# Error in the REMD md run **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [October 4, 2023, 6:33am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328 "2023-10-04T06:33:53Z")\ **Posts on this page:** 15\ **Page:** 1
**Author:** ![Akhilesh](https://avatars.discourse-cdn.com/v4/letter/a/35a633/32.png) [@Akhilesh](https://gromacs.bioexcel.eu/u/Akhilesh)\ **Post date:** [October 4, 2023, 6:33am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/1 "2023-10-04T06:33:53Z")
GROMACS version: 2021.5 GROMACS modification: No Dear users, I am trying to run a REMD simulation, with the replica files in the working directory having names like testrun\_0.tpr, testrun\_1.tpr, etc. However, upon running the command as below: gmx\_mpi mdrun -v -deffnm remd\_.tpr -multidir remd\_0.tpr remd\_1.tpr remd\_2.tpr -replex 500 or gmx\_mpi mdrun -v -deffnm remd\_ -multidir 0 1 2 -replex 500 I get errors like: Program: gmx mdrun, version 2021.5 Program: gmx mdrun, version 2021.5 Program: gmx mdrun, version 2021.5 Source file: src/gromacs/utility/futil.cpp (line 739) Source file: src/gromacs/utility/futil.cpp (line 739) Function: void gmx\_chdir(const char \*) Source file: src/gromacs/utility/futil.cpp (line 739) Function: void gmx\_chdir(const char \*) Function: void gmx\_chdir(const char \*) MPI rank: 0 (out of 3) MPI rank: 1 (out of 3) MPI rank: 2 (out of 3) System I/O error: System I/O error: System I/O error: While changing directory for multi-simulation to remd\_0.tpr Cannot change directory to ‘remd\_0.tpr’. Reason: Not a directory For more information and tips for troubleshooting, please check the GROMACS website at [http://www.gromacs.org/Documentation/ErrorsWhile](http://www.gromacs.org/Documentation/ErrorsWhile) changing directory for multi-simulation to remd\_2.tpr While changing directory for multi-simulation to remd\_1.tpr * * * Cannot change directory to ‘remd\_2.tpr’. Reason: Not a directory Cannot change directory to ‘remd\_1.tpr’. Reason: Not a directory ## For more information and tips for troubleshooting, please check the GROMACS website at [http://www.gromacs.org/Documentation/ErrorsFor](http://www.gromacs.org/Documentation/ErrorsFor) more information and tips for troubleshooting, please check the GROMACS * * * Rank 1 [Thu Sep 28 12:13:22 2023] [c0-0c1s0n1] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 1 Rank 2 [Thu Sep 28 12:13:22 2023] [c0-0c1s0n1] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 2 Rank 0 [Thu Sep 28 12:13:22 2023] [c0-0c1s0n1] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 0 \_pmiu\_daemon(SIGCHLD): [NID 00065] [c0-0c1s0n1] [Thu Sep 28 12:13:22 2023] PE RANK 1 exit signal Aborted [NID 00065] 2023-09-28 12:13:22 Apid 21544482: initiated application termination Please suggest on how to proceed further regarding this. Thanks a lot. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [October 4, 2023, 6:42am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/2 "2023-10-04T06:42:21Z")
The `-multidir` option implies that you have one directory for each simulation, and you specify the names of the directories with this option. That is why it says that the directories don’t exist. I would suggest creating directories called `remd_0`, `remd_1` etc. Then just put your tpr files in there - one in tpr in each directory. Easiest is if you use the default name `topol.tpr`. Then `gmx_mpi mdrun -multidir remd_0 remd_1 [...] -replex 500` should work. Easiest is of course to avoid writing all the directory names and just use wildcards, such as `gmx_mpi mdrun -multidir remd_* -replex 500` or `gmx_mpi mdrun -multidir remd_{0..49} -replex 500` or whatever fits your situation. ---
