Thread: Access the LSF APIs in Python (with help of SWIG)

To access the LSF APIs in Python I used SWIG to map lsf.h (Adding lsbatch is possible but left out to reduce complexity). First step is the creation of the lsf.i file which SWIG will use:

Code:

/* File: lsf.i */
%module lsf

%{
#define SWIG_FILE_WITH_INIT
#include "lsf/lsf.h"
%}
%ignore ls_placeoftype;
%ignore ls_loadoftype;
%ignore ls_lostconnection;
%ignore ls_gethostrespriority;
%ignore ls_verrlog;
%ignore getBEtime;
%ignore ls_nioinit;
%ignore ls_nioselect;
%ignore ls_nioctl;
%ignore ls_nionewtask;
%ignore ls_nioremovetask;
%ignore ls_niowrite;
%ignore ls_nioclose;
%ignore ls_nioread;
%ignore ls_niotasks;
%ignore ls_niostatus;
%ignore ls_niokill;
%ignore ls_niosetdebug;
%ignore ls_niodump;
%ignore ls_readrexlog;

// howto handle char**
%typemap(in) char ** {
    int size = PyList_Size($input);
    int i = 0;
    $1 = (char **) malloc((size+1)*sizeof(char *));
    for (i = 0; i < size; i++) {
      PyObject *o = PyList_GetItem($input,i);
      $1[i] = PyBytes_AsString(PyUnicode_AsUTF8String(PyList_GetItem($input,i)));
    }
    $1[i] = 0;
}
// cleanup char**
%typemap(freearg) char ** {
  free((char *) $1);
}
//
%include "lsf/lsf.h"

It does nothing more then saying: please provided me with all which is defined in the lsf.h file. This will not work out of the box and some routines need to be excluded/ignored. Next to that we need to define a so called typemap to convert a Python list to a char **. More typemaps might be needed for e.g. return values, and other LSG APIs calls but are left out to reduce complexity.

Now run SWIG and compile the code:

Code:

swig -python lsf.i
gcc -c lsf_wrap.c -I/usr/include/python3.1
ld -shared lsf_wrap.o -o _lsf.so ${LSF_LIBDIR}/liblsf.a ${LSF_LIBDIR}/libbat.a -lc

The result will be a _lsf.so and lsf.py file which now can be used:

Code:

import lsf

if __name__ == '__main__':
    print(lsf.ls_getclustername())
    print(lsf.ls_initrex(1, 0))
    print(lsf.ls_rexecv("ubuntu", ["/bin/ls"], 0))

I run this example on a Ubuntu 10.04 machine running Python 3.1; SWIG 1.3.40 and LSF 7.0.6

The example of a job submission in the Platform LSF Programmer's Guide written in C (Page 64, LSF Version 7.0.6) would reflect to the following code in Python:

Code:

    submitreq = lsf.submit()
    submitreq.command = "/bin/sleep 1000"
    submitreq.options = 0
    submitreq.options2 = 0

    limits = []
    for i in range (0, lsf.LSF_RLIM_NLIMITS):
        limits.append(lsf.DEFAULT_RLIMIT)

    submitreq.rLimits = limits

    submitreq.beginTime = 0
    submitreq.termTime = 0
    submitreq.numProcessors = 1
    submitreq.maxNumProcessors = 1;

    submitreply = lsf.submitReply()

    print(lsf.lsb_init("test"))
    print(lsf.lsb_submit(submitreq, submitreply))

The following lsf.i file was used for SWIG:

Code:

/* File: lsf.i */
%module lsf

%{
#define SWIG_FILE_WITH_INIT
#include "/opt/lsf/7.0/include/lsf/lsf.h"
#include "/opt/lsf/7.0/include/lsf/lsbatch.h"
%}

%ignore ls_placeoftype;
%ignore ls_loadoftype;
%ignore ls_lostconnection;
%ignore ls_gethostrespriority;
%ignore ls_verrlog;
%ignore getBEtime;
%ignore ls_nioinit;
%ignore ls_nioselect;
%ignore ls_nioctl;
%ignore ls_nionewtask;
%ignore ls_nioremovetask;
%ignore ls_niowrite;
%ignore ls_nioclose;
%ignore ls_nioread;
%ignore ls_niotasks;
%ignore ls_niostatus;
%ignore ls_niokill;
%ignore ls_niosetdebug;
%ignore ls_niodump;
%ignore ls_readrexlog;

// howto handle char **
%typemap(in) char ** {
    int size = PyList_Size($input);
    int i = 0;
    $1 = (char **) malloc((size+1)*sizeof(char *));
    for (i = 0; i < size; i++) {
      PyObject *o = PyList_GetItem($input,i);
      $1[i] = PyBytes_AsString(PyUnicode_AsUTF8String(PyList_GetItem($input,i)));
    }
    $1[i] = 0;
}

// cleanup of char **
%typemap(freearg) char ** {
  free((char *) $1);
}

// typemap for time_t
%typemap(in) time_t {
    $1 = (time_t) PyLong_AsLong($input);
}

%typemap(out) time_t {
    $result = PyLong_FromLong((long)$1);
}

%typemap(freearg) time_t {
    free((time_t *) $1);
}

// handle int arrays in struct...
%typemap(in) int [ANY] (int temp[$1_dim0]) {
  int i;
  for (i = 0; i < $1_dim0; i++) {
    PyObject *o = PySequence_GetItem($input,i);
      temp[i] = (int) PyInt_AsLong(o);
  }
  $1 = temp;
}
// allow to set members of int array
%typemap(memberin) int [ANY] {
  int i;
  for (i = 0; i < $1_dim0; i++) {
      $1[i] = $input[i];
  }
}
// access int arrays
%typemap(out) int [ANY] {
  int i;
  $result = PyList_New($1_dim0);
  for (i = 0; i < $1_dim0; i++) {
    PyObject *o = PyLong_FromDouble((int) $1[i]);
    PyList_SetItem($result,i,o);
  }
}

//
%include "/opt/lsf/7.0/include/lsf/lsf.h"
%include "/opt/lsf/7.0/include/lsf/lsbatch.h"

This is released under an LGPL license: https://github.com/tmetsch/pylsf