netpyne.batchtools.submits

Classes:

`SHSubmit`(**kwargs)
`SHSubmitSFS`(**kwargs)
`SHSubmitSOCK`(**kwargs)
`SGESubmit`(**kwargs)
`SGESubmitSSH`(**kwargs)
`SlurmSubmitSSH`(**kwargs)
`SGESubmitSFS`(**kwargs)
`SGESubmitSOCK`(**kwargs)
`SlurmSubmit`(**kwargs)
`SlurmSubmitSOCK`(**kwargs)

class netpyne.batchtools.submits.SHSubmit(**kwargs)[source]

Bases: Submit

Attributes:

`script_args`
`script_template`
`script_handles`

Methods:

`set_handles`()
`submit_job`(**kwargs)

script_args = {'command', 'env', 'label', 'output_path', 'project_path'}

script_template = '#!/bin/sh\ncd {project_path}\nexport JOBID=$$\n{env}\nnohup {command} > {output_path}/{label}.run 2>&1 &\npid=$!\necho $pid >&1\n'

script_handles = {'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh'}

set_handles()[source]

submit_job(**kwargs)[source]

class netpyne.batchtools.submits.SHSubmitSFS(**kwargs)[source]

Bases: SHSubmit

Attributes:

`script_args`
`script_template`
`script_handles`

script_args = {'command', 'env', 'label', 'output_path', 'project_path'}

script_template = '#!/bin/sh\ncd {project_path}\nexport MSGFILE="{output_path}/{label}.out"\nexport SGLFILE="{output_path}/{label}.sgl"\nexport JOBID=$$\n{env}\nnohup {command} > {output_path}/{label}.run 2>&1 &\npid=$!\necho $pid >&1\n'

script_handles = {'signal_file': '{output_path}/{label}.sgl', 'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh', 'write_file': '{output_path}/{label}.out'}

class netpyne.batchtools.submits.SHSubmitSOCK(**kwargs)[source]

Bases: SHSubmit

Attributes:

`script_args`
`script_template`
`script_handles`

script_args = {'command', 'env', 'label', 'output_path', 'project_path', 'sockname'}

script_template = '#!/bin/sh\ncd {project_path}\nexport SOCNAME="{sockname}"\nexport JOBID=$$\n{env}\nnohup {command} > {output_path}/{label}.run 2>&1 &\npid=$!\necho $pid >&1\n'

script_handles = {'socket_name': '{sockname}', 'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh'}

class netpyne.batchtools.submits.SGESubmit(**kwargs)[source]

Bases: Submit

Attributes:

`script_args`
`script_template`
`script_handles`

Methods:

`submit_job`(**kwargs)
`set_handles`()

script_args = {'command', 'cores', 'env', 'label', 'output_path', 'project_path', 'queue', 'vmemrealtime'}

script_template = '#!/bin/bash\n#$ -N job{label}\n#$ -q {queue}\n#$ -pe smp {cores}\n#$ -l h_vmem={vmem}\n#$ -l h_rt={realtime}\n#$ -o {output_path}/{label}.run\nsource ~/.bashrc\ncd {project_path}\nexport JOBID=$JOB_ID\n{env}\n{command}\n'

script_handles = {'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh'}

submit_job(**kwargs)[source]

set_handles()[source]

class netpyne.batchtools.submits.SGESubmitSSH(**kwargs)[source]

Bases: Submit

Attributes:

`script_args`
`script_template`
`script_handles`

Methods:

`submit_job`(**kwargs)
`set_handles`()

script_args = {'command', 'cores', 'env', 'label', 'output_path', 'project_path', 'queue', 'vmemrealtime'}

script_template = '#!/bin/bash\n#$ -N job{label}\n#$ -q {queue}\n#$ -pe smp {cores}\n#$ -l h_vmem={vmem}\n#$ -l h_rt={realtime}\n#$ -o {output_path}/{label}.run\nsource ~/.bashrc\ncd {project_path}\nexport JOBID=$JOB_ID\nexport MSGFILE="{output_path}/{label}.out"\nexport SGLFILE="{output_path}/{label}.sgl"\n{env}\ntouch $MSGFILE\n{command}\n'

script_handles = {'signal_file': '{output_path}/{label}.sgl', 'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh', 'write_file': '{output_path}/{label}.out'}

submit_job(**kwargs)[source]

set_handles()[source]

class netpyne.batchtools.submits.SlurmSubmitSSH(**kwargs)[source]

Bases: Submit

Attributes:

`script_args`
`script_template`
`script_handles`

Methods:

