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| This page is targeted at those who have access to the FreeSurfer source code, and wish to build this source code on their own Unix platform (whether it be an NMR Martinos Center platform, which has all required libraries, or on some arbitrary Unix platform, where the dependent libraries must be installed prior to building FreeSurfer). | This page is targeted at Martinos Center users who wish to inspect, build or develop within the !FreeSrufer code base. Non-Martinos users wishing to work with the !FreeSrufer code base should consult the read-only git repo http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page |
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| Users can download !FreeSurfer source code via the git repo: | First thing users at the Martinos Center will need to do is add the newer version of the {{{git}}} and {{{git-annex}}} software to their PATH environment variable. This should be added to the {{{.cshrc}}} or {{{.bashrc}}} file in the users home directory: {{{ ## csh $> setenv PATH /usr/pubsw/packages/git-annex/current/bin:$PATH ## bash $> export PATH=/usr/pubsw/packages/git-annex/current/bin:$PATH }}} Users can then clone !FreeSurfer repository as follows: |
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| The !FreeSurfer repository contains a large number data files, distributed via the {{{git-annex}}} software, which are not included with a default {{{git clone}}} of the repo. Users who only want the repository for the purposes of compiling binaries and/or inspecting source code, the {{{git clone}}} command from above is all you need to do. Users at the Center who want to run build time checks, or perform a full local installation, or just want all the contents of the repository, will need to run the following commands: Put {{{git-annex}}} in your PATH: {{{ (bash) $> export PATH=/usr/pubsw/packages/git-annex/current/bin:$PATH (csh) $> setenv PATH /usr/pubsw/packages/git-annex/current/bin:$PATH }}} Get the data files: {{{ $> git annex get . }}} ==== Remote git Access ==== Outside of the Martinos Center, users can download !FreeSurfer source code via the read-only git repo: {{{ $> git clone https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/freesurfer.git }}} === Configuring === It is necessary to run a pre-configure script, to create the platform specific tools required by configure (execute in the {{{freesurfer}}} directory created by {{{git clone}}}): {{{ $> ./setup_configure }}} This script runs a set of commands (aclocal, libtoolize, automake v1.9.6, autoconf v2.59) that creates the platform specific files for configure and puts them in the 'dev/config' directory. Now you need to configure your building parameters for your machine: {{{ ./configure }}} This runs the {{{configure}}} script which checks a bunch of local settings and libraries that are needed. Users at the Martinos Center should for the most part fine with the default settings, but the {{{configure}}} script does accept many options for pointing to specific libraries and other build specific parameters. Type {{{./configure --help}}} for a full list of options. The one exception is if a user want to perform a local installation of the freesurfer, he/she should use the {{{--prefix}}} flag. For example: |
The !FreeSurfer repository contains a large number of data files (pdfs, test data, etc) which are not normally included with a default {{{git clone}}} of the repo. Users who wish to clone the repository for the purposes of just inspecting source code and/or build the code, the {{{git clone}}} command from above is all that is required. Users who want to run build time checks, or perform a full local installation, or just want all the data files contained in the repository, will need to run the following command: |
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| $> ./configure --prefix=~/work/freesurfer | ## Change directories $> cd freesurfer ## Get only the data files required for build time checks (1.9 GB) $> git annex get --metadata fstags=makecheck . ## Get only the data files required for local installation (4.3 GB) $> git annex get --metadata fstags=makeinstall . ## Just give me everything! Not Recommended (6.8 GB) $> git annex get . |
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| You can now run 'make', edit and build code, etc. The first thing you should do is 'make' to build libraries like libutils. (Note that all libs will be built to your local checkout directory.) To just build libutils, cd into utils/ and run make. | ==== Setup Configure ==== |
