Download & install
Get RELION to run on your computer in 4 easy steps:
Download
Download RELION for free from here
Install
First unpack the tar-ball, and enter the relion directory using:
tar -jxf relion-1.4.tar.bz2
cd relion-1.4
Note that compilation of the parallel version of RELION needs an existing MPI installation on your system. And you'll need the -devel version to link against. We use the open-source flavour openMPI, but in principle any flavour should do. However, in case of trouble, please do try compiling openMPI (with the correct --with_tm reference to your queue setup) on your system before contacting us. Just make sure the mpi executables (e.g. mpiCC and mpirun) are in your PATH and the libraries are in your LD_LIBRARY_PATH. We use the following lines in our .cshrc:
setenv PATH /public/EM/OpenMPI/bin:$PATH
setenv LD_LIBRARY_PATH /public/EM/OpenMPI/lib:$LD_LIBRARY_PATH
For compilation on Mac OSX, also use: "setenv MAC_OSX".
Together with the RELION source code, come tar.gz files for fftw-3.2.2 and fltk-1.3.0. These two external libraries are needed to build RELION. Standard installation of the whole package is performed by executing the following command:
./INSTALL.sh -j 8
Where -j 8 indicates that 8 threads may be used in parallel for compilation. By default the package will be built inside the relion directory. Move the resulting bin/ and lib/ directories to a different place if you want to install RELION elsewhere.
Set-up queue job submission
The GUI allows user to submit jobs to a job queueing system with a single click. For this to work, a template job submission script needs to be provided for the queueing system at hand (e.g. TORQUE, PBS, SGE). In this script a set of strings (variables) in the template script is replaced by the values given in the GUI. The following table contains all defined variables:
| String | Variable type | Meaning |
|---|---|---|
| XXXcommandXXX | string | relion command + arguments |
| XXXqueueXXX | string | Name of the queue to submit job to |
| XXXmpinodesXXX | integer | The number of MPI processes to use |
| XXXthreadsXXX | integer | The number of threads to use on each MPI process |
| XXXcoresXXX | integer | The number of MPI processes times the number of threads |
| XXXdedicatedXXX | integer | The minimum number of cores on each node that should be dedicated to the job (use this to fill entire nodes) |
| XXXnodesXXX | integer | The total number of nodes to be requested |
| XXXextra1XXX | string | Installation-specific, see below |
| XXXextra2XXX | string | Installation-specific, see below |
There are two environment variables that control the use of the entry of the 'Minimum number of dedicated cores per node' on the Running tabs of the GUI: $RELION_MINIMUM_DEDICATED sets its default value (1 if not set); $RELION_ALLOW_CHANGE_MINIMUM_DEDICATED sets whether the user will be able to change this entry. At LMB, we set the default to 24 and do not allow users to change it. In this way, we enforce that our hyper-threaded 12-core nodes get filled up entirely by individual RELION jobs.
By default, the XXXextra1XXX and XXXextra2XXX variables are not used. They provide additional flexibility for queueing systems that require additional variables. They may be activated by setting the $RELION_QSUB_EXTRA1, and $RELION_QSUB_EXTRA2 environment variables, respectively. This will result in extra input fields in the GUI, with the label text being equal to the value of the environment variable. Likewise, their default values (upon starting the GUI) can be set through environment variables $RELION_QSUB_EXTRA1_DEFAULT and $RELION_QSUB_EXTRA2_DEFAULT, respectively. But note that (unlike all other entries in the GUI) the extra values are not remembered from one run to the other.
The template job submission script may be saved in any location. By default, the one used at the LMB is present as gui/qsub.csh in the relion tar-ball. Upon installation this file is copied to the bin directory. It is convenient for the user if he does not have to select this file each time he opens the RELION GUI in a new directory. Therefore, one may set the environment variable $RELION_QSUB_TEMPLATE to point to the location of the script for the system at hand. This value will be pre-set as default in the GUI. (Note the user still has the liberty to define and use his own template!)
IMPORTANT NOTE: If somehow the job queue submission cannot be set up, RELION may still be run in parallel and on a job queueing system. The GUI comprises a Print command button that prints the entire RELION command, including all arguments, to the screen. Pasting of this command to a job queue submission script, and manual submission of this script may then be used to submit the parallel job to a queueing system.
For illustrative purposes, have a look at the following examples:
- SGE template script example used at the LMB
- TORQUE template script example used at the CNB-CSIC
- manual machinefile script example used at Columbia (no queueing system involved)
Edit the environment set-up
The following assumes the program was built in /lmb/home/scheres/app/relion-1.3/; the template script for the queueing system is located in /lmb/home/scheres/app/relion-1.3/bin/qsub.csh; the ctffind3 executable is located in /public/EM/CTFFIND/ctffind3.exe, the resmap executable is in /public/EM/ResMap/ResMap-1.1.4-linux64; and no extra variables are required in this template script.
For csh or tcsh, add the following lines to your ~/.cshrc:
setenv LD_LIBRARY_PATH /lmb/home/scheres/app/relion-1.3/lib:$LD_LIBRARY_PATH
setenv PATH /lmb/home/scheres/app/relion-1.3/bin:$PATH
setenv RELION_QSUB_TEMPLATE "/lmb/home/scheres/app/relion-1.3/bin/qsub.csh"
setenv RELION_CTFFIND3_EXECUTABLE "/public/EM/CTFFIND/ctffind3.exe"
setenv RELION_RESMAP_EXECUTABLE "/public/EM/ResMap/ResMap-1.1.4-linux64"
For bash, add the following lines to your ~/.bashrc:
export LD_LIBRARY_PATH=/lmb/home/scheres/app/relion-1.3/lib:$LD_LIBRARY_PATH
export PATH=/lmb/home/scheres/app/relion-1.3/bin:$PATH
export RELION_QSUB_TEMPLATE="/lmb/home/scheres/app/relion-1.3/bin/qsub.csh"
export RELION_CTFFIND3_EXECUTABLE="/public/EM/CTFFIND/ctffind3.exe"
export RELION_RESMAP_EXECUTABLE="/public/EM/ResMap/ResMap-1.1.4-linux64"