Infiniband and other.

roles/scipion/tasks/main.yaml

@@ -8,14 +8,14 @@
 - name: Change owner
   file:
     path: "{{ scipion_home_dir }}"
-    owner: centos
-    group: centos
+    owner: "{{ user_name }}"
+    group: "{{ user_name }}"
     recurse: yes
 
 - name: Run config
   command: "/usr/bin/python {{ scipion_home_dir }}/scipion config --overwrite"
   become: yes
-  become_user: centos
+  become_user: "{{ user_name }}"
 
 - name: Change scipion.config 1
   lineinfile:
@@ -38,15 +38,15 @@
 - name: Run config
   command: "/usr/bin/python {{ scipion_home_dir }}/scipion config"
   become: yes
-  become_user: centos
+  become_user: "{{ user_name }}"
 
 
 - name: Create directory /services
   file:
     path: /services
     state: directory
-    owner: centos
-    group: centos
+    owner: "{{ user_name }}"
+    group: "{{ user_name }}"
 
 - name: Web protocols
   blockinfile:
@@ -71,8 +71,8 @@
   lineinfile:
     dest: "{{ scipion_home_dir }}/config/hosts.conf"
     regexp: '^PARALLEL_COMMAND'
-    line: "PARALLEL_COMMAND = /usr/lib64/openmpi/bin/mpirun -hostfile /home/centos/mpi_hosts -np %_(JOB_NODES)d -bynode -x LD_LIBRARY_PATH={{ scipion_home_dir }}/software/lib:$LD_LIBRARY_PATH -x PATH={{ scipion_home_dir }}/software/em/xmipp/bin:$PATH %_(COMMAND)s"
-
+#    line: "PARALLEL_COMMAND = /usr/lib64/openmpi/bin/mpirun -hostfile /home/centos/mpi_hosts -np %_(JOB_NODES)d -bynode -x LD_LIBRARY_PATH={{ scipion_home_dir }}/software/lib:$LD_LIBRARY_PATH -x PATH={{ scipion_home_dir }}/software/em/xmipp/bin:$PATH %_(COMMAND)s"
+    line: "PARALLEL_COMMAND = /usr/lib64/openmpi/bin/mpirun -hostfile /home/centos/mpi_hosts --mca pml obl -np %_(JOB_NODES)d --mca plm_rsh_no_tree_spawn true --map-by node -x LD_LIBRARY_PATH={{ scipion_home_dir }}/software/lib:$LD_LIBRARY_PATH -x PATH={{ scipion_home_dir }}/software/em/xmipp/bin:$PATH %_(COMMAND)s"
 - name: Change mpi hostfile
   lineinfile:
     dest: "{{ mpi_hosts_file }}"

roles/scipion/vars/main.yml

@@ -5,3 +5,4 @@ alig_url: "http://dior.ics.muni.cz/~cuda/aliment.tar.gz"
 scipion_config_file: "/opt/scipion-web/config/scipion.conf"
 mpi_hosts_file: "/home/centos/mpi_hosts"
 scipion_home_dir: "/opt/scipion-web"
+user_name: "centos"

ostack.yml → scipion.yml

@@ -2,20 +2,22 @@
   hosts: localhost
   gather_facts: false
   vars:
+    cluster_id: "ng"
     os_image: "MU-CentOS-7-64-bit"
     flavor_name: "m1.medium"
     network_name: "private"
     key_name: "debian"
-    volume_name: "scipion_volume_ng"
-    master_name: "masterng"
-    worker_name: "workerng"
+    volume_name: "scipion_volume_{{ cluster_id }}"
+    volume_size: 50
+    master_name: "master_{{ cluster_id }}"
+    worker_name: "worker_{{ cluster_id }}"
     count: 5
 
   tasks:
     - name: Create a volume
       os_volume:
         state: present
-        size: 50
+        size: {{ volume_size }}
         display_name: "{{ volume_name }}"
 
     - name: Deploy a master