[BioMart Users] (no subject)

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[BioMart Users] (no subject)

zhilianghu
Thanks to the hard work by the Biomart team - I was able to download the
new Biomart version 0.8 to install and deploy on my RH Linux server...
Everything seems working alright, except that the serve "ram away" a few
times (quitely die).  The observations are:

I use Xming to operate remote Biomart GUI on my Windows XP. I can start
the Biomart with "biomart-server.sh" GUI.  When done I can close the GUI
and release the shell to it prompt, and even logout from the shell, while
Biomart is running.  However I have to keep my Xming alive in the
background. When I attempt to turn off Xming, it warns:

  There are currently 2 clients connected; Shut down these client/server?

If I close Xming on my PC, the Biomart on my remote Linux dies.

I also tried to run the server from the command line, as in:
  > /usr/local/biomart/dist/scripts/biomart-server.sh start

Sometimes it complains there is already a biomart running, while
"biomart-server.sh stop" won't really stop it, that I had to kill the
process (it's a short process name, different from normal) to try again.

Sometimes it starts, but I got errors on the http/web:
  HTTP Error, problem accessing /.Reason: Cannot find

Any advice please?

Zhiliang
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Re: [BioMart Users] (no subject)

Jack Hsu
Re: [BioMart Users] (no subject) Hi Zhiliang,

The “biomart-server.sh stop” command will look at the biomart.pid file inside dist directory and kill that process. It may be that the process was already killed but the pid file still remained.

I’m not sure how Xming works, but the “biomart-server.sh start” script should be launching the BioMart process as a daemon process. You could try running the script through a “screen”, which you can detach from using ^A^D (Ctlr+A, Ctlr+D), and reattach using “screen -r”. This will allow you to resume previous screen sessions on the Linux server even if your client disconnects.

The “HTTP Error” occurs during querying when an URL source is not accessible by the BioMart server. Do you have a firewall that prevents access to outside resources?

-jack


On 11-05-19 9:55 AM, "Zhiliang" <hu@...> wrote:

Thanks to the hard work by the Biomart team - I was able to download the
new Biomart version 0.8 to install and deploy on my RH Linux server...
Everything seems working alright, except that the serve "ram away" a few
times (quitely die).  The observations are:

I use Xming to operate remote Biomart GUI on my Windows XP. I can start
the Biomart with "biomart-server.sh" GUI.  When done I can close the GUI
and release the shell to it prompt, and even logout from the shell, while
Biomart is running.  However I have to keep my Xming alive in the
background. When I attempt to turn off Xming, it warns:

  There are currently 2 clients connected; Shut down these client/server?

If I close Xming on my PC, the Biomart on my remote Linux dies.

I also tried to run the server from the command line, as in:
  > /usr/local/biomart/dist/scripts/biomart-server.sh start

Sometimes it complains there is already a biomart running, while
"biomart-server.sh stop" won't really stop it, that I had to kill the
process (it's a short process name, different from normal) to try again.

Sometimes it starts, but I got errors on the http/web:
  HTTP Error, problem accessing /.Reason: Cannot find

Any advice please?

Zhiliang
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Users mailing list
Users@...
https://lists.biomart.org/mailman/listinfo/users


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Re: [BioMart Users] (no subject)

zhilianghu
In reply to this post by zhilianghu
Hi Jack,

"screen" over Xming didn't help - close of Xming still shuts down biomart
and "screen" (there is no screen to resume).

My server does not block outgoing URL or alike.

But I think I have found it - by looking through the stdouterr logs in
"dist/logs".  When I tried to start it with womething like:
   /full/path/to/biomart/dist/scripts/biomart-server.sh start
from an arbitrary location, it keeps looking for
./conf/xml/AttributeTableConfig.xml in my current dir (don't find it),
thus complains several "(Unknown Source)".  So I had to start it by
  1>  cd /usr/local/biomart
  2>  ./dist/scripts/biomart-server.sh start
so that it sees /usr/local/biomart/conf/xml/AttributeTableConfig.xml

Thanks!

Zhiliang

> Date: Thu, 19 May 2011 12:01:03 -0400
> From: Jack Hsu <[hidden email]>
> To: Zhiliang <[hidden email]>, BioMart Users <[hidden email]>
> Subject: Re: [BioMart Users] (no subject)
>
> Hi Zhiliang,
>
> The "biomart-server.sh stop" command will look at the biomart.pid file inside
> dist directory and kill that process. It may be that the process was already
> killed but the pid file still remained.
>
> I'm not sure how Xming works, but the "biomart-server.sh start" script should
> be launching the BioMart process as a daemon process. You could try running
> the script through a "screen", which you can detach from using ^A^D (Ctlr+A,
> Ctlr+D), and reattach using "screen -r". This will allow you to resume
> previous screen sessions on the Linux server even if your client disconnects.
>
> The "HTTP Error" occurs during querying when an URL source is not accessible
> by the BioMart server. Do you have a firewall that prevents access to outside
> resources?
>
> -jack
>
>
> On 11-05-19 9:55 AM, "Zhiliang" <[hidden email]> wrote:
>
> Thanks to the hard work by the Biomart team - I was able to download the
> new Biomart version 0.8 to install and deploy on my RH Linux server...
> Everything seems working alright, except that the serve "ram away" a few
> times (quitely die).  The observations are:
>
> I use Xming to operate remote Biomart GUI on my Windows XP. I can start
> the Biomart with "biomart-server.sh" GUI.  When done I can close the GUI

I should correct myself - I had a wrong copy/paste here, it should be
"/usr/local/biomart/dist/scripts/martconfigurator.sh" to launch the GUI.

> and release the shell to it prompt, and even logout from the shell, while
> Biomart is running.  However I have to keep my Xming alive in the
> background. When I attempt to turn off Xming, it warns:
>
>  There are currently 2 clients connected; Shut down these client/server?
>
> If I close Xming on my PC, the Biomart on my remote Linux dies.
>
> I also tried to run the server from the command line, as in:
>  > /usr/local/biomart/dist/scripts/biomart-server.sh start
>
> Sometimes it complains there is already a biomart running, while
> "biomart-server.sh stop" won't really stop it, that I had to kill the
> process (it's a short process name, different from normal) to try again.
>
> Sometimes it starts, but I got errors on the http/web:
>  HTTP Error, problem accessing /.Reason: Cannot find
>
> Any advice please?
>
> Zhiliang
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