rbbt-util 5.26.99 → 5.26.101
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +13 -4
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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metadata.gz: 1c25e0ed9f390b6cfe9f13d8a25f9818f01ebeb18721bffe457f2addf13519c3
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4
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data.tar.gz: 5ef61ec1c11a6993a37043004306c4a85a96d27dd6e391fdb0a32ecf882fb695
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5
5
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SHA512:
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6
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metadata.gz:
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7
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data.tar.gz:
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6
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metadata.gz: 43c13e02b198f133a37f8368ac53471ddd456fb6267c902c1acc2c100c6cfd9322002d216e305b21c1e44745d858fe9d18ee782b39cc7a7a94527c010df729fc
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7
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data.tar.gz: dce15b38e52af3e5acc274418ef7cdeb9ea1e5b454ebd1ae0e4045182a4585694b23e33ae61876e28f65e8d57ae7100609d70e2abbca7309876a9782a5ea2576
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data/lib/rbbt/hpc.rb
CHANGED
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@@ -18,8 +18,8 @@ module Marenostrum
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singularity = options.delete :singularity
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contain = options.delete :contain
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sync = options.delete :sync
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user_group = options.delete :user_group
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contain_and_sync = options.delete :contain_and_sync
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group = options.delete :user_group
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wipe_container = options.delete :wipe_container
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copy_image = options.delete :copy_image
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exclusive = options.delete :exclusive
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@@ -142,7 +142,7 @@ mkdir -p "$SINGULARITY_RUBY_INLINE"
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if contain
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user = ENV['USER'] || `whoami`.strip
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-
group = File.basename(File.dirname(ENV['HOME']))
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group = File.basename(File.dirname(ENV['HOME']))
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scratch_group_dir = File.join('/gpfs/scratch/', group)
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projects_group_dir = File.join('/gpfs/projects/', group)
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@@ -173,8 +173,16 @@ echo "user_scratch: $CONTAINER_DIR/scratch/#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}
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[[ -a "$CONTAINER_DIR/projects" ]] || ln -s '#{projects_group_dir}' "$CONTAINER_DIR/projects"
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[[ -a "$CONTAINER_DIR/scratch" ]] || ln -s '#{scratch_group_dir}' "$CONTAINER_DIR/scratch"
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-
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-
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EOF
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if group != user_group
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env +=<<-EOF
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# Add user_group search_path
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echo "#{user_group}: /gpfs/projects/#{user_group}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> $CONTAINER_DIR/.rbbt/etc/search_paths
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EOF
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end
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if inputs_dir
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env +=<<-EOF
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@@ -213,6 +221,7 @@ EOF
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-B ~/git:"$CONTAINER_DIR/git":ro \
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-B ~/.rbbt/software/opt/:"/opt/":ro \
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-B ~/.rbbt:"$CONTAINER_DIR/home/":ro \
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#{ group != user_group ? "-B /gpfs/projects/#{user_group}" : "" } \
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-B #{scratch_group_dir} \
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-B #{projects_group_dir} \
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"$SINGULARITY_IMG")
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