**Author:** ![Akhilesh](https://avatars.discourse-cdn.com/v4/letter/a/35a633/32.png) [@Akhilesh](https://gromacs.bioexcel.eu/u/Akhilesh)\ **Post date:** [October 9, 2023, 5:03am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/3 "2023-10-09T05:03:19Z")
Thank you for your suggestions. I was applied the and now getting the following error after running the “gmx\_mpi mdrun -multidir remd\_0 remd\_1 remd\_2 -replex 500” GROMACS: gmx mdrun, version 2021.5 Executable: /scratch/apps/gromacs\_cray-2021.5/bin/gmx\_mpi Data prefix: /scratch/apps/gromacs\_cray-2021.5 Working dir: /home/PrecisionOncologyGrp/20003317/AKT/L1 Command line: gmx\_mpi mdrun -multidir remd\_0 remd\_1 remd\_2 -replex 500 * * * * * * Program: gmx mdrun, version 2021.5 Program: gmx mdrun, version 2021.5 Source file: src/gromacs/utility/futil.cpp (line 481) Source file: src/gromacs/utility/futil.cpp (line 481) MPI rank: 1 (out of 3) MPI rank: 2 (out of 3) File input/output error: File input/output error: topol.tpr * * * topol.tpr ## Program: gmx mdrun, version 2021.5 For more information and tips for troubleshooting, please check the GROMACS website at [http://www.gromacs.org/Documentation/ErrorsFor](http://www.gromacs.org/Documentation/ErrorsFor) more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) Source file: src/gromacs/utility/futil.cpp (line 481) * * * MPI rank: 0 (out of 3) File input/output error: topol.tpr * * * Rank 1 [Sun Oct 8 17:31:43 2023] [c0-0c0s14n3] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 1 Rank 2 [Sun Oct 8 17:31:43 2023] [c0-0c0s14n3] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 2 Rank 0 [Sun Oct 8 17:31:43 2023] [c0-0c0s14n3] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 0 \_pmiu\_daemon(SIGCHLD): [NID 00059] [c0-0c0s14n3] [Sun Oct 8 17:31:43 2023] PE RANK 2 exit signal Aborted [NID 00059] 2023-10-08 17:31:43 Apid 21599487: initiated application termination Please suggest on how to proceed further regarding this. Thanks a lot. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [October 9, 2023, 6:50am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/4 "2023-10-09T06:50:50Z")
`gmx mdrun` cannot find your input files (`topol.tpr`) Have you checked that you’ve got one `topol.tpr` file in each of the directories `remd_0`, `remd_1` and `remd_2`? ---
**Author:** ![Akhilesh](https://avatars.discourse-cdn.com/v4/letter/a/35a633/32.png) [@Akhilesh](https://gromacs.bioexcel.eu/u/Akhilesh)\ **Post date:** [October 9, 2023, 7:13am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/5 "2023-10-09T07:13:59Z")
Yes, My each folder named with `remd_0` , `remd_1` and `remd_2` have remd\_0.tpr’ , `remd_1.tpr` and `remd_2.tpr`. with their mdp file Is any thing ealse I have to put in the folder. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [October 9, 2023, 7:50am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/6 "2023-10-09T07:50:21Z")
I think things get significantly easier if you stick to the default names (`topol.tpr`), at least when using `-multidir`. At least they should not have different names in the different directories. ---
**Author:** ![Akhilesh](https://avatars.discourse-cdn.com/v4/letter/a/35a633/32.png) [@Akhilesh](https://gromacs.bioexcel.eu/u/Akhilesh)\ **Post date:** [October 10, 2023, 4:49am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/7 "2023-10-10T04:49:42Z")
Hi, I am agetting again same error while i have changed the .tpr file name with topol.tpr gmx\_mpi mdrun -multidir remd\_0 remd\_1 remd\_2 -replex 500 Back Off! I just backed up md.log to ./#md.log.1# Back Off! I just backed up md.log to ./#md.log.1# Back Off! I just backed up md.log to ./#md.log.1# * * * Program: gmx mdrun, version 2021.5 Source file: src/gromacs/utility/futil.cpp (line 481) MPI rank: 2 (out of 3) File input/output error: topol.tpr … This is my md.mdp file please check it and suggest me ; Run control integrator = md dt = 0.002 ; ps ! nsteps = 50000000; total 10 ns. ; Output control nstxout = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 nstenergy = 100 ; Neighbor searching cutoff-scheme = group rlist = 5 pbc = no ns\_type = simple ; Electrostatics and VdW rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off ;Langevin dynamics bd\_fric = 0 ld\_seed = -1 ; Bonds constraints = all-bonds lincs\_order = 4 lincs\_iter = 1 lincs-warnangle = 30 ; Temperature and