Simplification of xml jobs, added option for VIRGO cluster.

features/io/NicaJobs.cxx

@@ -23,37 +23,41 @@ NicaJobs::NicaJobs(TString name) : fArray(kFALSE), fFile(name), fStartJob(1), fE
   NicaXMLNode* options  = root->GetChild("job_options");
   NicaXMLNode* commands = root->GetChild("job_commands");
   NicaXMLNode* submit   = settings->GetChild("submit");
-  NicaXMLNode* array    = settings->GetChild("array");
   NicaXMLNode* shell    = settings->GetChild("shell");
   fSubmitCommand        = submit->GetValue();
   fSubmitCommand.ReplaceAll("${NICA_PWD}", gSystem->pwd());
+  TString Shell;
   if (shell != nullptr)
-    fShell = shell->GetValue();
+    Shell = shell->GetValue();
   else
-    fShell = "";
+    Shell = "";
+  fCommands.push_back(Shell);
   NicaXMLNode* start_id = settings->GetChild("submit_start");
   NicaXMLNode* end_id   = settings->GetChild("submit_end");
 
   fStartJob = start_id->GetValue().Atoi();
   fEndJob   = end_id->GetValue().Atoi();
+  fSubmitCommand.ReplaceAll("${NICA_START_ARRAY}", Form("%i", fStartJob));
+  fSubmitCommand.ReplaceAll("${NICA_END_ARRAY}", Form("%i", fStartJob));
+
+  if (options->GetAttrib("array")->GetValue() == "yes") { fArray = kTRUE; }
 
-  if (array) {
-    if (array->GetValue().Length() > 0) fArray = kTRUE;
-  }
-  if (fArray) {
-    TString array_command = array->GetValue();
-    array_command.ReplaceAll("${NICA_START_ARRAY}", Form("%i", fStartJob));
-    array_command.ReplaceAll("${NICA_END_ARRAY}", Form("%i", fStartJob));
-    fOptions.push_back(array_command.Data());
-  }
   for (int i = 0; i < options->GetNChildren(); i++) {
     NicaXMLNode* command = options->GetChild(i);
-    fOptions.push_back(command->GetValue());
+    fCommands.push_back(command->GetValue());
   }
+
   for (int i = 0; i < commands->GetNChildren(); i++) {
     NicaXMLNode* command = commands->GetChild(i);
     fCommands.push_back(command->GetValue());
   }
+
+  TString pwd = gSystem->pwd();
+  for (unsigned int i = 0; i < fCommands.size(); i++) {
+    fCommands[i].ReplaceAll("${NICA_START_ARRAY}", Form("%i", fStartJob));
+    fCommands[i].ReplaceAll("${NICA_END_ARRAY}", Form("%i", fStartJob));
+    fCommands[i].ReplaceAll("${NICA_PWD}", pwd);
+  }
 }
 
 void NicaJobs::SubmitJobs() {
@@ -82,16 +86,9 @@ void NicaJobs::SubmitJobs() {
 }
 
 void NicaJobs::CreateJobs() {
-  for (unsigned int i = 0; i < fCommands.size(); i++) {
-    fCommands[i].ReplaceAll("${NICA_PWD}", gSystem->pwd());
-  }
   if (fArray) {
     std::ofstream job_array;
     job_array.open("jobs/job_array");
-    if (fShell.Length() > 0) job_array << fShell << std::endl;
-    for (unsigned int i = 0; i < fOptions.size(); i++) {
-      job_array << fOptions[i] << std::endl;
-    }
     for (unsigned int i = 0; i < fCommands.size(); i++)
       job_array << fCommands[i] << std::endl;
     job_array.close();
@@ -100,12 +97,6 @@ void NicaJobs::CreateJobs() {
     for (int iJob = fStartJob; iJob <= fEndJob; iJob++) {
       std::ofstream job_file;
       job_file.open(Form("jobs/job_%i", iJob));
-      if (fShell.Length() > 0) job_file << fShell << std::endl;
-      for (unsigned int i = 0; i < fOptions.size(); i++) {
-        TString option = fOptions[i];
-        option.ReplaceAll("${NICA_JOB_ID}", Form("%i", iJob));
-        job_file << option << std::endl;
-      }
       for (unsigned int i = 0; i < fCommands.size(); i++) {
         TString commands = fCommands[i];
         commands.ReplaceAll("${NICA_JOB_ID}", Form("%i", iJob));
@@ -117,9 +108,7 @@ void NicaJobs::CreateJobs() {
   }
 }
 