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| You can now compile individual programs or all of them at once. To compile all of them, just run 'make' from dev/. Binaries will automatically be placed in their individual subdirectories. Like this: | It is necessary to run a pre-configure script, to create the platform specific tools required by configure (execute in the {{{freesurfer}}} directory created by {{{git clone}}}). This script runs a set of commands (aclocal, libtoolize, automake v1.9.6, autoconf v2.59) that creates the platform specific files for configure and puts them in the 'fsdev/config' directory. |
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| cd dev make -j 9 |
$> ./setup_configure |
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| Handy hint: the -j 9 option to make tells it to run nine simultaneous make processes, which, if building on a multi-processor machine, can speed-up the build. | ==== Configure ==== |
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| You may just want to compile one binary at a time, for instance, if you are developing an app. To do so, cd to the directory of the program you want and use 'make' to compile it: {{{ cd mri_info make }}} This creates mri_info in the mri_info/ directory. === Adding a new binary to the tree === Assuming that you have a source file {{{MYPROG.c}}} that compiles into MYPROG and want to add it to the FreeSurfer tree: 1) Make the directory in dev and copy the source file there. Name the directory MYPROG and the source file {{{MYPROG.c}}}. |
Now you need to configure your building parameters for your machine by running the {{{configure}}} script. Users at the Martinos Center should for the most part be fine with the default settings, but the {{{configure}}} script does accept many options for pointing to specific libraries and other build specific parameters. One exception is if a user wants to perform a local installation of !FreeSurfer, he/she should use the {{{--prefix}}} flag. Type {{{./configure --help}}} for a full list of options. For example: |
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| mkdir dev/MYPROG cp MYPROG.c dev/MYPROG |
## Default configuration $> ./configure ## Specify an installation location $> ./configure --prefix=~/freesurfer_install_dir ## See all possible options $> ./configure --help |
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| 2) Tell the autotools to build your program when you type {{{make}}} from the top dir: | |
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| a) Modify {{{dev/configure.in}}} to add {{{MYPROG/Makefile}}} to the list of files in the definition of {{{AC_OUTPUT}}} (these are in roughly alphabetical order). | !FreeSurfer builds against the following set of open-sourced libraries, which are installed under the {{{/usr/pubsw/packages}}} directory on all NMR computers: || Package || Version || || Package || Version || || CUDA || v5.0.35-rh5 || || ANN || v1.1 || || tiffjpegglut || v3.6, v6b, v3.7 || || itk || v3.16 || || VTK || v5.6 || || VXL || v1.14 || || MNI || v1.5 || || tcltktixblt || v8.4, v8.4, v8.1, v2.4z || || KWWWidgets || CVS checkout || || Qt || v4.7 || || wxWidgets || v2.8 || || cppunit || v1.10 || || xawplus || v3.1 || || petsc || v2.3 || All these packages will be found by default by the {{{./configure}}} script. But there are options to specify where certain packages exists if a user wishes to build against a different version of one of the open-source libraries. For example: |
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| AC_OUTPUT( ... other files ... MYPROG/Makefile ) |
## Specify a specific version of qt $> ./configure --with-qt=/usr/pubsw/packages/qt/4.8.5 |
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| b) Modify {{{dev/Makefile.am}}} to add {{{MYPROG}}} to the {{{SUBDIRS}}} definition. (You can also alternatively add it to the end of {{{MRISUBDIRS}}} or {{{MRISSUBDIRS}}} if more appropriate.) | ==== Compile ==== You can now run 'make' to build the all individual programs in the !FreeSurfer source tree. Binaries will automatically be placed in their individual subdirectories. |
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| SUBDIRS= ... other directories ... MYPROG | $> make -j 4 }}} ''Handy hint: the -j 4 option to make tells it to run four simultaneous make processes, which, if building on a multi-processor machine, can speed-up the build.'' If you want to compile just one binary at a time, for example, if you are developing an app, than {{{cd}}} to the directory of the program you want and use 'make' to compile it: {{{ $> cd mri_info $> make }}} This creates mri_info in the mri_info/ directory. However, be aware the many program depends on the existence of libraries having already been build like libutils. Therefore users will need to build a few of the library directories first (e.g. utils, fsgdf, xml2, etc). ==== Install ==== To install all binaries and support files into your private !FreeSurfer installation, type 'make install' from the toplevel fsdev/ directory, like this: {{{ $> make install |
