Difference: SoftwareInstallation (1 vs. 15)

Revision 152019-05-07 - MartinMarinus

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Revision 142019-04-04 - ReneJanssen

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SoftwareInstallation

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  If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell.
Changed:
<
<

Making software available using guix

>
>

Making software available using GUIX

 Guix is a package manager and is installed for general use.
Line: 136 to 136
 

Making software available using LMOD

Deleted:
<
<
 #Making software available using LMOD.
Added:
>
>

Making software available using SINGULARITY

Singularity (docker compatible but more secure) is available on the compute-nodes (n00XX).
You can download docker- or singularity- images and run your programs in singularty.
p.e. R and SAIGE module :

You can execute this in a qlogin session.

SAIGE on singularity(image)
# Download a singularty image for SAIGE:
singularity pull shub://singularity-hub.org/statgen/singularity-saige

# Login into the container
singularity shell ./statgen-singularity-saige-master-latest.simg

# Check if SAIGE is available

R
installed.packages() 
q()
n

# run a R script in the container
# create 1.R
library("SAIGE") 
print("Hello World!") 

# You can run this in a qsub script
# Run your code by :
singularity exec ./saige-0.35.8.1.simg Rscript 1.R

SAIGE on singularity with docker image

singularity pull docker://wzhou88/saige:0.35.8.1
singularity shell ./saige:0.35.8.1
R
installed.packages()
q()
n

# run
singularity exec ./saige-0.35.8.1.simg Rscript 1.R

Revision 132018-02-20 - ReneJanssen

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 61 to 61
  Now, we'll have to "configure" and "make" this:
Changed:
<
<
./configure --prefix=/hpc/local/CentOS6/bofh/R-3.0.2

>
>
./configure --prefix=/hpc/local/CentOS7/bofh/R-3.0.2

 make make install
Changed:
<
<
Where you replace "/hpc/local/CentOS6/bofh/R-3.0.2" with some path where you have write-access. Something like "/hpc/local/CentOS6/YOURGROUP/R-3.0.2" would probably be a good choice.
>
>
Where you replace "/hpc/local/CentOS7/bofh/R-3.0.2" with some path where you have write-access. Something like "/hpc/local/CentOS7/YOURGROUP/R-3.0.2" would probably be a good choice.
  Now, you would start this version of R by entering the full path:
Changed:
<
<
/hpc/local/CentOS6/bofh/R-3.0.2/bin/R
>
>
/hpc/local/CentOS7/bofh/R-3.0.2/bin/R
 
Changed:
<
<
Or by adding the directory /hpc/local/CentOS6/YOURGROUP/R-3.0.2/bin to your own PATH (e.g. in your $HOME/.bash_profile).
>
>
Or by adding the directory /hpc/local/CentOS7/YOURGROUP/R-3.0.2/bin to your own PATH (e.g. in your $HOME/.bash_profile).
 

R packages

Revision 122018-01-31 - ReneJanssen

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 111 to 111
  If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell.
Changed:
<
<

Making software available using LMOD

>
>

Making software available using guix

Guix is a package manager and is installed for general use.
You can find information in the and

Add these lines in your ~/.bash_profile file to enable guix .

# guix environment 
# see : https://hpcguix.op.umcutrecht.nl/getting-started 

export PATH=$PATH:"/gnu/profiles/base/bin"

GX_PROFILE="$HOME/.guix-profile"
if [ -f "$GX_PROFILE/etc/profile" ]; then
  . "$GX_PROFILE/etc/profile"
fi

Making software available using LMOD

  #Making software available using LMOD.

Revision 112017-12-21 - ReneJanssen

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 44 to 44
 pip list
pip install --user <module>

Added:
>
>
Create your virtual software environment for a specific Python project with Python Virtual Environment :
see : http://docs.python-guide.org/en/latest/dev/virtualenvs
 

Your own R version

Revision 102017-03-27 - ReneJanssen

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 83 to 83
  Alternatively, you can customize your Linux environment variables and set R_LIBS to /hpc/local/osversion/group/path. This way, you can leave out the path specification in R.
Added:
>
>
Check
module load R
R
find.package('<mypackage>')

 

Perl libraries

To install CPAN perl libraries, you first have to instruct CPAN which directory to use. You can do this by modifying your CPAN configuration, from within the CPAN shell:

Revision 92016-12-07 - ReneJanssen

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META TOPICPARENT name="WebHome"

SoftwareInstallation

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  That is it! You can check the user documentation of the installed software for details of how to run the application.
Added:
>
>

Python modules

use pip to install python modules.
module load python
module list
pip list
pip install --user <module>

 

Your own R version

Go to http://cran-mirror.cs.uu.nl/, download the latest "R-3.0.whatever.tar.gz" file to a submit host (hpcs01/hpcs02).

