Every thing Ok in PC end Error on Server

This topic has 8 replies, 2 voices, and was last updated 8 years, 7 months ago by Anonymous.

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- March 22, 2016 at 2:21 pm #2395
  Anonymous
  Hi everyone
  
  I’m using a script to relax with rosetta_scripts. So, the script work on the PC lab but when i put in the server that error is show.
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level contextERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level contextERROR: Option matching -mp:setup:spanfiles not found in command line top-level contextERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level contextERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  mpiexec has exited due to process rank 22 with PID 5760 on
  
  node r1i2n15 exiting improperly. There are two reasons this could occur:
  
  1. this process did not call “init” before exiting, but others in
  
  the job did. This can cause a job to hang indefinitely while it waits
  
  for all processes to call “init”. By rule, if one process calls “init”,
  
  then ALL processes must call “init” prior to termination.
  
  2. this process called “init”, but exited without calling “finalize”.
  
  By rule, all processes that call “init” MUST call “finalize” prior to
  
  exiting or it will be considered an “abnormal termination”
  
  This may have caused other processes in the application to be
  
  terminated by signals sent by mpiexec (as reported here).
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  ERROR: Option matching -mp:setup:spanfiles not found in command line top-level context
  
  The script is the same, i just put some questions only to call the MPI.
  
  Sugestions?
- March 22, 2016 at 2:46 pm #11481
  Anonymous
  The version of Rosetta on your server doesn’t have the option “-mp:setup:spanfiles”. Presumably the version on your PC does not match the version on your cluster?
- March 22, 2016 at 3:53 pm #11483
  Anonymous
  If you aren’t using -mute all, the first line of the log file ought to be something like “core.init: Rosetta version 5512591becb785321f20e0491cbdcfc36af4a0f7 2016-03-06 16:19:51 -0700 from [git]” – except for the release versions, we’ve replaced it with a string that says which release it’s from.
- March 23, 2016 at 2:46 am #11487
  Anonymous
  Hi again
  
  that is the result.
  
  jrcfer@gauss:~> grep spanfiles ~/rosetta/main/source/src/basic/options/options_rosetta.py
  
  Option( ‘spanfiles’, ‘StringVector’, desc=”Spanning topology file from Octopus” ),
  
  I think, the rosetta version is the same of my PC, it is strange to me.
- March 22, 2016 at 3:46 pm #11482
  Anonymous
  Hi SMLEWIS
  
  I think is the same.
  
  how can i confirm that? or how can i identify if the option exist in that version of the rosetta?
- March 22, 2016 at 5:00 pm #11484
  Anonymous
  I’m using this flag -out:levels all:warning core.init:info protocols.jd2.JobDistributor:info
  
  without;
  
  core.init: (0) Rosetta version exported from http://www.rosettacommons.org
  
  core.init: (0) command: /home/u/jrcfer/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease -jd2:mpi_work_partition_job_distributor -database /home/u/jrcfer/rosetta/main/database
  
  and
  
  core.init: (1) command: /home/u/jrcfer/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease -jd2:mpi_work_partition_job_distributor -database /home/u/jrcfer/rosetta/main/database
  
  core.init: (1) ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1699493606 seed_offset=0 real_seed=1598830808
  
  core.init.random: (1) RandomGenerator:init: Normal mode, seed=1598830808 RG_type=mt19937
  
  protocols.jd2.MPIWorkPartitionJobDistributor: (4) RANK: 4 NUM_PROCS: 5 NUM_JOBS: 1 START_ID: 2 END_ID: 1
  
  protocols.jd2.JobDistributor: (4) Parser is present. Input mover will be overwritten with whatever the parser creates.
  
  protocols.jd2.JobDistributor: (4) no more batches to process…
  
  protocols.jd2.JobDistributor: (4) 1 jobs considered, 0 jobs attempted in 0 seconds
  
  protocols.jd2.JobDistributor: (4) no jobs were attempted, did you forget to pass -overwrite?
  
  protocols.evaluation.ChiWellRmsdEvaluatorCreator: (3) Evaluation Creator active …
  
  protocols.jd2.MPIWorkPartitionJobDistributor: (3) RANK: 3 NUM_PROCS: 5 NUM_JOBS: 1 START_ID: 2 END_ID: 1
  
  protocols.jd2.JobDistributor: (3) Parser is present. Input mover will be overwritten with whatever the parser creates.
  
  protocols.jd2.JobDistributor: (3) no more batches to process…
  
  protocols.jd2.JobDistributor: (3) 1 jobs considered, 0 jobs attempted in 0 seconds
  
  protocols.jd2.JobDistributor: (3) no jobs were attempted, did you forget to pass -overwrite?
  
  protocols.evaluation.ChiWellRmsdEvaluatorCreator: (1) Evaluation Creator active …
  
  protocols.jd2.MPIWorkPartitionJobDistributor: (1) RANK: 1 NUM_PROCS: 5 NUM_JOBS: 1 START_ID: 2 END_ID: 1
  
  protocols.jd2.JobDistributor: (1) Parser is present. Input mover will be overwritten with whatever the parser creates.
  
  protocols.jd2.JobDistributor: (1) no more batches to process…
  
  protocols.jd2.JobDistributor: (1) 1 jobs considered, 0 jobs attempted in 0 seconds
  
  protocols.jd2.JobDistributor: (1) no jobs were attempted, did you forget to pass -overwrite?
  
