Building OVJ on Linux

See README.ovj
v0.3
11 September 2015
Dan Iverson & John Ryan

BUILD REQUIREMENTS

EL6 (RHEL/CentOS 6)

The minimum package requirement for EL6 assumes that your system was installed with the “Software Development Workstation” package selection as required by VnmrJ. This build configuration has been tested on CentOS 6.6 but should work for any RHEL or CentOS 6.x.

yum install compat-gcc-34-g77 glibc-devel.i686 libstdc++.i686 libX11-devel.i686 libXt-devel.i686 openmotif-devel.i686 scons

Optionally, you can also install gsl-devel and libtiff-devel if you wish to compile using the GNU scientific library. Code compiled with the GSL will be subject to license restrictions.

Ubuntu Trusty Tahr 14.04 LTS

The minimum package requirement for Ubuntu Trusty Tahr 14.04 LTS assumes that you have installed the standard desktop edition of Ubuntu. A minimal install may require additional packages including but not limited to make, unzip and zip. This build configuration has been tested on Ubuntu but should work for any *buntu Trusty Tahr 14.04 LTS distribution.

sudo apt-get install fort77 g++ lib32stdc++-4.8-dev libc6-dev-i386 libglu1-mesa-dev libmotif-dev:i386 libx11-dev:i386 libxt-dev:i386 scons

Optionally, you can also install libgsl0-dev and libtiff5-dev if you wish to compile components using the GNU scientific library. Code compiled with the GSL will be subject to license restrictions.

Full package requirements including dependent packages are listed in the appendix of this document.

INSTALLATION & COMPILATION

Make a directory. Lets call it ovjbuild. unzip the source code file inside that directory. It will add a git-repo. The git-repo directory contains the following directories and files. These files may be open-sourced.

SConstruct This is the definition file used by scons. It is similar to Makefile used by the make command. scripts This contains tools used by scons. src This contains the source code for OpenVnmrJ. Some of these directories also contain a SConstruct file that is used to build / compile that specific program.

The ovjTools can be unzipped in the ovjbuild directory or anyplace that you want to put it. The ovjTools directory contains code from external sources. This code should not be open-sourced by OpenVnmrJ. It contains the following directories. (In earlier edition, this was the 3rdParty directory.

fftw Used by xrecon (imaging program)
fftw_mac Used by xrecon MacOS version (imaging program)
gsllibs Used by programs in bin_image
java Used by all java programs. It is a soft link to the java jdk.
JavaPackages Used by vjmol and vnmrj
jdk1.6.0_39_64 Java jdk.
JMF-2.1.1e Used by vnmrj (simplemovie.jar)
junit Used by apt, probeid, and vjclient
NDDS Used by nvlocki, nvexpproc, nvinfoproc, nvrecvproc, nvsendproc
pgsql Postgress / Locator code
tcl This contains headers and libraries for compiling programs that require tcl (Roboproc)

We compile VnmrJ java programs with jdk1.6.0_39_64. The java in ovjTools should be a soft link to the actual java JDK.

At the same level as the git-repo directory, do the following

  mkdir bin
  cp git-repo/src/scripts/buildovj bin
  cp git-repo/src/scripts/makeovj bin
  cd bin

Edit the buildovj script and set the ovjBuildDir and OVJ_TOOLS parameters for your environment. The OVJ_TOOLS parameter should point to the ovjTools directory. The ovjTools directory does not necessarily need to be in the same directory as the git-repo directory, although that may be a convenient place.

Other options are described in that file but the defaults should be okay. The buildovj script collects all the options and the makeovj script does all the work. In general, the makeovj script does three things. The first is to update the sources from git. Since we are not yet actually using git, this part is turned off (doGitClone=no). The second part compiles everything. This step is equivalent to what was done in the previous two versions of OVJ (doScons=yes). The third part collects files into the DVD images (buildOVJ=yes).

Run the command

  ./buildovj

This command will compile the entire OVJ package. It will use the SConstruct file to compile the programs in src and place the results in directories at the same level as the git-repo level. The console directory will contain console-specific files.

The vnmr directory will contain files that are generic. The options directory contains optional software and code that may be optionally installed. If the buildOVJ and / or buildOVJMI parameters are set to yes in the buildovj script, additional directories will be built that are an image of the DVD installer. A log of the build process will be placed in a logs direcory. In summary, before running the buildovj script, your build directory will have bin, git-repo, and ovjTools directories. If you have previously run the buildovj script, there will also be console, logs, options, and vnmr directories. Depending on your selections in the buildovj script, the default DVD images dvdimageOVJ and dvdimageOVJMI may also be present. When the buildovj script is executed, one of the first things it does is remove any preexisting console, options, vnmr, and dvd image directories.

