Rosetta3.5 src/core/pack/dunbrack/ permission problem

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    • #1627

        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/ 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 is creating temporary files where only root can write?



      • #8976

          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.

        • #8977

            Thanks for solving the puzzle!

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