-NicaJobs::~NicaJobs() {
-  // TODO Auto-generated destructor stub
-}
+NicaJobs::~NicaJobs() {}
 
 Int_t NicaJobs::GetNVariables(TString textfile) {
   if (textfile.EndsWith(".xml")) { return GetNVariablesXML(textfile); }

features/io/NicaJobs.h

@@ -19,9 +19,7 @@ class NicaJobs : public TObject {
   TString fFile;
   TString fSubmitCommand;
   Int_t fStartJob, fEndJob;
-  TString fShell;
   std::vector<TString> fCommands;
-  std::vector<TString> fOptions;
   static Int_t GetNVariablesTxt(TString textfile);
   static Int_t GetNVariablesXML(TString xmlfile);
   static TString GetParameterTxt(TString textfile, Int_t job, Int_t var);

features/nicafemto_plus/job_patterns/pbs_array.xml

@@ -3,14 +3,14 @@
 <settings>
   <!--submit command-->
   <submit>qsub ${NICA_JOB_FILE}</submit>
-  <!--array command in options, ${NICA_START_ARRAY}/${NICA_END_ARRAY} will
-   be replaced by submit start/end -->
-  <array>#PBS -t ${NICA_START_ARRAY}-${NICA_END_ARRAY}</array>
   <submit_start>1</submit_start>
   <submit_end>1</submit_end>
   <shell>#!/bin/bash</shell>
 </settings>
-<job_options>
+<job_options array="yes">
+  <!--array command in options, ${NICA_START_ARRAY}/${NICA_END_ARRAY} will
+   be replaced by submit start/end -->
+  <command>#PBS -t ${NICA_START_ARRAY}-${NICA_END_ARRAY}</command>
 <!--job array ids-->
   <!--number of nodes, cores per node walltime-->
   <command>#PBS -l nodes=1:ppn=1,walltime=30:00</command>

features/nicafemto_plus/job_patterns/pbs_single.xml

@@ -3,14 +3,12 @@
 <settings>
   <!--submit command-->
   <submit>qsub ${NICA_JOB_FILE}</submit>
-  <!-- must be emtpy -->
-  <array></array>>
   <!--job ids-->
   <submit_start>1</submit_start>
   <submit_end>1</submit_end>
   <shell>#!/bin/bash</shell>
 </settings>
-<job_options>
+<job_options array="no">
   <!--number of nodes, cores per node walltime-->
   <command>#PBS -l nodes=1:ppn=1,walltime=30:00</command>
   <!--output logs ${NICA_JOB_ID} will be replaced by id-->

features/nicafemto_plus/job_patterns/sbatch_array.xml

@@ -3,14 +3,19 @@
 <settings>
   <!--submit command-->
   <submit>sbatch ${NICA_JOB_FILE}</submit>
-    <!--array command in options, ${NICA_START_ARRAY}/${NICA_END_ARRAY} will
-   be replaced by submit start/end -->
-  <array>#SBATCH --array=${NICA_START_ARRAY}-${NICA_END_ARRAY}</array>
+  <!--  submit command for VIRGO
+  <submit>sbatch --output=${NICA_PWD}/ana2021/%j.out 
+  --error=${NICA_PWD}/%j.errors --time=36:00:00 --array=${NICA_START_ARRAY}-${NICA_END_ARRAY}
+   -p long -- ${NICA_PWD}/${NICA_JOB_FILE}</submit>
+   -->
   <submit_start>1</submit_start>
   <submit_end>2</submit_end>
   <shell>#!/bin/bash</shell>
 </settings>
-<job_options>
+<job_options array="yes">
+  <!--array command in options, ${NICA_START_ARRAY}/${NICA_END_ARRAY} will
+   be replaced by submit start/end -->
+  <command>#SBATCH --array=${NICA_START_ARRAY}-${NICA_END_ARRAY}</command>
   <!--walltime-->
   <command>#SBATCH --time=01:30:00</command>
   <!--errors logs-->

features/nicafemto_plus/job_patterns/sbatch_single.xml

@@ -3,14 +3,12 @@
 <settings>
   <!--submit command-->
   <submit>sbatch ${NICA_JOB_FILE}</submit>
-  <!-- must be emtpy -->
-  <array></array>
   <!--job ids-->
   <submit_start>1</submit_start>
   <submit_end>1</submit_end>
   <shell>#!/bin/bash</shell>
 </settings>
-<job_options>
+<job_options array="no">
   <!--walltime-->
   <command>#SBATCH --time=01:30:00</command>
 </job_options>