You can also change into specific directories in src and run scons. That will build that specific program. To compile the java programs, the OVJ_TOOLS env parameter must be set to point to the ovjTools directory. In a bash shell, the command would be ` export OVJ_TOOLS= ` In a csh, the command would be ` setenv OVJ_TOOLS ` For example,

cd git-repo/src/vnmrbg
scons

will build only the Vnmrbg program.

For Linux systems: Once the buildovj script is complete, and you had selected the buildOVJ and / or buildOVJMI parameters, you can cd dvdimageOVJ or dvdimageOVJMI and run ./load.nmr to install a complete OpenVnmrJ package. If a prior VJ42 install is present (/vnmr is a symbolic link to the VJ42 installation), then the OpenVnmrJ installation will collect various files from the VJ42 install so that the OpenVnmrJ install should be complete. See the src/scripts/update_OpenVnmrJ.sh script. Assuming the VJ42 directory was available, this installed OVJ should be a complete system capable of data acquisition. After installation, the only thing that should be needed is su acqproc to start the OVJ version of the procs.

For MacOS systems: Once the buildovj script is complete, and you had selected the buildOVJ parameter, you will have a dvd image that is constructed so that the MacOS utility PackageMaker can be used to build a MacOS installer. Instructions for building the installer are in git-repo/src/macos/readme_packagemaker. If a prior VJ42 install is present (/vnmr is a symbolic link to the VJ42 installation), then the OpenVnmrJ installation will collect various files from the VJ42 install so that the OpenVnmrJ install should be complete.

The src directory has a number of subdirectories. In general, each subdirectory corresponds to one or more programs that need to be compiled. Some of the subdirectories contain code that is shared by several programs. Some directories also contain a special sconsPostAction file. These typically are a shell script with symbolic link commands. For example, src/common/maclib has a sconsPostAction files which creates aliases of some of the macros. The SConstuct must explicitly execute the sconsPostAction. See the git-repo/SConstruct file for an example.

The src directory contains the following subdirectories.

3D Code for compressfid, ft3d, getplane
acqproc Shared files
admin VnmrJ installer java program
aip Shared files used by vnmrbg. (aip -> advanced image processing)
apt Auto ProTune java program
aslmirtime Imaging program (requires GPL license)
Asp Shared files used by vnmrbg. (Asp -> advanced spectral processing)
atproc Code for Atproc
autotest Autotest appdir
backproj Imaging back-projection tool
bin Compiled programs in /vnmr/bin
bin_image Compiled imaging programs in /vnmr/bin (requires GPL license)
biopack Biopack appdir
biosolidspack Biosolidspack appdir
bootpd.rh51 Bootp program for Inova and Mercury
cgl Imaging library libcgl.so
common This contains text files that do not need further processing / compiling, including CRAFT.
cryo Cryobay communications java program
cryomon Cryo monitor communications java program
ddl Shared files
ddr Protocols for DDR
dicom_store Imaging DICOM tool
DOSY DOSY files
expproc Expproc for Inova and Mercury
gif Tools used to build a release DVD
Gilson VAST files
gxyzshim 3D gradient shimming
ib Shared files (image browser)
IMAGE Files for imaging
infoproc Infoproc for Inova and Mercury
inova Files to support Inova
ipsglib Inova specific pulse sequences
jaccount Accounting program
jplot jplot program
kpsg PSG for Mercury
kpsglib Pulse sequences for Mercury
languages Support for Chinese and Japanese
layouts layout XML files
LCNMR LC-NMR files
license Current license statements
macos Tools used to build the MacOS version
magic Shared files
managedb Program used by Locator and dbsetup
masproc Masproc for Inova
mercury Files to support Mercury
nacqi Shared files
nautoproc Autoproc
ncomm Shared files and acqproc and ncomm libraries.
nvacq Shared files with DDR console software
nvexpproc Expproc for DDR systems
nvinfoproc Infoproc for DDR systems
nvpsg PSG for DDR systems
nvpsglib DDR specific pulse sequences
nvrecvproc Recvproc for DDR systems
nvsendproc Sendproc for DDR systems
p11 Files for Part 11 option
patch Tools used to make patches
probeid probeid communications program
procproc Procproc
psg PSG for Inova
psglib Pulse sequences shared by Inova and DDR
recvproc Recvproc for Inova and Mercury systems
roboproc Roboproc
scripts Scripts in /vnmr/bin (and other scripts used for install, etc)
sendproc Sendproc for Inova and Mercury systems
solidspack Solidspack appdir
stars The STARS solid-state NMR simulation package
stat Code for Infostat and showstat
tcl tcl scripts (autotest, etc)
veripulse veripulse appdir
vjclient Program used by probeid
vjmol Auxiliary java program to connect jmol with vnmrj
vnmr Shared files
vnmrbg Code for Vnmrbg
vnmrj vnmrj java program (requires GPL license)
vobj Shared files
vwacq Shared files with Inova console software
web Programs to support tablet
xracq Shared files with VXR console software
xrecon Imaging reconstruction program (requires GPL license)
yacc Original yacc tool for helping to make Magical (no longer used)