Pressure coupling Tcoupl = v-rescale tau\_t = 1.0 tc-grps = Protein ref\_t = 300 Pcoupl = no ; Velocity generation gen\_vel = yes gen\_temp = 300 gen\_seed = 173529 ;[[gmx-users] Temperature in Brownian Dynamics simulation](http://www.mail-archive.com/gmx-users@gromacs.org/msg20866.html) ;mine addition comm\_mode = angular nstcomm = 10 ; IMPLICIT SOLVENT ALGORITHM implicit\_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb\_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb\_epsilon\_solvent = 80 ; Salt concentration in M for Generalized Born models gb\_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb\_obc\_alpha = 1 gb\_obc\_beta = 0.8 gb\_obc\_gamma = 4.85 gb\_dielectric\_offset = 0.009 sa\_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa\_surface\_tension = -1 ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [October 10, 2023, 5:54am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/8 "2023-10-10T05:54:54Z")
That’s strange. Could you do `ls */` in the directory from where you are starting the simulations? So that we can see that the topol.tpr files are present in all the subdirectories. I’m getting exactly the same error as you get when there is no `topol.tpr` file in each of the `remd_0/`, `remd_1/` and `remd_2/` directories. ---
**Author:** ![Akhilesh](https://avatars.discourse-cdn.com/v4/letter/a/35a633/32.png) [@Akhilesh](https://gromacs.bioexcel.eu/u/Akhilesh)\ **Post date:** [October 10, 2023, 6:17am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/9 "2023-10-10T06:17:13Z")
yes sure ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/6d858d364efc0ddd818b2c80dfde623203d4eff2.png) this is snapshot of directories. all folder have the topol.tpr file. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [October 10, 2023, 6:53am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/10 "2023-10-10T06:53:04Z")
Your image doesn’t show the `remd_2` directory, but I trust the `topol.tpr` file is there. I’m fairly sure the problem is not caused by the mdp file settings. In the output you posted two hours ago, did you remove anything? Were there any other error messages? Because before, it complained that it could not find tpr files in any of the run directories. In your last output it only complained on MPI rank 2 (indicating a problem with the `remd_2` directory). You could start a simulation (just `gmx_mpi mdrun`) only from that directory and see if that works. If that works you could try the same from the other two directories. Finally, if nothing else helps, it would be good to test with a more recent version of GROMACS (2023.2) to see if it works better with that. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [October 10, 2023, 4:10pm UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/11 "2023-10-10T16:10:14Z")
Having a closer look at your mdp options I see that you are running with implicit solvent. That is not possible since GROMACS 2018. You should also have a closer look at your Electrostatics and VdW settings and make sure that they match the settings to be used with whatever forcefield you are using. ---
**Author:** ![Akhilesh](https://avatars.discourse-cdn.com/v4/letter/a/35a633/32.png) [@Akhilesh](https://gromacs.bioexcel.eu/u/Akhilesh)\ **Post date:** [October 11, 2023, 4:34am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/12 "2023-10-11T04:34:55Z")
Thank you for suggestions. But now am getting other type of error as … Command line: gmx\_mpi mdrun -multidir remd\_0 remd\_1 remd\_2 -replex 500 Reading file topol.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision) Reading file topol.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision) Reading file topol.