nocompress notagstring'
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perl -e 'print "O"'| parallel --pipe --line-buffer cat
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echo "K"
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echo 'nopipe compress tagstring'
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parallel --compress --tagstring {#} --line-buffer echo {} O ::: -n
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echo "K"
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echo 'nopipe compress notagstring'
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parallel --compress --line-buffer echo {} O ::: -n
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echo "K"
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echo 'nopipe nocompress tagstring'
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parallel --tagstring {#} --line-buffer echo {} O ::: -n
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echo "K"
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echo 'nopipe nocompress notagstring'
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parallel --line-buffer echo {} O ::: -n
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echo "K"
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echo 'bug #41412: --timeout + --delay causes deadlock';
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seq 10 | parallel -j10 --timeout 1 --delay .3 echo;
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@ -9,13 +9,14 @@ Sleeping 1s
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Running 2s
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Sleeping 1s
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Running 2s
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bug #38908: niceload: Ctrl-C/TERM should resume jobs if using -p
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Sleeping 1s
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Running 10s
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bug #38908: niceload: Ctrl-C/TERM should resume jobs if using -p - Order may change, but not output
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done
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10
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Finished
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Sleeping 1s
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Running 10s
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bug #38908: niceload: Ctrl-C should resume jobs if using -p
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Sleeping 1s
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Running 10s
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done
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10
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Sleeping 1s
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Running 10s
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@ -1,6 +1,6 @@
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### Test --pipe
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### Test 200M records with too small block
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parallel: Warning: A full record was not matched in a block. Increasing to --blocksize 260000001
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parallel: Warning: A record was longer than 200000000. Increasing to --blocksize 260000001
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303111434
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303111434
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303111434
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@ -127,10 +127,10 @@ c
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1>01a02a0a
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2>0a12a34a
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3>45a6a
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parallel: Warning: A full record was not matched in a block. Increasing to --blocksize 3
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parallel: Warning: A full record was not matched in a block. Increasing to --blocksize 5
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parallel: Warning: A record was longer than 1. Increasing to --blocksize 3
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parallel: Warning: A record was longer than 3. Increasing to --blocksize 5
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1>01a02a0a
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parallel: Warning: A full record was not matched in a block. Increasing to --blocksize 8
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parallel: Warning: A record was longer than 5. Increasing to --blocksize 8
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2>0a12a34a
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3>45a6a
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### Test 10M records with too big block
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@ -4,6 +4,23 @@ bug #41613: --compress --line-buffer no --tagstring
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Good: --line-buffer matters
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bug #41613: --compress --line-buffer with --tagstring
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Good: --line-buffer matters
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bug #41613: --compress --line-buffer - no newline
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pipe compress tagstring
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1 OK
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pipe compress notagstring
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OK
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pipe nocompress tagstring
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1 OK
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pipe nocompress notagstring
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OK
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nopipe compress tagstring
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1 OK
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nopipe compress notagstring
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OK
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nopipe nocompress tagstring
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1 OK
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nopipe nocompress notagstring
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OK
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bug #41412: --timeout + --delay causes deadlock
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1
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2
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