Line: 93 to 101
  If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell.
Deleted:
<
<
 

Making software available using LMOD

#Making software available using LMOD.

Revision 82016-03-09 - HinriKerstens

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META TOPICPARENT name="WebHome"

SoftwareInstallation

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  If you find a software to be of general interest to HPC users, let us know. We can provide is as an software module or install it as a system package (rpm) and update it on a regular basis.
Changed:
<
<
However, if you are dependent on a specific version of a software package and don't want regular updates, we advise you to install it yourself and encourage you to take the benefits of using the lmod software module system.
>
>
However, if you are dependent on a specific version of a software package and don't want regular updates, we advise you to install it yourself and encourage you to take the benefits of #Making software available using LMOD.
 

How to install your own software

Line: 96 to 96
 

Making software available using LMOD

Added:
>
>
#Making software available using LMOD.

Revision 72016-03-09 - HinriKerstens

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 13 to 14
 

Software of general interest

Changed:
<
<
If you find a software to be of general interest to HPC users, let us know. We can install it and update it on a regular basis. There is one condition: the software of interest needs to be available as an RPM package.
>
>
If you find a software to be of general interest to HPC users, let us know. We can provide is as an software module or install it as a system package (rpm) and update it on a regular basis.
 
Changed:
<
<
However, if you are dependent on a specific version of a software package and don't want regular updates, we advise you to install it yourself.
>
>
However, if you are dependent on a specific version of a software package and don't want regular updates, we advise you to install it yourself and encourage you to take the benefits of using the lmod software module system.
 

How to install your own software

Line: 41 to 46
  Go to http://cran-mirror.cs.uu.nl/, download the latest "R-3.0.whatever.tar.gz" file to a submit host (hpcs01/hpcs02). Copy this file to a directory that has enough space (about 300M). In this case, let's assume /tmp, but your homedir probably has enough space as well.
Changed:
<
<
cd /tmp

>
>
cd /tmp

 wget http://cran-mirror.cs.uu.nl/src/base/R-3/R-3.0.2.tar.gz tar -zxvf R-3.0.2.tar.gz cd R-3.0.2

Now, we'll have to "configure" and "make" this:

Changed:
<
<
./configure --prefix=/hpc/local/CentOS6/bofh/R-3.0.2

>
>
./configure --prefix=/hpc/local/CentOS6/bofh/R-3.0.2

 make make install
Line: 60 to 61
 Where you replace "/hpc/local/CentOS6/bofh/R-3.0.2" with some path where you have write-access. Something like "/hpc/local/CentOS6/YOURGROUP/R-3.0.2" would probably be a good choice.

Now, you would start this version of R by entering the full path:

Changed:
<
<
/hpc/local/CentOS6/bofh/R-3.0.2/bin/R

>
>
/hpc/local/CentOS6/bofh/R-3.0.2/bin/R

 

Or by adding the directory /hpc/local/CentOS6/YOURGROUP/R-3.0.2/bin to your own PATH (e.g. in your $HOME/.bash_profile).

Line: 74 to 72
 
R
install.packages( "yourLibrary", lib = "/hpc/local/osversion/group/path" )
Changed:
<
<
library( "yourLibrary", lib.loc = "/hpc/local/osversion/group/path" )
>
>
library( "yourLibrary", lib.loc = "/hpc/local/osversion/group/path" )
  Alternatively, you can customize your Linux environment variables and set R_LIBS to /hpc/local/osversion/group/path. This way, you can leave out the path specification in R.
Line: 89 to 85
 o conf makepl_arg "INSTALLDIRS=site INSTALL_BASE=/hpc/local/osversion/group" o conf prefer_installer MB o conf prerequisites_policy follow
Changed:
<
<
o conf commit
>
>
o conf commit
  After this, CPAN should install all perl libraries in the appropriate directory such that they are available on the entire cluster. Your PERLLIB environment variable should be set to include /hpc/local/OSVERSION/GROUP/lib/perl5.
Line: 99 to 94
 If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell.

Added:
>
>

Making software available using LMOD

Revision 62015-03-17 - PatrickKemmeren

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 97 to 97
 In the past, the environment variable PERL_INSTALL_ROOT used to be used for cpan installs, but that doesn't work anymore and wreaks havoc on the install if you use the cpan configuration shown above. I.o.w., be sure not to define PERL_INSTALL_ROOT.

