Index: /issm/trunk-jpl/src/m/classes/clusters/saga.py
===================================================================
--- /issm/trunk-jpl/src/m/classes/clusters/saga.py	(revision 25818)
+++ /issm/trunk-jpl/src/m/classes/clusters/saga.py	(revision 25818)
@@ -0,0 +1,174 @@
+import subprocess
+from fielddisplay import fielddisplay
+from pairoptions import pairoptions
+from issmssh import issmssh
+from issmscpin import issmscpin
+from issmscpout import issmscpout
+from QueueRequirements import QueueRequirements
+from IssmConfig import IssmConfig
+import datetime
+try:
+    from saga_settings import saga_settings
+except ImportError:
+    print('You need saga_settings.py to proceed, check presence and sys.path')
+
+
+class saga(object):
+    """
+    Saga cluster class definition
+    This is a SLURM queue
+
+       Usage:
+          cluster = saga()
+    """
+
+    def __init__(self, *args):  # {{{
+        self.name = 'saga'
+
+        self.numnodes = 1
+        self.cpuspernode = 20
+        self.mem = 2
+        self.queue = 'normal'
+        self.time = 2 * 60
+
+        self.port = []
+        #set by setting file
+        self.login = ''
+        self.codepath = ''
+        self.executionpath = ''
+        self.accountname = ''
+
+        self.interactive = 0
+        self.profiling = 0
+
+        self.valgrind = '/cluster/software/Valgrind/3.16.1-gompi-2019b/bin/valgrind'
+
+    #use provided options to change fields
+        options = pairoptions(*args)
+    #initialize cluster using user settings if provided
+        self = saga_settings(self)
+    #OK get other fields
+        self = options.AssignObjectFields(self)
+        self.np = self.numnodes * self.cpuspernode
+    # }}}
+
+    def __repr__(self):  # {{{
+        #  display the object
+        s = "class vilje object:"
+        s = "%s\n%s" % (s, fielddisplay(self, 'name', 'name of the cluster'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'login', 'login'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'numnodes', 'number of nodes'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'cpuspernode', 'number of CPUs per nodes'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'mem', 'memory per CPU'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'queue', 'name of the queue (normal (D), bigmem, devel)'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'time', 'walltime requested in minutes'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'codepath', 'code path on the cluster'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'executionpath', 'execution path on the cluster'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'interactive', ''))
+        s = "%s\n%s" % (s, fielddisplay(self, 'accountname', 'your cluster account'))
+        s = "%s\n%s" % (s, fielddisplay(self, 'profiling', 'enable profiling if 1 default is 0'))
+        return s
+    # }}}
+
+    def checkconsistency(self, md, solution, analyses):  # {{{
+        #Queue dictionarry  gives queue name as key and max walltime, cpus and memory (GB) as var
+        queuedict = {'normal': [7 * 24 * 60, 256, 8],
+                     'bigmem': [14 * 24 * 60, 256, 10],
+                     'devel': [2 * 60, 256, 8]}
+        QueueRequirements(queuedict, self.queue, self.np, self.time)
+
+    #Miscelaneous
+        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')
+        if self.interactive == 1:
+            md = md.checkmessage('interactive mode not implemented')
+        return self
+    # }}}
+
+    def BuildQueueScript(self, dirname, modelname, solution, io_gather, isvalgrind, isgprof, isdakota, isoceancoupling):  # {{{
+
+        executable = 'issm.exe'
+        if isdakota:
+            version = IssmConfig('_DAKOTA_VERSION_')[0:2]
+            version = float(version)
+            if version >= 6:
+                executable = 'issm_dakota.exe'
+        if isoceancoupling:
+            executable = 'issm_ocean.exe'
+    #write queuing script
+        shortname = modelname[0:min(12, len(modelname))]
+        timeobj = datetime.timedelta(minutes=self.time)
+        m, s = divmod(timeobj.total_seconds(), 60)
+        h, m = divmod(m, 60)
+        d, h = divmod(h, 24)
