[BioBrew Users] Trouble running mpiBlast

[shalini sharon]

Hi Glen,

Is the rpms ready? And if they r , where can I download them?

Rgs, Sharon.


>From: Glen Otero <gotero at linuxprophet.com>
>Reply-To: BioBrew-Users at bioinformatics.org
>To: BioBrew-Users at bioinformatics.org
>Subject: Re: [BioBrew Users] Trouble running mpiBlast
>Date: Mon, 15 Mar 2004 22:44:18 -0800
>
>
>On Mar 15, 2004, at 10:34 PM, shalini sharon wrote:
>
>>Hi Glen,
>>
>>
>>
>>Thanks for ur reply. Can u send us an email notifying us when the rpms  
>>are done?
>
>Absolutely.
>
>>Are we suppose to download the rpms from www.bioinformatics.org  website?
>
>That may be one way. But I may be able to email them to you as well.
>>
>>We faced another error while running EMBOSS. Do u have any ideas
>>what this error means?
>>
>>Error message:
>>======================================================================= 
>>=========
>>pwd: /opt/BioBrew/EMBOSS/2.6.0/bin
>>[root at frontend-0 bin]./wossname
>>./wossname: error while loading shared libraries libnucleus.so.0:  cannot 
>>open shared object file: No such file or direectory
>>======================================================================= 
>>=========
>>
>>The pointer seems to point to /usr/local/lib for the file, but the  file 
>>are located at /opt/BioBrew/EMBOSS/2.6.0/lib. Is there any where  to 
>>change the pointer?? And which file contain the pointer code?
>
>Can you make a symbolic link that points to the proper library?
>
>Glen
>
>>
>>
>>Rgds
>>Sharon
>>
>>>From: Glen Otero <gotero at linuxprophet.com>
>>>Reply-To: BioBrew-Users at bioinformatics.org
>>>To: BioBrew-Users at bioinformatics.org
>>>Subject: Re: [BioBrew Users] Trouble running mpiBlast
>>>Date: Mon, 15 Mar 2004 19:50:31 -0800
>>>
>>>Sharon-
>>>
>>>We should have new rpms by Tuesday or Wednesday (California time) ; )
>>>
>>>Glen
>>>
>>>On Mar 15, 2004, at 4:53 PM, shalini sharon wrote:
>>>
>>>>
>>>>Hi, Glen
>>>>
>>>>Can we know by when u will be able to send urs the rpms?
>>>>
>>>>Thank U
>>>>
>>>>Rgs, sharon
>>>>
>>>>
>>>>>From: Glen Otero <gotero at linuxprophet.com>
>>>>>Reply-To: BioBrew-Users at bioinformatics.org
>>>>>To: BioBrew-Users at bioinformatics.org
>>>>>Subject: Re: [BioBrew Users] Trouble running mpiBlast
>>>>>Date: Mon, 15 Mar 2004 12:19:01 -0800
>>>>>
>>>>>Soumyadeep-
>>>>>
>>>>>No need to switch over to BioBrew 3.0 just yet. We should be able  to 
>>>>>send you new rpms for BLAST, lam-mpi, and vmi (if necessary) to  take 
>>>>>care of the problems on 1.0.
>>>>>
>>>>>Glen
>>>>>
>>>>>On Mar 15, 2004, at 9:45 AM, Soumyadeep nandi wrote:
>>>>>
>>>>>>Hi Glen,
>>>>>>
>>>>>>>You're running BioBrew 1.0, correct?
>>>>>>
>>>>>>We are using BioBrew 1.0 and isos are downloaded from
>>>>>>ftp://ftp.bay13.net/pub/BioBrew/.
>>>>>>Moreover, you have released version 3.0, that is
>>>>>>available in "Massachusetts, USA --
>>>>>>http://bioinformatics.org/ftp/biobrew/", should we
>>>>>>switch over to this latest version.
>>>>>>
>>>>>>Regards,
>>>>>>Soumyadeep
>>>>>>
>>>>>>--- Glen Otero <gotero at linuxprophet.com> wrote:
>>>>>>>Soumyadeep-
>>>>>>>
>>>>>>>You're running BioBrew 1.0, correct?
>>>>>>>
>>>>>>>Glen
>>>>>>>
>>>>>>>On Mar 13, 2004, at 7:40 AM, Soumyadeep nandi wrote:
>>>>>>>
>>>>>>>>--- Glen Otero <gotero at linuxprophet.com> wrote:
>>>>>>>>>>The pvm we were using in production mode was
>>>>>>>>>>HMMER-2.3.2 compiled with the intel compiler.
>>>>>>>>>
>>>>>>>>>What flags did you use to compile HMMER with the
>>>>>>>>>Intel compiler? We'll
>>>>>>>>>be offering the Intel compilers and tools in our
>>>>>>>>>distro soon.
>>>>>>>>
>>>>>>>>We used the precompiled version from the hmmer
>>>>>>>site -
>>>>>>>>here is the listing:
>>>>>>>>
>>>>>>>>  Intel GNU/Linux
>>>>>>>>     Download: hmmer-2.3.2.bin.intel-linux.tar.gz
>>>>>>>>     Or, as an RPM:
>>>>>>>hmmer-2.3.2-1static_pvm.i686.rpm
>>>>>>>>     Dell 6450; 4xPIII/700/2; Red Hat Linux 7.2;
>>>>>>>>--enable-threads --enable-lfs --enable-pvm; CC=icc
>>>>>>>>CFLAGS="-O3 -axMKW -static"
>>>>>>>>     the RPM spec file is available: hmmer-pvm.spec
>>>>>>>>
>>>>>>>>Soumyadeep
>>>>>>>>
>>>>>>>>__________________________________
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>>>>>>>>_______________________________________________
>>>>>>>>BioBrew-Users mailing list
>>>>>>>>BioBrew-Users at bioinformatics.org
>>>>>>>>
>>>>>>>
>>>>>>https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>>>>>>>>
>>>>>>>>
>>>>>>>Glen Otero, Ph.D.
>>>>>>>Linux Prophet
>>>>>>>619.917.1772
>>>>>>>
>>>>>>>_______________________________________________
>>>>>>>BioBrew-Users mailing list
>>>>>>>BioBrew-Users at bioinformatics.org
>>>>>>>
>>>>>>https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>>>>>>
>>>>>>
>>>>>>__________________________________
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>>>>>>Yahoo! Mail - More reliable, more storage, less spam
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>>>>>>_______________________________________________
>>>>>>BioBrew-Users mailing list
>>>>>>BioBrew-Users at bioinformatics.org
>>>>>>https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>>>>>>
>>>>>>
>>>>>Glen Otero, Ph.D.
>>>>>Linux Prophet
>>>>>619.917.1772
>>>>>
>>>>>_______________________________________________
>>>>>BioBrew-Users mailing list
>>>>>BioBrew-Users at bioinformatics.org
>>>>>https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>>>>
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>>>>
>>>>
>>>Glen Otero, Ph.D.
>>>Linux Prophet
>>>619.917.1772
>>>
>>>_______________________________________________
>>>BioBrew-Users mailing list
>>>BioBrew-Users at bioinformatics.org
>>>https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>>
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>>https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>>
>>
>Glen Otero, Ph.D.
>Linux Prophet
>619.917.1772
>
>_______________________________________________
>BioBrew-Users mailing list
>BioBrew-Users at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/BioBrew-Users

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