  ^[[0m^[[1m^[[31m
  
  ERROR: Attempting to initiate job distribution for input job ‘S’, but the generated pose has no residues.make sure you specified a valid input PDB, silent file or database.
  
  ERROR:: Exit from: src/protocols/jd2/Parser.cc line: 60
  
  ^[[0m/home/u/jrcfer/rosetta/main/source/build/src/release/linux/2.6/64/x86/gcc/4.8/mpi/libutility.so(print_backtrace()+0x26) [0x2ad714556486]
  
  /home/u/jrcfer/rosetta/main/source/build/src/release/linux/2.6/64/x86/gcc/4.8/mpi/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0xd4) [0x2ad7145561c4]
  
  /home/u/jrcfer/rosetta/main/source/build/src/release/linux/2.6/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::Parser::generate_mover_from_job(boost::shared_ptr<protocols::jd2::Job>, core::pose::Pose&, boost::shared_ptr<protocols::moves::Mover>&, bool, bool, bool)+0x618) [0x2ad7107e3ed8]
  
  /home/u/jrcfer/rosetta/main/source/build/src/release/linux/2.6/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(boost::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0xea2) [0x2ad7107c4ca2]
  
  /home/u/jrcfer/rosetta/main/source/build/src/release/linux/2.6/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(boost::shared_ptr<protocols::moves::Mover>)+0xb9) [0x2ad7107c5cb9]
  
  /home/u/jrcfer/rosetta/main/source/build/src/release/linux/2.6/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::MPIWorkPartitionJobDistributor::go(boost::shared_ptr<protocols::moves::Mover>)+0x22) [0x2ad7107dcd92]
  
  /home/u/jrcfer/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease(main+0xb9) [0x402689]
  
  /lib64/libc.so.6(__libc_start_main+0xe6) [0x2ad716ac3bc6]
  
  /home/u/jrcfer/rosetta/main/source/bin/rosetta_scripts.mpi.linuxgccrelease() [0x402829]
  
  Error: (0) ERROR: Exception caught by JobDistributor while trying to get pose from job ‘S_0001’
  
  Error: (0)
  
  [ERROR] EXCN_utility_exit has been thrown from: src/protocols/jd2/Parser.cc line: 60
  
  ERROR: Attempting to initiate job distribution for input job ‘S’, but the generated pose has no residues.make sure you specified a valid input PDB, silent file or database.
  
  Error: (0) Treating failure as bad input; canceling similar jobs
  
  protocols.jd2.MPIWorkPartitionJobDistributor: (0) job failed, reporting bad input; other jobs of same input will be canceled: S_0001
  
  protocols.jd2.JobDistributor: (0) no more batches to process…
  
  protocols.jd2.JobDistributor: (0) 1 jobs considered, 1 jobs attempted in 0 seconds
  
  Error: (0) ERROR: Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages
  
  Error: (0)
  
  mpiexec has exited due to process rank 0 with PID 18874 on
  
  node r1i2n15 exiting improperly. There are two reasons this could occur:
  
  1. this process did not call “init” before exiting, but others in
  
  the job did. This can cause a job to hang indefinitely while it waits
  
  for all processes to call “init”. By rule, if one process calls “init”,
  
  then ALL processes must call “init” prior to termination.
  
  2. this process called “init”, but exited without calling “finalize”.
  
  By rule, all processes that call “init” MUST call “finalize” prior to
  
  exiting or it will be considered an “abnormal termination”
  
  This may have caused other processes in the application to be
  
  terminated by signals sent by mpiexec (as reported here).
  
  /var/spool/PBS/mom_priv/jobs/83454.gauss.SC: line 18: -parser:protocol: command not found
  
  now I’m more lost than ever.
- March 22, 2016 at 9:08 pm #11485
  Anonymous
  Right, so the release version isn’t in there correctly. I’ll check the release script and figure out why, but it won’t help your actual problem.
  
  If you don’t know the Rosetta versions, the easiest solution is probably to just get the newest one and recompile it, for both your local machine and the server.
  
  I can see mp:setup:spanfiles in recent versions of the code, so presumably the server version is the one that’s out of date. You can do “grep spanfiles /path/to/Rosetta/main/source/src/basic/options/options_rosetta.py” to see if it shows up in that file (that’s where options are defined) to confirm that the version on your cluster doesn’t have it.
- March 23, 2016 at 2:59 pm #11488
  Anonymous
  OK, another option is to try recompiling. With developer versions under version control, we get these problems all the time due to stale executables not matching the code if we forgot to recompile. For you, I don’t see how you’d have gotten new code text under older stale executables unless you went out of your way to do that, but I guess it’s worth trying. If the executables aren’t stale, recompiling does nothing and is fast; if they are stale, then you needed to do it anyway.
  
  I guess you don’t want to try just reinstalling with known identical versions to be sure they match?
- March 23, 2016 at 7:16 pm #11489
  Anonymous
  Thank’s
  
  If i will recompiling, should i use the most recent version? or i just recompile the version the server?
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