Install relax cloud.sagemath.com
Contents
Purpose
Why ?
- The first installation of relax can be an energy barrier
- It could be of interest to make relax available in "the cloud" for the first analysis, so time is not used on solving software dependencies
Problems with "the cloud"
- Very time consuming to "run an online" cloud.
- The benefits of cloud.sagemath.com are well explained here: http://www.sagemath.org/library-why.html
Other info
- The prizing is here: https://cloud.sagemath.com/policies/pricing.html
- There is also the Bio-NMR initiative: http://www.bio-nmr.net
- And a web service with all NMR software - WeNMR: http://www.wenmr.eu
Possibilities with cloud.sagemath.com
cloud.sagemath.com currently don't provide admin account or dedicated SMC servers.
A purchase for a subscription for $ 49 / month (or $499/year), one can apply the quotas listed here to any projects:
* 16 upgrades Member hosting
* 40 upgrades Network access
* 8 days Idle timeout
* 24 GB Memory
* 40 GB Disk space
* 4 shares CPU shares
* 2 cores CPU cores
The procedure should be
- A new interested scientist would go to SMC, create a project.
- Add relax as a collaborator to their free project, and we would click a button to upgrade their project to member hosting.
- This add network access, increase the cpu shares, etc.
- "We" have a page which lists, for each project, what upgrades "we" have applied
- "We" can also see if the project is being used.
- "We" can remove upgrades at any time (in any granularity).
The value of upgrading to "member hosting" is:
- Computation is much faster. The free pool of computers are typically massively loaded during the week.
- The "free servers" work fine, but they can easily be 15% of the speed of the members-only machines.
- With the $49/month subscription, "we" get to move 16 projects to members-only machines.
Installation and analysis in the cloud
Installation of relax in cloud.sagemath.com
- Instead of making "relax" available for all users on cloud.sagemath.com, each user should install their local copy of relax
- When using svn to checkout relax, there will be a: install_relax_cloud_sagemath_com.sh bash script
- The user now have full control over any version of relax
- The user can potentially "develop" online with subversion
To do Analysis
- Use ssh to send data to the server
- Supported right now, even for free projects. See the button "ssh to your project" in project settings.
- The uploaded data for the researcher is private:
- Even for free projects, data in projects is only visible to collaborators on that project and nobody else.
- SMC is not like github, where free = public by default.
- With SMC everything is private by default, even for free users.
- However, people can also explicitly share any file or directory tree, and that makes it publicly available
- Could be a way to share data related to a paper or research project
- Use relax in the terminal in the server
- Fine for free projects.
The test project at cloud.sagemath.com
This audit was performed: 2015/11/24
Project location
https://cloud.sagemath.com/projects/9cd9d431-3eb2-4cde-a03a-4b9c6b49a1c2/files/test%20ipyth.ipynb
Project resources
Disk space: 3000 MB disk space available - 59 MB used 3000 MB given by free project
Memory: 1000 MB RAM memory available - 133 MB used 1000 MB given by free project
CPU cores:1 core 1 core given by free project
CPU shares: 1 share 1 share given by free project
Idle timeout: 1 hour of non-interactive use before project stops 1 hour given by free project
Network access: Yes 1 upgrade given by free project
Member hosting: No 0 upgrades given by free project
Software at cloud.sagemath.com
Is subversion available
~$ svn --version
svn, version 1.8.10 (r1615264)
Is scons available
~$ which scons
/usr/bin/scons
~$ scons --version
SCons by Steven Knight et al.:
script: v2.3.1, 2014/03/02 14:18:15, by garyo on lubuntu
engine: v2.3.1, 2014/03/02 14:18:15, by garyo on lubuntu
engine path: ['/usr/lib/scons/SCons']
Is xmgrace available
~$ xmgrace
The program 'xmgrace' is currently not installed. To run 'xmgrace' please ask your administrator to install the package 'grace'
~$ grace
The program 'grace' is currently not installed. To run 'grace' please ask your administrator to install the package 'grace'
Is mpirun available
~$ which mpicc
/usr/bin/mpicc
~$ which mpiexec
/usr/bin/mpiexec
~$ which mpirun
/usr/bin/mpirun
~$ mpirun --version
mpirun (Open MPI) 1.6.5
Report bugs to http://www.open-mpi.org/community/help/
~$ mpirun --report-bindings -np 4 echo "hello world"
hello world
hello world
hello world
hello world
python packages at cloud.sagemath.com
Start python
python
Version of python
Python 2.7.9 (default, Apr 2 2015, 15:33:21)
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Paste in
try:
import wx
print wx.__file__
print wx.version()
print wx.__version__
except ImportError:
print "no wx module"
try:
import bmrblib
print bmrblib.__file__
print bmrblib.__version__
except ImportError:
print "no bmrblib module"
try:
import minfx
print minfx.__file__
print minfx.__version__
except ImportError:
print "no minfx module"
try:
import mpi4py
print mpi4py.__file__
print mpi4py.__version__
except ImportError:
print "no mpi4py module"
Output
>>> try:
... import wx
... print wx.__file__
... print wx.version()
... print wx.__version__
... except ImportError:
... print "no wx module"
...
