Index: /issm/trunk-jpl/src/m/classes/clusters/smce_eis.py
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/smce_eis.py	(revision 26419)
+++ /issm/trunk-jpl/src/m/classes/clusters/smce_eis.py	(revision 26419)
@@ -0,0 +1,222 @@
+import subprocess
+
+try:
+    from smce_eis_settings import smce_eis_settings
+except ImportError:
+    print('You need smce_eis_settings.py to proceed, check presence and sys.path')
+from fielddisplay import fielddisplay
+from helpers import *
+from IssmConfig import IssmConfig
+from issmscpin import issmscpin
+from issmscpout import issmscpout
+from issmssh import issmssh
+from MatlabFuncs import *
+from pairoptions import pairoptions
+from QueueRequirements import QueueRequirements
+
+class smce_eis(object):
+    """SMCE_EIS cluster class definition
+
+    Usage:
+        cluster = smce_eis()
+        cluster = smce_eis('np', 3)
+        cluster = smce_eis('np', 3, 'login', 'username')
+    """
+
+    def __init__(self, *args):  # {{{
+        self.name = oshostname()
+        self.login = ''
+        self.modules = []
+        self.numnodes = 20
+        self.cpuspernode = 8
+        self.port = 0
+        self.queue = 'general'
+        self.time = 12 * 60 * 60
+        self.processor = 'west'
+        self.srcpath = '/shared/issm/issm/trunk-jpl'
+        self.codepath = '/shared/issm/issm/trunk-jpl/bin'
+        self.executionpath = ''
+        self.grouplist = ''
+        self.interactive = 0
+        self.bbftp = 0
+        self.numstreams = 8
+        self.hyperthreading = 0
+        self.email = ''
+
+        # Use provided options to change fields
+        options = pairoptions(*args)
+
+        # Initialize cluster using user settings if provided
+        try:
+            self = smce_eis_settings(self)
+        except NameError:
+            print('smce_eis_settings.py not found, using default settings')
+
+        # OK get other fields
+        self = options.AssignObjectFields(self)
+    # }}}
+
+    def __repr__(self):  # {{{
+        # Display the object
+        s = 'class smce_eis object\n'
+        s += '    name: {}\n'.format(self.name)
+        s += '    login: {}\n'.format(self.login)
+        s += '    modules: {}\n'.format(strjoin(self.modules, ', '))
+        s += '    numnodes: {}\n'.format(self.numnodes)
+        s += '    cpuspernode: {}\n'.format(self.cpuspernode)
+        s += '    np: {}\n'.format(self.nprocs())
+        s += '    port: {}\n'.format(self.port)
+        s += '    queue: {}\n'.format(self.queue)
+        s += '    time: {}\n'.format(self.time)
+        s += '    processor: {}\n'.format(self.processor)
+        s += '    srcpath: {}\n'.format(self.srcpath)
+        s += '    codepath: {}\n'.format(self.codepath)
+        s += '    executionpath: {}\n'.format(self.executionpath)
+        s += '    grouplist: {}\n'.format(self.grouplist)
+        s += '    interactive: {}\n'.format(self.interactive)
+        s += '    bbftp: {}\n'.format(self.bbftp)
+        s += '    numstreams: {}\n'.format(self.numstreams)
+        s += '    hyperthreading: {}\n'.format(self.hyperthreading)
+        return s
+    # }}}
+
+    def nprocs(self):  # {{{
+        return self.numnodes * self.cpuspernode
+    # }}}
+
+    def checkconsistency(self, md, solution, analyses):  # {{{
+        queuedict = {'long': [24 * 60 * 60, 560],
+                     'allnccs': [12 * 60 * 60, 6000],
+                     'debug': [1 * 60 * 60, 532]}
+        QueueRequirements(queuedict, self.queue, self.nprocs(), self.time)
+
+        # Now, check cluster.cpuspernode according to processor type
+        if self.processor == 'sand':
+            if self.cpuspernode > 16 or self.cpuspernode < 1:
+                md = md.checkmessage('cpuspernode should be between 1 and 16 for \'sand\' processors in hyperthreading mode')
+        elif self.processor == 'hasw':
+            if self.cpuspernode > 28 or self.cpuspernode < 1:
+                md = md.checkmessage('cpuspernode should be between 1 and 28 for \'hasw\' processors in hyperthreading mode')
+        else:
+            md = md.checkmessage('unknown processor type, should be \'sand\' or \'hasw\'')
+
+        # Miscellaneous
+        if not self.login:
+            md = md.checkmessage('login empty')
+        if not self.codepath:
+            md = md.checkmessage('codepath empty')
+        if not self.executionpath:
+            md = md.checkmessage('executionpath empty')
+
+        return self
+    # }}}
+
+    def BuildQueueScript(self, dirname, modelname, solution, io_gather, isvalgrind, isgprof, isdakota, isoceancoupling):  # {{{
+        if isgprof:
+            print('gprof not supported by cluster, ignoring...')
+
+        executable = 'issm.exe'
+        if isdakota:
+            version = IssmConfig('_DAKOTA_VERSION_')[0:2]
+            version = float(str(version[0]))
+            if version >= 6:
+                executable = 'issm_dakota.exe'
+        if isoceancoupling:
+            executable = 'issm_ocean.exe'
+
+        # Write queuing script
+        fid = open(modelname + '.queue', 'w')
+
+        fid.write('#!/bin/bash\n')
+        fid.write('#SBATCH -J {} \n'.format(modelname))
+        fid.write('#SBATCH --qos={} \n'.format(self.queue))
+        fid.write('#SBATCH -o {}.outlog \n'.format(modelname))
+        fid.write('#SBATCH -e {}.errlog \n'.format(modelname))
+        fid.write('#SBATCH -n {} \n'.format(self.nprocs()))
+        fid.write('#SBATCH -N {} \n'.format(self.numnodes))
+        fid.write('#SBATCH -t {:02d}:{:02d}:00 \n'.format(int(floor(self.time / 3600)), int(floor(self.time % 3600) / 60)))
+        fid.write('#SBATCH -A {} \n\n'.format(self.grouplist))
+        if (self.email.find('@')>-1):
+            fid.write('#SBATCH --mail-user={} \n'.format(self.email))
+            fid.write('#SBATCH --mail-type=end \n\n')
+        # fid.write('. /usr/share/modules/init/bash\n\n')
+        # for i in range(len(self.modules)):
+        #     fid.write('module load {}\n'.format(self.modules[i]))
+        fid.write('export MPI_GROUP_MAX=64\n\n')
+        fid.write('export MPI_UNBUFFERED_STDIO=true\n\n')
+        fid.write('export PATH="$PATH:."\n\n')
+        fid.write('export ISSM_DIR="{}"\n'.format(self.srcpath)) # FIXME
+        fid.write('source $ISSM_DIR/etc/environment.sh\n') # FIXME
+        fid.write('cd {}/{}/\n\n'.format(self.executionpath, dirname))
+
+        fid.write('mpiexec -np {} {}/{} {} {}/{} {}\n'.format(self.nprocs(), self.codepath, executable, solution, self.executionpath, dirname, modelname))
+
+        if not io_gather: # concatenate the output files
+            fid.write('cat {}.outbin.* > {}.outbin'.format(modelname, modelname))
+        fid.close()
+
+        # In interactive mode, create a run file, and errlog and outlog file
+        if self.interactive:
+            fid = open(modelname + '.run', 'w')
+            if not isvalgrind:
+                fid.write('mpiexec -np {} {}/{} {} {}/{} {}\n'.format(self.nprocs(), self.codepath, executable, solution, self.executionpath, dirname, modelname))
+            else:
+                fid.write('mpiexec -np {} valgrind --leak-check=full {}/{} {} {}/{} {}\n'.format(self.nprocs(), self.codepath, executable, solution, self.executionpath, dirname, modelname))
+            if not io_gather: # concatenate the output files
+                fid.write('cat {}.outbin.* > {}.outbin'.format(modelname, modelname))
+            fid.close()
+            fid = open(modelname + '.errlog', 'w') # TODO: Change this to system call (touch <file>)?
+            fid.close()
+            fid = open(modelname + '.outlog', 'w') # TODO: Change this to system call (touch <file>)?
+            fid.close()
+    # }}}
+
+    def UploadQueueJob(self, modelname, dirname, filelist):  # {{{
+        # Compress the files into one zip
+        compressstring = 'tar -zcf {}.tar.gz'.format(dirname)
+        for file in filelist:
+            compressstring += ' {}'.format(file)
+        if self.interactive:
+            compressstring += ' {}.run {}.errlog {}.outlog'.format(modelname, modelname, modelname)
+        subprocess.call(compressstring, shell=True)
+
+        print('uploading input file and queueing script')
+        if self.interactive:
+            directory = '{}/Interactive{}'.format(self.executionpath, self.interactive)
+        else:
+            directory = self.executionpath
+
+        if self.bbftp:
+            issmbbftpout(self.name, directory, self.login, self.port, self.numstreams, '{}.tar.gz'.format(dirname))
+        else:
+            issmscpout(self.name, directory, self.login, self.port, ['{}.tar.gz'.format(dirname)])
+    # }}}
+
+    def LaunchQueueJob(self, modelname, dirname, filelist, restart, batch):  # {{{
+        if self.interactive:
+            if not isempty(restart):
+                launchcommand = 'cd {}/Interactive{}'.format(self.executionpath, self.interactive)
+            else:
+                launchcommand = 'cd {}/Interactive{} && tar -zxf {}.tar.gz'.format(self.executionpath, self.interactive, dirname)
+        else:
+            if not isempty(restart):
+                launchcommand = 'cd {} && cd {} && sbatch {}.queue'.format(self.executionpath, dirname, modelname)
+            else:
+                launchcommand = 'cd {} && rm -rf ./{} && mkdir {} && cd {} && mv ../{}.tar.gz ./ && tar -zxf {}.tar.gz && sbatch {}.queue'.format(self.executionpath, dirname, dirname, dirname, dirname, dirname, modelname)
+
+        print('launching solution sequence on remote cluster')
+        issmssh(self.name, self.login, self.port, launchcommand)
+    # }}}
+
+    def Download(self, dirname, filelist):  # {{{
+        # Copy files from cluster to current directory
+        if self.interactive:
+            directory = '{}/Interactive{}'.format(self.executionpath, self.interactive)
+        else:
+            directory = '{}/{}/'.format(self.executionpath, dirname)
+
+        if self.bbftp:
+            issmbbftpin(self.name, self.login, self.port, self.numstreams, directory, filelist)
+        else:
+            issmscpin(self.name, self.login, self.port, directory, filelist)
+    # }}}