[BioBrew Users] mpiblast and other biobrew apps

Tue May 2 00:38:48 EDT 2006

On May 1, 2006, at 9:46 AM, kannaiah at bsd.uchicago.edu wrote:

> Hi Glen,
>
> Thanks for the info. We had the 4.1 version of ROcks and Biobrew.
> I will download the 4.1.1 version and install.
> Few questions:
>
> 1)Should i stop all the jobs running before installation? (i would  
> think so,
> just thought i would confirm)

Yep.

> 2)Also, once i edit the extend-compute.xml file and run the rocks- 
> dist dist,
> does it install it on all the compute nodes as well?

It should.

> 3) Do i need to reinstall the compute nodes after the biobrew  
> installation?

Yep.
>
> I am still trying to understand how all this installation thing  
> works on rocks.
> Sorry if this is a repeat question from earlier posts.
>
> -Kiran
>
>>
>> Today's Topics:
>>
>>    1. mpiblast and other biobrew apps (kannaiah at bsd.uchicago.edu)
>>    2. Re: mpiblast and other biobrew apps (Glen Otero)
>>
>>
>> --------------------------------------------------------------------- 
>> -
>>
>> Message: 1
>> Date: Mon,  1 May 2006 09:13:30 -0500
>> From: kannaiah at bsd.uchicago.edu
>> Subject: [BioBrew Users] mpiblast and other biobrew apps
>> To: BioBrew-Users at bioinformatics.org
>> Message-ID: <1146492810.4456178af3177 at netmail.bsd.uchicago.edu>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hello,
>>
>> We installed Biobrew roll on our Rocks cluster. But i dont see any  
>> of the
>> Biobrew apps having installed on the cluster. I only see their  
>> rpms sitting
>> in
>> certain folders. I checked on mpiblast and this is what i found  
>> (output of
>> FIND
>> command)
>>
>>
> /home/install/ftp.rocksclusters.org/pub/rocks/rocks-4.1/rocks-dist/ 
> rolls/biobrew/4.1/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
>>
> /home/install/rocks-dist/lan/x86_64/RedHat/RPMS/ 
> mpiblast-1.4.0-1.x86_64.rpm.torrent
>> /home/install/rocks-dist/lan/x86_64/RedHat/RPMS/ 
>> mpiblast-1.4.0-1.x86_64.rpm
>>
> /share/install/ftp.rocksclusters.org/pub/rocks/rocks-4.1/rocks-dist/ 
> rolls/biobrew/4.1/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
>>
> /share/install/rocks-dist/lan/x86_64/RedHat/RPMS/ 
> mpiblast-1.4.0-1.x86_64.rpm.torrent
>> /share/install/rocks-dist/lan/x86_64/RedHat/RPMS/ 
>> mpiblast-1.4.0-1.x86_64.rpm
>>
>> Do i need to manually install these rpms? Or did the Biobrew not  
>> install
>> correctly?
>>
>> I have not run mpiblast before, but shouldnt i be able to type  
>> "mpiblast" on
>> the
>> command line?
>> Likewise Hmmer and other packages of Biobrew.
>>
>> Thanks for the help
>>
>> -Kiran
>>
>>
>>
>>
>>
>>
>>
>>
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 1 May 2006 08:44:09 -0700
>> From: Glen Otero <glen at callident.com>
>> Subject: Re: [BioBrew Users] mpiblast and other biobrew apps
>> To: The Virtual BioBrew Think Tank
>> 	<BioBrew-Users at bioinformatics.org>
>> Message-ID: <C45059D0-ADA2-4E9C-86E4-DFFA1B694CFB at callident.com>
>> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>>
>> Hi Kiran-
>>
>> The version of the BioBrew roll you have does have a few problems
>> that prevent the rpms from installing automatically. So you will have
>> to install the rpms yourself. But if you download and install the
>> latest roll, 4.1.1, the rpms should install automatically.
>>
>> Glen
>>
>> On May 1, 2006, at 7:13 AM, kannaiah at bsd.uchicago.edu wrote:
>>
>>> Hello,
>>>
>>> We installed Biobrew roll on our Rocks cluster. But i dont see any
>>> of the
>>> Biobrew apps having installed on the cluster. I only see their rpms
>>> sitting in
>>> certain folders. I checked on mpiblast and this is what i found
>>> (output of FIND
>>> command)
>>>
>>> /home/install/ftp.rocksclusters.org/pub/rocks/rocks-4.1/rocks-dist/
>>> rolls/biobrew/4.1/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
>>> /home/install/rocks-dist/lan/x86_64/RedHat/RPMS/
>>> mpiblast-1.4.0-1.x86_64.rpm.torrent
>>> /home/install/rocks-dist/lan/x86_64/RedHat/RPMS/
>>> mpiblast-1.4.0-1.x86_64.rpm
>>> /share/install/ftp.rocksclusters.org/pub/rocks/rocks-4.1/rocks-dist/
>>> rolls/biobrew/4.1/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
>>> /share/install/rocks-dist/lan/x86_64/RedHat/RPMS/
>>> mpiblast-1.4.0-1.x86_64.rpm.torrent
>>> /share/install/rocks-dist/lan/x86_64/RedHat/RPMS/
>>> mpiblast-1.4.0-1.x86_64.rpm
>>>
>>> Do i need to manually install these rpms? Or did the Biobrew not
>>> install correctly?
>>>
>>> I have not run mpiblast before, but shouldnt i be able to type
>>> "mpiblast" on the
>>> command line?
>>> Likewise Hmmer and other packages of Biobrew.
>>>
>>> Thanks for the help
>>>
>>> -Kiran
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>>> intended
>>> recipient, you are hereby notified that any dissemination,
>>> distribution, or
>>> copying of this communication is prohibited.  If you have received
>>> this email
>>> in error, please notify the sender and destroy/delete all copies of
>>> the
>>> transmittal.  Thank you.
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>>
>>
>>
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>>
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>>
>> End of BioBrew-Users Digest, Vol 12, Issue 1
>> **********************************************
>>
>>
>>
>
>
>
>
>
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