# Gmx mdrun -deffnm md\_0\_1 -nb gpu \*\* GPU command line error
**URL:** https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177
**Category:** User discussions
**Created:** [May 24, 2020, 3:42pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177 "2020-05-24T15:42:14Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 24, 2020, 3:42pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/1 "2020-05-24T15:42:14Z")
GROMACS version:
GROMACS modification: Yes/No
Here post your question
Command line:
gmx mdrun -deffnm md\_0\_1 -nb gpu
Compiled SIMD: SSE2, but for this host/run AVX2\_256 might be better (see log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX\_USE\_RDTSCP=ON CMake option.
Reading file md\_0\_1.tpr, VERSION 2018.1 (single precision)
Changing nstlist from 10 to 80, rlist from 1 to 1.147
Using 1 MPI thread
Using 8 OpenMP threads
* * *
Program: gmx mdrun, version 2018.1
Source file: src/programs/mdrun/runner.cpp (line 1001)
Fatal error:
Cannot run short-ranged nonbonded interactions on a GPU because there is none
detected.
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [May 24, 2020, 6:12pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/2 "2020-05-24T18:12:32Z")
Your GROMACS installation is not optimally compiled (see note about SSE2 vs. AVX2\_256) and it seems you do not have a GPU installed on this system. If this is not the case, we will need a lot more information about your hardware and what you have done to verify that any GPU is working properly.
---
### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 24, 2020, 7:06pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/3 "2020-05-24T19:06:57Z")
Dear Dr. Lemkul sir
Please find the atatchments to see that gpu is enabled, i hope
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### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 24, 2020, 7:07pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/4 "2020-05-24T19:07:29Z")
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [May 24, 2020, 7:45pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/5 "2020-05-24T19:45:14Z")
What does the `.log` file say about GPU detection? How did you install GROMACS? What was your exact `cmake` command?
---
### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 25, 2020, 11:14am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/6 "2020-05-25T11:14:06Z")
GROMACS version: 2018.1
Precision: single
Memory model: 64 bit
MPI library: thread\_mpi
OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64)
GPU support: disabled
SIMD instructions: SSE2
FFT library: fftw-3.3.7-sse2-avx
RDTSCP usage: disabled
TNG support: enabled
Hwloc support: hwloc-1.11.6
Tracing support: disabled
Built on: 2018-03-31 17:12:46
Built by: buildd@debian [CMAKE]
Build OS/arch: Linux x86\_64
Build CPU vendor: Intel
Build CPU brand: Westmere E56xx/L56xx/X56xx (Nehalem-C)
Build CPU family: 6 Model: 44 Stepping: 1
Build CPU features: aes apic clfsh cmov cx8 cx16 intel lahf mmx msr pcid pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 x2apic
C compiler: /usr/bin/cc GNU 7.3.0
C compiler flags: -msse2 -g -O2 -fdebug-prefix-map=/build/gromacs-Fqu8ou/gromacs-2018.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D\_FORTIFY\_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 7.3.0
C++ compiler flags: -msse2 -g -O2 -fdebug-prefix-map=/build/gromacs-Fqu8ou/gromacs-2018.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D\_FORTIFY\_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
---
### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 25, 2020, 11:15am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/7 "2020-05-25T11:15:20Z")
---
### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 25, 2020, 11:16am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/8 "2020-05-25T11:16:58Z")
> **[Run GROMACS 3X Faster on NVIDIA GPUs](https://www.nvidia.com/en-sg/data-center/gpu-accelerated-applications/gromacs/)**
>
> Complete your molecular dynamics simulations in hours instead of days. Learn more.
i have used the above protocol to install GROMACS dear sir
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [May 25, 2020, 12:13pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/9 "2020-05-25T12:13:49Z")
> [@abraham](#):
>
> GPU support: disabled
Apparently not, because the `.log` file shows you did not enable GPU support. Please provide the actual `cmake` command you gave to install GROMACS.
