rbbt-util 5.26.36 → 5.26.37
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +16 -5
- 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: 8e4344a2ec967804100fde955c1e8b4e71ba3985cdd24322fdac97641fbefd41
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4
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+
data.tar.gz: 6753f2431714d64a64a8764ebea61f8ae338a4b244bcd0c93764a681a03a8cd6
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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: 13e3c5553cc5364cbbb0d54aecc333cba23c20240dc18839b8f98c726cf55c5c2e66c6a13ad7b3c921676e8cab823c4f534421ba0344046fa7431b28f910e628
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|
7
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+
data.tar.gz: 73873821fee4f6d60f6b2d9f91fd073cee06084b92fe76de00bcd75a023683e7e37bdb8c58667df60e252cdca151f6cb9449f259bc4d057647c38c124b056694
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data/lib/rbbt/hpc.rb
CHANGED
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@@ -124,6 +124,7 @@ let "MAX_MEMORY=$SLURM_MEM_PER_CPU * $SLURM_CPUS_ON_NODE"
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124
124
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module load intel/2018.1
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125
125
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module load singularity
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126
126
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SINGULARITY_IMG="$HOME/projects/rbbt.singularity.img"
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|
127
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+
SINGULARITY_OVERLAY_DIR="$HOME/projects/rbbt.singularity.overlays"
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127
128
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SINGULARITY_RUBY_INLINE="$HOME/.singularity_ruby_inline"
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128
129
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mkdir -p "$SINGULARITY_RUBY_INLINE"
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129
130
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EOF
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@@ -197,9 +198,14 @@ EOF
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197
198
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# RUN
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|
198
199
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run = ""
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199
200
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201
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+
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202
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+
exec_cmd = %(env _JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m)
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|
203
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+
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200
204
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if singularity
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205
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+
singularity_exec = %(singularity exec -e $(ls $SINGULARITY_OVERLAY_DIR/*.img |xargs -l echo -n " " --overlay) )
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206
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+
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201
207
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if contain
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202
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-
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208
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+
singularity_exec << %( -C -H "$CONTAINER_DIR" \
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|
203
209
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-B /apps/ \
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|
204
210
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-B /scratch/tmp \
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205
211
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-B "$SINGULARITY_RUBY_INLINE":"$CONTAINER_DIR/.ruby_inline":rw \
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@@ -208,16 +214,21 @@ EOF
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208
214
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-B ~/.rbbt:"$CONTAINER_DIR/home/":ro \
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209
215
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-B #{scratch_group_dir} \
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|
210
216
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-B #{projects_group_dir} \
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|
211
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-
"$SINGULARITY_IMG"
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|
217
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+
"$SINGULARITY_IMG")
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|
218
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+
exec_cmd << ' TMPDIR="$CONTAINER_DIR/.rbbt/tmp" '
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|
212
219
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else
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|
213
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-
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|
220
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+
singularity_exec = %(-B /apps/ -B "$SINGULARITY_RUBY_INLINE":"$HOME/.ruby_inline":rw "$SINGULARITY_IMG")
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|
214
221
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end
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|
215
222
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|
|
216
223
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if development
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|
217
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-
exec_cmd += ' --dev=git'
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|
224
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+
exec_cmd += 'rbbt --dev=git'
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|
225
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+
else
|
|
226
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+
exec_cmd += 'rbbt'
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|
218
227
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end
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|
228
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+
|
|
229
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+
exec_cmd = singularity_exec + " " + exec_cmd
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|
219
230
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else
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|
220
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-
exec_cmd
|
|
231
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+
exec_cmd << %(~/git/rbbt-util/bin/rbbt --dev=~/git/)
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|
221
232
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end
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222
233
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223
234
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