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

[Anonymous]

Compilation
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]

I could have sworn I answered this yesterday, I must have failed to hit save…

A) Nobody is using Rosetta 2 anymore, and I don’t know anyone who is capable and willing to help debug MPI compilation in 2.3.1.

SnugDock derives no speed benefit from MPI. The MPI layer (which is jobdistributor.cc) just organizes the processes so that they each write outputs to separate files. You can get the same effect by running N Rosetta jobs in N directories using separate random number seeds.

C) If you need MPI because the cluster administrators say so, there is a Rosetta-compatible MPI wrapper floating around which wraps a Rosetta job in MPI camouflage. It’s not easy to use. I can ask its author if he’ll release it if you need it.

[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!

[Anonymous]

I’ve been told Snugdock is being ported to Rosetta3; should come out in a year or so. Other than that there’s no more advice I can offer.

[Anonymous]

I’ve made it by commenting out everything about “pathways” and recompile and link the objects. I’ve made some tests on sungdock, it looks fine to me. Thanks anyway.

[Author]

Posts