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Commit ee369609 authored by Radim Peša's avatar Radim Peša
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ubuntu changes

parent 7bcc0c77
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......@@ -15,10 +15,11 @@ Default number of worker nodes is 5, but it can be changed by setting variable *
Scipion Web Tools cluster can be started in the following way:
```bash
ansible-playbook scipion.yml -e count=3 -e cluster_id=cl -e os=centos
ansible-playbook scipion.yml -e count=3 -e number_of_mpi=24 -e cluster_id=cl -e os=centos
```
where
* **count** is number of worker nodes
* **number_of_mpi** is number of MPI for XmippProtReconstructSignificant
* **cluster_id** is cluster identification, it is used as suffix in instances and volume names
* **os** is preferred operating system, Two options (centos and ubuntu) are supported.
---
#user_name: "centos"
#home_dir: "/home/centos"
......@@ -18,5 +18,4 @@
- gsl-devel.x86_64
- libX11.x86_64
- gcc-gfortran.x86_64
- mc
- screen
......@@ -60,7 +60,7 @@
[WEB_PROTOCOLS]
XmippProtRansac = {"useQueue": 0, "numberOfThreads": 4, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
EmanProtInitModel = {"useQueue": 0, "numberOfThreads": 4, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
XmippProtReconstructSignificant = {"useQueue": 0, "numberOfThreads": 1, "numberOfMpi": 16, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
XmippProtReconstructSignificant = {"useQueue": 0, "numberOfThreads": 1, "numberOfMpi": {{ number_of_mpi }}, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
XmippProtAlignVolumeForWeb = {"useQueue": 0, "numberOfThreads": 4, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
ProtMovieAlignment = {"useQueue": 0, "numberOfThreads": 1, "numberOfMpi": 1, "queueParams" : ["gpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
XmippProtCreateMask3D = {"useQueue": 0, "numberOfThreads": 1, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
......@@ -77,7 +77,7 @@
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 --mca pml ob1 -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"
line: "PARALLEL_COMMAND = {{ mpi_bin_dir }}/mpirun -hostfile {{ home_dir }}/mpi_hosts --mca pml ob1 -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 }}"
......
---
#binary_url: "http://dior.ics.muni.cz/~cuda/scipion_web_bin.tgz"
#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"
---
#user_name: "centos"
#home_dir: "/home/centos"
---
- name: Update operating system
yum: name=* state=latest update_cache=yes
- name: install scipion prerequisities
yum: name={{ item }} state=present
with_items:
- screen
- mc
......@@ -4,4 +4,9 @@
apt: update_cache=yes
- name: upgrade a server
apt: upgrade=dist
- name: install packages
apt: name={{ item }} state=present
with_items:
- screen
- mc
---
#home_dir: "/home/centos"
......@@ -4,3 +4,4 @@ user_name: "centos"
home_dir: "/home/centos"
mpi_hosts_file: "/home/centos/mpi_hosts"
binary_url: "http://dior.ics.muni.cz/~cuda/scipion_web_bin.tgz"
mpi_bin_dir: "/usr/lib64/openmpi/bin"
---
count: 5
count: 2
cluster_id: "ngc"
flavor_name: "m1.xlarge"
network_name: "private"
......@@ -13,3 +13,4 @@ worker_name: "worker_{{ cluster_id }}"
alig_url: "http://dior.ics.muni.cz/~cuda/aliment.tar.gz"
scipion_config_file: "/opt/scipion-web/config/scipion.conf"
scipion_home_dir: "/opt/scipion-web"
number_of_mpi: 16
......@@ -7,3 +7,4 @@ home_dir: "/home/ubuntu"
mpi_hosts_file: "/home/ubuntu/mpi_hosts"
binary_url: "http://dior.ics.muni.cz/~cuda/scipion_web_bin_u.tgz"
#binary_url: "http://dior.ics.muni.cz/~cuda/scipion_v1.0.1_2016-06-30_linux64.tgz"
mpi_bin_dir: "/usr/bin"
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