rbbt-util 5.26.39 → 5.26.40
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +7 -3
- metadata +1 -1
checksums.yaml
CHANGED
@@ -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: c402dd55adf3e0a67b17b70c55550033e5c49d8662d9a299fb11247c602b4d9a
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4
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+
data.tar.gz: 48bea651b2efa8ef85e0dd34cfccd3ceb446dd4353c41a482fe8ba08b382f88b
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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: 96cfd11c662b6fb442687fd1b545344ef9c1834f8800bd9cd29985507824df45fe3ab2d6b68c2d9ee03bb696aae287dc6e877b154c65e5f3fb5c27a1adba35a4
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7
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+
data.tar.gz: a6b4eee7818f876694d30050044cd2ae885eb2c52f32ba3dd41444904d9e4ef4bbfeaa09a49a3f7b38f94e15c2e81f5d4295c0c25c0c6d0ac1590a6da8bc6aeb
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data/lib/rbbt/hpc.rb
CHANGED
@@ -123,8 +123,9 @@ let "MAX_MEMORY=$SLURM_MEM_PER_CPU * $SLURM_CPUS_ON_NODE"
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123
123
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env +=<<-EOF
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124
124
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module load intel/2018.1
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125
125
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module load singularity
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126
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-
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127
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-
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126
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+
PROJECTS_ROOT="/gpfs/projects/bsc26/"
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127
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+
SINGULARITY_IMG="$PROJECTS_ROOT/rbbt.singularity.img"
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128
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+
SINGULARITY_OVERLAY_DIR="$PROJECTS_ROOT/rbbt.singularity.overlays"
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128
129
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SINGULARITY_RUBY_INLINE="$HOME/.singularity_ruby_inline"
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129
130
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mkdir -p "$SINGULARITY_RUBY_INLINE"
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130
131
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EOF
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@@ -181,6 +182,9 @@ echo "/scratch/tmp/rbbt/projects/rbbt/workflows/" > $CONTAINER_DIR/.rbbt/etc/wor
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181
182
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# Copy image
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182
183
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rsync -avz "$SINGULARITY_IMG" "$CONTAINER_DIR/rbbt.singularity.img" 1>&2
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183
184
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SINGULARITY_IMG="$CONTAINER_DIR/rbbt.singularity.img"
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185
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+
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186
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+
rsync -avz "$SINGULARITY_OVERLAY_DIR"/ "$CONTAINER_DIR/rbbt.singularity.overlays/" 1>&2
|
187
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+
SINGULARITY_OVERLAY_DIR="$CONTAINER_DIR/rbbt.singularity.overlays"
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184
188
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EOF
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185
189
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end
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186
190
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@@ -202,7 +206,7 @@ EOF
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|
202
206
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exec_cmd = %(env _JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m")
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203
207
|
|
204
208
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if singularity
|
205
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-
singularity_exec = %(singularity exec -e $(ls $SINGULARITY_OVERLAY_DIR/*.img
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209
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+
singularity_exec = %(singularity exec -e $(for f in `ls $SINGULARITY_OVERLAY_DIR/*.img`; do echo -n --overlay "'$f' "; done) )
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206
210
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|
207
211
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if contain
|
208
212
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singularity_exec << %( -C -H "$CONTAINER_DIR" \
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