rbbt-util 5.31.15 → 5.32.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9616d2b1893ed3444d432e99b4ef6ddaf7d61836ee1c23dbd4deb1efa767b80d
-  data.tar.gz: c5dc433a171c909eb2711ee37832fb094d271fcf6099f0394706af3cd8da1520
+  metadata.gz: ef9271207cbe69c725a4ab3a8553295d3b68e5f04ec1bfd25ad4654f162ed9cb
+  data.tar.gz: '087009c9ac6b4fee6d9fa7bceb003e050a0cc1e73f96987ec792c07388760633'
 SHA512:
-  metadata.gz: efe3b9c85ec947f900283ca4b2a3e651617558bfd7d85dbea80180ad377e18150df8fccde9efecdd2493d9e4f0ed7979dbdefe2f815e2480d910d5e507670422
-  data.tar.gz: 24bc0e0e6dda34cbf7ad4ea08cb1cbeb18b3bb55b42a79a4590183fd86e7247d7aeb648c31673ef5601f632828d71ae29594e3c6b8f5c7c860dab6592a373f68
+  metadata.gz: b031c1143992b4c75eeeabcb231d656af2927a5bc46a0ea3527c4c90b7ffcc5eb44b0ec02ef9e31d4879fcf2b3192165ba5b22cd1978dc5250eec355f2556bdc
+  data.tar.gz: eb43875132a5f4ddc7ff9ae5dcaed7677c6bff84a4d61454cad9a83361d2a3dd63432cd5b28c656cd9e7bb589b8517bbdd3b57c0fa370527724d3ae55810b0cb

data/lib/rbbt/hpc/lsf.rb

@@ -7,10 +7,13 @@ module HPC
 
     def self.batch_system_variables
       <<-EOF
-[[ -z $LSB_MAX_MEM_RUSAGE ]] || MAX_MEMORY=$LSB_MAX_MEM_RUSAGE 
-[[ -z $MAX_MEMORY ]] && let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
-BATCH_JOB_ID=$LSF_JOBID
-BATCH_SYSTEM=LSF
+let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
+let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $SLURM_CPUS_PER_TASK )"
+[ ! -z $LSB_MAX_MEM_RUSAGE ] && let MAX_MEMORY="$LSB_MAX_MEM_RUSAGE" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
+export MAX_MEMORY_DEFAULT
+export MAX_MEMORY
+export BATCH_JOB_ID=$LSF_JOBID
+export BATCH_SYSTEM=LSF
       EOF
     end
 

data/lib/rbbt/hpc/slurm.rb

@@ -8,7 +8,8 @@ module HPC
 
     def self.batch_system_variables
       <<-EOF
-let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( 1024 * $(nproc) / $SLURM_CPUS_PER_TASK )"
+let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
+let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $SLURM_CPUS_PER_TASK )"
 [ ! -z $SLURM_MEM_PER_CPU ] && let MAX_MEMORY="$SLURM_MEM_PER_CPU * $SLURM_CPUS_PER_TASK" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
 export MAX_MEMORY_DEFAULT
 export MAX_MEMORY

data/lib/rbbt/workflow/step.rb

@@ -458,6 +458,10 @@ class Step
   end
 
   def clean
+    if ! Open.exists?(info_file)
+      Log.high "Refusing to clean step with no .info file: #{path}"
+      return self
+    end
     status = []
     status << "dirty" if done? && dirty?
     status << "not running" if ! done? && ! running? 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.31.15
+  version: 5.32.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-14 00:00:00.000000000 Z
+date: 2021-04-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake