[BioBrew Users] Trouble running mpiBlast

[Glen Otero]

On Mar 15, 2004, at 11:00 PM, shalini sharon wrote:

> Hi Glen,
>
> sorry to distrub u again.
>
> I've no idea what symbolic link means? Any examples that u can offer?
>

http://www.freebsddiary.org/ln.php
http://www.scit.wlv.ac.uk/cgi-bin/mansec?1+ln

>
> 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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>>>>>>> _______________________________________________
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>>>>>>> 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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>>>>> _______________________________________________
>>>>> BioBrew-Users mailing list
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>>>>> https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>>>>>
>>>>>
>>>> Glen Otero, Ph.D.
>>>> Linux Prophet
>>>> 619.917.1772
>>>>
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>>>> 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
>
> _________________________________________________________________
> 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