+        timestring = "%02d-%02d:%02d:%02d" % (d, h, m, s)
+        print('timestring')
+        fid = open(modelname + '.queue', 'w')
+        fid.write('#!/bin/bash -l\n')
+        fid.write('#SBATCH --job-name=%s \n' % shortname)
+        if self.queue in ['devel']:
+            fid.write('#SBATCH --partition=normal \n')
+            fid.write('#SBATCH --qos=%s \n' % self.queue)
+        else:
+            fid.write('#SBATCH --partition=%s \n' % self.queue)
+
+        fid.write('#SBATCH --nodes=%i \n' % self.numnodes)
+        fid.write('#SBATCH --ntasks-per-node=%i \n' % self.cpuspernode)
+        fid.write('#SBATCH --time={}\n'.format(timestring))  #walltime is minutes
+        fid.write('#SBATCH --mem-per-cpu={}MB\n'.format(int(1000 * self.mem)))  # mem is in MB
+
+        fid.write('#SBATCH --account=%s\n' % self.accountname)
+        fid.write('#SBATCH --output %s/%s/%s.outlog \n' % (self.executionpath, dirname, modelname))
+        fid.write('#SBATCH --error %s/%s/%s.errlog \n\n' % (self.executionpath, dirname, modelname))
+
+        fid.write('export ISSM_DIR="%s/../"\n' % self.codepath)
+        fid.write('module purge\n')
+        fid.write('module load CMake/3.15.3-GCCcore-8.3.0\n')
+        fid.write('module load PETSc/3.12.4-intel-2019b\n')
+        fid.write('module load ParMETIS/4.0.3-iimpi-2019b\n')
+        if isvalgrind:
+            fid.write('module --ignore-cache load Valgrind/3.16.1-gompi-2019b \n')
+
+        fid.write('cd %s/%s/ \n\n' % (self.executionpath, dirname))
+        if isvalgrind:
+            # profiling
+            #fid.write('mpirun {} --tool=callgrind {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog \n'.format(self.valgrind, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname))
+            # leak check
+            fid.write('mpirun {} --leak-check=full {}/{} {} {}/{} {} 2>{}.errlog>{}.outlog '.format(self.valgrind, self.codepath, executable, solution, self.executionpath, dirname, modelname, modelname, modelname))
+        else:
+            fid.write('time mpirun {}/{} {} {}/{} {}\n'.format(self.codepath, executable, solution, self.executionpath, dirname, modelname))
+        fid.close()
+
+    # }}}
+    def UploadQueueJob(self, modelname, dirname, filelist):  # {{{
+        #compress the files into one zip.
+        compressstring = 'tar -zcf %s.tar.gz ' % dirname
+        for file in filelist:
+            compressstring += ' %s' % file
+        subprocess.call(compressstring, shell=True)
+
+        print('uploading input file and queueing script')
+        issmscpout(self.name, self.executionpath, self.login, self.port, [dirname + '.tar.gz'])
+
+    # }}}
+
+    def LaunchQueueJob(self, modelname, dirname, filelist, restart, batch):  # {{{
+
+        print('launching solution sequence on remote cluster')
+        if restart:
+            launchcommand = 'cd %s && cd %s && sbatch %s.queue' % (self.executionpath, dirname, modelname)
+        else:
+            launchcommand = 'cd %s && rm -rf ./%s && mkdir %s && cd %s && mv ../%s.tar.gz ./ && tar -zxf %s.tar.gz  && sbatch %s.queue' % (self.executionpath, dirname, dirname, dirname, dirname, dirname, modelname)
+        issmssh(self.name, self.login, self.port, launchcommand)
+
+    # }}}
+
+    def Download(self, dirname, filelist):  # {{{
+        #copy files from cluster to current directory
+        directory = '%s/%s/' % (self.executionpath, dirname)
+        issmscpin(self.name, self.login, self.port, directory, filelist)
+    # }}}
Index: /issm/trunk-jpl/src/m/classes/model.py
===================================================================
--- /issm/trunk-jpl/src/m/classes/model.py	(revision 25817)
+++ /issm/trunk-jpl/src/m/classes/model.py	(revision 25818)
@@ -42,4 +42,5 @@
 from cyclone import cyclone
 from stallo import stallo
+from saga import saga
 from balancethickness import balancethickness
 from stressbalance import stressbalance
@@ -867,13 +868,13 @@
         md.stressbalance.referential = project2d(md, md.stressbalance.referential, md.mesh.numberoflayers)
         md.stressbalance.loadingforce = project2d(md, md.stressbalance.loadingforce, md.mesh.numberoflayers)
-        # TODO: 
+        # TODO:
