View source for Install relax cloud.sagemath.com

== 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. <br>
A purchase for a subscription for $ 49 / month (or $499/year), one can apply the quotas listed here to any projects:

<source lang="text">
* 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
</source>

'''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===
<source lang="bash">
https://cloud.sagemath.com/projects/9cd9d431-3eb2-4cde-a03a-4b9c6b49a1c2/files/test%20ipyth.ipynb
</source>

===Project resources===
<source lang="bash">
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
</source>

==Software at cloud.sagemath.com==
===Is subversion available===
<source lang="bash">
~$ svn --version
svn, version 1.8.10 (r1615264)
</source>

===Is scons available===
<source lang="bash">
~$ 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']
</source>

===Is xmgrace available===
<source lang="bash">
~$ 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'
</source>

===Is mpirun available===
<source lang="bash">
~$ 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
</source>

==python packages at cloud.sagemath.com==
Start python
<source lang="bash">
python
</source>

Version of python
<source lang="bash">
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.
</source>

Paste in
<source lang="python">
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"
</source>

Output
<source lang="python">
>>> 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
</source>

== Install python modules ==

===Bmrblib===
See [[Bmrblib]]
<source lang="bash">
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 ..
</source>

===minfx===
See [[Minfx]]
<source lang="bash">
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 ..
</source>

===mpi4py===
See [[OpenMPI#Install_mpi4py]]
<source lang="bash">
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 ..
</source>

===Test python packages===
Paste in
<source lang="python">
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"
</source>

Output
<source lang="python">
>>> 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
</source>

==Checkout relax and build==
<source lang="bash">
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
</source>

'''relax works!'''

== See also ==
[[Category:Devel tutorial]]