---
### Author:  [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)
#### Post date: [May 25, 2020, 12:56pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/10 "2020-05-25T12:56:46Z")
Please follow the official GROMACS installation guide and use a recent release:
[http://manual.gromacs.org/documentation/current/install-guide/index.html](http://manual.gromacs.org/documentation/current/install-guide/index.html)
---
### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 25, 2020, 1:18pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/11 "2020-05-25T13:18:09Z")
root@linux-pc:/home/tom# BUILD AND INSTALL^C
root@linux-pc:/home/tom# # CC=gcc CXX=g++ cmake /home/tom/gromacs-5.1.4 -DGMX\_OPENMP=ON -DGMX\_GPU=ON -DGMX\_BUILD\_OWN\_FFTW=ON -DGMX\_PREFER\_STATIC\_LIBS=ON -DCMAKE\_BUILD\_TYPE=Release -DCMAKE\_INSTALL\_PREFIX=/opt/gromacs
root@linux-pc:/home/tom# CC=gcc CXX=g++ cmake /home/tom/gromacs-5.1.4 -DGMX\_OPENMP=ON -DGMX\_GPU=ON -DGMX\_BUILD\_OWN\_FFTW=ON -DGMX\_PREFER\_STATIC\_LIBS=ON -DCMAKE\_BUILD\_TYPE=Release -DCMAKE\_INSTALL\_PREFIX=/opt/gromacs
– Could NOT find LibXml2 (missing: LIBXML2\_LIBRARY LIBXML2\_INCLUDE\_DIR)
CMake Error at CMakeLists.txt:552 (message):
Cannot build unit tests without libxml2. Either set
GMX\_BUILD\_UNITTESTS=OFF or tell CMake how to find a working version of
libxml2.
– Configuring incomplete, errors occurred!
See also “/home/tom/gromacs-5.1.4/CMakeFiles/CMakeOutput.log”.
See also “/home/tom/gromacs-5.1.4/CMakeFiles/CMakeError.log”.
root@linux-pc:/home/tom#
---
### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 25, 2020, 1:48pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/12 "2020-05-25T13:48:15Z")
Dear justin lemkul sir
Have i to re install sir
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [May 25, 2020, 2:55pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/13 "2020-05-25T14:55:37Z")
Yes. You need to satisfy all dependencies, and above you get a clear failure message about why `cmake` failed.
---
### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 25, 2020, 7:25pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/14 "2020-05-25T19:25:17Z")
Dear sir
I installed new version successfully after my first installation i could able to run 2020.2 version and after closing the terminal and again opened it, when i type gmx command it says, command not found and install with sudo apt install gromacs and if try installing it, again it is installing 2018-1 old version. How to open new version with gmx command
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### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 25, 2020, 7:50pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/15 "2020-05-25T19:50:10Z")
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### Author:  [@abraham](https://gromacs.bioexcel.eu/u/abraham)
#### Post date: [May 25, 2020, 7:51pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/16 "2020-05-25T19:51:24Z")
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### Author:  [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)
#### Post date: [May 25, 2020, 10:41pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/17 "2020-05-25T22:41:06Z")
There is no need to install another copy/version of GROMACS. What has happened is you have failed to point to the GROMACS installation so that each time you start up a terminal window the OS can find it. When you first installed it, if you notice at the end of the quick and dirty instructions that is at the top of [http://manual.gromacs.org/documentation/current/install-guide/index.html](http://manual.gromacs.org/documentation/current/install-guide/index.html) there was this command:
source /usr/local/gromacs/bin/GMXRC
That command needs to be run each time that you open a terminal window. You can either do it by hand, or better you put it into the shell command that will do it automatically each time for you. For myself I have to add the above line into my .bashrc script (located in my home directory). Yours may be different, so find out what shell you are running, then add the command appropriately to the shell script/command file that is run each time you open a terminal.