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| c) Copy {{{dev/dummy/Makefile.am}}} into {{{MYPROG/}}} and customize it, replacing 'dummy' with 'MYPROG'. Be sure to change: {{{ bin_PROGRAMS = MYPROG }}} and also delete the notes that are there. d) Copy in the additional testing file {{{dev/dummy/myown.c}}}. You can customize it for your test program later. 3) Run {{{./setup_configure}}} from {{{dev/}}}. This runs aclocal, autoconf and automake. You should get no errors. If you do, make sure you followed the above instructions properly. Also try the AutoconfTroubleshooting page. Verify that this step worked by checking if {{{MYPROG/Makefile.in}}} was created. 4) Run {{{./configure}}} with the parameters you previously used. To check these out, run {{{head config.log}}} from {{{dev/}}}, assuming you have run configure successfully on some prior occasion. The output should include the {{{./configure}}} line you used. Copy it, but leave out the {{{--no-create --no-recursion}}} options if present. {{{ [dev/]$ head config.log This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by Freesurfer configure dev3, which was generated by GNU Autoconf 2.59. Invocation command line was $ ./configure --prefix=/space/minerva/1/users/nicks/freesurfer \ --with-mni-dir=/usr/pubsw/packages/mni/current \ --with-vxl-dir=/usr/pubsw/packages/vxl/current \ --with-tcl-dir=/usr/pubsw/packages/tcltktixblt/current \ --with-tixwish=/usr/pubsw/packages/tcltktixblt/current/bin/tixwish8.1.8.4 ## --------- ## ## Platform. ## [dev/]$ /configure --prefix=/space/minerva/1/users/nicks/freesurfer \ --with-mni-dir=/usr/pubsw/packages/mni/current \ --with-vxl-dir=/usr/pubsw/packages/vxl/current \ --with-tcl-dir=/usr/pubsw/packages/tcltktixblt/current \ --with-tixwish=/usr/pubsw/packages/tcltktixblt/current/bin/tixwish8.1.8.4 }}} Note: Do not just copy this example, use what's in your own {{{config.log}}} file! 5) Run {{{make}}} and verify that your binary program {{{MYPROG/MYPROG}}} was created. 6) Check in your changes (note: do not commit Makefile.in, only Makefile.am is necessary). {{{ [dev/] cvs ci -m "Added MYPROG" configure.in Makefile.am [dev/] cvs add MYPROG [dev/] cd MYPROG [MYPROG/] cvs add Makefile.am MYPROG.c myown.c [MYPROG/] cvs commit -m "First checkin." Makefile.am MYPROG.c myown.c }}} === Installing === To install all binaries and support files into your private FreeSurfer, use 'make install' from the toplevel dev/ directory, like this: {{{ cd dev make install }}} This will make a directory called freesurfer/ in the directory specified by the --prefix option to configure, above. Note that if you do not specify this location, it will try to install to /usr/local, which you probably don't have permission to do. Even if you do, i.e. you are installing on a laptop, it's generally better to specify a prefix of /usr/local/freesurfer to keep everything in the same place. |
This will create a local !FreeSurfer installation in the directory specified by the {{{--prefix}}} option to {{{configure}}} scipt (see above). Note that if you do not specify this location, it will try to install to /usr/local, which will probably require root access. |
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| === Using CVS === | === Adding a new binary to the tree === |
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| When you want to commit your changes, use the cvs commit command. However, you must first check to see if the file(s) in the archive have changed since the last time you checked them out. To do so, run the cvs update command on the files you have changed. The -P option will purge (remove) files that have been removed from the CVS and the -d option will add any new directories that have been added since your last update (unsure why this isnt the default behavior). | For this example we will assume you want to create a program called 'MYPROG' and want to add it to the !FreeSurfer tree: 1) Make a directory called {{{MYPROG}}} under the {{{freesurfer}}} directory, and put your source code there. In the simplest case you will have a single source code file called {{{MYPROG.c}}}. |
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| cvs update -d -P }}} If any have changed, you will see the letter U followed by the file name. {{{ U myFile.c }}} This means somebody else committed a newer version of the file, and your copy was just updated. If you and somebody else have made changes on the same file that conflict each other, you will see the letter C along with a message about the conflicts. {{{ C myFile.c }}} If the message states the conflicts have been resolved, you don't have to worry: cvs has merged the differences properly. If it says it couldn't merge the differences, you need to open the file in question, search for the string >>>, and merge the differences yourself. Once the up to date check has been performed, you can commit your changes. If you are in a directory and want to commit all the files in that directory that you have changed, just use: {{{ cvs commit }}} This will commit changes in the current directory and any subdirectories. If you want to commit only certain files, use: {{{ cvs commit <filename> |
