My original message is shown below.
The first question: Is it possible to run vnmrj 2.2D on RHEL 5.5 or CentOS 5.5? The answer, from the responses I received is YES, it is possible and a number of locations are doing that.
The second question then is: Is it possible to install vnmrj 2.2D over Centos 5.4 or 5.5 as I was trying to do? This question is more difficult to answer because no one who responded had done that; most had installed on a lower version of RHEL and upgraded. However, after some "messing around" I found that it can be done. I give a brief procedure below in case anyone is searching the archives trying to do this:
1. After installing Centos 5.4 or 5.5, proceed with installation of vnmrj 2.2D as outlined in the document "VnmrJLinuxSupport.pdf" - which is extremely useful for this purpose.
2. The first major hurdle is installing the pre-patch prior to installation of vnmrj. This installation fails under Centos because the structure of the Centos installation DVD is not the same as a RHEL installation DVD. This is easily remedied by changing the references to "Client" and "Server" DVD directories in the "setupyumrepo" script to the base DVD directory "/". After this is done, the pre-patch installs fine.
3. Proceed to install vnmrj, and the vnmrj patch referenced in the document.
4. Now, when sysprofiler is run, you will find that pulse sequence generation fails. This is due to the fact that gcc has not been installed. You can install it several ways, but I chose to install all of the development tools: "yum groupinstall 'Development Tools'". After doing this, there is still a pulse sequence compilation error due to a missing header file, so one more installation is needed: "yum -y install glibc_devel".
5. At this point, sysprofiler gives no errors or recommendations (other than saying that you are running a non-supported version of Linux). However, vnmrj still hangs (does not completely come up).
6. In order to debug this, I used the strace command to log all of the system calls associated with any process or subprocess spawned by vnmrj (e.g. 'strace -f -ff -o filename vnmrj'). This generates a HUGE amount of output, but from that I could see that I was missing the library libstdc++.so.5, which was then loaded using "yum install compat-libstdc++.33".
7. After this was done SUCCESS!!!
I would like the thank the following who responded to the original message: Dave VanderVelde, Scott Burt, Eugenio Alverado, Jerry Hu, and Mike Strain.
Tom P.
On Nov 5, 2010, at 4:13 PM, Tom Pratum wrote:
> Hello All-
> I do realize that Varian does not currently recommend the use of RHL 5.5 with Vnmrj, however I am wondering if anyone is currently using such a setup. I attempted to install vnmrj 2.2D on Centos 5.5 using the instructions and patches for RHL 5.4 (I did need to make some minor changes to the patch scripts for Centos), and found that although I can communicate with the console, the entire Vnmrj graphical interface does not come up when the program is started. Sysprofiler only give one apparent "error" - that psg generation does not complete due to a missing header file. I can downgrade to 5.4 and reinstall, but before I do that I am checking to see if it is possible to get vnmrj to run on 5.5 (RHL/Centos).
>
> Thanks in advance for any comments - I will post any useful info I get.
>
>
> Tom Pratum
> Dept of Chemistry, MS 9150
> Western Washington University
> pratum_at_chem.wwu.edu
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Tom Pratum
Dept of Chemistry, MS 9150
Western Washington University
pratum_at_chem.wwu.edu
Received on Mon Nov 15 2010 - 13:22:03 MST