We provided simple installation scripts for each software package for your convenience; however, we cannot guarantee that they will be sufficient to successfully complete installation. Please, contact SLIM's developers (see SUPPORT section) with any questions or problems encountered during installation.
The 3-rd party software packages included with SLIM software release might require additional prerequisites depending on the version of the operating system and type and/or completeness of its installation. This installation was tested and completes successfully on full installation of x86_64 Linux with operating systems CentOS 5.5 or later (equivalent to RedHat 5.5 or later).
If any step of the installation fails for the 3-rd party software, it might be more effective to consult first your IT support if some of the prerequisites are missing or the included web site for specific instructions suitable for your operating system.
Note! This document covers only installation of SLIM-release-apps-public part of software release. For notes on installation of SLIM-release-comp-public refer to INSTALLATION file in SLIM-release-comp-public repository.
Here are the potential strategies for installing our software in single-/multi-user environment.
Note, that each user must have a personal (or at the very least has to have write permissions) copy of SLIM-release-apps-public in order to to run any applications, since each application is configured to look for data and create directories inside of its own directory.
Personal installation for single user, both SLIM-release-comp-public and SLIM-release-apps-public.
User installs both SLIM-release-comp-public and SLIM-release-apps-public in personal directories.
Multi-user installation of SLIM-release-comp-public and personal installation of SLIM-release-apps-public.
Designated person instals SLIM-release-comp-public in common directory and user installs personal SLIM-release-apps-public.
Multi-user installation of SLIM-release-comp-public, multi-user installation of SLIM-release-apps-public, and personal copy of SLIM-release-apps-public
Designated person instals both SLIM-release-comp-public and SLIM-release-apps-public in common directories, and user obtains personal copy of SLIM-release-apps-public (no installation needed).
In terminal, change directory to the location where you want to install the software and execute the following git command:
git clone git@github.com:SINBADconsortium/SLIM-release-apps-public.git
and the cloned software will be in SLIM-release-apps-public sub-directory.
SLIM is using master branch to develop/add software to repository. To
avoid using the software that is not complete or fully tested, you
might want to use use stable branch. You may switch to stable
branch using the following:
git checkout stable
You must configure your shell environment before you can proceed with installation.
Open terminal window, change directory to the home of SLIM-release-apps-public and do either of the following:
cp environment.sh.template environment.sh
cp environment.csh.template environment.csh
Edit the file created above in an editor and make the following changes accordingly to chosen installation strategy.
Note: if you skipped the installation of SLIM-release-comp-public, leave SLIM_COMP environment as it is in any of the options below.
In personal SLIM-release-apps-public/environment.{sh,csh}:
- SLIM_COMP points to absolute path of user's personal SLIM-release-comp-public
- SLIM_APPS points to absolute path of user's personal SLIM-release-apps-public
- SLIM_APPS_RUNS points to $SLIM_APPS
In personal SLIM-release-apps-public/environment.{sh,csh}:
- SLIM_COMP points to absolute path of common SLIM-release-comp-public
- SLIM_APPS points to absolute path of user's personal SLIM-release-apps-public
- SLIM_APPS_RUNS points to $SLIM_APPS
In common SLIM-release-apps-public/environment.{sh,csh}:
- SLIM_COMP points to absolute path of common SLIM-release-comp-public
- SLIM_APPS points to absolute path of common SLIM-release-apps-public
- SLIM_APPS_RUNS points to $SLIM_APPS
In personal SLIM-release-apps-public/environment.{sh,csh}:
- SLIM_COMP points to absolute path of common SLIM-release-comp-public
- SLIM_APPS points to absolute path of common SLIM-release-apps-public
- SLIM_APPS_RUNS points to absolute path of user's personal SLIM-release-apps-public
In terminal window, in the home of SLIM-release-apps-public do either of the following:
. environment.sh
source environment.csh
Add the following to your default-shell's startup script to make the permanent change to the environment. You will not need then to source environment.sh/csh manually.
. path_to-SLIM-release-apps-public/environment.sh
source path_to-SLIM-release-apps-public/environment.csh
Once configured, you can check if the SLIM_COMP , SLIM_APPS, and SLIM_APPS_RUNS environments are set correctly and verify if MATLAB executables are in the PATH using the following:
test_env4slim.sh
test_env4slim.csh
Users who intend to run their jobs in non-interactive batch mode must add those extra steps. Note, it is not necessary to do those modification while only installing the software for other users.