New since last version:

ampfit Tools for amplifier linearization (DDR systems)
shuffler xml files used by the Locator

APPENDIX

EL6 (RHEL/CentOS 6)

Full list of required packages for EL 6 starting from a “Software Development Workstation” configuration:

compat-gcc-34
compat-gcc-34-g77
compat-libf2c-34
expat.i686
fontconfig.i686
freetype.i686
glibc.i686
glibc-devel.i686
libgcc.i686
libICE.i686
libjpeg-turbo.i686
libpng.i686
libstdc++.i686
libSM.i686
libuuid.i686
libX11.i686
libX11-devel.i686
libXau.i686
libxcb.i686
libXext.i686
libXft.i686
libXmu.i686
libXp.i686
libXrender.i686
libXt.i686
libXt-devel.i686
nss-softokn-freebl.i686
openmotif.i686
openmotif-devel.i686
scons
zlib.i686  

And optionally:

gsl
gsl-devel
libtiff-devel

Ubuntu Trusty Tahr 14.04 LTS Full list of required packages for Ubuntu Trusty Tahr 14.04 LTS starting from a standard desktop edition installation:

f2c
fort77
g++
g++-4.8
gcc-4.8-multilib
gcc-4.9-base:i386
gcc-multilib
lib32asan0
lib32atomic1
lib32gcc-4.8-dev
lib32gcc1
lib32gomp1
lib32itm1
lib32quadmath0
lib32stdc++-4.8-dev
lib32stdc++6
libc6-dev-i386
libc6-dev-x32
libc6-i386
libc6-x32
libc6:i386
libdrm-dev
libexpat1:i386
libf2c2
libf2c2-dev
libfontconfig1:i386
libfreetype6:i386
libgcc1:i386
libgl1-mesa-dev
libglu1-mesa-dev
libice-dev:i386
libice6:i386
libjpeg-turbo8:i386
libjpeg8:i386
libmotif-common
libmotif-dev:i386
libmrm4
libmrm4:i386
libpng12-0:i386
libpthread-stubs0-dev
libpthread-stubs0-dev:i386
libsm-dev:i386
libsm6:i386
libstdc++-4.8-dev
libuil4
libuil4:i386
libuuid1:i386
libx11-6:i386
libx11-dev
libx11-dev:i386
libx11-doc
libx11-xcb-dev
libx32asan0
libx32atomic1
libx32gcc-4.8-dev
libx32gcc1
libx32gomp1
libx32itm1
libx32quadmath0
libxau-dev
libxau-dev:i386
libxau6:i386
libxcb-dri2-0-dev
libxcb-dri3-dev
libxcb-glx0-dev
libxcb-present-dev
libxcb-randr0-dev
libxcb-render0-dev
libxcb-shape0-dev
libxcb-sync-dev
libxcb-xfixes0-dev
libxcb1-dev
libxcb1-dev:i386
libxcb1:i386
libxdamage-dev
libxdmcp-dev
libxdmcp-dev:i386
libxdmcp6:i386
libxext-dev
libxext6:i386
libxfixes-dev
libxft2:i386
libxm4
libxm4:i386
libxmu6:i386
libxrender1:i386
libxshmfence-dev
libxt-dev:i386
libxt6:i386
libxxf86vm-dev
mesa-common-dev
scons
uil
x11proto-core-dev
x11proto-damage-dev
x11proto-dri2-dev
x11proto-fixes-dev
x11proto-gl-dev
x11proto-input-dev
x11proto-kb-dev
x11proto-xext-dev
x11proto-xf86vidmode-dev
xorg-sgml-doctools
xtrans-dev
zlib1g:i386

And optionally:

libgsl0-dev
libgsl0ldbl
libjbig-dev
libjpeg-dev
libjpeg-turbo8-dev
libjpeg8-dev
liblzma-dev
libtiff5-dev
libtiffxx5
zlib1g-dev