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haddocking / haddock3

Official repo of the modular BioExcel version of HADDOCK
https://www.bonvinlab.org/haddock3
Apache License 2.0
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mdmdscoring error #1147

Open bestz123 opened 2 weeks ago

bestz123 commented 2 weeks ago

Question

I am using the prediction structure to run haddock to calculate mdscoring and the following error occurs. How can I solve it?

Code snippet

Traceback (most recent call last): File "/mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/libs/libutil.py", line 335, in log_error_and_exit yield File "/mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/clis/cli.py", line 195, in main workflow.run() File "/mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/libs/libworkflow.py", line 43, in run step.execute() File "/mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/libs/libworkflow.py", line 162, in execute self.module.run() # type: ignore File "/mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/modules/base_cns_module.py", line 61, in run self._run() File "/mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/modules/topology/topoaa/init.py", line 334, in _run self.export_io_models(faulty_tolerance=self.params["tolerance"]) File "/mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/modules/init.py", line 309, in export_io_models self.finish_with_error(_msg) File "/mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/modules/init.py", line 317, in finish_with_error raise RuntimeError(reason) RuntimeError: 100.00% of output was not generated for this module and tolerance was set to 0.00%.

amjjbonvin commented 2 weeks ago

Most likely an issue with the CNS executable.

How did you install haddock3?

On which operating system?

bestz123 commented 2 weeks ago

Hello @amjjbonvin, I installed it using the following command on ubuntu20.04: conda create -n haddock3 python=3.10 conda activate haddock3 pip install haddock3

amjjbonvin commented 2 weeks ago

And what is the hardware? Which processor?

Can you try to test the CNS binary? In your installation it should be in /mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/bin/

Try starting cns it at the command line level

Hello @amjjbonvin https://github.com/amjjbonvin, I installed it using the following command on ubuntu20.04: conda create -n haddock3 python=3.10 conda activate haddock3 pip install haddock3

bestz123 commented 2 weeks ago

Hello, @amjjbonvin I use is AMD EPYC 9654 96-Core Processor. After I executed ./cns in the command line, the following error was reported: ./cns: /lib/x86_64-linux-gnu/libc.so.6: version GLIBC_2.33' not found (required by ./cns) ./cns: /lib/x86_64-linux-gnu/libc.so.6: versionGLIBC_2.34' not found (required by ./cns)

amjjbonvin commented 1 week ago

If you can locate where haddock3 was installed in your python path you should be able to find a bin directory containing the CNS executable. Try calling it from the command line to see if it starts or gives an error.

Try cloning the haddock3 repo and then installing CNS from scratch. You will have to follow the instructions from haddock3/varia/cns1.3 to copy the CNS files coming with HADDOCK3 to your CNS installation prior to compiling.

Instructions can be found at: https://www.bonvinlab.org/haddock3/CNS.html

bestz123 commented 1 week ago

Hi @amjjbonvin , When I was compiling CNS, when I executed the ./intel-x86_64bit-linux/source/cns_solve-2411181800.exe command, the following error occurred: %SETFPEPS increase value of MXFPEPS2 and recompile %SETFPEPS error encountered: Could not determine machine epsilon (CNS is in mode: SET ABORT=NORMal END) WARNING: program encountered a fatal error. However, in interactive mode, program execution will continue. Proceed at your own risk. Program will stop immediately.

       Maximum dynamic memory allocation:           0 bytes
       Maximum dynamic memory overhead:             0 bytes
       Program started at:  on 
       Program stopped at: 18:08:29 on 18-Nov-2024
       CPU time used:       0.0037 seconds
      ============================================================

Note: The following floating-point exceptions are signalling: IEEE_DENORMAL

amjjbonvin commented 1 week ago

Did you follow all the instructions from the varia/cns1.3/README.md file?

The issue must come from the machine.c file.