## Create the MYPROG directory and 'cd' into it $> mkdir MYPROG $> cd MYPROG ## The MYPROG.c file goes here |
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| Or you can only commit the code in the current directory with the -l switch: | 2) Copy {{{freesurfer/dummy/Makefile.am}}} into {{{MYPROG/}}} and customize it, replacing 'dummy' with 'MYPROG'. Also delete the notes that are there. Be sure to change: |
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| cvs commit -l }}} Each time, an editor will open and ask you to enter a log message. To bypass this, use the -m option and enter your log message on the command line: {{{ cvs commit -m "some descriptive changelog comment" <filename> }}} A synonym for commit is ci, so you can just: {{{ cvs ci -m "fixed stuff" <filename> }}} Periodically, you should update your working copy to be in sync with the archive. CVS will look at all your files and see if the ones in the archive are different. If so, it will update your copy. CVS will not delete local modifications you have made. To do this update: {{{ cvs update -d -P }}} The -d switch adds any new directories and is not strictly necessary, but is a good habit, because if you don't use it you will update existing files but will now add new directories. The -P option purges directories of files that have been removed in the past. Similarly, you can update an entire directory or a single file. To commit all the code in the current directory (code that has not been changed will not be commited): {{{ cvs ci -m "fixed many things" }}} To restore an edited version to the version in the archive, either delete the file and cvs update, and the archive version will be copied to the local work area, or use the -C option to cvs update to replace your copy with one from the archive. To add a new file to the archive, use the add command and then commit the file: {{{ cvs add <filename> cvs commit -m "added the file" <filename> }}} To remove a file, remove in cvs and locally (with the -f flag), and commit: {{{ cvs remove -f <filename> cvs commit -m "removed the file" <filename> }}} That covers most of the CVS commands you'll have to to use. For more info on CVS, check out www.cvshome.org or the CVS man pages. Summary: check in a file {{{ cvs commit }}} get newest versions. merges newer versions than the ones you had with your working versions. {{{ cvs update -A |
bin_PROGRAMS = MYPROG |
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| add a new file: | 3) Modify {{{configure.in}}} to add {{{MYPROG/Makefile}}} to the list of files in the definition of {{{AC_OUTPUT}}} (these are in roughly alphabetical order). |
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| cvs add file; cvs commit file | ## configure.in ## AC_OUTPUT( ... <list of files> ... MYPROG/Makefile ... <list of files> ... ) |
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| remove a file (but keep in older revisions): | 4) Modify {{{freesurfer/Makefile.am}}} to add {{{MYPROG}}} to the {{{MRISUBDIRS}}} or {{{MRISSUBDIRS}}} definition. (You can also alternatively add it to the end of any of the *SUBDIRS categories.) |
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| rm file; cvs remove file; cvs commit file | ## Makefile.am ## MRISUBDIRS= \ ... <list of files> ... MYPROG \ ... <list of files> ... |
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| rename a file: | Once these 4 steps are complete MYPROG should automatically be built with the rest of !FreeSurfer. === Using Git === If your program successfully builds/installs/runs and is thus ready to be checked into the repository, you can commit the files as follows: |
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| mv old new; cvs remove old; cvs add new; cvs commit old new | $> cd MYPROG $> git add MYPROG.c Makefile.am $> git commit -m "Initial add of MRPROG." MYPROG.c Makefile.am $> git push |
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| See also: [[http://www.bioinf.uni-freiburg.de/~mmann/HowTo/cvs_branches.html|CVS Branch and Tag Primer]] and [[http://badgertronics.com/writings/cvs/keywords.html|CVS Keywords]] |
Data files represent a special use-case, and they should not go into the normal Git repository. Instead {{{git-annex}}} is used to store all data files that are part of the !FreeSurfer repository. Generally speaking, data files are anything not source code related - pdfs, compressed tarballs, test data, precompiled binaries, and image files are all examples of data files that should be stored in {{{git-annex}}}. Simple text files like Look-up tables, configuration files, etc., while not exactly source code, are NOT considered data files. Those files CAN go in the normal repository. The following webpage provides instructions on how to manage data files in the !FreeSurfer repository. |