Make sure to follow the steps in the section above to automatically source environment.* from shell's startup scripts.
First. create ~/matlab directory if it does not exists.
Execute the following command in terminal:
cp $SLIM_APPS/skel/startup_SLIM.m ~/matlab
First, create ~/matlab/startup.m if it does not exist.
Add the following line at the end of ~/matlab/startup.m:
startup_SLIM
The installation relies on correctly set shell environment (see SHELL ENVIRONMENT section) and should be executed in the terminal window only after that particular terminal session have the environment configured. Before starting/continuing with the installation, make sure that your environment was setup according to the instruction above.
7.1 MATLAB version R2014a or later (http://www.mathworks.com/)
We cannot provide here the installation for MATLAB software due to MATLAB license limitation. However, please, make sure to have version R2014a installed at the very least. The test_env4slim.* (mentioned above in SHELL environment section) will check the if necessary MATLAB commands are present, and warn you if version of MATLAB is too old.
Running installation script does not require much time, and typically takes a couple of seconds. The script prints to the screen the information about current stage and the name of the output log. This information will be needed if you encounter any errors during compilation.
To compile MATLAB's mex binaries in SLIM's MATLAB toolboxes execute the following in the terminal:
install_MEX
If you encounter problems during installation (FATAL ERRORS), please, remember to attach the log files from the failing stage of installation while contacting us for support.
To complete the installation, one should run an extra script that will test MATLAB mex binaries. Contrary to installation scripts, the testing script will output its progress to the terminal. Please, check the output for potential errors.The comments in the subsections below explain the meaning of each test.
To run test suite execute the following from the terminal:
install_test4matlab
Note, that the testing suite will stop for a few seconds between each test.
Contact SLIM's developers if any of those tests fail.
This test runs a series of SPOT unit tests and will report results to
the terminal. All tests should report pass in the 3-rd column.
We did not devise yet a proper unit test for SPGL1, so SPGL1 part of the test executes suite of demos. Some of the demos are expected to fail. However the test should neither produce any MATLAB errors nor stop during execution.
This test runs a single Quasi-Newton solver test. It should report
PASSED.
The test runs a few serial tests in Hierarchical Tucker Optimization
toolbox. It should report PASSED.
The test for Linearized Bregman method. It should report PASSED.
This test runs a dot-test for 2D curvelet interface, and only if
SLIM-release-comp-public is installed. It should report PASSED.
This test runs a dot-test for 3D curvelet interface, and only if
SLIM-release-comp-public is installed. It should report PASSED.
This a short test to check MATLAB's RSF interface, and only if
SLIM-release-comp-public is installed. It should report PASSED.
Series of tests for algorithm in tools/algorithms/3DFreqModeling. It
should report PASSED.
Series of tests for algorithm in tools/algorithms/2DFreqModeling. It
should report PASSED.
Unit tests for miscellaneous operators in directory tools/operators/misc
Tests in this category require parallel MATLAB license. All tests use
default MATLAB's parallel pool configuration with 2 workers.
This test runs a series of pSPOT unit tests and will report results to
the terminal. It will utilize 2 workers to check parallel
functionality. All tests should report pass in the 3-rd column.
Note, this test will fail if you do not have working (not installed of lacking the license) at the least MATLAB's Parallel Toolbox, or your worker configuration is constrained for minimum number of workers bigger then 2. Then the test will report that it is not able to open properly parallel session, so called 'parallel pool'.
The test runs a few parallel tests in Hierarchical Tucker Optimization
toolbox. It should report PASSED.
Series of tests for algorithm in tools/algorithms/2DFreqModeling. It
should report PASSED.
Series of tests for functions in tools/algorithms/3DFreqModeling/
including tools/solvers/Krylov. It should report PASSED.
Series of tests for algorithm in tools/algorithms/2DFreqModeling. It
should report PASSED.
You may contact developers of SINBAD software by means of:
Subscribe to [SINBAD software mailing list] (http://slim.eos.ubc.ca/mailman/listinfo/slimsoft) and e-mail your question to the mailing list.
Contact SLIM administrator with any questions related to the SINBAD software release.