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Concise Instruction for a Beginner needed. #78

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osparking opened this issue Dec 3, 2016 · 24 comments
Closed

Concise Instruction for a Beginner needed. #78

osparking opened this issue Dec 3, 2016 · 24 comments

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@osparking
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Well, I'm new to VnmrJ completely, as a matter of fact. I heard the word itself only a couple of days ago.
Still I want to get at this kind of status (see figure below.)

Image of Desktop

These are my current position.

  • Desktop computer running Windows 7
  • Installed VirtualBox on Win7, and Ubuntu 14.04 machine in VBox.

What I don't know:

  1. The relationship of Vagrant and buildovj.

What I need:

  1. Rough (maybe 5 to 10) (1 line) steps to arrive at the above image(I don't know what to call it, maybe desktoop?)

End.
@tesch1
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tesch1 commented Dec 5, 2016

What are you trying to accomplish with OpenVnmrJ? Do you have some NMR data you want to process, or do you have a magnet? By to the image above, it looks like you have already successfully installed OpenVnmrJ.

Vagrant is a tool to manage the creation and setup of virtual machines. You can find more information with google.

The build script for building OpenVnmrJ in a Vagrantfile-described VM is build_vm.sh, which calls build_box.sh to setup the VM. buildovj is not used by these scripts.

Have you installed Vagrant? Have you tried the steps from the 'development' branch README for building "In a Virtual Machine"? What happened?

@osparking
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osparking commented Dec 5, 2016 via email

@tesch1
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tesch1 commented Dec 5, 2016 •
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It would be nice to improve the build process. I've tried to make some steps in that direction, for example by abstracting/standardizing the build platform from the build via the Vagrant layer. I'm sure any contributions you can make to improving the situation would be appreciated.

The source code is chock full of warning messages, due to a number of factors, one being that the original code is >30 years old, and C was a somewhat different language back then. Two, compiler warnings have changed continuously over the last 30 years.

@osparking
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osparking commented Dec 5, 2016 via email

@DanIverson
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OpenVnmrJ (OVJ) can be customized at several different levels. The GUI part uses java and xml. If you just want to customize the interface with modified panels or menus, you can do that without modifying the java code. There is a built-in panel editor. Perhaps if we had a better idea of the changes your physics professor wants to implement we could direct you to the correct tools.

@osparking
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osparking commented Dec 5, 2016 via email

@DanIverson
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Also, if you just want to get it running in virtualbox, follow the installation instructions here https://github.com/OpenVnmrJ/OpenVnmrJ/releases

@osparking
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osparking commented Dec 6, 2016 via email •
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@DanIverson
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Neither the image nor log file seem to be attached to your last message

@osparking
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osparking commented Dec 6, 2016 via email •
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@DanIverson
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You can probably ignore the postgres error. Login in as the vnmr1 account. There should be a OpenVnmrJ or VnmrJ icon on the desktop that you can double-click. Or you can open a terminal and enter vnmrj on the command line.

@osparking
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I don't have any icon on the desktop.
(A user 'vnmr1' was created during installation I guess. I had to change it's password though.)
So, I logged in as 'vnmr1' and tried the command vnmrj as follows:

vnmr1@JB-VBOX-Ubt:~/orun$ vnmrj
No protocol specified
xrdb: Permission denied
xrdb: Can't open display ':0'
vnmr1@JB-VBOX-Ubt:~/orun$ No protocol specified
Exception in thread "main" java.lang.InternalError: Can't connect to X11 window server using ':0' as the value of the DISPLAY variable.
	at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
	at sun.awt.X11GraphicsEnvironment.access$100(X11GraphicsEnvironment.java:52)
	at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:155)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:131)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:171)
	at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:68)
	at sun.awt.X11.XToolkit.<clinit>(XToolkit.java:89)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:171)
	at java.awt.Toolkit$2.run(Toolkit.java:834)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:826)
	at vnmr.images.VnmrImageUtil.<init>(VnmrImageUtil.java:23)
	at vnmr.util.Util.getImageIcon(Util.java:591)
	at vnmr.ui.VNMRFrame.main(VNMRFrame.java:80)
 
vnmr1@JB-VBOX-Ubt:~/orun$

Did I miss any step?

@DanIverson
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You are very close. The error is related to X-windows. Did to su vnmr1 or actually login as vnmr1. If you did "su", use "su - vnmr1". Also, try running "xhost +" prior to running vnmrj. I have not actually run OVJ under Ubuntu. Perhaps @tesch1 has run into this problem and knows the solution.

@osparking
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I'm back and tried
$ ./load.nmr
"Postgres Not Installed" error,
(waited 5 to 10 minutes => percentage became 100% and "Done" button appeared.

// clicked [Done] button.

I had this terminal output

110percent

// I didn't think my system is spectrometer and

$ su vnmr1
pw: ...

