[BioBrew Users] Trouble running mpiBlast

[Glen Otero]

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
>>>>>>>
>>>>>>> __________________________________
>>>>>>> Do you Yahoo!?
>>>>>>> Yahoo! Mail - More reliable, more storage, less
>>>>>> spam
>>>>>>> http://mail.yahoo.com
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>
>>>>>
>>>>> __________________________________
>>>>> Do you Yahoo!?
>>>>> Yahoo! Mail - More reliable, more storage, less spam
>>>>> http://mail.yahoo.com
>>>>> _______________________________________________
>>>>> 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
>>>
>>> _________________________________________________________________
>>> Keep track of Singapore & Malaysia stock prices.  
>>> http://www.msn.com.sg/money/
>>>
>>> _______________________________________________
>>> 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
>
> _________________________________________________________________
> Download games, logos, wallpapers and lots more at MSN Mobile!  
> http://www.msn.com.sg/mobile/
>
> _______________________________________________
> 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