Merge branch 'develop'

docker/slurm/Dockerfile

@@ -1,6 +1,6 @@
 FROM ubuntu:latest
-
-RUN apt update && apt install slurmd slurmctld munge openssh-server -y
+ENV DEBIAN_FRONTEND "noninteractive"
+RUN apt update && apt install slurmd slurmctld munge openssh-server openmpi-bin -y
 RUN mkdir -p /home/slurm/
 RUN usermod --shell /bin/bash --home /home/slurm slurm
 RUN chown slurm:slurm /home/slurm

frontend/calcusliveserver.py

@@ -142,6 +142,8 @@ def _test_wrapper(self):
                 else:
                     num += 1
                 print("Test failed, trying again (attempt {}/{})".format(num, MAX_ATTEMPTS))
+                self.cleanupCalculations()
+                self.lget("/home/")
                 time.sleep(3)
             else:
                 break

frontend/cluster_daemon.py

@@ -301,7 +301,7 @@ def _process_command(self, lines):
                     calc.status = 3
                     calc.error_message = "Job cancelled"
                     calc.save()
-                    return
+                return
 
             access = calc.order.resource
 

frontend/gen_calc.py

@@ -50,11 +50,6 @@ def gen_param(params):
         solvation_model = params['solvation_model']
         if 'solvation_radii' in params.keys():
             solvation_radii = params['solvation_radii']
-        else:
-            if solvation_model == "SMD":
-                solvation_radii = "Default"
-            if solvation_model in ["PCM", "CPCM"]:
-                solvation_radii = "UFF"
 
     if 'basis_set' in params.keys():
         basis_set = params['basis_set']

frontend/models.py

@@ -754,7 +754,7 @@ def delete(self, *args, **kwargs):
         if self.new_status:
             with transaction.atomic():
                 p = Profile.objects.select_for_update().get(id=self.author.id)
-                p.unseen_calculations -= 1
+                p.unseen_calculations = max(0, p.unseen_calculations-1)
                 p.save()
         super(CalculationOrder, self).delete(*args, **kwargs)
 

frontend/tasks.py

@@ -93,9 +93,15 @@ def retry():
     try:
         response = conn[1].run("source ~/.bashrc; " + command, hide='both')
     except invoke.exceptions.UnexpectedExit as e:
-        logger.info(f"Got exception {e} for command {command}")
         lock.release()
+        if e.result.exited == 1 and e.result.stderr.find("Invalid job id specified") != -1:
+            return []
+
+        logger.info(f"Command {command} terminated with exception: {e}")
         return []
+    except ConnectionResetError as e:
+        logger.debug("Connection reset")
+        return self.retry()
 
     lock.release()
 
@@ -1498,9 +1504,6 @@ def xtb_stda(in_file, calc):#TO OPTIMIZE
     return ErrorCodes.SUCCESS
 
 def calc_to_ccinput(calc):
-    global PAL
-    global MEM
-
     if calc.parameters.method != "":
         _method = calc.parameters.method
     elif calc.parameters.theory_level.lower() == "hf":
@@ -1515,8 +1518,11 @@ def calc_to_ccinput(calc):
     if software in ['gaussian', 'orca']:
         _specifications += ' ' + getattr(calc.order.author, "default_" + software)
 
+    PAL = int(os.environ.get("NUM_CPU", 1))
+    MEM = int(os.environ.get("OMP_STACKSIZE", "1G")[:-1])*1024*PAL
+
     if is_test:
-        _nproc = PAL
+        _nproc = min(4, PAL)
         _mem = 2000
     else:
         if calc.local:
@@ -2499,7 +2505,7 @@ def analyse_opt_Gaussian(calc):
             s_ind += 1
             xyz += "{}\n\n".format(num_atoms)
             ind += 5
-            while lines[ind].find("---------") == -1:
+            while ind < len(lines) - 2 and lines[ind].find("---------") == -1:
                 try:
                     n, z, T, X, Y, Z = lines[ind].strip().split()
                 except ValueError:
@@ -2957,6 +2963,10 @@ def get_calc(calc_id):
 
     return ret
 
+@app.task
+def del_order(order_id):
+    _del_order(order_id)
+
 @app.task
 def del_project(proj_id):
     _del_project(proj_id)
@@ -2969,6 +2979,16 @@ def del_molecule(mol_id):
 def del_ensemble(ensemble_id):
     _del_ensemble(ensemble_id)
 
