Can not build the parallel version of rosetta-2.3.1 (the SnugDock). Help!!

[Anonymous]

Hi all,

I was trying to build a parallel version of Rosetta-2.3.1(SnugDock) on my workstation. My OS is RHEL 5.4(32-bit), and I use Openmpi-1.4.3.

I tried to compile it as I did to Rosetta2.3.0 on the same computer and the very same OS and MPI compilier, but it didn’t work.

I got the following errors:

######################
job_distributor.cc:(.text+0x5ada): undefined reference to `pathways::pathways_generator_main(bool&)’
collect2: ld return 1
make: *** [rosetta.mpilam] error 1

######################

Looks like there is something wrong with compiling “job_distributor.cc”?

Looking forwards to your help!!!!! Thanks in advance!!!!

Best wishes and thanks!!!!

Ming

from BJUT

[Anonymous]

There is little if any experience left in the community for tweaking compilation on Rosetta 2. The best I can do is offer alternatives:

A) I strongly suspect that MPI will only work at the job distribution level anyway; I think there is no multithreaded code inside the SnugDock part. This means you can get the same speedup by just running independent Rosetta jobs in separate directories (remember to use unique RNG seeds).

I know a guy who wrote an MPI “wrapper” for the use of Rosetta on clusters where MPI is required by the cluster administrator. If that is your situation, I’ll ask if he wants to let you borrow the code. It works great, but it is extremely challenging to get it working.

[Anonymous]

Hi

I want to use the SnuDock. I can not find it in any other versions of Reosetta…
so I have to use 2.3.1…..

I, myself, can compile and build Rosetta2.3.0 with openmpi/mpilam/mpich2 successfully, and to some extent, the “paralleled” version is more convenient to me. so I just want to do the same thing to SnugDock.

Any further suggestions?

Thanks!

[Author]

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