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Excessive disk use in Rosetta download and build processes

Submitted by bene on Tue, 2011-02-01 11:44

The software I build and install gets pushed to standalone installations on about 100 different machines, and the installation usually lives on higher-cost storage (i.e. RAID or a SAN, etc), and then all those installations are backed up somewhere or other, so I usually take the time to weed out as many unnecessary files as possible. It makes everyone's life a little better.

Looking at the Rosetta packaging, there are a number of opportunities for improvements. The first one is very easy. Here's an expanded rosetta3.2_bundles.tgz:

$ du -k --max-depth=1 | sort -n
48 ./.svn

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Rosetta 3 - Build/Install

Error during installation of rosetta2.3 in Blue gene

Submitted by anusmita on Mon, 2011-01-31 09:49

Hi

I am trying to install rosetta2.3 in IBM Blue gene
Compiler: xlc++
Mpi : mpixlC

The error got during compilation:
mpixlC -c -I. -Isrc -Iexternal/include -Isrc/platform/linux/ -O3 -qhot=nosimd -DNDEBUG -DUSEMPI -qarch=440 -qtune=440 -qmaxmem=-1 -qlanglvl=c99__func__ -MT.xlc++_ppc.map_sequence.d -MF.xlc++_ppc.map_sequence.d map_sequence.cc -o .xlc++_ppc.map_sequence.o
"src/ObjexxFCL/FArray1DB.hh", line 477.29: 1540-0274 (S) The name lookup for "equal_dimensions" did not find a declaration.

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Rosetta++ - Build/Install

Build Error, ubuntu 10.10, scons 2.0, python 2.6.6 and gcc 4.4.5, truncation

Submitted by meghrig on Mon, 2011-01-31 08:02

Hello,
I'm using ubuntu 10.10, scons 2.0, python 2.6.6 and gcc 4.4.5
I built a release version of Rosetta, here are the last few lines of the building process
sh: o: not found
Install file: "build/src/release/linux/2.6/32/x86/gcc/rna_extract.linuxgccrelease" as "bin/rna_extract.linuxgccrelease"

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Rosetta 3 - Build/Install

(drluca77) python/gcc combo for mac build, pyrosetta 2.0

Submitted by smlewis on Mon, 2011-01-31 07:25

(This comment copied from a different topic)

Hello.

I downloaded and tried to use the Mac version, but I get this error:

Python 2.6.5 (r265:79063, Mar 20 2010, 11:39:18)
[GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rosetta import *
Traceback (most recent call last):
File "", line 1, in
File "rosetta/__init__.py", line 11, in
import utility
File "rosetta/utility/__init__.py", line 1, in
from __utility_all_at_once_ import *

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PyRosetta - Build/Install

3.2 with Intel Compilers on OS X Intel

Submitted by bene on Fri, 2011-01-28 10:19

Is building Rosetta 3.2 with the Intel compilers on OS X Intel supported? I ran the build like so:

./scons.py bin mode=release cxx=icc

And the resulting commands look like this:

g++ -o build/src/release/macos/10.5/64/x86/icc/super_aln.macosiccrelease build/src/release/macos/10.5/64/x86/icc/apps/public/comparative_modeling/super_aln.o -Llib -Lexternal/lib -Lbuild/src/release/macos/10.5/64/x86/icc -Lsrc -L/usr/local/lib -L/usr/lib -ldevel -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz

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Rosetta 3 - Build/Install

3.2 and Intel Compilers 12.0

Submitted by bene on Fri, 2011-01-28 08:24

It looks like there is some buggy interaction between Rosetta, Scons and the latest version of the Intel compilers.

I edited tools/build/options.settings to enable the 12.0 compiler version and tools/build/user.settings to find the Intel compilers and the error looks like this:


$ ./scons.py bin mode=release cxx=icc extras=static tatic
scons: Reading SConscript files ...
svn: '.' is not a working copy
scons: done reading SConscript files.
scons: Building targets ...

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Rosetta 3 - Build/Install

Rosetta parallel installation

Submitted by vamsi on Fri, 2011-01-28 03:31

Hi all,
have been using Rosetta for a while, but could not figure out exactly how to install parallel. I am very happy to see Rosetta3.2 latest version. I will be grateful to you if anyone suggest me how to install (best way)parallel and how to run applications in parallel.

Thank you in advance

Best regards,
vamsi

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Rosetta 3 - Build/Install

Rosetta 3.2

Submitted by knutjbj on Thu, 2011-01-27 08:18

I used pc with Fedora 14. I used gcc 4.5 and mpich2 to compile Rosetta 3.2. However I encounter this erros when I try to compile Rosetta 3,2 with scons.

src/core/conformation/symmetry/util.cc: In function 'void core::conformation::symmetry::make_symmetric_pose(core::pose::Pose&, core::conformation::symmetry::SymmetryInfo)':
src/core/conformation/symmetry/util.cc:360:37: error: expected type-specifier
src/core/conformation/symmetry/util.cc:360:37: error: conversion from 'int*' to non-scalar type 'core::pose::PDBInfoOP' requested

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Rosetta 3 - Build/Install

unable to propagate location of libraries to scons for Rosetta 3.1 [FIXED...SORT OF...]

Submitted by smg3d on Thu, 2011-01-27 07:14

I am unable to propagate our cluster environment to the Rosetta scons scripts (most likely the library environment)

Here is my situation:

On our cluster, compilers are loaded using "module" (e.g. "module load compilers/gcc/4.4.2" or "module load mpi/openmpi/1.4.3_gcc").
-> Consequently, compilers (gcc, g++, ...) are not in "normal" PATH, and the same goes for some required libraries (and for INCLUDE paths also)

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Rosetta 3 - Build/Install

Docking an iron atom to a peptide

Submitted by buzb on Wed, 2011-01-26 09:49

Hi All,

This is my first post to the form. I'm a new user to Rosetta.

I am using the ligand_docking application to dock an Fe(III) atom to a protein structure, and am running into difficulty. A few questions:

1. Is ligand_docking appropriate for docking a single atom to a protein molecule?

2. If ligand_docking is appropriate, what is the best way to do it? When I try to use the 1_setup.sh script produced by arls.py to set up a ligand docking run, it complains that I need to have at least 3 atoms in the Mol2 file used to define the ligand (the Fe atom).

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Rosetta 3 - General

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