[BioBrew Users] Biobrew 4.1.1 installation on a running cluster

Thu May 4 12:42:52 EDT 2006

Hmmm... Not sure why the rpms aren't being installed. Go ahead and  
install the rpms with 'rpm -i' on the frontend. You'll have to  
reinstall the compute nodes for the biobrew rpms to be
installed.

Glen

On May 4, 2006, at 8:50 AM, kannaiah at bsd.uchicago.edu wrote:

> Hello there
>
> I just installed Biobrew 4.1.1 (prev version i had was the 4.1) on  
> our cluster
> frontend. I followed the steps below as given in the docs for a  
> installing a
> roll on a running system:
> But i still dont see the biobrew packages installed on the  
> frontend. They are
> just stored as rpm files. Do i need to restart the frontend?
> I still havent reinstalled the compute nodes, i was waiting to see  
> if they
> installed correctly on the frontend first.
> ----------------
> # cd /tmp
> # wget
> http://www.rocksclusters.org/ftp-site/pub/rocks/extras/4.1/x86_64/ 
> app-trace-4.1-0.x86_64.disk1.iso
> # mount -o loop app-trace-4.1-0.x86_64.disk1.iso /mnt/cdrom
> # cd /home/install
> # rocks-dist --install copyroll
> # umount /mnt/cdrom
> # rocks-dist dist
> ---------------------
>
> Any suggestions?
>
> Thank you
> Kiran Annaiah
> Dept of Human Genetics
> Univ of Chicago
>
>> 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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>> entity to
>> which
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>> intended
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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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>>> to which
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>>> confidential.  If the reader of this email message is not the  
>>> 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.
>>> -------------------------------------------------
>>> _______________________________________________
>>> BioBrew-Users mailing list
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>>
>>
>>
>> ------------------------------
>>
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>>
>> End of BioBrew-Users Digest, Vol 12, Issue 1
>> **********************************************
>>
>>
>>
>
>
>
>
>
> -------------------------------------------------
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