$ /vnmr/bin/makeuser

I had "Updating for vnmr1 complete" on the terminal.

Now, my question is "What is the VnmrJ interface?", what do I do after that? Do you my log?

@DanIverson
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That all looks good. You are not a spectrometer so you don't need to run the /vnmr/bin/setacq command. Use su - vnmr1 rather than su vnmr1 when you switch to vnmr1 account. The vnmrj command should start the "VnmrJ interface". If you get the "Can't connect to X11 window" error, enter xhost + and then try vnmrj again.

@osparking
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As "xhost +" didn't work. I followed next steps refering No protocol specified.

$ export LOGIN_USER="vnmr1" 
$ su - $LOGIN_USER 
$ /vnmr/bin/makeuser 
$ sudo xhost local:$LOGIN_USER &>/dev/null 
$ vnmrj adm

And the result is this,

define_vnmr1_user

How would I be able to define user 'vnmr1' in the userlist file?

@DanIverson
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Could you do the following:
cd /vnmr/adm
zip -r adm.zip groups users
Attach the adm.zip file to an email and send it to me at daniverson2016@gmail.com

@tesch1
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tesch1 commented Dec 8, 2016 •
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I suspect this is something that's already fixed in the development branch. There were some small changes to the install scripts to deal with similar issues.

The install and startup does work on the Vagrant-described Ubuntu installs (last I checked). The Vagrant VMs would be a good place to debug these things because they let us all use exactly the same environment.

@osparking
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Dear Iverson, let me get back to you later.

Now I'm using Vagrant and Vagrantfile that you provide for Ubuntu-14.
When I followed https://github.com/OpenVnmrJ/OpenVnmrJ/releases
and ran

$ ./load.nmr

I had following error list. Do I need to install each package one by one?

vagrant@vagrant-ubuntu-trusty-64:/vagrant/project/dvdimageOVJ$ ./load.nmr
VnmrJ required Ubuntu package "openjdk-6-jre" NOT installed
VnmrJ required Ubuntu package "csh" NOT installed
VnmrJ required Ubuntu package "libmotif-dev" NOT installed
VnmrJ required Ubuntu package "expect" NOT installed
VnmrJ required Ubuntu package "tcl8.4-dev" NOT installed
VnmrJ required Ubuntu package "tk8.4-dev" NOT installed
VnmrJ required Ubuntu package "rarpd" NOT installed
VnmrJ required Ubuntu package "rsh-server" NOT installed
VnmrJ required Ubuntu package "tftpd" NOT installed
VnmrJ required Ubuntu package "mutt" NOT installed
VnmrJ required Ubuntu package "sharutils" NOT installed
VnmrJ required Ubuntu package "sendmail-cf" NOT installed
VnmrJ required Ubuntu package "gnome-power-manager" NOT installed
VnmrJ required Ubuntu package "k3b" NOT installed
VnmrJ required Ubuntu package "kdiff3" NOT installed
VnmrJ required Ubuntu package "ghostscript" NOT installed
VnmrJ required Ubuntu package "imagemagick" NOT installed
 Standby........
chmod: cannot access ‘/tmp/agilent_preinstall/*’: No such file or directory

==================================================================

There are RHEL packages required by OpenVnmrJ that are not installed

OpenVnmrJ Installation can not proceed until the required Linux packages are Installed.


Please following the instructions below to install the Linux packages:

Eject the OpenVnmrJ Installation CD and go to the directory /tmp/agilent_preinstall
Insert your systems RHEL 5 Installation DVD and run the installpkgs script
e.g.:

cd /tmp/agilent_preinstall
./installpkgs


After completion Eject RHEL DVD, insert the OpenVnmrJ CD and start the OpenVnmrJ install.

==================================================================

@tesch1
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tesch1 commented Dec 9, 2016

Ok, looks like we need to figure out a process for providing development branch install packages.

You're trying to install a version that doesn't have the "fixes" (I think this stuff is fixed, but only after the 1.1A release) onto a machine that is tested with the latest development branch with the fixes.

You can try building the development branch and then installing it, using the instructions in the README for the development branch... (it should only take an hour or so)... or wait until we have a way to provide intermediate packages... or work through the failures...

@tesch1
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tesch1 commented Dec 19, 2016

@osparking could you try the REL_TEST7_linux package at https://github.com/tesch1/OpenVnmrJ/releases ?
You'll probably still need to do xhost + before ./load.nmr but I think the other issues should be resolved -- just tried it here successfully on the ubuntu14 Vagrant-defined VM.

@osparking
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osparking commented Dec 19, 2016 via email

@tesch1
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tesch1 commented Dec 19, 2016

Sounds like this issue can be closed?

@osparking
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osparking commented Dec 20, 2016 via email

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@tesch1 @osparking @DanIverson