`submit_job`(**kwargs)
`set_handles`()

script_args = {'allocation', 'command', 'coresPerNode', 'custom', 'email', 'env', 'label', 'nodes', 'output_path', 'partition', 'project_path', 'realtime'}

script_template = '#!/bin/bash\n#SBATCH --job-name={label}\n#SBATCH -A {allocation}\n#SBATCH -t {realtime}\n#SBATCH --nodes={nodes}\n#SBATCH --ntasks-per-node={coresPerNode}\n#SBATCH --cpus-per-task=1\n#SBATCH --mem={mem}\n#SBATCH --partition={partition}\n#SBATCH -o {output_path}/{label}.run\n#SBATCH -e {output_path}/{label}.err\n#SBATCH --mail-user={email}\n#SBATCH --mail-type=end\n#SBATCH --export=ALL\nexport JOBID=$SLURM_JOB_ID\nexport MSGFILE="{output_path}/{label}.out"\nexport SGLFILE="{output_path}/{label}.sgl"\n{env}\n{custom}\ncd {project_path}\n{command}\nwait\n'

script_handles = {'signal_file': '{output_path}/{label}.sgl', 'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh', 'write_file': '{output_path}/{label}.out'}

submit_job(**kwargs)[source]

set_handles()[source]

class netpyne.batchtools.submits.SGESubmitSFS(**kwargs)[source]

Bases: SGESubmit

Attributes:

`script_args`
`script_template`
`script_handles`

script_args = {'command', 'cores', 'env', 'label', 'output_path', 'project_path', 'queue', 'vmemrealtime'}

script_template = '#!/bin/bash\n#$ -N job{label}\n#$ -q {queue}\n#$ -pe smp {cores}\n#$ -l h_vmem={vmem}\n#$ -l h_rt={realtime}\n#$ -o {output_path}/{label}.run\nsource ~/.bashrc\ncd {project_path}\nexport JOBID=$JOB_ID\nexport MSGFILE="{output_path}/{label}.out"\nexport SGLFILE="{output_path}/{label}.sgl"\n{env}\ntouch $MSGFILE\n{command}\n'

script_handles = {'signal_file': '{output_path}/{label}.sgl', 'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh', 'write_file': '{output_path}/{label}.out'}

class netpyne.batchtools.submits.SGESubmitSOCK(**kwargs)[source]

Bases: SGESubmit

Attributes:

`script_args`
`script_template`
`script_handles`

script_args = {'command', 'cores', 'env', 'label', 'output_path', 'project_path', 'queue', 'sockname', 'vmemrealtime'}

script_template = '#!/bin/bash\n#$ -N job{label}\n#$ -q {queue}\n#$ -pe smp {cores}\n#$ -l h_vmem={vmem}\n#$ -l h_rt={realtime}\n#$ -o {output_path}/{label}.run\nsource ~/.bashrc\ncd {project_path}\nexport JOBID=$JOB_ID\nexport SOCNAME="{sockname}"\n{env}\n{command}\n'

script_handles = {'socket_name': '{sockname}', 'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh'}

class netpyne.batchtools.submits.SlurmSubmit(**kwargs)[source]

Bases: Submit

Attributes:

`script_args`
`script_template`
`script_handles`

Methods:

`submit_job`(**kwargs)
`set_handles`()

script_args = {'allocation', 'command', 'coresPerNode', 'custom', 'email', 'label', 'nodes', 'output_path', 'project_path', 'reservation', 'walltime'}

script_template = '#SBATCH --job-name={label}\n#SBATCH -A {allocation}\n#SBATCH -t {walltime}\n#SBATCH --nodes={nodes}\n#SBATCH --ntasks-per-node={coresPerNode}\n#SBATCH -o {output_path}/{label}.run\n#SBATCH -e {output_path}/{label}.err\n#SBATCH --mail-user={email}\n#SBATCH --mail-type=end\nexport JOBID=$SLURM_JOB_ID\n{custom}\n{env}\ncd {project_path}\n{command}\n'

script_handles = {'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh'}

submit_job(**kwargs)[source]

set_handles()[source]

class netpyne.batchtools.submits.SlurmSubmitSOCK(**kwargs)[source]

Bases: SlurmSubmit

Attributes:

`script_args`
`script_template`
`script_handles`

script_args = {'allocation', 'command', 'coresPerNode', 'custom', 'email', 'label', 'nodes', 'output_path', 'project_path', 'reservation', 'walltime'}

script_template = '#SBATCH --job-name={label}\n#SBATCH -A {allocation}\n#SBATCH -t {walltime}\n#SBATCH --nodes={nodes}\n#SBATCH --ntasks-per-node={coresPerNode}\n#SBATCH -o {output_path}/{label}.run\n#SBATCH -e {output_path}/{label}.err\n#SBATCH --mail-user={email}\n#SBATCH --mail-type=end\nexport JOBID=$SLURM_JOB_ID\nexport SOCNAME="{sockname}"\n{custom}\n{env}\ncd {project_path}\n{command}\n'

script_handles = {'socket_name': '{sockname}', 'stdout': '{output_path}/{label}.run', 'submit': '{output_path}/{label}.sh'}