         # - Check if md.mesh.numberoflayershould really be offset by 1.
-        # - Find out why md.masstransport.spcthickness is not offset, but the 
+        # - Find out why md.masstransport.spcthickness is not offset, but the
         #   other fields are.
-        # - If offset is required, figure out if it can be abstarcted away to 
+        # - If offset is required, figure out if it can be abstarcted away to
         #   another part of the API.
         if np.size(md.masstransport.spcthickness) > 1:
             md.masstransport.spcthickness = project2d(md, md.masstransport.spcthickness, md.mesh.numberoflayers)
-        if np.size(md.damage.spcdamage) > 1 and not np.isnan(md.damage.spcdamage).all():
+        if np.size(md.damage.spcdamage) > 1:  # and not np.isnan(md.damage.spcdamage).all():
             md.damage.spcdamage = project2d(md, md.damage.spcdamage, md.mesh.numberoflayers - 1)
         if np.size(md.levelset.spclevelset) > 1:
@@ -883,20 +884,20 @@
         # Hydrologydc variables
         if md.hydrology.__class__.__name__ == 'hydrologydc':
-            md.hydrology.spcsediment_head = project2d(md, md.hydrology.spcsediment_head, 1)
-            md.hydrology.mask_eplactive_node = project2d(md, md.hydrology.mask_eplactive_node, 1)
-            md.hydrology.sediment_transmitivity = project2d(md, md.hydrology.sediment_transmitivity, 1)
-            md.hydrology.basal_moulin_input = project2d(md, md.hydrology.basal_moulin_input, 1)
-            if md.hydrology.isefficientlayer == 1:
-                md.hydrology.spcepl_head = project2d(md, md.hydrology.spcepl_head, 1)
-            # hydrofields = md.hydrology.__dict__.keys()
-            # for field in hydrofields:
-            #     try:
-            #         isvector = np.logical_or(np.shape(md.hydrology.__dict__[field])[0] == md.mesh.numberofelements,
-            #                                  np.shape(md.hydrology.__dict__[field])[0] == md.mesh.numberofvertices)
-            #     except IndexError:
-            #         isvector = False
-            #     #we collapse only fields that are vertices or element based
-            #     if isvector:
-            #         md.hydrology.__dict__[field] = project2d(md, md.hydrology.__dict__[field], 1)
+            # md.hydrology.spcsediment_head = project2d(md, md.hydrology.spcsediment_head, 1)
+            # md.hydrology.mask_eplactive_node = project2d(md, md.hydrology.mask_eplactive_node, 1)
+            # md.hydrology.sediment_transmitivity = project2d(md, md.hydrology.sediment_transmitivity, 1)
+            # md.hydrology.basal_moulin_input = project2d(md, md.hydrology.basal_moulin_input, 1)
+            # if md.hydrology.isefficientlayer == 1:
+            #     md.hydrology.spcepl_head = project2d(md, md.hydrology.spcepl_head, 1)
+            hydrofields = md.hydrology.__dict__.keys()
+            for field in hydrofields:
+                try:
+                    isvector = np.logical_or(np.shape(md.hydrology.__dict__[field])[0] == md.mesh.numberofelements,
+                                             np.shape(md.hydrology.__dict__[field])[0] == md.mesh.numberofvertices)
+                except IndexError:
+                    isvector = False
+                #we collapse only fields that are vertices or element based
+                if isvector:
+                    md.hydrology.__dict__[field] = project2d(md, md.hydrology.__dict__[field], 1)
 
         # Materials