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| See also: [[DevelopersGuide/CVSTips]] | [[git-annex page that doesnt exist yet.|git-annex page that doesnt exist yet.]] |
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| === Troubleshooting autoconf issues === | Additional information on how to use Git can be found on the Atlassian websites which has decent tutorials and examples to help users getting started with Git: |
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| [[AutoconfTroubleshooting|Here's a list of common problems and solutions for autotools problems.]] === Martinos Center issues === see [[DevelopersGuide/MartinosCenter|Martinos Center issues]] page Note: On this page, there are also instructions on how commit messages can be sent to an additional person for documentation purposes, etc. === Coding Guide === This page deals specifically with coding issues. [[DevelopersGuide/CodingGuide|CodingGuide]] === Docs and Testing === [[NewProgramDocAndTest]] === Developing for a Mac === Info can be found [[http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page|here]]. |
https://www.atlassian.com/git/tutorials/saving-changes |
Index
This page is targeted at Martinos Center users who wish to inspect, build or develop within the FreeSrufer code base. Non-Martinos users wishing to work with the FreeSrufer code base should consult the read-only git repo http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
1. Git Clone
First thing users at the Martinos Center will need to do is add the newer version of the git and git-annex software to their PATH environment variable. This should be added to the .cshrc or .bashrc file in the users home directory:
## csh $> setenv PATH /usr/pubsw/packages/git-annex/current/bin:$PATH ## bash $> export PATH=/usr/pubsw/packages/git-annex/current/bin:$PATH
Users can then clone FreeSurfer repository as follows:
## Get source code files (206 MB) $> git clone file:///space/freesurfer/repo/freesurfer
1.1. Getting the Data Files
The FreeSurfer repository contains a large number of data files (pdfs, test data, etc) which are not normally included with a default git clone of the repo. Users who wish to clone the repository for the purposes of just inspecting source code and/or build the code, the git clone command from above is all that is required. Users who want to run build time checks, or perform a full local installation, or just want all the data files contained in the repository, will need to run the following command:
## Change directories $> cd freesurfer ## Get only the data files required for build time checks (1.9 GB) $> git annex get --metadata fstags=makecheck . ## Get only the data files required for local installation (4.3 GB) $> git annex get --metadata fstags=makeinstall . ## Just give me everything! Not Recommended (6.8 GB) $> git annex get .
2. Building
2.1. Setup Configure
It is necessary to run a pre-configure script, to create the platform specific tools required by configure (execute in the freesurfer directory created by git clone). This script runs a set of commands (aclocal, libtoolize, automake v1.9.6, autoconf v2.59) that creates the platform specific files for configure and puts them in the 'fsdev/config' directory.
$> ./setup_configure
2.2. Configure
Now you need to configure your building parameters for your machine by running the configure script. Users at the Martinos Center should for the most part be fine with the default settings, but the configure script does accept many options for pointing to specific libraries and other build specific parameters. One exception is if a user wants to perform a local installation of FreeSurfer, he/she should use the --prefix flag. Type ./configure --help for a full list of options. For example:
## Default configuration $> ./configure ## Specify an installation location $> ./configure --prefix=~/freesurfer_install_dir ## See all possible options $> ./configure --help
FreeSurfer builds against the following set of open-sourced libraries, which are installed under the /usr/pubsw/packages directory on all NMR computers:
Package
Version
Package
Version
CUDA
v5.0.35-rh5
ANN
v1.1
tiffjpegglut
v3.6, v6b, v3.7
itk
v3.16
VTK
v5.6
VXL
v1.14
MNI
v1.5
tcltktixblt
v8.4, v8.4, v8.1, v2.4z
KWWWidgets
CVS checkout
Qt
v4.7
wxWidgets
v2.8
cppunit
v1.10
xawplus
v3.1
petsc
v2.3
All these packages will be found by default by the ./configure script. But there are options to specify where certain packages exists if a user wishes to build against a different version of one of the open-source libraries. For example:
## Specify a specific version of qt $> ./configure --with-qt=/usr/pubsw/packages/qt/4.8.5
2.3. Compile
You can now run 'make' to build the all individual programs in the FreeSurfer source tree. Binaries will automatically be placed in their individual subdirectories.
