batch_command.h

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#include "function_set.h"
 
#include <map>
#include <string>
 
struct batch_commands
{
    string scheduler_run_job;
    string array_dependency_option, job_dependency_option;
    string sheduler_priority_option, sheduler_queue_option, sheduler_qos_option, sheduler_workdir_option;
    string operative_memory1_option;
    string sheduler_hosts_option;
    string sheduler_exclude_hosts_option;
    char sheduler_hosts_separation;
    string set_job_variables, check_status_command, queue_count_command, cancel_command, run_command,
        container_run_command;
    string batch_temp_directory, batch_task_id;
    string job_begin;
    char job_dependency_separator;
    batch_commands()
        : scheduler_run_job("")
        , array_dependency_option("")
        , job_dependency_option("")
        , sheduler_priority_option("")
        , sheduler_queue_option("")
        , sheduler_qos_option("")
        , sheduler_workdir_option("")
        , operative_memory1_option("")
        , sheduler_hosts_option("")
        , sheduler_exclude_hosts_option("")
        , sheduler_hosts_separation(',')
        , set_job_variables("")
        , check_status_command("")
        , queue_count_command("")
        , cancel_command("")
        , run_command("")
        , container_run_command("")
        , batch_temp_directory("")
        , batch_task_id("")
        , job_begin("")
        , job_dependency_separator(':')
    {}
    batch_commands(string str_scheduler_run_job,
                   string str_array_dependency_option,
                   string str_job_dependency_option,
                   string str_sheduler_priority_option,
                   string str_sheduler_queue_option,
                   string str_sheduler_qos_option,
                   string str_sheduler_workdir_option,
                   string str_operative_memory1_option,
                   string str_sheduler_hosts_option,
                   string str_sheduler_exclude_hosts_option,
                   char c_sheduler_hosts_separation,
                   string str_set_job_variables,
                   string str_check_status_command,
                   string str_queue_count_command,
                   string str_cancel_command,
                   string str_run_command,
                   string str_container_run_command,
                   string str_batch_temp_directory,
                   string str_batch_task_id,
                   string str_job_begin,
                   char c_job_dependency_separator)
        : scheduler_run_job(str_scheduler_run_job)
        , array_dependency_option(str_array_dependency_option)
        , job_dependency_option(str_job_dependency_option)
        , sheduler_priority_option(str_sheduler_priority_option)
        , sheduler_queue_option(str_sheduler_queue_option)
        , sheduler_qos_option(str_sheduler_qos_option)
        , sheduler_workdir_option(str_sheduler_workdir_option)
        , operative_memory1_option(str_operative_memory1_option)
        , sheduler_hosts_option(str_sheduler_hosts_option)
        , sheduler_exclude_hosts_option(str_sheduler_exclude_hosts_option)
        , sheduler_hosts_separation(c_sheduler_hosts_separation)
        , set_job_variables(str_set_job_variables)
        , check_status_command(str_check_status_command)
        , queue_count_command(str_queue_count_command)
        , cancel_command(str_cancel_command)
        , run_command(str_run_command)
        , container_run_command(str_container_run_command)
        , batch_temp_directory(str_batch_temp_directory)
        , batch_task_id(str_batch_task_id)
        , job_begin(str_job_begin)
        , job_dependency_separator(c_job_dependency_separator)
    {}
};
 
