Re: [phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS

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

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Message: 3 Date: Tue, 05 Nov 2013 14:26:00 +0100 From: Jan Gebauer mailto:[email protected]> To: PHENIX user mailing list mailto:[email protected]> Subject: Re: [phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS Message-ID: <[email protected] mailto:[email protected]> 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/