arvados-cli 0.1.20151202215640 → 0.1.20151207150126
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- checksums.yaml +4 -4
- data/LICENSE-2.0.txt +202 -0
- data/bin/crunch-job +19 -10
- metadata +4 -3
checksums.yaml
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: a03f2e5b32fbb7baa6118dc0381dbe5e615a24fc
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data.tar.gz: 7376e517abb7f4917476b08337ae991d548613ba
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metadata.gz:
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metadata.gz: defe3a8d77c8d1f477b6873a1980f612d90471b34ffbd23c05b6732f4d3e4e9ca4ec0d5713a1c132588805e04c405fe1d5dde58fd2a3d099ad5afd9b376e811f
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data.tar.gz: 8c0d79d77b92623a178bf5f3f05febfa4caeee080964166ae26978a9c688f2e099498e572c59f6031739ac45604aed7561a19da10744d855e8f460587a45ebf3
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data/LICENSE-2.0.txt
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Apache License
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Version 2.0, January 2004
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data/bin/crunch-job
CHANGED
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@@ -872,11 +872,12 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
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$ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
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$ENV{"TASK_WORK"} = $ENV{"CRUNCH_TMP"}."/task/$childslotname";
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$ENV{"HOME"} = $ENV{"TASK_WORK"};
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$ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}.".keep";
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$ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
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$ENV{"CRUNCH_NODE_SLOTS"} = $round_max_slots{$ENV{TASK_SLOT_NODE}};
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$ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"};
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my $keep_mnt = $ENV{"TASK_WORK"}.".keep";
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$ENV{"GZIP"} = "-n";
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my @srunargs = (
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}
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my $command =
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"if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
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."mkdir -p $ENV{CRUNCH_TMP} $ENV{JOB_WORK} $ENV{TASK_WORK} $
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."&& cd $ENV{CRUNCH_TMP} "
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"if [ -e \Q$ENV{TASK_WORK}\E ]; then rm -rf \Q$ENV{TASK_WORK}\E; fi; "
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."mkdir -p \Q$ENV{CRUNCH_TMP}\E \Q$ENV{JOB_WORK}\E \Q$ENV{TASK_WORK}\E \Q$keep_mnt\E "
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."&& cd \Q$ENV{CRUNCH_TMP}\E "
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# These environment variables get used explicitly later in
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# $command. No tool is expected to read these values directly.
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.q{&& MEM=$(awk '($1 == "MemTotal:"){print $2}' </proc/meminfo) }
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.q{&& SWAP=$(awk '($1 == "SwapTotal:"){print $2}' </proc/meminfo) }
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."&& MEMLIMIT=\$(( (\$MEM * 95) / ($ENV{CRUNCH_NODE_SLOTS} * 100) )) "
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."&& let SWAPLIMIT=\$MEMLIMIT+\$SWAP ";
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-
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$command .= "&& exec arv-mount --read-write --mount-by-pdh=by_pdh --mount-tmp=tmp --crunchstat-interval=10 --allow-other $arv_file_cache \Q$keep_mnt\E --exec ";
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$ENV{TASK_KEEPMOUNT} = "$keep_mnt/by_pdh";
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$ENV{TASK_KEEPMOUNT_TMP} = "$keep_mnt/tmp";
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if ($docker_hash)
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{
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my $containername = "$Jobstep->{arvados_task}->{uuid}-$Jobstep->{failures}";
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@@ -924,14 +929,18 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
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$command .= "--volume=\Q$ENV{CRUNCH_SRC}:$ENV{CRUNCH_SRC}:ro\E ";
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$command .= "--volume=\Q$ENV{CRUNCH_INSTALL}:$ENV{CRUNCH_INSTALL}:ro\E ";
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-
# Currently, we make arv-mount's mount
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# inside the container (instead of using
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# host like we do with CRUNCH_SRC and
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# crunch scripts and utilities must
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931
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# use $TASK_KEEPMOUNT.
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932
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# Currently, we make the "by_pdh" directory in arv-mount's mount
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933
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# point appear at /keep inside the container (instead of using
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934
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# the same path as the host like we do with CRUNCH_SRC and
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935
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# CRUNCH_INSTALL). However, crunch scripts and utilities must
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936
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# not rely on this. They must use $TASK_KEEPMOUNT.
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932
937
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$command .= "--volume=\Q$ENV{TASK_KEEPMOUNT}:/keep:ro\E ";
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933
938
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$ENV{TASK_KEEPMOUNT} = "/keep";
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934
939
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940
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# Ditto TASK_KEEPMOUNT_TMP, as /keep_tmp.
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941
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$command .= "--volume=\Q$ENV{TASK_KEEPMOUNT_TMP}:/keep_tmp\E ";
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942
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$ENV{TASK_KEEPMOUNT_TMP} = "/keep_tmp";
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943
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935
944
|
# TASK_WORK is almost exactly like a docker data volume: it
|
|
936
945
|
# starts out empty, is writable, and persists until no
|
|
937
946
|
# containers use it any more. We don't use --volumes-from to
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: arvados-cli
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.1.
|
|
4
|
+
version: 0.1.20151207150126
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Arvados Authors
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2015-12-
|
|
11
|
+
date: 2015-12-07 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: arvados
|
|
@@ -178,7 +178,7 @@ dependencies:
|
|
|
178
178
|
- - "<"
|
|
179
179
|
- !ruby/object:Gem::Version
|
|
180
180
|
version: 1.0.0
|
|
181
|
-
description: Arvados command line tools, git commit
|
|
181
|
+
description: Arvados command line tools, git commit 1a0c39586b5c73f083b7dad4d3017c5c4ffe5bf4
|
|
182
182
|
email: gem-dev@curoverse.com
|
|
183
183
|
executables:
|
|
184
184
|
- arv
|
|
@@ -188,6 +188,7 @@ executables:
|
|
|
188
188
|
extensions: []
|
|
189
189
|
extra_rdoc_files: []
|
|
190
190
|
files:
|
|
191
|
+
- LICENSE-2.0.txt
|
|
191
192
|
- bin/arv
|
|
192
193
|
- bin/arv-crunch-job
|
|
193
194
|
- bin/arv-run-pipeline-instance
|