If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell. \ No newline at end of file

Added:
>
>

Revision 52014-01-13 - MartinMarinus

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 39 to 39
 

Your own R version

Changed:
<
<
to be written
>
>
Go to http://cran-mirror.cs.uu.nl/, download the latest "R-3.0.whatever.tar.gz" file to a submit host (hpcs01/hpcs02). Copy this file to a directory that has enough space (about 300M). In this case, let's assume /tmp, but your homedir probably has enough space as well.

cd /tmp
wget http://cran-mirror.cs.uu.nl/src/base/R-3/R-3.0.2.tar.gz
tar -zxvf R-3.0.2.tar.gz
cd R-3.0.2

Now, we'll have to "configure" and "make" this:

./configure --prefix=/hpc/local/CentOS6/bofh/R-3.0.2
make
make install

Where you replace "/hpc/local/CentOS6/bofh/R-3.0.2" with some path where you have write-access. Something like "/hpc/local/CentOS6/YOURGROUP/R-3.0.2" would probably be a good choice.

Now, you would start this version of R by entering the full path:

/hpc/local/CentOS6/bofh/R-3.0.2/bin/R

Or by adding the directory /hpc/local/CentOS6/YOURGROUP/R-3.0.2/bin to your own PATH (e.g. in your $HOME/.bash_profile).

 

R packages

Revision 42013-08-27 - PhilipLijnzaad

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META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 7 to 7
 

Can I install my own software?

The answer is: yes, (of course) you can. There is a group-specific directory that is made available for this purpose:

Changed:
<
<
/hpc/local/version/group/
>
>
/hpc/local/osversion/group/
 
Changed:
<
<
Note that version is the current Linux version and group is your own group name. Here, you can install any software you like and maintain it yourself. See here for explanations how to install C, Perl or R packages.
>
>
Note that osversion is the current Linux version and group is your own group name. Here, you can install any software you like and maintain it yourself. See here for explanations how to install C, Perl or R packages.
 

Software of general interest

Added:
>
>
 If you find a software to be of general interest to HPC users, let us know. We can install it and update it on a regular basis. There is one condition: the software of interest needs to be available as an RPM package.

However, if you are dependent on a specific version of a software package and don't want regular updates, we advise you to install it yourself.

Line: 19 to 20
 

How to install your own software

A specific directory is made available for group-specific software to be installed:

Changed:
<
<
/hpc/local/version/group/
>
>
/hpc/local/osversion/group/
 

C software

You can download your C software of interest and unpack it in this directory. Typically, a pre-installation configuration is done by executing:

Changed:
<
<
./configure --prefix /hpc/local/version/group/package
>
>
./configure --prefix /hpc/local/osversion/group/package

This will create a "Makefile" which explains to the "make" utility how the software should be compiled, and where the software will be installed. The 'prefix' is the top directory under which the whole package will be installed. You may want to include the package version number in the name of this directory; that way you can install more than one version next to each other. Use symlinks to point to the 'default' installation.

 
Changed:
<
<
This will create a "Makefile" which explains to the "make" utility how the software should be compiled. Compiling of the software is done using:
>
>
After the configure step, you compile the software using:
 
make

The Makefile will be read, building the application binaries. To install these binaries, use:

Line: 44 to 47
 
R
Changed:
<
<
install.packages( "yourLibrary", lib = "/hpc/local/version/group/path" ) library( "yourLibrary", lib.loc = "/hpc/local/version/group/path" )
>
>
install.packages( "yourLibrary", lib = "/hpc/local/osversion/group/path" ) library( "yourLibrary", lib.loc = "/hpc/local/osversion/group/path" )
 
Changed:
<
<
Alternatively, you can customize your Linux environment variables and set R_LIBS to /hpc/local/version/group/path. This way, you can leave out the path specification in R.
>
>
Alternatively, you can customize your Linux environment variables and set R_LIBS to /hpc/local/osversion/group/path. This way, you can leave out the path specification in R.
 

Perl libraries

Line: 57 to 59
 
cpan
Changed:
<
<
o conf mbuildpl_arg "installdirs=site install_base=/hpc/local/version/group" o conf makepl_arg "INSTALLDIRS=site INSTALL_BASE=/hpc/local/version/group"
>
>
o conf mbuildpl_arg "installdirs=site install_base=/hpc/local/osversion/group" o conf makepl_arg "INSTALLDIRS=site INSTALL_BASE=/hpc/local/osversion/group"
 o conf prefer_installer MB o conf prerequisites_policy follow o conf commit
Changed:
<
<
After this, CPAN should install all perl libraries in the appropriate directory such that they are available on the entire cluster.
>
>
After this, CPAN should install all perl libraries in the appropriate directory such that they are available on the entire cluster. Your PERLLIB environment variable should be set to include /hpc/local/OSVERSION/GROUP/lib/perl5.