You can also try to indeed increase the value of MXFPEPS2 defined in machine.inc in the source directory and recompile. No idea though what a proper value would be.

bestz123 commented 1 week ago

Hi @amjjbonvin ， I installed CNS again according to https://www.bonvinlab.org/haddock3/CNS.html. When I did make install compiler=gfortran, the following error was reported: Installation directory: /mnt/zyz/package/cns_solve_1.3/intel-x86_64bit-linux copying files in instlib directory intel-x86_64bit-linux to intel-x86_64bit-linux 0read.me arch_env machine_c.c machine_f.f Makefile.header.1.ifort Makefile.header.2.gfortran Makefile.header.3.ifort_mp Makefile.header.4.pgf95 Makefile.header.5.ifort_mp_profile Makefile.header.6.ifort_mp_tcheck Makefile.header.7.gfortran Makefile.header.7.gfortran_mp Using Makefile template for compiler: gfortran ln: 目标'Makefile.header' 不是目录 removing old source files linking source files to intel-x86_64bit-linux/source linking machine_f.f to source directory linking machine_c.c to source directory linking generic fft file to source directory making Makefile in source directory testing Fortran and C compilers compiling: gcc -O -DINTEGER='long int' -DCNS_ARCH_TYPE_LINUX C compiler passes test compiling: gfortran -fdefault-integer-8 -w -fallow-argument-mismatch -O3 -funroll-loops -ffast-math -static
gfortran: error: unrecognized command line option ‘-fallow-argument-mismatch’; did you mean ‘-Wno-argument-mismatch’? linking: gfortran -w -static-libgfortran gfortran: error: test_f.o: 没有那个文件或目录 /bin/sh: 1: ./test_f: not found ERROR: problem with Fortran compiler make[3]: [Makefile:18：fortran-test] 错误 2 make[2]: [Makefile:205：compiler-test] 错误 2 make[1]: [Makefile:68：compiler-test] 错误 2 compiler problems - stopping installation please check compilers before retrying installation make: [Makefile:38：install] 错误 1

amjjbonvin commented 1 week ago

Do you have gfortran installed?

May-be update your compiler versions

bestz123 commented 1 week ago

Hi @amjjbonvin， I executed this command gfortran --version, and the following is displayed GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 Copyright (C) 2019 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. It seems that I have installed the latest version.

amjjbonvin commented 1 week ago

On our linux cluster we have version 13 and I even have 14 on my laptop…

@.*** ~]$ gfortran --version GNU Fortran (GCC) 13.1.0 Copyright (C) 2023 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

On 18 Nov 2024, at 14:00, xiao zhu @.***> wrote:

Hi @amjjbonvin https://github.com/amjjbonvin， I executed this command gfortran --version, and the following is displayed GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 Copyright (C) 2019 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. It seems that I have installed the latest version.

— Reply to this email directly, view it on GitHub https://github.com/haddocking/haddock3/issues/1147#issuecomment-2482983036, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABOH5IHAWV26GAMVXEUKLLT2BHQIRAVCNFSM6AAAAABR2YZGI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOBSHE4DGMBTGY. You are receiving this because you were mentioned.

bestz123 commented 17 hours ago

hi @amjjbonvin ： I upgraded gfortran version to 13 and recomplied CNS, GNU Fortran (Ubuntu 13.1.0-8ubuntu1~20.04.2) 13.1.0 Copyright (C) 2023 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

but the same error still occurs：

[2024-11-29 10:31:11,947 cli INFO] ##############################################

HADDOCK3

##############################################

!! Some of the HADDOCK3 components use CNS (Crystallographic and NMR System) which is free of use for non-profit applications. !! !! For commercial use it is your own responsibility to have a proper license. !! !! For details refer to the DISCLAIMER file in the HADDOCK3 repository. !!

Starting HADDOCK3 v2024.10.0b7 on 2024-11-29 10:31:00

Python 3.11.10 | packaged by conda-forge | (main, Oct 16 2024, 01:27:36) [GCC 13.3.0]