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### Author:  [@sam](https://gromacs.bioexcel.eu/u/sam)
#### Post date: [November 2, 2020, 1:25am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/18 "2020-11-02T01:25:29Z")
did you solve it ?
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### Author:  [@an\_n](https://gromacs.bioexcel.eu/u/an_n)
#### Post date: [July 9, 2021, 8:40pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/20 "2021-07-09T20:40:29Z")
Hi,
I ran across the same error. Here’s my log file output:
> GROMACS version: 2021.2
> Verified release checksum is d91a739522d82c53dc47c2276b9ac5fae3b2119283e84e3a1c7bed8ce741fda2
> Precision: mixed
> Memory model: 64 bit
> MPI library: thread\_mpi
> OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 64)
> **GPU support: CUDA**
> SIMD instructions: AVX2\_256
> FFT library: fftw-3.3.8-sse2-avx
> RDTSCP usage: enabled
> TNG support: enabled
> Hwloc support: disabled
> Tracing support: disabled
> C compiler: /usr/bin/gcc GNU 9.3.0
> C compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
> C++ compiler: /usr/bin/c++ GNU 9.3.0
> C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp
> CUDA compiler: /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Sun\_Jul\_28\_19:07:16\_PDT\_2019;Cuda compilation tools, release 10.1, V10.1.243
> CUDA compiler flags:-std=c++14;-gencode;arch=compute\_30,code=sm\_30;-gencode;arch=compute\_35,code=sm\_35;-gencode;arch=compute\_37,code=sm\_37;-gencode;arch=compute\_50,code=sm\_50;-gencode;arch=compute\_52,code=sm\_52;-gencode;arch=compute\_60,code=sm\_60;-gencode;arch=compute\_61,code=sm\_61;-gencode;arch=compute\_70,code=sm\_70;-gencode;arch=compute\_75,code=sm\_75;-gencode;arch=compute\_35,code=compute\_35;-gencode;arch=compute\_32,code=compute\_32;-use\_fast\_math;-D\_FORCE\_INLINES;-mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp
> CUDA driver: 11.20
> CUDA runtime: N/A
My cmake command was:
> sudo cmake … -DGMX\_BUILD\_OWN\_FFTW=OFF -DREGRESSIONTEST\_DOWNLOAD=OFF -DCMAKE\_C\_COMPILER=gcc -DGMX\_GPU=CUDA -DGMX\_MPI=OFF -DREGRESSIONTEST\_PATH=gmx\_2021.2/regressiontests-2021.2
Any idea how to fix this? Any help is much appreciated.
Thanks!
An
---
### Author:  [@H3nrasouli](https://gromacs.bioexcel.eu/u/H3nrasouli)
#### Post date: [March 25, 2022, 10:13am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177/21 "2022-03-25T10:13:23Z")
Dear all,
I have a smilar problem when I run gromacs-2019.5 on my HPC cluster
This is the message I faced with:
Back Off! I just backed up md\_0\_1.log to ./#md\_0\_1.log.6#
:-) GROMACS - gmx mdrun, 2019.5 (-:
```
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
```
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out [http://www.gromacs.org](http://www.gromacs.org) for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2019.5
Executable: /share/apps/GROMACS/gromacs-2019.5/build/bin/gmx\_mpi
Data prefix: /share/apps/GROMACS/gromacs-2019.5/build
Working dir: /home/hpcuser120/phz
Command line:
gmx\_mpi mdrun -v -deffnm md\_0\_1
## Sorry couldn’t backup md\_0\_1.log to ./#md\_0\_1.log.7# Compiled SIMD: SSE4.1, but for this host/run AVX2\_256 might be better (see log). Reading file md\_0\_1.tpr, VERSION 2019.5 (single precision)
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[51499,1],5]
Exit code: 1
[Next page](https://gromacs.bioexcel.eu/t/gmx-mdrun-deffnm-md-0-1-nb-gpu-gpu-command-line-error/177.md?page=2)