no wx module
>>> try:
... import bmrblib
... print bmrblib.__file__
... print bmrblib.__version__
... except ImportError:
... print "no bmrblib module"
...
no bmrblib module
>>> try:
... import minfx
... print minfx.__file__
... print minfx.__version__
... except ImportError:
... print "no minfx module"
...
no minfx module
>>> try:
... import mpi4py
... print mpi4py.__file__
... print mpi4py.__version__
... except ImportError:
... print "no mpi4py module"
...
no mpi4py module
Install python modules
Bmrblib
See Bmrblib
v={{current version bmrblib}}
mkdir -p $HOME/Downloads
cd $HOME/Downloads
curl http://download.gna.org/bmrblib/bmrblib-$v.tar.gz -o bmrblib-$v.tar.gz
tar -xzf bmrblib-$v.tar.gz
cd bmrblib-$v
pip install .
cd ..
minfx
See Minfx
v=1.0.12
mkdir -p $HOME/Downloads
cd $HOME/Downloads
curl http://download.gna.org/minfx/minfx-$v.tar.gz -o minfx-$v.tar.gz
tar -xzf minfx-$v.tar.gz
cd minfx-$v
pip install .
cd ..
mpi4py
v=2.0.0
mkdir -p $HOME/Downloads
cd $HOME/Downloads
wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-$v.tar.gz
tar -xzf mpi4py-$v.tar.gz
cd mpi4py-$v
pip install .
cd ..
Test python packages
Paste in
try:
import bmrblib
print bmrblib.__file__
print bmrblib.__version__
except ImportError:
print "no bmrblib module"
try:
import minfx
print minfx.__file__
print minfx.__version__
except ImportError:
print "no minfx module"
try:
import mpi4py
print mpi4py.__file__
print mpi4py.__version__
except ImportError:
print "no mpi4py module"
Output
>>> try:
... import bmrblib
... print bmrblib.__file__
... print bmrblib.__version__
... except ImportError:
... print "no bmrblib module"
...
/projects/9cd9d431-3eb2-4cde-a03a-4b9c6b49a1c2/.local/lib/python2.7/site-packages/bmrblib/__init__.pyc
1.0.4
>>> try:
... import minfx
... print minfx.__file__
... print minfx.__version__
... except ImportError:
... print "no minfx module"
...
/projects/9cd9d431-3eb2-4cde-a03a-4b9c6b49a1c2/.local/lib/python2.7/site-packages/minfx/__init__.pyc
1.0.12
>>> try:
... import mpi4py
... print mpi4py.__file__
... print mpi4py.__version__
... except ImportError:
... print "no mpi4py module"
...
/projects/9cd9d431-3eb2-4cde-a03a-4b9c6b49a1c2/.local/lib/python2.7/site-packages/mpi4py/__init__.pyc
2.0.0
Checkout relax and build
cd $HOME
svn co svn://svn.gna.org/svn/relax/trunk relax_trunk
# Build
cd relax_trunk
scons
# Link to executable
cd $HOME
mkdir -p $HOME/bin
ln -s $HOME/relax_trunk/relax $HOME/bin
# Test all of relax with unittests and systemtests
relax --time -u
relax --time -s
relax works!