+def _del_order(id):
+    o = CalculationOrder.objects.get(pk=id)
+    for c in o.calculation_set.all():
+        _del_calculation(c)
+
+    if o.result_ensemble:
+        _del_ensemble(o.result_ensemble.id)
+
+    # The order is automatically deleted with the last calculation
+
 def _del_project(id):
     proj = Project.objects.get(pk=id)
     proj.author = None
@@ -2983,6 +3003,20 @@ def _del_molecule(id):
         _del_ensemble(e.id)
     mol.delete()
 
+def _del_calculation(calc):
+    if calc.status == 1 or calc.status == 2:
+            kill_calc(calc)
+
+    calc.delete()
+    try:
+        rmtree(os.path.join(CALCUS_SCR_HOME, str(calc.id)))
+    except OSError:
+        pass
+    try:
+        rmtree(os.path.join(CALCUS_RESULTS_HOME, str(calc.id)))
+    except OSError:
+        pass
+
 def _del_ensemble(id):
     try:
         e = Ensemble.objects.get(pk=id)
@@ -2993,35 +3027,14 @@ def _del_ensemble(id):
         _del_structure(s)
 
     for c in e.calculation_set.all():
-        if c.status == 1 or c.status == 2:
-            kill_calc(c)
+        _del_calculation(c)
 
-        c.delete()
-        try:
-            rmtree(os.path.join(CALCUS_SCR_HOME, str(c.id)))
-        except OSError:
-            pass
-        try:
-            rmtree(os.path.join(CALCUS_RESULTS_HOME, str(c.id)))
-        except OSError:
-            pass
     e.delete()
 
 def _del_structure(s):
     calcs = s.calculation_set.all()
     for c in calcs:
-        if c.status == 1 or c.status == 2:
-            kill_calc(c)
-
-        c.delete()
-        try:
-            rmtree(os.path.join(CALCUS_SCR_HOME, str(c.id)))
-        except OSError:
-            pass
-        try:
-            rmtree(os.path.join(CALCUS_RESULTS_HOME, str(c.id)))
-        except OSError:
-            pass
+        _del_calculation(c)
 
     s.delete()
 

frontend/templates/frontend/calculation.html

@@ -303,9 +303,9 @@
 	</script>
 	{% endif %}
 	<script>
-		frame_num = document.getElementById("opt_scroll").value;
 
 		$('#launch_frame_form').submit(function(){
+			frame_num = document.getElementById("opt_scroll").value;
 			$('<input />').attr('type', 'hidden')
 				.attr('name', "frame_num")
 				.attr('value', frame_num)

frontend/templates/frontend/calculationorder.html

@@ -5,56 +5,47 @@
 {% block extrahead %}
 	<link rel="stylesheet" href="{% static 'frontend/uis/jquery-ui-1.11.4.css' %}" type="text/css">
 	<script src="{% static 'frontend/jquery.min.js' %}"></script>
-
-	<script>
-		function cancel(id) {
-			$("#cancel_button_" + id).addClass("is-loading");
-			$.ajax({
-				method: "POST",	 	 
-				url: "/cancel_calc/",
-				headers: {
-					"X-CSRFToken": '{{ csrf_token }}',
-				},
-				data: {'id': id},
-				success: function() {
-					$("#cancel_button_" + id).removeClass("is-loading");
-					$("#cancel_button_" + id).addClass("has-background-success");
-				}
-			});
-
+	<style>
+		#delete_order_button {
+			margin: 50 auto;
+			margin-bottom: 10px;
+			display: block;
 		}
-		function relaunch(id) {
-			$("#relaunch_button_" + id).addClass("is-loading");
+	</style>
+	<script>
+		function calc_action(id, action) {
+			$("#" + action + "_button_" + id).addClass("is-loading");
 			$.ajax({
 				method: "POST",	 	 
-				url: "/relaunch_calc/",
+				url: "/" + action + "_calc/",
 				headers: {
 					"X-CSRFToken": '{{ csrf_token }}',
 				},
 				data: {'id': id},
 				success: function() {
-					$("#relaunch_button_" + id).removeClass("is-loading");
-					$("#relaunch_button_" + id).addClass("has-background-success");
+					$("#" + action + "_button_" + id).removeClass("is-loading");
+					$("#" + action + "_button_" + id).addClass("has-background-success");
 				}
 			});
 
