I downloaded the 2016 linux release of Rosetta3 (rosetta_bin_linux_2016.32.58837_bundle) about 6 months ago. I have just now found that the partial_thread.default.linuxgccrelease executable needed for RosettaCM is missing. Is there any particular reason why it would not have been built? How do I fix it?
Does src/apps/public/comparative_modeling/partial_thread.cc exist? What does 'find . -name "partial_thread*"' return? The file exists for more recent Rosettas. I don't think it's changed since 3.6.
I do not beleive that I have an src/apps/public/comparative_modeling/partial_thread.cc directory
Are you getting *anything* in Rosetta/main/source/bin/ directory? If so, is there anything there which starts with `partial_thread`?
If you're expecting to get the binaries from the pre-built download, one thing to double check is if your download is good. If you still have the tarball you downloaded, run the program `md5sum` on it, and then compare the value you get from that with the value you get from the "MD5 checksum of all files" link on the download page for the version you downloaded. It should match. If no, the download you got may be corrupted. (I've been having issues downloading that file, though it might be the fact that my network connection is very flakey at the moment.)
I have many executable files in my Rosetta/main/source/bin directory, but none of them are default files. There is a partial_thread.linuxgccrelease and a partial_thread.static.linixgccrelease. I do not know what the difference is between these files and the default file I don't have. I have discovered that there are two other executables of the format "name.default.linuxgccrelease" that I am also missing. I think I am missing all default executables. And I don't think I kept the original tar file.
"default" means you specified no extra bells or whistles. It looks like you compiled only the static build. The one with no item in the middle (the name that has two parts instead of three) probably symlinks to the tame target as the static build.
You have only the static build because either you compiled it that way (with extras=static), or maybe if you have the binary download they come that way. In any case, the static executable probably works fine.
Ok, thank you for your help. I have someone helping me who knows more about compiling programs that will probably be able to recompile it for me. If not, I will just use the static executables if you think they will do the same thing.
If you have partial_thread.static.linuxgccrelease (or partial_thread.static.linuxclangrelease ) that will work just as well as partial_thread.default.linuxgccrelease - the static just means "statically linked" which is an implementation detail. (Basically, it means the programs can easily be moved from one computer to the other without worrying too much about where things are installed.)
You can certainly recompile Rosetta if you want to, though. See https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation for information on how to build Rosetta on your local machine -- the with-binaries download of Rosetta should also contain the source code, so you can certainly recompile for your local system.