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision) Changing nstlist from 20 to 100, rlist from 1.222 to 1.343 Changing nstlist from 20 to 100, rlist from 1.227 to 1.353 Changing nstlist from 20 to 100, rlist from 1.23 to 1.359 1 GPU selected for this run. Mapping of GPU IDs to the 6 GPU tasks in the 3 ranks on this node: PP:0,PME:0,PP:0,PME:0,PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU PME tasks will do all aspects on the GPU 1 GPU selected for this run. Mapping of GPU IDs to the 6 GPU tasks in the 3 ranks on this node: PP:0,PME:0,PP:0,PME:0,PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU PME tasks will do all aspects on the GPU 1 GPU selected for this run. Mapping of GPU IDs to the 6 GPU tasks in the 3 ranks on this node: PP:0,PME:0,PP:0,PME:0,PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PP task will update and constrain coordinates on the CPU PME tasks will do all aspects on the GPU * * * Program: gmx mdrun, version 2021.5 Program: gmx mdrun, version 2021.5 Source file: src/gromacs/gpu\_utils/cudautils.cuh (line 81) Source file: src/gromacs/gpu\_utils/cudautils.cuh (line 81) Function: void gmx::\_GLOBAL\_\_N\_\_66ca6d5f\_16\_device\_stream\_cu\_cfe55bbe::checkDeviceError(const cudaError\_t, const std::\_\_cxx11::string &) Function: void gmx::\_GLOBAL\_\_N\_\_66ca6d5f\_16\_device\_stream\_cu\_cfe55bbe::checkDeviceError(const cudaError\_t, const std::\_\_cxx11::string &) MPI rank: 2 (out of 3) MPI rank: 1 (out of 3) Internal error (bug): Internal error (bug): Could not create CUDA stream. CUDA error #46 (cudaErrorDevicesUnavailable): Could not create CUDA stream. CUDA error #46 (cudaErrorDevicesUnavailable): CUDA-capable device(s) is/are busy or unavailable. CUDA-capable device(s) is/are busy or unavailable. * * * Rank 1 [Tue Oct 10 18:46:22 2023] [c0-0c0s6n3] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 1 Rank 2 [Tue Oct 10 18:46:22 2023] [c0-0c0s6n3] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 2 \_pmiu\_daemon(SIGCHLD): [NID 00027] [c0-0c0s6n3] [Tue Oct 10 18:46:22 2023] PE RANK 2 exit signal Aborted [NID 00027] 2023-10-10 18:46:22 Apid 21604357: initiated application termination … Please suggest on how to proceed further regarding this. Thanks a lot. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [October 11, 2023, 5:39am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/13 "2023-10-11T05:39:33Z")
It seems like there are problems with running on your GPU - or at least that the multidir run can only use the GPU for the first run (flagged as busy for two processes). This might be due to a CUDA or Gromacs issue, but I cannot say for sure. If so, it’s hopefully fixed in recent versions. There’s not much point in digging deep into it - before upgrading to a supported Gromacs version. If you cannot upgrade to a supported version you can run with the options `-nb cpu -pme cpu`. ---
**Author:** ![Akhilesh](https://avatars.discourse-cdn.com/v4/letter/a/35a633/32.png) [@Akhilesh](https://gromacs.bioexcel.eu/u/Akhilesh)\ **Post date:** [November 6, 2023, 5:20am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/14 "2023-11-06T05:20:37Z")
Hi, I am getting an other error as below GROMACS: gmx mdrun, version 2021.5 Executable: /scratch/apps/gromacs\_cray-2021.5/bin/gmx\_mpi Data prefix: /scratch/apps/gromacs\_cray-2021.5 Working dir: /home/PrecisionOncologyGrp/sushil.kumar/AKM/L2/L2 Command line: gmx\_mpi mdrun -deffnm -pin on -cpi md\_0\_10 * * * Program: gmx mdrun, version 2021.5 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int \*, char \*\*) ## Error in user input: Invalid command-line options In command-line option -deffnm Too few (valid) values Rank 0 [Sat Nov 4 21:46:53 2023] [c0-0c0s14n0] application called MPI\_Abort(MPI\_COMM\_WORLD, 1) - process 0 \_pmiu\_daemon(SIGCHLD): [NID 00056] [c0-0c0s14n0] [Sat Nov 4 21:46:53 2023] PE RANK 0 exit signal Aborted … Please suggest on how to proceed further regarding this Regards ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [November 6, 2023, 9:26am UTC](https://gromacs.bioexcel.eu/t/error-in-the-remd-md-run/7328/15 "2023-11-06T09:26:19Z")
The `-deffnm` option requires that you specify what name you want to use for your simulation input/output. You don’t have to use `-deffnm` at all, as long as you separate your simulations in different directories.