Error in running runall.sh with GROMACS2021

[camputchem]

Hi,

After running the prepare_dual_topology.py, I was trying to run bash runall.py and got following error. I am using GROMACS 2021 version. /water/md/rerun folder is empty. Am I missing any other files?

(PyAutoFEP) chemco:~/Desktop/new/tutorial$ bash runall.sh tar: /water/md/rerun/.pkl: Cannot stat: No such file or directory tar: /water/md/rerun/.xvg: Cannot stat: No such file or directory tar: /water/md/rerun/.edr: Cannot stat: No such file or directory tar: /protein/md/rerun/.pkl: Cannot stat: No such file or directory tar: /protein/md/rerun/.xvg: Cannot stat: No such file or directory tar: /protein/md/rerun/.edr: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda_pbcfit.xtc: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda_nocont.tpr: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda.tpr: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda.log: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda.edr: Cannot stat: No such file or directory tar: /water/md/lambda/lambda.xtc: Cannot stat: No such file or directory tar: /water/md/lambda/lambda_nocont.tpr: Cannot stat: No such file or directory tar: /water/md/lambda/lambda.tpr: Cannot stat: No such file or directory tar: /water/md/lambda/lambda.log: Cannot stat: No such file or directory tar: /water/md/lambda/lambda.edr: Cannot stat: No such file or directory tar: /protein/md/lambda/analysis.log: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors

[xy21hb]

If you are running Tutorial example, just check /PyAutoFEP-master/docs/tutorial01/tutorial/FXR_12-FXR_74/water/md/feprun_..._14082023.log or similar file.

[sarahmarie935]

Hi,

I have been having this same issue but I am not running it with the tutorial.

[sarahmarie935]

Hi,

I have been having this same issue but I am not running it with the tutorial.

Also, I am running with gromcas 2021 @camputchem. Have you figured out a resolution to this problem?

[sarahmarie935]

Here are my specific error details:

tar: /water/md/rerun/.pkl: Cannot stat: No such file or directory tar: /water/md/rerun/.xvg: Cannot stat: No such file or directory tar: /water/md/rerun/.edr: Cannot stat: No such file or directory tar: /protein/md/rerun/.pkl: Cannot stat: No such file or directory tar: /protein/md/rerun/.xvg: Cannot stat: No such file or directory tar: /protein/md/rerun/.edr: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda_pbcfit.xtc: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda_nocont.tpr: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda.tpr: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda.log: Cannot stat: No such file or directory tar: /protein/md/lambda/lambda.edr: Cannot stat: No such file or directory tar: /water/md/lambda/lambda.xtc: Cannot stat: No such file or directory tar: /water/md/lambda/lambda_nocont.tpr: Cannot stat: No such file or directory tar: /water/md/lambda/lambda.tpr: Cannot stat: No such file or directory tar: /water/md/lambda/lambda.log: Cannot stat: No such file or directory tar: /water/md/lambda/lambda.edr: Cannot stat: No such file or directory tar: /protein/md/lambda/analysis.log: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors

[AzraelXu]

check your gromacs path using "which gmx" and "which gmx_mpi"

[luancarvalhomartins]

Sorry for the tardiness. I was out of office for some days.

Your output suggest FEP did not run. Make sure GROMACS with MPI support is correctly installed and working fine in your compute node and that gmx_bin_run is correctly set.

[pcardonap]

I am also having thee same problem while working through the tutorial and running runall.sh.

However my output is this:

FXR_12-FXR_74/runall_FXR_12-FXR_74_water.sh: line 8: 247687 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_74/runall_FXR_12-FXR_74_protein.sh: line 8: 247975 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_76/runall_FXR_12-FXR_76_water.sh: line 8: 248242 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_76/runall_FXR_12-FXR_76_protein.sh: line 8: 248508 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_84/runall_FXR_12-FXR_84_water.sh: line 8: 248774 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_84/runall_FXR_12-FXR_84_protein.sh: line 8: 249040 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_85/runall_FXR_12-FXR_85_water.sh: line 8: 249306 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_85/runall_FXR_12-FXR_85_protein.sh: line 8: 249572 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_88/runall_FXR_12-FXR_88_water.sh: line 8: 249838 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
FXR_12-FXR_88/runall_FXR_12-FXR_88_protein.sh: line 8: 250104 Aborted                 /pdc/software/22.06/eb/software/gromacs/2021.7-cpeCray-22.06/bin/gmx_mpi mdrun --deffnm min01 > min01_mdrun_log.log 2>&1
tar: */water/md/rerun/*.pkl: Cannot stat: No such file or directory
tar: */water/md/rerun/*.xvg: Cannot stat: No such file or directory
tar: */water/md/rerun/*.edr: Cannot stat: No such file or directory
tar: */protein/md/rerun/*.pkl: Cannot stat: No such file or directory
tar: */protein/md/rerun/*.xvg: Cannot stat: No such file or directory
tar: */protein/md/rerun/*.edr: Cannot stat: No such file or directory
tar: */protein/md/lambda*/lambda_pbcfit.xtc: Cannot stat: No such file or directory
tar: */protein/md/lambda*/lambda_nocont.tpr: Cannot stat: No such file or directory
tar: */protein/md/lambda*/lambda.tpr: Cannot stat: No such file or directory
tar: */protein/md/lambda*/lambda.log: Cannot stat: No such file or directory
tar: */protein/md/lambda*/lambda.edr: Cannot stat: No such file or directory
tar: */water/md/lambda*/lambda.xtc: Cannot stat: No such file or directory
tar: */water/md/lambda*/lambda_nocont.tpr: Cannot stat: No such file or directory
tar: */water/md/lambda*/lambda.tpr: Cannot stat: No such file or directory
tar: */water/md/lambda*/lambda.log: Cannot stat: No such file or directory
tar: */water/md/lambda*/lambda.edr: Cannot stat: No such file or directory
tar: */protein/md/lambda*/analysis.log: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors

The binaries are being called correctly, yet the problem is still there.

[pcardonap]

After looking more carefully at the files. I realized that the error occurred due to GROMACS trying to run using more OpenMP threads that I have access to in my HPC enviroment. Setting OMP_NUM_THREADS, fixed it.

[Jiang-Lu-CAS]

After looking more carefully at the files. I realized that the error occurred due to GROMACS trying to run using more OpenMP threads that I have access to in my HPC enviroment. Setting OMP_NUM_THREADS, fixed it.

@pcardonap Hi, I also met the same problem. How to set the OMP_NUM_THREADS? Thanks.

[pcardonap]

Hi @Jiang-Lu-CAS, I'm running the tutorial so I simply added the variable in step2.ini output_runbefore = export OMP_NUM_THREADS=256 Just replace 256 with a number appropriate for you.

[Jiang-Lu-CAS]

export OMP_NUM_THREADS

@pcardonap Thanks.