Tools and libraries to build OpenVnmrJ.
OpenVnmrJ has been built on CentOS 6, 7, and 8 and on Ubuntu 18 and 20 and on MacOS 10.10 (Yosemite). The CentOS and Ubuntu builds make a combination of 32-bit and 64-bit executables. The MacOS build makes only 64-bit executables. To build on MacOS, see the OSX.md document.
The only requirement to build in a VM is to have the free tools VirtualBox and Vagrant installed on your build machine. This will save you the trouble of installing and configuring an operating system. Build instructions for VM containers are below.
There are several ready-to-use VM descriptions (using Vagrant ) for CentOS 6/7 and Ubuntu 14.04 16.04, and 18.04. These automatically create and configure the OS in a VM for building and running OpenVnmrJ. The Vagrant files and machines live in the vms/ directory.
To build OpenVnmrJ using one of these machine descriptions, install
Vagrant and the vbguest
plugin, then from this
repository (ovjTools) run the VM build script
build_vm.sh:
(in this example CentOS 6)
git clone [email protected]:OpenVnmrJ/ovjTools.git
cd ovjTools
./bin/build_vm.sh centos6 # do the actual build, may take ~1 h the first timeto build for multiple OS targets at the same time, just add the target
name to the command line, currently tested targets are centos6,
centos7, ubuntu14, ubuntu16, and ubuntu18. By default, the
build_vm.sh script performs a full "from scratch" clean + build +
install + test cycle, but it can be limited to do any one or
combination of these by simply specifying the action on the command
line, a basic: ./build_vm.sh build centos6 would just build
OpenVnmrJ on an existing centos6 without cleaning it, and without
installing or testing it.
The build_vm.sh script can specify the git branch and github username. To build the "development" branch from a github user "ghuser" on both centos6 and ubuntu14 :
./bin/build_vm.sh centos6 ubuntu14 --gitname ghuser --branch development If there are any build errors, you can log into the VM locally through ssh and inspect the build.log:
ovjTools $ cd ./vms/centos6
centos6 $ vagrant up
centos6 $ vagrant ssh
[now logged into a shell on the VM...]
vagrant $ cd $ovjBuildDir/logs/
vagrant $ more build*The actual install of OpenVnmrJ (currently) requires graphical user interaction with the java gui, so to complete the install of OpenVnmrJ, you have to boot the VM with the GUI enabled and run the installer manually:
cd ${OVJ_TOOLS}/vms/centos6
VMGUI=y vagrant up
[open a terminal in the VM]
cd $ovjBuildDir/dvdimageOVJ_.../
./load.nmrThese instructions work for Ubuntu and CentOS (RHEL).
Make a directory. Let us call it ovjbuild and change into that directory. Check out the ovjTools repository from GitHub with
mkdir ovjbuild && cd ovjbuild
git clone https://github.com/OpenVnmrJ/ovjTools.git
or Download it from the GitHub web site. If you download it, move it to the ovjbuild directory and unzip it with the commands
mv ~/Downloads/ovjTools-master.zip .
unzip ovjTools-master.zip
rm ovjTools-master.zip
At the same level as the ovjTools directory, do the following
cp -r ovjTools/bin .
cd bin
The bin directory contains several scripts.
The toolChain script installs all the Linux packages required to build OpenVnmrJ. This includes things like the gcc compiler and assorted libraries and development header files. You need network access in order to run this script. The toolChain script only needs to be executed once.
The buildovj script controls the overall build process. By default, it should work correctly. However, if you wish to customize the build process, edit this script. For example, you may decide not to build the Mercury / Inova version. Or you may decide to move the ovjTools directory to a different location. The buildovj script is commented to describe various options.
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 or clone OpenVnmrJ from git. The second part compiles everything (doScons=yes). The third part collects files into the DVD images (buildOVJ=yes).
