- This topic has 2 replies, 2 voices, and was last updated 10 years, 5 months ago by Anonymous.
June 28, 2013 at 7:13 pm #1627Anonymous
Hi Rosetta community,
I’m trying to run the rosetta 3.5 FloppyTail app and encoutered a permission error:
ERROR: Failed to open temporary file with mkstemp
ERROR:: Exit from: src/core/pack/dunbrack/RotamerLibrary.cc line: 1388
MPI_ABORT was invoked on rank 36 in communicator MPI_COMM_WORLD
with errorcode 911.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
mpiexec has exited due to process rank 36 with PID 19669 on
node compute-0-17.local exiting without calling “finalize”. This may
have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
The rosetta 3.5 software was installed by root on our cluster and a separate linux server, and I encountered this error on both cluster and server when running as normal user.
When I ran the script as root, the script finished running without error. Is it possible RotamerLibrary.cc is creating temporary files where only root can write?
June 28, 2013 at 9:59 pm #8976Anonymous
Yes, the rotamer database comes in a text format, but after it’s loaded and parsed the first time, a quicker-loading binary representation is written to the database directory.
This only happens once, so if you can get the database owner to run a quick scoring job (or temporarily change permissions to allow you to do it) it should write the binary format, and you’ll not have to worry about it again. (So since you’ve run a job as root already, you should be good to go.)
The other option would be to pass the “-no_binary_dunlib” flag to Rosetta every time you run to keep it from attempting to read/write the Dunbrack rotamer library binary representation.
June 28, 2013 at 10:34 pm #8977Anonymous
Thanks for solving the puzzle!
- You must be logged in to reply to this topic.