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Compilation

ubuntu 16.04 install

Category: 
Compilation

Do I assume correctly in a 8 core hyperthreaded machine openmpi runs will be faster than normal static compilations? Has anyone managed to compile  the openmpi version on ubuntu 16.04?   I did have to edit the tools/build/options.settings and add 5.4 otherwise scons wont run.  I assume that the compiler is too new for this? Any work around? Thanks

PS:My tools/build/site.settings is empty

Post Situation: 

Rosetta on CentOS 7 using GCC-5.5

Category: 
Compilation

Hello

I am trying to compile rosetta_src_2017.45.59812 using gcc-5.5 on a centos machine.

First of all,

./rosetta_compiler_test.py /home/ertinaz/gcc-install/gcc-5.5.0/bin/g++-5.5

gives

Summary:
Main Tests:             	16 of 16 passed
Optional Tests:         	5 of 6 passed

REGEX:                  	<<<FAILED! (Compiled but did not run.)>>>

First question is which gcc version would pass the entire test?

Post Situation: 

FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py

Category: 
Compilation

Dears,

After installing Rosetta 3.9 in a cluster and trying to run the simple command:

helix_preassemble_setup.py -fasta NFKB_1OOA_RNAStructure_2D.fasta -secstruct NFKB_1OOA_RNAStructure.secstruct

we get the following error:

Post Situation: 

FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py

Category: 
Compilation

Dears,

After installing Rosetta 3.9 in a cluster and trying to run the simple command:

helix_preassemble_setup.py -fasta NFKB_1OOA_RNAStructure_2D.fasta -secstruct NFKB_1OOA_RNAStructure.secstruct

we get the following error:

Post Situation: 

PyRosetta compiled with GLIBC 2.12

Category: 
Compilation
PyRosetta

Hello,

We are trying to install PyRosetta on CentOS 6.  The current compilation of PyRosetta (PyRosetta4.Release.python27.linux.release-171.tar.bz2) requires GLIBC_2.14.

However, our system's GLIBC version is 2.12 and the compilation of PyRosetta stop with the error

                          ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cm/shared/apps/pyrosetta/python/2.7/4.171/lib/python2.7/site-packages/pyrosetta-2018.9+release.333d996-py2.7-linux-x86_64.egg/pyrosetta/rosetta.so)

Post Situation: 

rosetta_mpi error

Category: 
Compilation

Hello!

I'd compiled rosetta using using extra=mpi and it was successful (no errors). moreover, I already have rosetta running without mpi options. 

when i am trying to run any application (let say abinitio) it pop up an error " AbinitioRelax.mpi.linuxgccrelease: error while loading shared libraries: libcppdb.so: cannot open shared object file: No such file or directory"

Post Situation: 

Only Link to executables in bin

Category: 
Compilation

Hi

Im new to Ubuntu and Rosetta. Installed Rosetta as per the guildelines and released bin by

./scons.py -j2 mode=release

But the bin only contains link to executables and hence when I try to run the De novo structure prediction tutorials, getting error message,

AbinitioRelax.default.linuxgccrelease: No such file or directory

can you please help.

Many thanks

Siaseb
 

Post Situation: 

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