If this is the first time you are building OpenVnmrJ on this PC, run the command
./toolChain
To build OpenVnmrJ, run the command
./buildovj
During the build, a log file is kept in the ovjbuid/logs directory. You can use a command such as
tail -f ~/ovjbuild/logs/makeovj.<DATE>
to monitor the build. The whatsin script scans the log file and gives a summary of the build process. It identifies any errors that may have occurred.
You can also build specific programs in the OpenVnmrJ package. For example, to build the Vnmrbg program, assuming ovjbuild is in your home directory, you can use the following commands
cd ~/ovjbuild/OpenVnmrJ/src/vnmrbg
scons
Note that on newer operating systems, such as CentOS 8, the scons command may be called scons-3
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=<path>
In a csh, the command would be
setenv OVJ_TOOLS <path>
Then, to build vnmrj.jar, use the commands
cd ~/ovjbuild/OpenVnmrJ/src/vnmrj
scons
The buildovj script will compile the entire OVJ package. It will use the OpenVnmrJ/SConstruct file to compile the programs in src and place the results in directories at the same level as the OpenVnmrJ 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 directory. The script whatsin in the bin directory will produce a summary of the content of the build log file.
In summary, before running the buildovj script, your build directory will have bin
and ovjTools directories and optionally, an OpenVnmrJ directory. 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.
Once the buildovj script is complete, and you had selected the buildOVJ and / or buildOVJMI
parameters, you can cd dvdimageOVJ or cd dvdimageOVJMI and run ./load.nmr to install a complete
OpenVnmrJ package. For complete details see the OpenVnmrJ/Install.md file.
The ovjTools directory contains the following directories and files.
bin Scripts to build the OpenVnmrJ package
console programs for spectrometer control
dicom3tools Used by imaging
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
kermit_8.0.211 The kermit program used for field mapping
LICENSE The Apache II license used by OpenVnmrJ
linux Some Linux rpm packages
logs Directory used by VM builds to save log files
NDDS Used by nvlocki, nvexpproc, nvinfoproc, nvrecvproc, nvsendproc
OSX.md Build instructions for MacOS
pgsql Postgress / Locator code
pgsql.osx Postgress / Locator code for MacOS
tcl This contains headers and libraries for compiling programs that
require tcl (Roboproc)
wkhtmltopdf Used by vnmrj
The OpenVnmrJ directory contains the following directories and files. These files are open-sourced under the Apache II license.
Install.md Installation instructions for OpenVnmrJ
LICENSE A copy of the Apache II license, under which OpenVnmrJ is licensed.
Notes.txt Release notes for OpenVnmrJ
README.md A description of the OpenVnmrJ project
RELEASE.md A Document describing OpenVnmrJ releases
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.
site_scons Some MacOS specific tools.
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 OpenVnmrJ/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 OpenVnmrJ/SConstruct file for an example.
The src directory contains the following subdirectories. Note that the CRAFT included here is version 1 and is obsolete. See a description of the new CRAFT here.
3D Code for compressfid, ft3d, getplane
acqproc Shared files
admin VnmrJ installer java program
aip Shared files used by vnmrbg. (aip -> advanced image processing)
ampfit Tools for amplifier linearization (DDR systems)
apt Auto ProTune java program
apt_32_MMI Auto ProTune java program for Mercury and Inova systems
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
craft CRAFT version 1.
cryo Cryobay communications java program
cryomon Cryo monitor communications java program
ddl Shared files
ddr Protocols for DDR
dialog java dialog program
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
kvwacq Example code for Mercury console programs
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 and example programs
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
passwd java passwd program
patch Tools used to make patches
probeid probeid communications programPlease
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
shuffler xml files used by the Locator
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
vjqa Some quality assurance tests
vnmr Shared files
vnmrbg Code for Vnmrbg
vnmrj vnmrj java program (requires GPL license)
vobj Shared files
vwacq Shared files with Inova console software
vwauto Example code for Inova automation board
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)
