Abinitio.relax problem on centos

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    • #2004

        Hi everyone,
        I just compiled rosetta (2014.20.56838_bundle) on a cluster with Centos, using the following command:
        ./scons.py -j16 bin

        Everything went ok, but when i’m trying to create a model with AbinitioRelax.linuxgccdebug binary my works for some reason stop in an specific line:
        Log file:
        core.init: Rosetta version exported from http://www.rosettacommons.org
        core.init: command: ../../rosetta_2014.20.56838_bundle/main/source/bin/AbinitioRelax.linuxgccdebug -database ../../rosetta_2014.20.56838_bundle/main/database/ -in:file:fasta ./COR15A.fasta -in:file:frag3 ./aat000_03_05.200_v1_3 -in:file:frag9 ./aat000_09_05.200_v1_3 -abinitio:relax -relax:fast -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -constant_seed -jran 8 -abinitio::rsd_wt_loop 0.5 -use_filters true -psipred_ss2 ./t000_.psipred_ss2 -kill_hairpins ./t000_.psipred_ss2 -out:file:silent COR15A_silent.out -nstruct 1
        core.init: Constant seed mode, seed=8 seed_offset=0 real_seed=8
        core.init.random: RandomGenerator:init: Normal mode, seed=8 RG_type=mt19937
        protocols.abinitio.AbrelaxApplication: read fasta sequence: 89 residues
        protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
        core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1010 residue types
        core.io.fragments: reading fragments from file: ./aat000_09_05.200_v1_3 …
        core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
        core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file ./aat000_09_05.200_v1_3
        core.io.fragments: reading fragments from file: ./aat000_03_05.200_v1_3 …
        core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
        core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ./aat000_03_05.200_v1_3
        core.fragment: compute strand/loop fractions for 89 residues…
        protocols.abinitio.AbrelaxApplication: run ClassicAbinitio…..
        basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
        basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
        basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
        basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
        basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth
        basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth
        basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv
        basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv
        basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv
        basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
        basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
        basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
        basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
        basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt
        basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt
        basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt
        basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt
        core.scoring: ATOM_VDW set to CENTROID_ROT
        core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
        basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
        core.scoring.CartesianBondedEnergy: Read 770 bb-independent lengths.
        basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
        core.scoring.CartesianBondedEnergy: Read 1464 bb-independent angles.
        basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt

        If i make a top, i can see that the process is still running, but its not doing anything :/
        This is really weird, because i installed rosetta on my PC (ubuntu) and it works perfectly :/

        I’m using the following command:
        nohup ../../rosetta_2014.20.56838_bundle/main/source/bin/AbinitioRelax.linuxgccdebug -database ../../rosetta_2014.20.56838_bundle/main/database/ -in:file:fasta ./COR15A.fasta -in:file:frag3 ./aat000_03_05.200_v1_3 -in:file:frag9 ./aat000_09_05.200_v1_3 -abinitio:relax -relax:fast -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -constant_seed -jran 8 -abinitio::rsd_wt_loop 0.5 -use_filters true -psipred_ss2 ./t000_.psipred_ss2 -kill_hairpins ./t000_.psipred_ss2 -out:file:silent COR15A_silent.out -nstruct 1 > COR15A.log &

        Hope someone can help me,
        Best Regards,
        Carlos Navarro Retamal

      • #10331

          When you redirect standard output to a file or through a pipe, the standard output becomes buffered. This means that only when a certain amount of text is output does it actually get passed to the file or through the pipe. This can often happen in the middle of a line. So one possibility is that Rosetta is still working, it just hasn’t printed enough to standard output to trigger a dump to the file. Recheck your COR15A.log file now that some time has passed, and see if there’s any additional output.

          If there isn’t, then it’s helpful to know exactly where the program is hanging, which the output buffering make difficult. Can you re-run the program, this time without the nohup and output redirection to see what the last line is? If you’re redoing the run, adding the flag “-out:levels all:debug” will increase the amount of text printed, and permit finer-grained determination of where things might be going wrong.

        • #10340

            First of all thanks for your reply.
            According to the first point the Abinitio command was working for almost 3 hours (just to generate 1 model) and the .log file didn’t continue. Sadly it doesn’t even generate the respective -out-silent file.
            I re-run the program (without the nohup and the > to redirect the output) and its working (really slow, but is working) thanks.
            The problem is that without the nohup command i don’t know how to avoid the crashing of the program when i logout from the cluster at my university.
            Is there a way to avoid this?
            Thanks in advance,

            ps- never mind, just by typing exit it works just fine.
            So probably the problem was that the output wasn’t writing properly in the .log file.

          • #10353

              Usually with cluster systems there is some sort of job control system such that you can submit commands to run, and the job control handles running them. I’d look into what sort of system your cluster has along those lines – usually if such a thing is available, it’s the preferred way to run compute-heavy jobs like Rosetta.)

              In the keep-running-in-the-background lines, I’d recommend looking into the “screen” program. This is a way to have a persistent terminal session that keeps running even if you log out. In addition to keeping the programs running, it also saves your terminal session, including things like environment variables and current directory. (See https://www.mattcutts.com/blog/a-quick-tutorial-on-screen/ and http://www.gnu.org/software/screen/ )

            • #10409

                You will also want to run the release mode executables instead of the debug mode executables by using mode=release with the Rosetta compilation. Debug mode is slow. Release mode is fast.

                You can also try MPI executables (I believe AbInitio now supports it, but I may very well be wrong). These are covered in the Setting Up Rosetta 3 page: https://www.rosettacommons.org/docs/latest/Build-Documentation.html

                You can run compile and run MPI locally on a single node/computer or on a cluster. For ubuntu it is usually (but not nessessarily) straightforward to install openmpi via the package manager. Then, when you pass nstruct, it will divy out what needs to be done for each processor. You will run with mpiexec -np 16 (or whatever) rosetta_executable.xxxx options.

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