map<BATCH_SYSTEM_NAME, batch_commands> mapBS = {
    {SGE_BATCH_SYSTEM,   // Sun Grid Engine commands
     {/*string scheduler_run_job = */ "qsub -N %s %s -t 1-%d -tc %d",
      /*string array_dependency_option = */ "-hold_jid_ad ",
      /*string job_dependency_option = */ "-hold_jid ",
      /*string sheduler_priority_option = */ " -p %d",
      /*string sheduler_queue_option = */ " -q %s",
      /*string sheduler_qos_option = */ "",
      /*string sheduler_workdir_option = */ " -wd %s",
      /*string operative_memory1_option = */ " -l h_vmem=%sM",
      /*string sheduler_hosts_option = */ " -l h=\"(%s)\"",
      /*string sheduler_exclude_hosts_option = */ " -l h=\"!(%s)\"",
      /*char   sheduler_hosts_separation = */ '|',
      /*string set_job_variables = */ " -v ",
      /*string check_status_command = */ "qstat",
      /*string queue_count_command = */ "qstat -u \"$USER\" 2>/dev/null | awk 'NR>2 {count++} END {print count+0}'",
      /*string cancel_command = */ "qdel %s",
      /*string run_command = */ "qsub",
      /*string container_run_command = */ "qrsh",
      /*string batch_temp_directory = */ "${TMPDIR}",
      /*string batch_task_id = */ "$SGE_TASK_ID",
      /*string job_begin = */
      "#!/bin/bash\n#$ -j y\n#$ -cwd\n#$ -S /bin/bash\n\n"
      "echo \"Start date: `date` (host: `hostname`)\"\n"
      "echo \"Current directory: `pwd`\"\n\n",
      /*char   job_dependency_separator = */ ','}},
    {SLURM_BATCH_SYSTEM,   // SLURM commands
     {/*string scheduler_run_job = */ "sbatch -J %s %s -a 1-%d%%%d",
      /*string array_dependency_option = */ "-d aftercorr:",
      /*string job_dependency_option = */ "-d afterany:",
      /*string sheduler_priority_option = */ " --nice=%d",
      /*string sheduler_queue_option = */ " -p %s",
      /*string sheduler_qos_option = */ " -q %s",
      /*string sheduler_workdir_option = */ " -D %s",
      /*string operative_memory1_option = */ " --mem-per-cpu=%sM",
      /*string sheduler_hosts_option = */ " -w %s",
      /*string sheduler_exclude_hosts_option = */ " -x %s",
      /*char   sheduler_hosts_separation = */ ',',
      /*string set_job_variables = */ " --export=",
      /*string check_status_command = */ "squeue",
      /*string queue_count_command = */ "squeue -h -u \"$USER\" 2>/dev/null | wc -l",
      /*string cancel_command = */ "scancel %s",
      /*string run_command = */ "sbatch",
      /*string container_run_command = */ "srun",
      /*string batch_temp_directory = */ "${TMPDIR}",
      /*string batch_task_id = */ "$SLURM_ARRAY_TASK_ID",
      /*string job_begin = */
      "#!/bin/bash\n\n"
      "echo \"Start date: `date` (host: `hostname`)\"\n"
      "echo \"Current directory: `pwd`\"\n\n",
      /*char   job_dependency_separator = */ ':'}},
    {TORQUE_BATCH_SYSTEM,   // Torque commands
     {/*string scheduler_run_job = */ "qsub -N %s %s -t 1-%d%%%d",
      /*string array_dependency_option = */ "-W depend=afteranyarray:",   //? unclear for implementation
      /*string job_dependency_option = */ "-W depend=afterany:",
      /*string sheduler_priority_option = */ " -p %d",
      /*string sheduler_queue_option = */ " -q %s",
      /*string sheduler_qos_option = */ " -l qos=%s",
      /*string sheduler_workdir_option = */ " -w %s",
      /*string operative_memory1_option = */ " -l pmem=%smb",
      /*string sheduler_hosts_option = */ " -l nodes=%s",
      /*string sheduler_exclude_hosts_option = */ " -l excludenodes=%s",
      /*char  sheduler_hosts_separation = */ '+',
      /*string set_job_variables = */ " -v ",
      /*string check_status_command = */ "qstat",
      /*string queue_count_command = */
      "qstat -u \"$USER\" 2>/dev/null | awk -v user=\"$USER\" '$0 ~ user {count++} END {print count+0}'",
      /*string cancel_command = */ "qdel %s",
      /*string run_command = */ "qsub",
      /*string container_run_command = */ "qrsh",
      /*string batch_temp_directory = */ "${TMPDIR}",
      /*string batch_task_id = */ "$PBS_ARRAYID",
      /*string job_begin = */
      "#!/bin/bash\n#PBS -j oe\n#PBS -d .\n#PBS -S /bin/bash\n\n"
      "echo \"Start date: `date` (host: `hostname`)\"\n"
      "echo \"Current directory: `pwd`\"\n\n",
      /*char   job_dependency_separator = */ ':'}}};