 		}
 
-		function refetch(id) {
-			$("#refetch_button_" + id).addClass("is-loading");
-			$.ajax({
-				method: "POST",	 	 
-				url: "/refetch_calc/",
-				headers: {
-					"X-CSRFToken": '{{ csrf_token }}',
-				},
-				data: {'id': id},
-				success: function() {
-					$("#refetch_button_" + id).removeClass("is-loading");
-					$("#refetch_button_" + id).addClass("has-background-success");
-				}
-			});
-
+		function delete_order(id) {
+			var res = confirm('Delete this calculation order and all its calculations (including resulting structures and ensembles)"?');	
+			if (res) {
+				$("#delete_order_button_").addClass("is-loading");
+				$.ajax({
+					method: "POST",	 	 
+					url: "/delete_order/",
+					headers: {
+						"X-CSRFToken": '{{ csrf_token }}',
+					},
+					data: {'id': {{ order.pk }}},
+					success: function() {
+						window.location.replace("/calculations/");
+					}
+				});
+			}
 		}
 
 	</script>
@@ -91,14 +82,15 @@ <h3 class="title is-h3">Calculation Order {{ order.id }} - {{ order.structure.pa
 						<th><a class="button is-warning" href="/calculation/{{ calc.id}}">{{ calc.id }}</a></th>
 						<th>{{ calc.text_status }}{% if calc.status == 3%} - {{ calc.error_message }}{% endif %}</th>
 						<th>{{ calc.execution_time }}</th>
-						<th>{% if request.user.profile == order.author %}<a class="button is-danger" id="cancel_button_{{ calc.id }}" onclick="cancel({{ calc.id }});">Kill</a> {% if not calc.local %} <a class="button" id="relaunch_button_{{ calc.id }}" onclick="relaunch({{ calc.id }});">Relaunch</a><a class="button" id="refetch_button_{{ calc.id }}" onclick="refetch({{ calc.id }});">Refetch</a> {% endif %}{% endif %}</th>
+						<th>{% if request.user.profile == order.author %}<a class="button is-danger" id="cancel_button_{{ calc.id }}" onclick="calc_action({{ calc.id }}, 'cancel');">Kill</a> {% if not calc.local %} <a class="button" id="relaunch_button_{{ calc.id }}" onclick="calc_action({{ calc.id }}, 'relaunch');">Relaunch</a><a class="button" id="refetch_button_{{ calc.id }}" onclick="calc_action({{ calc.id }}, 'refetch');">Refetch</a> {% endif %}{% endif %}</th>
 					</tr>
 					{% endfor %}
 				</tbody>
 			</table>
 			<a class="button is-primary" href="/download_all_logs/{{ order.id }}">Download all logs</a>	
 		</center>
 	</div>
+	<button class="button is-danger" id="delete_order_button" onclick="delete_order()">Delete this calculation order</button>
 </div>
 <br />
 {% endblock %}

frontend/test_calculations.py

@@ -298,13 +298,16 @@ def test_DFT_default_pop(self):
         self.assertIn("Mulliken:", prop.charges)
         self.assertIn("Loewdin:", prop.charges)
 
+    '''
+    # Not valid with ccinput v1.3.2
     def test_DFT_hirshfeld_pop(self):
         self.assertTrue(self.run_test(type="Geometrical Optimisation", theory_level="DFT",
                 method="M062X", specifications="--phirshfeld",
                 callback=partial(self.cb_has_n_conformers, 1)))
 
         prop = Property.objects.latest('id')
         self.assertIn("Hirshfeld:", prop.charges)
+    '''
 
 class GaussianCalculationTests(CalculationUnitTest):
     @classmethod
@@ -470,14 +473,6 @@ def test_DFT_pop_HLY(self):
         prop = Property.objects.latest('id')
         self.assertIn("HLY:", prop.charges)
 
-    def test_DFT_max_step(self):
-        self.assertTrue(self.run_test(type="Geometrical Optimisation", theory_level="DFT",
-                method="M062X", specifications="opt(maxstep=5)",
-                callback=partial(self.cb_has_n_conformers, 1)))
-
-        calc = Calculation.objects.latest('id')
-        self.assertEqual(calc.parameters.specifications.strip(), 'opt(maxstep=5)')
-
     def test_scan_pop(self):
         self.assertTrue(self.run_test(theory_level="HF", type="Constrained Optimisation",
                 constraints="Scan_3.5_5.0_10/1_2;", specifications="pop(nbo)",