[2024-11-29 10:31:12,478 libworkflow INFO] Reading instructions step 0_topoaa [2024-11-29 10:31:12,478 libworkflow INFO] Reading instructions step 1_mdscoring [2024-11-29 10:31:12,478 libworkflow INFO] Reading instructions step 2_caprieval [2024-11-29 10:31:12,493 base_cns_module INFO] Running [topoaa] module [2024-11-29 10:31:12,493 init INFO] [topoaa] Molecule 1: T161-rescoring-ens.pdb [2024-11-29 10:31:12,507 init INFO] [topoaa] Sanitizing molecule T161-rescoring-ens_1.pdb [2024-11-29 10:31:12,518 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,518 init INFO] [topoaa] Sanitizing molecule T161-rescoring-ens_2.pdb [2024-11-29 10:31:12,529 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,529 init INFO] [topoaa] Sanitizing molecule T161-rescoring-ens_3.pdb [2024-11-29 10:31:12,540 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,540 init INFO] [topoaa] Sanitizing molecule T161-rescoring-ens_4.pdb [2024-11-29 10:31:12,550 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,550 init INFO] [topoaa] Sanitizing molecule T161-rescoring-ens_5.pdb [2024-11-29 10:31:12,561 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,561 init INFO] [topoaa] Molecule 2: protein-dna_1w.pdb [2024-11-29 10:31:12,562 init INFO] [topoaa] Sanitizing molecule protein-dna_1w.pdb [2024-11-29 10:31:12,565 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,565 init INFO] [topoaa] Molecule 3: protein-protein_1w.pdb [2024-11-29 10:31:12,566 init INFO] [topoaa] Sanitizing molecule protein-protein_1w.pdb [2024-11-29 10:31:12,570 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,570 init INFO] [topoaa] Molecule 4: protein-protein_2w.pdb [2024-11-29 10:31:12,571 init INFO] [topoaa] Sanitizing molecule protein-protein_2w.pdb [2024-11-29 10:31:12,576 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,576 init INFO] [topoaa] Molecule 5: protein-trimer_1w.pdb [2024-11-29 10:31:12,577 init INFO] [topoaa] Sanitizing molecule protein-trimer_1w.pdb [2024-11-29 10:31:12,584 init INFO] [topoaa] Topology CNS input created [2024-11-29 10:31:12,584 init INFO] [topoaa] Running CNS Jobs n=9 [2024-11-29 10:31:12,584 libutil INFO] Selected 9 cores to process 9 jobs, with 384 maximum available cores. [2024-11-29 10:31:12,586 libparallel INFO] Using 9 cores [2024-11-29 10:31:16,362 libparallel INFO] 9 tasks finished [2024-11-29 10:31:16,362 init INFO] [topoaa] CNS jobs have finished [2024-11-29 10:31:16,368 base_cns_module INFO] Module [topoaa] finished. [2024-11-29 10:31:16,368 init INFO] [topoaa] took 4 seconds [2024-11-29 10:31:16,405 base_cns_module INFO] Running [mdscoring] module [2024-11-29 10:31:16,423 init INFO] [mdscoring] Running CNS Jobs n=9 [2024-11-29 10:31:16,423 libutil INFO] Selected 9 cores to process 9 jobs, with 384 maximum available cores. [2024-11-29 10:31:16,423 libparallel INFO] Using 9 cores [2024-11-29 10:31:34,542 libparallel INFO] 9 tasks finished [2024-11-29 10:31:34,542 init INFO] [mdscoring] CNS jobs have finished [2024-11-29 10:31:34,543 init INFO] [mdscoring] Saving output to mdscoring.tsv [2024-11-29 10:31:34,552 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 20.00%. Traceback (most recent call last): File "/mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/libs/libutil.py", line 335, in log_error_and_exit yield File "/mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/clis/cli.py", line 195, in main workflow.run() File "/mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/libs/libworkflow.py", line 43, in run step.execute() File "/mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/libs/libworkflow.py", line 162, in execute self.module.run() # type: ignore ^^^^^^^^^^^^^^^^^ File "/mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/modules/base_cns_module.py", line 61, in run self._run() File "/mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/modules/scoring/mdscoring/init.py", line 102, in _run self.export_io_models(faulty_tolerance=self.params["tolerance"]) File "/mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/modules/init.py", line 309, in export_io_models self.finish_with_error(_msg) File "/mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/modules/init.py", line 317, in finish_with_error raise RuntimeError(reason) RuntimeError: 100.00% of output was not generated for this module and tolerance was set to 20.00%. [2024-11-29 10:31:34,553 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 20.00%. [2024-11-29 10:31:34,553 libutil ERROR] An error has occurred, see log file. And contact the developers if needed. [2024-11-29 10:31:34,553 libutil INFO] Finished at 29/11/2024 10:31:34. For any help contact us at https://github.com/haddocking/haddock3/issues. Tchau! Au revoir! Tot ziens!.

amjjbonvin commented 9 hours ago

Did you recompile CNS?