$> make -j 4
Handy hint: the -j 4 option to make tells it to run four simultaneous make processes, which, if building on a multi-processor machine, can speed-up the build.
If you want to compile just one binary at a time, for example, if you are developing an app, than cd to the directory of the program you want and use 'make' to compile it:
$> cd mri_info $> make
This creates mri_info in the mri_info/ directory. However, be aware the many program depends on the existence of libraries having already been build like libutils. Therefore users will need to build a few of the library directories first (e.g. utils, fsgdf, xml2, etc).
2.4. Install
To install all binaries and support files into your private FreeSurfer installation, type 'make install' from the toplevel fsdev/ directory, like this:
$> make install
This will create a local FreeSurfer installation in the directory specified by the --prefix option to configure scipt (see above). Note that if you do not specify this location, it will try to install to /usr/local, which will probably require root access.
Note that you can also run 'make release'. 'make install' makes and installs the NMR internal version of FreeSurfer, while 'make release' makes the public version which omits some stuff.
The first time you run 'make install', it will take a while to copy all the big data files to the new installation. Subsequent 'make installs' will only copy the changed files.
If you only want to install a single binary, run 'make install' from a subdirectory. For example, running 'make install' from the scuba/ directory will copy the scuba binary and its support script files to the proper locations. Running 'make install' from scripts/ will copy all the necessary scripts to the right location.
3. Adding a new binary to the tree
For this example we will assume you want to create a program called 'MYPROG' and want to add it to the FreeSurfer tree:
1) Make a directory called MYPROG under the freesurfer directory, and put your source code there. In the simplest case you will have a single source code file called MYPROG.c.
## Create the MYPROG directory and 'cd' into it $> mkdir MYPROG $> cd MYPROG ## The MYPROG.c file goes here
2) Copy freesurfer/dummy/Makefile.am into MYPROG/ and customize it, replacing 'dummy' with 'MYPROG'. Also delete the notes that are there. Be sure to change:
bin_PROGRAMS = MYPROG
3) Modify configure.in to add MYPROG/Makefile to the list of files in the definition of AC_OUTPUT (these are in roughly alphabetical order).
## configure.in ## AC_OUTPUT( ... <list of files> ... MYPROG/Makefile ... <list of files> ... )
4) Modify freesurfer/Makefile.am to add MYPROG to the MRISUBDIRS or MRISSUBDIRS definition. (You can also alternatively add it to the end of any of the *SUBDIRS categories.)
## Makefile.am ## MRISUBDIRS= \ ... <list of files> ... MYPROG \ ... <list of files> ...
Once these 4 steps are complete MYPROG should automatically be built with the rest of FreeSurfer.
4. Using Git
If your program successfully builds/installs/runs and is thus ready to be checked into the repository, you can commit the files as follows:
$> cd MYPROG $> git add MYPROG.c Makefile.am $> git commit -m "Initial add of MRPROG." MYPROG.c Makefile.am $> git push
Data files represent a special use-case, and they should not go into the normal Git repository. Instead git-annex is used to store all data files that are part of the FreeSurfer repository. Generally speaking, data files are anything not source code related - pdfs, compressed tarballs, test data, precompiled binaries, and image files are all examples of data files that should be stored in git-annex. Simple text files like Look-up tables, configuration files, etc., while not exactly source code, are NOT considered data files. Those files CAN go in the normal repository. The following webpage provides instructions on how to manage data files in the FreeSurfer repository.
git-annex page that doesnt exist yet.
Additional information on how to use Git can be found on the Atlassian websites which has decent tutorials and examples to help users getting started with Git: