rbbt-util 5.26.113 → 5.26.114

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: dca772b872b127233434d142720cdc4f05d32249fbb7c3480b6e97962b00b196
+  metadata.gz: 4f667fc42ef878fae10593c1ce3120644484bcd780f9992feac6d8f62eb20450
+  data.tar.gz: 5090c55a43b7487b2978d55f753ed79dc6d0dc389ccf915fdf0583e084ea4ea7
 SHA512:
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+  metadata.gz: bc8909d45725ca94c35ddf01a635fc92810f9cb90238045c0ba0bb9ead8a8937f5ab09b6c0a5cf7a87e42ec173ba5fb037035964d5ba4568e4259975a2f8832d
+  data.tar.gz: 20b90ae10e1012b768ad6c3127a52e3a0c8686ae9f97d3232e0294baadeedf73022a76c0e413921d9ddd2a8400f3141925773c16a4fd2ad0acfa46380bdad378

data/lib/rbbt/hpc.rb

@@ -146,11 +146,13 @@ SINGULARITY_RUBY_INLINE="$HOME/.singularity_ruby_inline"
 mkdir -p "$SINGULARITY_RUBY_INLINE"
         EOF
 
+        prep  = ""
+
         if contain
           scratch_group_dir = File.join('/gpfs/scratch/', group)
           projects_group_dir = File.join('/gpfs/projects/', group)
 
-          env +=<<-EOF
+          prep +=<<-EOF
 
 # Prepare container dir
 CONTAINER_DIR="#{contain}"
@@ -178,15 +180,15 @@ echo "user_scratch: #{scratch_group_dir}/#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}"
           EOF
 
           if user_group && group != user_group
-          env +=<<-EOF
+            prep +=<<-EOF
 
 # Add user_group search_path
 echo "#{user_group}: /gpfs/projects/#{user_group}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> $CONTAINER_DIR/.rbbt/etc/search_paths
-          EOF
+            EOF
           end
 
           if inputs_dir
-            env +=<<-EOF
+            prep +=<<-EOF
 
 # Copy inputs
 [[ -d '#{inputs_dir}' ]] && cp -R '#{inputs_dir}' $CONTAINER_DIR/inputs
@@ -195,7 +197,7 @@ echo "#{user_group}: /gpfs/projects/#{user_group}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}"
           end
 
           if copy_image
-            env +=<<EOF
+            prep +=<<EOF
 
 # Copy image
 rsync -avz "$SINGULARITY_IMG" "$CONTAINER_DIR/rbbt.singularity.img" 1>&2
@@ -205,7 +207,7 @@ EOF
 
           if  wipe_container == "pre" || wipe_container == "both"
             if singularity
-              env +=<<-EOF
+              prep +=<<-EOF
 
 # Clean container pre
 singularity exec -e -C -H "$CONTAINER_DIR" "$SINGULARITY_IMG" rm -Rfv .rbbt/var/jobs &>> #{fsync}
@@ -300,8 +302,8 @@ find '#{target}' -type l -ls | awk '$13 ~ /^#{target.gsub('/','\/')}/ { sub("#{s
 EOF
 
         if  contain && (wipe_container == "post" || wipe_container == "both")
-          run =<<-EOF + run
-if ls -A '#{contain}'; then
+          prep =<<-EOF + prep
+if ls -A '#{contain}' > /dev/null ; then
     echo "ERROR: Container directory not empty, refusing to wipe. #{contain}"
 fi
           EOF
@@ -342,7 +344,7 @@ else
 fi
 EOF
 
-      template = [header, env, run, coda] * "\n"
+      template = [header, env, prep, run, coda] * "\n"
 
       template
     end
@@ -482,7 +484,7 @@ EOF
       slurm_basedir = options.delete :SLURM_basedir
       slurm_basedir = "~/rbbt-slurm" if slurm_basedir.nil?
       TmpFile.with_file(nil, !keep_slurm_basedir, :tmpdir => slurm_basedir, :prefix => "SLURM_rbbt_job-") do |tmp_directory|
-        options[:slurm_basedir] ||= File.join(tmp_directory, 'workdir')
+        options[:slurm_basedir] ||= tmp_directory
         slurm_basedir = options[:slurm_basedir]
         inputs_dir = File.join(tmp_directory, 'inputs_dir')
         saved = Step.save_job_inputs(job, inputs_dir, options)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.113
+  version: 5.26.114
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-01-13 00:00:00.000000000 Z
+date: 2020-01-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake