espsite.py.example.suncatfifo

# cluster-dependent definitions
# espresso.py will make use of all "self" variables in config class
# although not necessary for the installation at the suncat cluster,
# we use a named pipe instead of stdio for sending coordinates back to pw.x
# as an example how to set this up
import os

class config:
    def __init__(self):
        self.scratch = '/scratch'
        if not os.path.exists(self.scratch):
            self.scratch = '/tmp'
        self.submitdir = os.getenv('LS_SUBCWD')
        self.batch = self.submitdir!=None
        #check for batch
        if self.batch:
            procs = os.getenv('LSB_HOSTS').split()
            self.procs = procs
            self.jobid = os.getenv('LSB_BATCH_JID')
    
            nprocs = len(procs)
            self.nprocs = nprocs
            d = {}
            for x in procs:
                d[x] = 1
                nodes = list(d.keys())
            nnodes = len(nodes)

            fin,fout = os.popen4('mpirun --version')
            mpiversion=fout.readlines()[0]
            mpiversion=mpiversion.split()[3]
            rsh_agent='orte_rsh_agent'
            if mpiversion[:3]=='1.4':
                rsh_agent='plm_rsh_agent'
        
            self.perHostMpiExec = 'mpiexec --mca '+rsh_agent+' /afs/slac.stanford.edu/package/lsf/bin.slac/gmmpirun_lsgrun.sh -host '+','.join(nodes)+' -np '+str(nnodes)
            self.perProcMpiExec = 'pam -g /afs/slac/g/suncat/bin/suncat-tsmpirun -x LD_LIBRARY_PATH -wdir %s %s'
            self.perSpecProcMpiExec = 'mpiexec --mca '+rsh_agent+' /afs/slac.stanford.edu/package/lsf/bin.slac/gmmpirun_lsgrun.sh -machinefile %s -np %d -wdir %s %s'
            # hack for suncat to make sure RHEL5 nfs disks are automounted
            # must be done before changing directories, otherwise mpirun
            # appears to do "getpwd" and sends the "/a" form of the name
            # to the slave nodes - cpo
            siteInit=self.perHostMpiExec + ' ls '+self.submitdir+'>/dev/null'
            os.system(siteInit)
            
            #how to create fifo
            self.fifogen = 'cd %s; [ -e ase3inpfifo ] || mkfifo ase3inpfifo'
            self.fifo = True

    def do_perProcMpiExec(self, workdir, program):
        os.system(self.fifogen%workdir)
        o = os.popen(self.perProcMpiExec % (workdir, program), 'r')
        return open(workdir+'/ase3inpfifo', 'w+'), o 

    def do_perProcMpiExec_outputonly(self, workdir, program):
        return os.popen(self.perProcMpiExec % (workdir, program), 'r')

    def runonly_perProcMpiExec(self, workdir, program):
        os.system(self.perProcMpiExec % (workdir, program))

    def do_perSpecProcMpiExec(self, machinefile, nproc, workdir, program):
        os.system(self.fifogen%workdir)
        i,o,e = os.popen3(self.perSpecProcMpiExec % (machinefile, nproc, workdir, program))
        return open(workdir+'/ase3inpfifo', 'w+'), o, e