In the past, the environment variable PERL_INSTALL_ROOT used to be used for cpan installs, but that doesn't work anymore and wreaks havoc on the install if you use the cpan configuration shown above. I.o.w., be sure not to define PERL_INSTALL_ROOT.

  If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell.

Revision 32013-05-31 - KatrinSameith

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

SoftwareInstallation

Line: 34 to 34
  That is it! You can check the user documentation of the installed software for details of how to run the application.
Added:
>
>

Your own R version

to be written

R packages

Packages can easily be installed inside R by providing a local path:

R
install.packages( "yourLibrary", lib = "/hpc/local/version/group/path" )
library( "yourLibrary", lib.loc = "/hpc/local/version/group/path" )

Alternatively, you can customize your Linux environment variables and set R_LIBS to /hpc/local/version/group/path. This way, you can leave out the path specification in R.

 

Perl libraries

To install CPAN perl libraries, you first have to instruct CPAN which directory to use. You can do this by modifying your CPAN configuration, from within the CPAN shell:

Line: 50 to 67
 After this, CPAN should install all perl libraries in the appropriate directory such that they are available on the entire cluster.

If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell.

Deleted:
<
<

R packages

Packages can easily be installed inside R by providing a local path:

R
install.packages( "yourLibrary", lib = "/hpc/local/version/group/path" )
library( "yourLibrary", lib.loc = "/hpc/local/version/group/path" )

Alternatively, you can customize your Linux environment variables and set R_LIBS to /hpc/local/version/group/path. This way, you can leave out the path specification in R.

Revision 22013-05-31 - KatrinSameith

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

SoftwareInstallation

Added:
>
>

Can I install my own software?

The answer is: yes, (of course) you can. There is a group-specific directory that is made available for this purpose:

/hpc/local/version/group/

Note that version is the current Linux version and group is your own group name. Here, you can install any software you like and maintain it yourself. See here for explanations how to install C, Perl or R packages.

 

Software of general interest

If you find a software to be of general interest to HPC users, let us know. We can install it and update it on a regular basis. There is one condition: the software of interest needs to be available as an RPM package.

However, if you are dependent on a specific version of a software package and don't want regular updates, we advise you to install it yourself.

Changed:
<
<

How to install group-specific software

>
>

How to install your own software

  A specific directory is made available for group-specific software to be installed:
/hpc/local/version/group/

Revision 12013-05-30 - KatrinSameith

Line: 1 to 1
Added:
>
>
META TOPICPARENT name="WebHome"

SoftwareInstallation

Software of general interest

If you find a software to be of general interest to HPC users, let us know. We can install it and update it on a regular basis. There is one condition: the software of interest needs to be available as an RPM package.

However, if you are dependent on a specific version of a software package and don't want regular updates, we advise you to install it yourself.

How to install group-specific software

A specific directory is made available for group-specific software to be installed:

/hpc/local/version/group/

C software

You can download your C software of interest and unpack it in this directory. Typically, a pre-installation configuration is done by executing:

./configure --prefix /hpc/local/version/group/package

This will create a "Makefile" which explains to the "make" utility how the software should be compiled. Compiling of the software is done using:

make

The Makefile will be read, building the application binaries. To install these binaries, use:

make install

That is it! You can check the user documentation of the installed software for details of how to run the application.

Perl libraries

To install CPAN perl libraries, you first have to instruct CPAN which directory to use. You can do this by modifying your CPAN configuration, from within the CPAN shell:

cpan
o conf mbuildpl_arg "installdirs=site install_base=/hpc/local/version/group"
o conf makepl_arg "INSTALLDIRS=site INSTALL_BASE=/hpc/local/version/group"
o conf prefer_installer MB
o conf prerequisites_policy follow
o conf commit

After this, CPAN should install all perl libraries in the appropriate directory such that they are available on the entire cluster.

If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell.

R packages

Packages can easily be installed inside R by providing a local path:

R
install.packages( "yourLibrary", lib = "/hpc/local/version/group/path" )
library( "yourLibrary", lib.loc = "/hpc/local/version/group/path" )

Alternatively, you can customize your Linux environment variables and set R_LIBS to /hpc/local/version/group/path. This way, you can leave out the path specification in R.

 
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