[phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS

[Jan Gebauer]

Hi Lee,

just to let you know:
For 1 processor, 600 Aa and 4 copy per asu, and ~60% solvent, my Ubuntu
needed 4.8GB of RAM and additionally 60% of the 1.4 GB Swap.
If I used more than one processor, RAM and Swap was completly filled and
execution failed with "Failed memory alloc" after a while.
Unfortunately Ubuntu tends to generate small swap partitions, a solution
might be to add a swap file (additionally to the partition...)
[http://goo.gl/RSLqT]
Just watch you "system  monitor"...

Regards,
Jan






Am 09.11.2013 16:35, schrieb qwertgfdsa78:
> Hi All,
>
> I tried Jan's tutorial and  finally I was able to install and
> ran phenix.rosetta with test set 1yjp successfully.
>  
> However, when I tried my data, I always got
> *
> *
> *"terminate called after throwing an instance of 'std::bad_alloc'"*
>  
> Google suggests maybe memory is not enough.
> I used VirutalBox and assign 8gb memory to it.
> My protein has ~3000 residues. I guess this will use more memory but
> how much RAM I need?
>
> Or the error is due to some other problem?
>
> Thank for any inputs.
>
> Lee
>
>
>
>     ------------------------------
>
>     Message: 3
>     Date: Tue, 05 Nov 2013 14:26:00 +0100
>     From: Jan Gebauer <jan.gebauer at uni-koeln.de
>     <mailto:jan.gebauer at uni-koeln.de>>
>     To: PHENIX user mailing list <phenixbb at phenix-online.org
>     <mailto:phenixbb at phenix-online.org>>
>     Subject: Re: [phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS
>     Message-ID: <5278F1E8.9020602 at uni-koeln.de
>     <mailto:5278F1E8.9020602 at uni-koeln.de>>
>     Content-Type: text/plain; charset="utf-8"
>
>     Hi David, hi all,
>
>     I now managed to at least get a test refinement working. What I mostly
>     changed was the Ubuntu version.
>     I have no idea why, but I managed to get it to work on Ubuntu 10.04.
>
>     In principle I installed 10.04 freshly in a virtualbox and from
>     their it
>     worked rather straight-forward.
>
>     Here is how I proceeded in detail for those of you who are interested:
>
>     1) Setting up a Virtualbox 4.3.2 r90405 on Ubuntu 12.04.3.
>     2) Installing the 64bit version of Ubuntu 10.04 in a virtualbox (4
>     processors / 90% speed cap / 4GB Ram /VT-x enabled)
>     3) Install VBoxAdditions
>     4) Update ubuntu (sudo apt-get update)
>     5) Installing g++ and zlib library (sudo apt-get install g++
>     zlib1g-dev)
>     6) Installing binary version of phenix-dev-1525 to
>     /usr/local/science/phenix-dev-1525 (sudo ./install
>     --prefix=/usr/local/science)
>     7) Unpack rosetta_2013_wk42_bundle to
>     /usr/local/science/rosetta_2013_wk42_bundle
>     8) set rossetta variables by inserting them at the start of
>     /usr/local/science/pheninx-dev-1525/phenix_env.sh (just in line 3ff):
>     export PHENIX_ROSETTA_PATH=/usr/local/science/rosetta_2013wk42_bundle
>     export
>     ROSETTA3_DB=/usr/local/science/rosetta_2013wk42_bundle/main/database
>     export
>     PATH=$PATH:/usr/local/science/rosetta_2013wk42_bundle/main/source/bin
>     9) assign ownership to active user (sudo chown gebauer:gebauer
>     /usr/local/science/ -R)
>     10) Compile it (phenix.build_phenix_interface nproc=4)
>     It should run without problems
>
>     Testing:
>     1) Create a new directory (mkdir test && cd test)
>     2) Download testset (suggested by Nat: phenix.fetch_pdb --mtz 1yjp)
>     3) Run rosetta_refine (phenix.rosetta_refine 1yjp.pdb 1yjp.mtz
>     nproc=4)
>     In my case rFree dropped from 18.21 to 14.90. It's not a low
>     resolution
>     dataset, but it show that it general works and lowRes would
>     potentially
>     take to long for a mere testing
>
>     My real data are still being processed so I have no idea how well it
>     will works... only thing I found out already:
>     4.5 GB RAM for 4 processes calculating ~500Aa via rosetta seems not to
>     be enough. I thereby reduced my "real run" to only one processor...
>
>     Regards,
>     Jan
>
>
>
>
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-- 
Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
Otto-Fischer-Str. 12-14 / 50674 Köln
Fon: +49 (221) 470 3212	
Fax: +49 (221) 470 5066

http://px.uni-koeln.de/

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