Can you try starting the CNS executable from the command line?

bestz123 commented 9 hours ago

Yes, this is the output when I execute the cns file：

      ============================================================
      |                                                          |
      |            Crystallography & NMR System (CNS)            |
      |                         CNSsolve                         |
      |                                                          |
      ============================================================
       Version: 1.3 at patch level U
       Status: Special UU release with Rg, paramagnetic
               and Z-restraints (A. Bonvin, UU 2013)
      ============================================================
       Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,
                   P.Gros, R.W.Grosse-Kunstleve,J.-S.Jiang,J.M.Krahn,
                   J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,
                   L.M.Rice, G.F.Schroeder, T.Simonson, G.L.Warren.
       Copyright (c) 1997-2010 Yale University
      ============================================================
       Running on machine: hostname unknown (x86_64/Linux,64-bit)
       Program started by: zyz
       Program started at: 10:30:50 on 29-Nov-2024
      ============================================================

FFT3C: Using FFTPACK4.1

CNSsolve>stop HEAP: maximum use = 8297488 current use = 96000 bytes HEAP: maximum overhead = 960 current overhead = 752 bytes

       Maximum dynamic memory allocation:     8297488 bytes
       Maximum dynamic memory overhead:           960 bytes
       Program started at: 10:30:50 on 29-Nov-2024
       Program stopped at: 10:30:55 on 29-Nov-2024
       CPU time used:       0.0019 seconds
      ============================================================
amjjbonvin commented 9 hours ago

Ok - that looks good.

Where is that CNS executable? In /mnt/zyz/anaconda3/envs/haddock3/lib/python3.10/site-packages/haddock/bin/ ? And called simply cns?

amjjbonvin commented 9 hours ago

Note that in the general section of your cfg file you can also define the CNS executable location to overwrite the default installation. This is defined in:

cns_exec = ''
bestz123 commented 9 hours ago

This is my complete command line，I have replaced the cns file in the original conda environment with the compiled cns file： (hdock3) zyz@aidd:~/work/$ /mnt/zyz/anaconda3/envs/hdock3/lib/python3.11/site-packages/haddock/bin/cns

this output：

      ============================================================
      |                                                          |
      |            Crystallography & NMR System (CNS)            |
      |                         CNSsolve                         |
      |                                                          |
      ============================================================
       Version: 1.3 at patch level U
       Status: Special UU release with Rg, paramagnetic
               and Z-restraints (A. Bonvin, UU 2013)
      ============================================================
       Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,
                   P.Gros, R.W.Grosse-Kunstleve,J.-S.Jiang,J.M.Krahn,
                   J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,
                   L.M.Rice, G.F.Schroeder, T.Simonson, G.L.Warren.
       Copyright (c) 1997-2010 Yale University
      ============================================================
       Running on machine: hostname unknown (x86_64/Linux,64-bit)
       Program started by: zyz
       Program started at: 10:30:50 on 29-Nov-2024
      ============================================================

FFT3C: Using FFTPACK4.1

CNSsolve>stop HEAP: maximum use = 8297488 current use = 96000 bytes HEAP: maximum overhead = 960 current overhead = 752 bytes

Maximum dynamic memory allocation: 8297488 bytes Maximum dynamic memory overhead: 960 bytes Program started at: 10:30:50 on 29-Nov-2024 Program stopped at: 10:30:55 on 29-Nov-2024 CPU time used: 0.0019 seconds

amjjbonvin commented 9 hours ago

Can you try a fresh run then and share (e.g. via email) the content of the generated run directory?

bestz123 commented 9 hours ago

run1-mdscoring-test.zip this is the content of the generated run directory。

amjjbonvin commented 9 hours ago

Can you please rerun it adding to the cfg file at the top section:

debug=true

In that way we should see the CNS output files.

This is the standard scoring example, correct?

bestz123 commented 8 hours ago

Can you please rerun it adding to the cfg file at the top section: debug=true

OK，this is the content of the generated run directory。 run1-mdscoring-test (2).zip

This is the standard scoring example, correct?

yes