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Hi Lee,<br>
<br>
just to let you know: <br>
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.<br>
If I used more than one processor, RAM and Swap was completly filled
and execution failed with "Failed memory alloc" after a while.<br>
Unfortunately Ubuntu tends to generate small swap partitions, a
solution might be to add a swap file (additionally to the
partition...) [<a class="moz-txt-link-freetext" href="http://goo.gl/RSLqT">http://goo.gl/RSLqT</a>]<br>
Just watch you "system monitor"...<br>
<br>
Regards,<br>
Jan<br>
<br>
<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 09.11.2013 16:35, schrieb
qwertgfdsa78:<br>
</div>
<blockquote
cite="mid:CAHFwYaDjQBLp9kBdANTvPai_HESiXW6cTwx0Yr0xtzrHUAMsEg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi All,
<div><br>
</div>
<div>I tried Jan's tutorial and finally I was able to install
and ran phenix.rosetta with test set 1yjp successfully.</div>
<div> <br>
<div class="gmail_extra">However, when I tried my data, I
always got</div>
<div class="gmail_extra"><b><br>
</b></div>
<div class="gmail_extra"><b>"terminate called after throwing
an instance of 'std::bad_alloc'"</b><br>
</div>
<div class="gmail_extra"> </div>
<div class="gmail_extra">
Google suggests maybe memory is not enough.</div>
<div class="gmail_extra">I used VirutalBox and assign 8gb
memory to it.</div>
<div class="gmail_extra">My protein has ~3000 residues. I
guess this will use more memory but how much RAM I need?<br>
</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Or the error is due to some other
problem?</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">Thank for any inputs.</div>
<div class="gmail_extra">
<br clear="all">
<div>Lee</div>
<br>
<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 05 Nov 2013 14:26:00 +0100<br>
From: Jan Gebauer <<a moz-do-not-send="true"
href="mailto:jan.gebauer@uni-koeln.de" target="_blank">jan.gebauer@uni-koeln.de</a>><br>
To: PHENIX user mailing list <<a
moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org"
target="_blank">phenixbb@phenix-online.org</a>><br>
Subject: Re: [phenixbb] Phenix.Rosetta_refine on Ubuntu
12.04 LTS<br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:5278F1E8.9020602@uni-koeln.de"
target="_blank">5278F1E8.9020602@uni-koeln.de</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi David, hi all,<br>
<br>
I now managed to at least get a test refinement working.
What I mostly<br>
changed was the Ubuntu version.<br>
I have no idea why, but I managed to get it to work on
Ubuntu 10.04.<br>
<br>
In principle I installed 10.04 freshly in a virtualbox
and from their it<br>
worked rather straight-forward.<br>
<br>
Here is how I proceeded in detail for those of you who
are interested:<br>
<br>
1) Setting up a Virtualbox 4.3.2 r90405 on Ubuntu
12.04.3.<br>
2) Installing the 64bit version of Ubuntu 10.04 in a
virtualbox (4<br>
processors / 90% speed cap / 4GB Ram /VT-x enabled)<br>
3) Install VBoxAdditions<br>
4) Update ubuntu (sudo apt-get update)<br>
5) Installing g++ and zlib library (sudo apt-get install
g++ zlib1g-dev)<br>
6) Installing binary version of phenix-dev-1525 to<br>
/usr/local/science/phenix-dev-1525 (sudo ./install<br>
--prefix=/usr/local/science)<br>
7) Unpack rosetta_2013_wk42_bundle to<br>
/usr/local/science/rosetta_2013_wk42_bundle<br>
8) set rossetta variables by inserting them at the start
of<br>
/usr/local/science/pheninx-dev-1525/phenix_env.sh (just
in line 3ff):<br>
export
PHENIX_ROSETTA_PATH=/usr/local/science/rosetta_2013wk42_bundle<br>
export
ROSETTA3_DB=/usr/local/science/rosetta_2013wk42_bundle/main/database<br>
export
PATH=$PATH:/usr/local/science/rosetta_2013wk42_bundle/main/source/bin<br>
9) assign ownership to active user (sudo chown
gebauer:gebauer<br>
/usr/local/science/ -R)<br>
10) Compile it (phenix.build_phenix_interface nproc=4)<br>
It should run without problems<br>
<br>
Testing:<br>
1) Create a new directory (mkdir test && cd
test)<br>
2) Download testset (suggested by Nat: phenix.fetch_pdb
--mtz 1yjp)<br>
3) Run rosetta_refine (phenix.rosetta_refine 1yjp.pdb
1yjp.mtz nproc=4)<br>
In my case rFree dropped from 18.21 to 14.90. It's not a
low resolution<br>
dataset, but it show that it general works and lowRes
would potentially<br>
take to long for a mere testing<br>
<br>
My real data are still being processed so I have no idea
how well it<br>
will works... only thing I found out already:<br>
4.5 GB RAM for 4 processes calculating ~500Aa via
rosetta seems not to<br>
be enough. I thereby reduced my "real run" to only one
processor...<br>
<br>
Regards,<br>
Jan<br>
<br>
<br>
</blockquote>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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
<a class="moz-txt-link-freetext" href="http://px.uni-koeln.de/">http://px.uni-koeln.de/</a></pre>
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