Use full paths to dx command

Switch to vfork/exec from system to avoid doubling memory reservation for dx command Reserve buffer of memory for OS when scheduling jobs
marbl · May 25, 2018 · 6f3c375 · 6f3c375
1 parent 2ff48f3
commit 6f3c375
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Showing 3 changed files with 21 additions and 6 deletions.
diff --git a/src/AS_UTL/objectStore.C b/src/AS_UTL/objectStore.C
@@ -29,6 +29,7 @@
 #include "splitToWords.H"
 
 #include <libgen.h>
+#include <sys/wait.h>
 
 
 static
@@ -235,12 +236,25 @@ fetchFromObjectStore(char *requested) {
   fprintf(stderr, "fetchFromObjectStore()-- found path '%s'\n", path);
 
   char *cmd = new char [FILENAME_MAX+1];
-
-  snprintf(cmd, FILENAME_MAX, "%s download --output \"%s\" \"%s:%s/%s\"", dx, requested, pr, ns, path);
+  snprintf(cmd, FILENAME_MAX, "%s:%s/%s", pr, ns, path);
+  char *args[8] = {"dx", "download", "--overwrite", "--no-progress", "--output", "", "", (char*)0};
+  args[5] = requested;
+  args[6] = cmd;
 
   fprintf(stderr, "fetchFromObjectStore()-- executing '%s'\n", cmd);
 
-  int32  err = system(cmd);
+  int32 err;
+  int32 pid = vfork();
+  if ( pid == -1)
+    fprintf(stderr, "vfork failed with error '%s'.\n", strerror(errno));
+
+  if ( pid == 0 ) {
+    execve(dx, args, environ);
+    fprintf(stderr, "execve failed with error '%s'.\n", strerror(errno));
+    _exit(-1);
+  }
+  waitpid(-1, (int*)&err, 0);
+  err = WEXITSTATUS(err);
 
   if (err == 127)
     fprintf(stderr, "Failed to execute '%s'.\n", cmd), exit(1);

diff --git a/src/dx-canu/src/canu.sh b/src/dx-canu/src/canu.sh
@@ -98,7 +98,8 @@ main() {
 
     if [ ! -s ${output_prefix}.contigs.fasta ]; then
        # save the command without the inputs
-       echo "canu executiveMemory=8 executiveThreads=2 objectStore=DNANEXUS objectStoreClient=dx objectStoreNameSpace=$output_path objectStoreProject=$DX_PROJECT_CONTEXT_ID -d . -p ${output_prefix} genomeSize=${genome_size} $parameters" > canu.sh
+       dx_command=`which dx`
+       echo "canu executiveMemory=8 executiveThreads=2 objectStore=DNANEXUS objectStoreClient=$dx_command objectStoreNameSpace=$output_path objectStoreProject=$DX_PROJECT_CONTEXT_ID -d . -p ${output_prefix} genomeSize=${genome_size} $parameters" > canu.sh
        # bash is set to quit in the app on any error (including file doesn't exist) so we only run rm on success of describe, otherwise nothing
        exists=`dx describe --name $DX_PROJECT_CONTEXT_ID:$output_path/canu.sh || true`
        if [[ -e canu.sh && x$exists != x ]] ; then
@@ -107,6 +108,6 @@ main() {
        dx upload --wait --parents --path $DX_PROJECT_CONTEXT_ID:$output_path/canu.sh canu.sh
 
        # run the canu command
-       canu executiveMemory=8 executiveThreads=2 objectStore=DNANEXUS objectStoreClient=dx objectStoreNameSpace=$output_path objectStoreProject=$DX_PROJECT_CONTEXT_ID -d . -p ${output_prefix} genomeSize=${genome_size} $parameters ${input_type} ${input_files_name[@]}
+       canu executiveMemory=8 executiveThreads=2 objectStore=DNANEXUS objectStoreClient=$dx_command objectStoreNameSpace=$output_path objectStoreProject=$DX_PROJECT_CONTEXT_ID -d . -p ${output_prefix} genomeSize=${genome_size} $parameters ${input_type} ${input_files_name[@]}
     fi
 }
diff --git a/src/pipelines/canu/Grid_DNANexus.pm b/src/pipelines/canu/Grid_DNANexus.pm
@@ -72,7 +72,7 @@ sub buildAvailableNodeList() {
         my @v = split '\|', $_;
 
         my $cpus = $v[$cpuIdx];
-        my $mem  = $v[$memIdx];
+        my $mem  = $v[$memIdx] * 0.85; # the machines don't have swap so save some space for OS overhead
         my $name = $v[$nameIdx];
 
         $mem  = int($mem);